Applied Bioinformatics Group - User contributions [en]

PAKAP

2018-05-02T07:07:31Z

Uqccha18:

INTRODUCTION

Presence/Absence variants (PAVs) have recently been shown to be abundant in plant and fungi genomes. Genome wide PAV detection is usually performed during the construction of pangenomes for species, using either the whole genome assembly and comparison or the iterative mapping and assembly approach. These rely on the presence of at least one reference genome, and can be confounded by variations in assembly and annotation quality.

We have established a Present/Absent Kmer Analysis Pipeline (PAKAP). By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

PAKAP consists of a series of scripts written in Perl, Python and Bash scripts and requires Jellyfish [Marcais 2011] as well as optionally [http://soap.genomics.org.cn/soapaligner.html SOAPaligner]. The scripts are freely available for non-commercial use.

== What PAKAP depends on ==

* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* Some non-standard Perl modules:
** BioPerl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)
* Python 2.7. The pipeline runs under Python 3, but is not tested extensively.
** BioPython
* Optional: [http://soap.genomics.org.cn/soapaligner.html SOAPaligner]

== Download ==
* Latest Version 1.7:
** [http://appliedbioinformatics.com.au/download/PAKAP_1.7.zip PAKAP_1.7.zip]

* Example data (244MB)
** [http://appliedbioinformatics.com.au/download/PAKAP_example_data.zip PAKAP_example_data.zip]

== How to install ==
* Download the package from above, then just extract the files to a directory of your choosing. Remember the directory, since you'll need that in the next step.

== How to prepare the pipeline ==

'''IMPORTANT:''' Currently, only single-line FASTA files are accepted by the pipeline, in other words, one line per identifier, one line per sequence. If you have FASTQ files, the included script FixFASTQ.py can transform them into the needed format. Usage:

python FixFASTQ.py your_reads.fastq single_line_reads.fasta

Create your project configuration file by using the example config file. Here it is:

<nowiki>
[PIPELINE]
# This should be the path to the directory containing the pipeline scripts.
SCRIPTS_PATH = /scratch/pipeline
# OPTIONAL: Path to reference
REFERENCE_PATH = /scratch/temp/ref.fasta
# OPTIONAL: Path to gene annotation on reference
GFF_PATH = /scratch/temp/ref.gff3

[JELLYFISH]
# The path to the local installation of jellyfish (http://www.cbcb.umd.edu/software/jellyfish/)
PATH = /scratch/bin
# The minimum k-mer size will be checked when KMER_SIZE=AUTO. Default is 5
MIN_KMER_SIZE=5
# The maximum k-mer size will be checked when KMER_SIZE=AUTO, jellyfish limits to the maximum k-mer size to 31. Default is 22
MAX_KMER_SIZE=22

[IDENTIFYKMERSIZE]
# Number of CPU will be used. Be aware of that the total amount of memory will be shared among all CPUs.
NUM_OF_PROCESSOR=4
# treatment 1 ID which will be used for naming files
T1_ID=CON
# treatment 2 ID which will be used for naming files
T2_ID=STE
# The output directory of the initial kmer counting, for jellyfish
OUT_DIR=/scratch/somewhere

# directory storing treatment 1 data files. The data files can be fasta or fastq formats.
DATA_DIR_T1=/scratch/somewhere/whole/whole_2.150.1sd/
# directory storing treatment 2 data files. The data files can be fasta or fastq formats.
DATA_DIR_T2=/scratch/somewhere/truncated/truncated_2.150.1sd/

[ADVANCED]
# Important setting in jellyfish for tuning jellyfish performance. A larger hash size, more memory will be used
# but less sub-count files will be generated. Default is 10000000.
JELLYFISH_HASH_SIZE=10000000
# Size of the jellyfish hash table. Use a size large enough to contain all of the K-mers such that 80% * s > number of distinct K-mers. [Default: 10000000].
#jellyfish_hash_size = 16G
# Length of counter in the hash table. See jellyfish manual for explanation. [Default: 4]
JELLYFISH_COUNTER_BITS = 18
# Number of bases used for splitting the k-mer files into sub-files. A larger number reduces RAM usage. Maximum at the moment is 3. [Default: 2]
N_SPLIT_BASES = 3
# Minimum occurrence count for a k-mer to be considered as a candidate Presence / Absence K-mer. [Default: 4]
MIN_OCC = 4</nowiki>

The most important settings are:

* SCRIPTS_PATH - this is where you extracted the pipeline
* REFERENCE_PATH - optional: if you have a reference fasta. SOAPaligner will be run if this is specified.
* GFF_PATH - optional: The SOAP results will be compared against genes if this is specified.
* JELLYFISH / PATH - the directory in which Jellyfish is located
* IDENTIFYKMERSIZE / OUT_DIR - the dirctory in which temporary kmers are stored (might get huge)
* DATA_DIR_T1 and DATA_DIR_T2 - where the fasta files for kmer counting are located

== How to run the pipeline ==

The pipeline takes four arguments: 's1' specifies reads from the first group (or treatment etc.), 's2' specifies reads from the second group, 'c' is the path to the configuration file, and 'o' specifies the path to the directory which will contain all results. Per condition s1 or s2, unlimited files are possible.

The command is:

python pipeline.py
--s1 ./truncated/truncated_2.150.1sd/truncated_2.150.1sd.R1.fasta ./truncated/truncated_2.150.1sd/truncated_2.150.1sd.R2.fasta
--s2 ./whole/whole_2.150.1sd/whole_2.150.1sd.R1.fasta ./whole/whole_2.150.1sd/whole_2.150.1sd.R2.fasta
-c default.config
-o output_folder/

or, easier:

python pipeline.py
--s1 ./truncated/truncated_2.150.1sd/truncated_2.150.1sd.R?.fasta
--s2 ./whole/whole_2.150.1sd/whole_2.150.1sd.R?.fasta
-c default.config
-o output_folder/

This will read the configuration from default.config and generate all output files, as well as a log-file, in output_folder.

== How to interpret the results ==
You can download the results of the sample data [link_here here].

In the given out_dir, between two and four folders will be created.

1. kmers - these are the k-mers present in s1 only, and in s2 only. K-mers present in s1 only start with s1.

2. PARs - this folder contains the reads present only in one of the two conditions:

2.1 ''s1_0_PARs_single.fasta'' - reads only present in s1

2.2 ''s2_0_PARs_single.fasta'' - reads only present in s2

3. SOAPs - optional, only when reference is specified: The SOAP results for aligning the reads only present in s1 or s2. Can be converted to SAM/BAM using SOAPaligner's soap2sam.pl and samtools view.

4. Results - optional, only when gff file and reference are specified: A table detailing how many genes there are in the given gff-file, how many reads were produced by the pipeline, how many reads could be aligned, how many reads hit inside the genes in the gff3 file, how many reads hit only with their start or their end inside genes, how many reads hit multiple times etc. Conditions that have no reads produced (like in the example data) are listed like with '-'. Example:

{| class="wikitable"
!Name
!Number_of_genes
!Aligned_reads
!Complete_hit
!Only_start
!Only_end
!Number_alignments_without_hit_to_gene
!Duplicate_hits
|-
|chr1.232_genes_vs_truncated_10.100.1sd_s2_0
|232
|2670
|2655
|8
|7
|0
|0
|-
|non_existing_condition
| -
| -
| -
| -
| -
| -
| -
|}

Here, the large majority of produced reads aligns completely inside the given 232 genes (2655 out of 2670 reads). 8 reads align only with their start and then stretch outside the gene, 7 reads start before the gene and then end inside the gene. 0 of the reads align somewhere else, and all reads align uniquely.

Here's one way to have all tables in one big table:

# first, get the header
head -n 1 some_results/gff_compared_to_soap_results.txt > Sorted_final_results.txt
# Append the sorted results from all other tables
find . -name gff_compared_to_soap_results.txt -exec tail -n +2 {} \; | sort >> Sorted_final_results.txt

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

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DaisyChain

2018-02-05T07:04:40Z

Uqccha18: Created page with "We have developed an assembly homology graph software named DaisyChain to produce interactive graph visualizations from custom-built homology databases. The gene-centric repre..."

We have developed an assembly homology graph software named DaisyChain to produce interactive graph visualizations from custom-built homology databases. The gene-centric representation includes local gene neighborhood in order to distinguish orthologs and paralogs by local synteny. The software supports genome sequences in FASTA format and GFF3 formatted annotation files and the process of building the homology database requires a minimum amount of user interaction. DaisyChain comes with an integrated web viewer which can be used for both data analysis and data publishing.

==Links==
[http://daisychain.appliedbioinformatics.com.au DaisyChain]

Kenneth Chan

2017-11-21T13:28:53Z

Uqccha18:

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2015 - present University of Western Australia. Senior Postdoctoral Bioinformatics Researcher
*2013 - 2014 University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ applied bioinformatics group in UQ. Since then, I have intensively worked with various NGS data. Following Dave's relocation to UWA in 2015, I have also moved from UQ to UWA.

My research interest is in NGS data management , analysis and visualisation, bioinformatics tool and pipeline development, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

===Contact:===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: kenneth.chan@uwa.edu.au

Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)

2017-10-23T03:43:11Z

Uqccha18: Created page with "== Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi) == === Academic history: === PhD Candidate (2014-current): Applied Bioinformatics, The University of Western Australia (UW..."

== Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi) ==
=== Academic history: ===
PhD Candidate (2014-current): Applied Bioinformatics, The University of Western Australia (UWA), Perth, Australia.
MSc (2008 –2010): Agricultural Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
BSc (2003 – 2007): Agronomy and Plant breeding, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran

=== Posts held: ===
• 2015- 2016, IT help desk, National eResearch Collaboration Tools and Resources (NeCTAR), Pawsey@UWA, Perth, Australia
• 2014- 2015, Lab helper, Molecular lab, School of Plant Biology, UWA, Perth, Australia
• 2011- 2013, Demonstrator ((1) Principle of plant breeding, (2) Genetics and their lab) Payame Noor University of Iran, branch of Sari, Sari, Iran

=== Publications: ===
• M. Mousavi-Derazmahalleh, B. Nevado, P. Bayer, D. Filatov, J. Hane, D. Edwards, W. Erskine, M. Nelson. 2017. Footprints of selection in a 20th century plant domesticate: The narrow-leafed lupin. Theoretical and Applied Genetics. (Submitted)

• M. Mousavi-Derazmahalleh, P. Bayer, B. Nevado, B. Hurgobin, D. Filatov, A. Kilian, L. Kamphuis, K. Singh, J. Berger, J. Hane, D. Edwards, W. Erskine, M. Nelson. 2017. Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: Narrow-leafed lupin. Theoretical and Applied Genetics. (Submitted & under revision)

• M. Mardi, M. Zeinalabedini, S. M. Mousavi-Derazmahalleh, A. A. Zeinanloo, P. Majidian, S. H. Kolahi-Zonoozi, M. R. Taslimpor, S. A. Masoomi-Majareh, F. A. Jamgardg and K. Mostafavi. 2016. Commercial Iranian olive cultivars: morphological traits, molecular diversity, and genetic structure. The Journal of Horticultural Science and Biotechnology, 91:4, 404-411.

• Ahmad Farhad Talebi, Masoud Tohidfar, Seyedeh Mahsa Mousavi Derazmahalleh, Alawi Sulaiman, Azhari Samsu Baharuddin, Meisam Tabatabaei. 2015. Biochemical modulation of lipid pathway in microalgae Dunaliella sp. for biodiesel production. BioMed Research International. Article ID 597198.

• SH. Kolahi-Zonoozi, M. Mardi, M. Zeinalabedini, S. M. Pirseyedi, P. Mahmoodi, I. Tabatabaei, S. M. Mousavi-Derazmahalleh, M. Farsi, M. A. Ebrahimi, S. M. Khayam-Nekoui , K. Ahmadi. 2014. Development of 12 new SSR markers for genetic diversity and structure analysis in Pistachio (Pistacia vera L.). Journal of horticultural science & biotechnology. 89(6):707-711.

• S. M. Mousavi Derazmahalleh, M. Mardi, M. Zeinalabedini, M. Kazemi, S. H. Marashi, S. Malekzadeh, S. M. khayam nekoui, T. Roodbar shojaie , Sh. Kolahi zenoozi. 2013. The Survey of Genetic Diversity & Population Structure Analysis of Iranian Sweet Pomegranate (Punica granatum L.) Germplasm Using SSR Markers. Acta Hort. (ISHS) 976:271-276.

• Mehrbanoo Kazemi alamuti, Mehrshad Zeinalabedini, Mahsa Mousavi Derazmahalleh,Taha RoodbarShojaie, Hashem Poor Irandoost, Mehdi Zahravi, Mohammad Vazifehshenas, Mohammad Ali Ebrahimi, Sayed Mojtaba Khayam Nekouei, Ghasem Hossini Salekdeh, Mohsen Mardi. 2012. Extensive genetic diversity in Iranian pomegranate (Punica granatum L.) germplasm revealed by microsatellite markers. Sci. Hortic. 146: 104-114.

=== Scholarship & Awards: ===
• 2016, UWA postgraduate research travel award, Australia
• 2014-2018, Endeavour Postgraduate Scholarship, Australia
• 2014, Student Travel Bursary awarded by Winter School in Mathematical & Computational Biology, University of Queensland, Brisbane, Australia

=== Contact: ===
University of Western Australia (UWA)
Perth, WA, Australia
Email: mahsa.mousaviderazmahalleh@research.uwa.edu.au
Linkedin: https://www.linkedin.com/in/mahsa-mousavi-77357758/

GitHub: https://github.com/mahsa-mousavi/PhD_Scripts

Publications KC

2017-10-03T03:56:52Z

Uqccha18:

==Publications - Chon Kit Kenneth Chan==

===JOURNAL ARTICLES:===
# Yuan Y, Bayer PE, Scheben A; Chan CKK and Edwards D. (2017) BioNanoAnalyst: A visualisation tool to assess genome assembly quality using BioNano data. BMC Bioinformatics. 2017;18 1:323. doi:10.1186/s12859-017-1735-4.
# Lim DKY, Schuhmann H, Thomas-Hall SR, Chan CKK, Wass TJ, Aguilera F, Adarme-Vega TC, Dal’Molin CGO, Thorpe GJ , Batley J, Edwards D, Schenk PM. (2017) RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 1 during nitrogen starvation reveals a 2 two-stage lipid accumulation mechanism Bioresource Technology. Bioresource Technology. 2017; doi:http://dx.doi.org/10.1016/j.biortech.2017.06.003
# Bayer PE, Hurgobin B, Golicz A, Chan K, Yuan Y, Lee HT, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King G, Batley J, Edwards D. (2017) Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnol J. 2017; doi:10.1111/pbi.12742 [doi].
# Montenegro JDM, Golicz AA, Bayer PE, Hurgobin B, Lee HT, Chan CKK, Visendi P, Lai K, Doležel J, Batley J, Edwards D. (2017) The pangenome of modern hexaploid bread wheat. The Plant Journal. 2017:n/a-n/a. doi:10.1111/tpj.13515
# Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP et al: The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications 2016, 7:13390.
# Lee H, Golicz AA, Bayer PE, Jiao Y, Tang H, Paterson AH, Sablok G, Krishnaraj RR, Chan CK, Batley J et al: The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri). Plant Physiol 2016, 172(1):272-283.
# Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan C-KK, Staňková H et al: An efficient approach to BAC based assembly of complex genomes. Plant Methods 2016, 12:2.
# Kaniewska P, Chan C-KK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg O, Dove S: Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change. PLoS ONE 2015, 10(10):e0139223.
# Bayer P, Ruperao P, Mason A, Stiller J, Chan C-KK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P et al: High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 2015, 128(6):1039-1047.
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015, 66(5):1489-1498.
# Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
# Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
# Ruperao P, Chan C-KK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
# Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
# Chan C-KK, Halgamuge SK: [http://www.google.com.au/url?sa=t&source=web&cd=1&ved=0CBYQFjAA&url=http%3A%2F%2Fwww.sersc.org%2Fjournals%2FIJBSBT%2Fvol1_no1%2F1.pdf&ei=EXWdTeimL4LovQO-mcCsBA&usg=AFQjCNF1LEKGsSVzWZ5Em6TBRlHgG8TTXA&sig2=WyfI3Q4Zd6lZRmohmDNziA A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature] International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
# Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: [http://www.biomedcentral.com/1471-2105/9/215 Binning sequences using very sparse labels within a metagenome] BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: [http://www.hindawi.com/journals/jbb/2008/513701/ref/ Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing] Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.
# Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

===BOOK CHAPER:===
# Yuan Y, Scheben A, Chan CKK and Edwards D. (2016) Databases for wheat genomics and crop improvement. Methods in Molecular Biology, Springer (USA)
# Ghosh S, Chan C-KK: Analysis of RNA-Seq Data Using TopHat and Cufflinks. In: Plant Bioinformatics: Methods and Protocols. Edited by Edwards D. New York, NY: Springer New York; 2016: 339-361.
# Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Sequences Using Very Sparse Labels Within a Metagenome. In: Encyclopedia of Metagenomics. Edited by Nelson EK. New York, NY: Springer New York; 2013: 1-13.
# Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Metagenomic Sequences Using Seeded GSOM. In: Handbook of Molecular Microbial Ecology I. John Wiley & Sons, Inc.; 2011: 369-378.

===CONFERENCE PAPERS:===
# Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
# Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: [http://bric.postech.ac.kr/vod/vod_detail.php?nNum=3326 Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes] In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
# Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
# Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
# Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

===MONSANTO INTERNAL CONFERENCE POSTERS:===
# Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

[[Kenneth_Chan|Back to Kenneth's Profile]]

DiffKAP

2017-08-14T08:26:35Z

Uqccha18: /* Download */

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version 0.9 (23/09/2013):
** [http://appliedbioinformatics.com.au/download/DiffKAP/DiffKAP_0.9.zip DiffKAP package]
** [http://appliedbioinformatics.com.au/download/DiffKAP/DiffKAP_sampleProj_testData.tar.gz Test Data]
** [http://appliedbioinformatics.com.au/download/DiffKAP/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

== Citation ==
* Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052

Back to [[Main_Page]]

Main Page

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==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (HueyTyng) Lee]]

[[Juan Montenegro]]

[[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

[[Ricky Hu]]

Positions available, please contact David Edwards if interested

=== Interns ===

[[Oliver Schliebs]]

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Publications DE

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Uqccha18: /* JOURNAL ARTICLES: */

==Publications - David Edwards==

===BOOKS:===

#Plant Genomics and Climate Change. Eds. Edwards D. and Batley J. Springer (USA). (2015) (in press)
#Plant Bioinformatics (Second Edition). Ed. Edwards D. Methods in Molecular Biology, Springer (USA). (2015) (in press)
#[http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA). (2012)
#[http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA). (2009)
#[http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (2007)

===BOOK CHAPTERS:===

#Yuan Y, Scheben A, Chan CKK and Edwards D. (2016) Databases for wheat genomics and crop improvement. Methods in Molecular Biology, Springer (USA), (in press)
#Edwards D. (2015) The impact of genomics technology on adapting plants to climate change. In: Plant Genomics and Climate Change. Eds. Edwards D. and Batley J. Springer (USA), (in press)
#Ruperao P and Edwards D. (2015) Bioinformatics: Identification of markers from next-generation sequence data. In: Plant Genotyping. Ed. Batley J. Methods in Molecular Biology, Springer (USA), pp. 29-47
#Lai K, Lorenc MT and Edwards D. (2015) Molecular marker databases. In: Plant Genotyping. Ed. Batley J. Methods in Molecular Biology, Springer (USA), pp. 49-62
#Golicz AA, Bayer PE and Edwards D. (2015) Skim-based genotyping by sequencing. In: Plant Genotyping. Ed. Batley J. Methods in Molecular Biology, Springer (USA), pp. 257-270
#Visendi P, Batley J and Edwards D. Next Generation Sequencing and Germplasm Resources. In Advances in Genomics of Plant Genetic resources. Volume 1. Genomics platforms, crop domestication and allele mining. Ed. Tuberosa R. Springer (USA), pp. 369-390
#Edwards D, Zander M, Dalton-Morgan J and Batley J. (2014) New technologies for ultra-high throughput genotyping in plant taxonomy. In: Molecular Plant Taxonomy. Ed. Besse P. Springer (USA), pp. 151-175
#Edwards D. (2013) Bioinformatics tools to assist breeding for climate change. In Genomics and breeding for climate resilient crops. Ed, Kole C. Springer (USA), pp 391-414
#Edwards D and Gupta PK. (2013) Sequence based DNA markers and genotyping for cereal genomics and breeding. In Cereal Genomics II. Eds. Gupta PK and Varshney, RK. Springer (USA) pp 57-76
#Edwards D and Wang X. (2012) Genome Sequencing Initiatives. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 152-157
#Lorenc M, Boskovic Z, Stiller J, Duran C and Edwards D. (2012) Role of Bioinformatics as a Tool for Oilseed Brassica Species. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 194-205
#Edwards D. (2011) Wheat Bioinformatics. In: [http://www.cplbookshop.com/contents/C63.htm The World Wheat Book II.] Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) pp 851-875
#Duran C, Boskovic Z, Batley J and Edwards D. (2011) Brassica Bioinformatics. In [http://www.scipub.net/agriculture/genetics-genomics-and-breeding-of-vegetable-brassicas.html Vegetable Brassicas] Ed. Sadowski J. Science Publishers, Inc., New Hampshire pp 406-418
#Edwards D, Hansen D and Stajich J. (2009) DNA Sequence Databases. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 1-11
#Duran C, Edwards D and Batley J. (2009) Molecular Marker Discovery and Genetic map Visualisation. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 165-189
#Imelfort M, Batley J, Grimmond S and Edwards D. (2009) Genome sequencing approaches and successes. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 345-358
#Batley J and Edwards D. (2009) Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/bioinformatics/book/978-1-58829-910-9 Bioinformatics for DNA Sequence Analysis.] Ed. Posada D. Methods in Molecular Biology, Humana Press (USA), pp 303-322
#Appleby N, Edwards D and Batley J. (2009) New technologies for ultra-high throughput genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press, (USA), pp 19-40
#Duran C, Edwards D and Batley J. (2009) Genetic maps and the use of synteny. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 41-56
#Edwards D and Batley J. (2008) Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding. In: [http://aob.oxfordjournals.org/content/102/5/879.full Principles and Practices of Plant Genomics.] Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA), pp 269-302
#Edwards D. (2007) Bioinformatics and plant genomics for staple crops improvement. In: [http://au.wiley.com/WileyCDA/WileyTitle/productCd-0813818354.html Breeding Major Food Staples.] Eds. Kang MS and Priyadarshan PM. Blackwell, pp 93-106
#Batley J, Jewell E and Edwards D. (2007) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA), pp. 473-494
#Love CG and Edwards D. (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (2007), pp. 229-244
#Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. (2007) Indian Mustard, in [http://www.springer.com/series/7367 Genome Mapping and Molecular Breeding in Plants, Vol. 2.] Ed. Kole C. Springer NY, pp 179-210
#Edwards D, Forster JW, Chagné D and Batley J. (2007) What are SNPs? In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 41-52.
#Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 53-76.
#Chagné D, Batley J, Edwards D, and Forster JW. (2007) Single Nucleotide Polymorphisms genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 77-94.
#Batley J and Edwards D. (2007) SNP applications in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 95-102.
#Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF and Dobrowolski M. (2005) Future Directions in the Molecular Breeding of Forage and Turf. In: [http://www.wageningenacademic.com/molecular Molecular Breeding for Genetic Improvement of Forage Crops and Turf.] Ed. Humphreys MO. Wageningen Academic Publishers, pp 83-97.
#Spangenberg GC, Felitti SA, Shields K, Ramsperger M, Tian P, Ong EK, Singh D, Logan E and Edwards D. (2005) Gene Discovery and Microarray-Based Transcriptome Analysis of the Grass-Endophyte Association. In: [http://onlinelibrary.wiley.com/book/10.1002/9780470384916 Neotyphodium in Cool Season Grasses.] Eds. Roberts CA, West CP and Spiers DE. Blackwell, pp 103-140

===JOURNAL ARTICLES:===

# Scheben A and Edwards D. (2017) Genome editors take on crops. [http://science.sciencemag.org/cgi/content/full/355/6330/1122?ijkey=9f1N4UfAGisKg&keytype=ref&siteid=sci Science 355 (6330): 1122-1123]
# Montenegro JDM, Golicz AA, Bayer PE, Hurgobin B, Lee HT, Chan CKK, Visendi P, Lai K, Doležel J, Batley J, Edwards D. (2017) The pangenome of modern hexaploid bread wheat. Plant Journal. (accepted February 2017)
# Hurgobin B and Edwards D. (2017) SNP discovery using a pangenome: has the single reference approach become obsolete? Biology (accepted March 2017)
# Li Y, Ruperao P, Batley J, Edwards D, Davidson J, Hobson K, Sutton T. (2017) Genome analysis identified novel candidate genes for ascochyta blight resistance in chickpea using whole genome re-sequencing data. Frontiers in Plant Science (accepted March 2017)
# Yuan Y, Bayer PE, Batley J and Edwards D. (2017) Improvements in genomic technologies: application to crop genomics. Trends in Biotechnology. (accepted January 2017)
# Kaur P, Bayer PE, Milec Z, Vrána J, Yuan Y, Appels R, Edwards D, Batley J, Nichols P, Erskine W, Doležel J. (2017) An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. Plant Biotechnology Journal. (accepted January 2017)
# Gacek K, Bayer PE, Bartkowiak-Broda I, Szala L, Bocianowski J, Edwards D and Batley J. (2017) Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus. Frontiers in Plant Science (accepted December 2016)
# Golicz AA, Bayer PE, Barker G, Edger PP, Kim HR, Martinez PA, Chan CKK, Severn-Ellis A, McCombie R, Parkin IAP, Paterson AH, Pires JC, Sharpe AG, Tang H, R. Teakle GR, Town CD, Batley J, Edwards D. (2016) The pangenome of an agronomically important crop Brassica oleracea. Nature Communications 7:13390
# Sablok G, Mudunuri S, Edwards D, Ralph PJ. (2016) Chloroplast Genomics: Expanding resources for an evolutionary conserved miniature molecule with enigmatic applications. Current Plant Biology. (accepted December 2016)
# Scheben A; Batley J and Edwards D. Genotyping by sequencing approaches to characterise crop genomes: choosing the right tool for the right application. Plant Biotechnology Journal. (accepted September 2016)
# Raman H, Raman R, Coombes N, Song J, Diffey S, Kilian A, Lindbeck K, DM Barbulescu, Batley J, Edwards D, Salisbury PA and Marcroft S. (2016) Genome-wide association study identifies new loci for resistance to Leptosphaeria maculans in canola. Frontiers in Plant Science. 7: 1513
# Scheben A, Yuan Y, Edwards D. (2016) Advances in genomics for adapting crops to climate change. Current Plant Biology. 6: 2-10
# Hane J, Ming Y, Kamphuis L, Nelson M, Garg, G, Atkins C, Bayer P, Bravo A, Bringans S, Cannon S, Edwards D, Foley R, Gao L, Harrison M, Huang W, Hurgobin B, Li S, Liu CW, McGrath A, Morahan G, Murray J, Weller J, Jian J and Singh K. (2016) A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: Insights into plant-microbe interactions and legume evolution. Plant Biotechnology Journal. (accepted August 2016)
# Davey PA, Pernice M, Sablok G, Larkum A, Lee HT, Golicz A, Edwards D, Dolferus R and Ralph P. (2016) The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses. Functional and Integrative Genomics. 16 (5): 465-80
# Lee HT, Golicz AA, Bayer P, Jiao Y, Tang H, Paterson AH, Sablok G, Krishnaraj RR, Chan CKK, Batley J, Kendrick GA, Larkum AW, Ralph PJ, Edwards D. (2016) The genome of a southern hemisphere seagrass species (Zostera muelleri). Plant Physiology. 172 (1): 272–283.
# Clarke WE, Higgins EE, Plieske J, Wieseke R, Sidebottom C, Khedikar Y, Batley J, Edwards D, Meng J, Li R, Lawley CT, Pauquet J, Laga B, Cheung W, Iniguez-Luy F, Dyrszka E, Rae S, Stich B, Snowdon RJ, Sharpe AG, Ganal MW, Parkin IA. (2016) A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. Theoretical and Applied Genetics. 129 (10): 1887-99
# Batley J and Edwards D. (2016) The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Current Opinion in Plant Biology. (accepted February 2016)
# Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Kenneth Chan CKK, Staňková H, Batley J, Šimková H, Doležel J and Edwards D. (2016) An efficient approach to BAC based assembly of complex genomes. Plant Methods. 12:2
# Doddamani D, Khan AW, Katta MAVSK, Agarwal G, Thudi M, Ruperao P, Edwards D and Varshney R. (2015) CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database bav079
# Staňková H, Hastie, A, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo MC, Batley J, Edwards D, Doležel J and Šimková H. BioNano Genome Mapping of Individual Chromosomes Supports Physical Mapping and Sequence Assembly in Complex Plant Genomes. Plant Biotechnology Journal. (accepted November 2015)
# Varshney RK, Singh VK, Xun X, Marshall DF, Wang J and Edwards D. (2015) Analytical and decision support tools for genomics-assisted breeding. Trends in Plant Science. (accepted October 2015)
# Golicz A, Batley J and Edwards D. (2015) Towards plant pangenomics. Plant Biotechnology Journal. (accepted October 2015)
# Kaniewska P, Chan CKK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg, Dove S. (2015) Transcriptomic changes in coral holobionts provide insights into physiological challenges of future climate and ocean change. PLOS ONE. (accepted September 2015)
# Kale SM, Jaganathan D, Ruperao P, Chen C, Punna R, Kudapa H, Thudi M, Roorkiwal M, Katta M, Doddamani D, Garg V, Kishor PBK, Gaur PM, Nguyen HT, Batley J, Edwards D, Sutton T and Varshney RK (2015) Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports (accepted September 2015)
# Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke L, Dempewolf H, De Pace C, Edwards D, Gepts P , Greenland A, Hall A, Henry R, Hori K, Howe G, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen H, Ogbonnaya F, Ortiz R, Paterson A, Tuberosa R, Valliyodan B, Varshney R, Yano M. (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal (accepted August 2015)
# Gou L, Hattori J, Fedak G, Balcerzak M, Klassen D, Sharpe A, Visendi P, Edwards D, Tinker N, Wei Y, Chen G and Ouellet T. (2015) Development and validation of Thinopyrum elongatum expressed molecular markers specific for the long arm of chromosome 7E. Crop Science Crop Science. 56: 354-364
# Staňková H, Valárik M, Lapitan NLV, Berkman PJ, Batley J, Edwards D, Luo MC, Tulpová Z, Kubaláková M, Stein N, Doležel J and Šimková H. (2015) Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. Theoretical and Applied Genetics. 128 (7): 1373-1383
# Cai G, Yang Q, Yi B, Fan C, Zhang C, Edwards D, Batley J and Zhou Y. (2015) A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics 16, 409
# Pang W, Li X, Choi SR, Nguyen VD, Dhandapani V, Kim YY, Ramchiary N, Kim JG, Edwards D, Batley J, Na J, Kim HR, Lim YP. (2015) Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L). Molecular Breeding 35:126
# Patel DA, Zander M, Van de Wouw AP, Mason AS, Edwards D, Batley J. (2015) Population Diversity of Leptosphaeria maculans in Australia. International Journal of Biology 7 (3): 18-36
# Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B and Batley J. (2015) Scanning ethyl methanesulphonate effects on the whole genome of Lotus japonicus using second generation sequencing analysis. G3. 5 (4): 559-67
# Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D. (2015) High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 128 (6): 1039-1047.
# Mason M, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources (Accepted January 2015).
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ, Edwards D. (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany. 66 (5):1489-98
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1):97-104.
# Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2015) Unfolding the secrets of coral-algal symbiosis. The ISME Journal. 9 (4): 844-56
# Golicz AA, Martinez PA, Zander M, Patel DA, Van De Wouw AP, Visendi P, Fitzgerald TL, Edwards D and Batley J. (2015) Gene loss in the fungal canola pathogen Leptosphaeria maculans. Functional and Integrative Genomics 15:189-196
# Saxena RK, Edwards D and Varshney RK. (2014) Structural variations in plant genomes. Briefings in Functional Genomics. 13 (4), 296-307
# Dalton-Morgan J, Hayward A, Alamery S, Tollenaere R, Mason AS, Campbell E, Patel D, Lorenc MT, Yi B, Long Y, Meng J, Raman R, Raman H, Lawley C, Edwards D and Batley J. (2014) A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Functional & Integrative Genomics. 14 (4): 643-655
# Cai G, Yang Q, Yi B, Fan C, Edwards D, Batley J and Zhou Y. (2014) A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map. PLOS ONE. 9 (10): e109910
# Rosic N, Kaniewska P, Chan K, Ling E, Edwards D, Dove D and Hoegh-Guldberg O. (2014) Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 15:1052.
# Shin SC, Ahn DH, Kim SJ, Pyo CW, Lee H, Kim MK, Lee J, Lee JE, H. Detrich III HW, Postlethwait JH, Edwards D, Lee SG, Lee JH, Park H. The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. (2014) Genome Biology 15:468.
# Chalhoub B., Denoeud F., Liu S., Parkin I.A.P., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., Corréa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento P., Noel B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.-C., Fan G., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.-H., Thi V.H.D., Chalabi S., Hu Q., Fan C., Tollenaere R., Lu Y., Battail C., Shen J., Sidebottom C.H.D., Wang X., Canaguier A., Chauveau A., Bérard A., Deniot G., Guan M., Liu Z., Sun F., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X., Meng J., Ma J., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.-M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y., Hua W., Sharpe A.G., Paterson A.H., Guan C., Wincker P. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. [http://www.sciencemag.org/content/345/6199/950.full Science 345:950-953.]
# Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2014) Unfolding the secrets of coral-algal symbiosis. The ISME Journal 9(4):844-56
# International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. [http://www.sciencemag.org/content/345/6194/1251788.abstract Science 345:1251788-1251788]
# Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. [http://www.sciencemag.org/content/345/6194/1250092.abstract Science 345:1250092-1250092]
# Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. [http://www.sciencemag.org/content/345/6194/1250091.abstract Science 345:1250091-1250091]
# Parkin, I., Koh, C., Tang, H., Robinson, S., Kagale, S., Clarke, W., Town, C., Nixon, J., Krishnakumar, V., Bidwell, S., Denoeud, F., Belcram, H., Links, M., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A., Pires, J., Barker, G., Moore, J., Walley, P., Manoli, S., Batley, J., Edwards, D., Nelson, M., Wang, X., Paterson, A., King, G., Bancroft, I., Chalhoub, B. and Sharpe, A. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. [http://genomebiology.com/2014/15/6/R77 Genome Biology 15, R77]
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. [http://www.onlinelibrary.wiley.com/doi/10.1111/pbi.12240/abstract Plant Biotechnology Journal 13 (1), 97-104]
# Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Kumar P, Parkin I, Batley J, Luckett D, and Wratten N. (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101673 PLOS ONE. 9(7): e101673]
# Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, SH, Wang X, Wang J, Lu K, Fan Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, L Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. [http://www.nature.com/ncomms/2014/140523/ncomms4930/full/ncomms4930.html Nature Communications. 5. DOI: 10.1038/ncomms4930]
# Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D and Batley, J. (2014) High-density SNP markers based map construction and genome-wide linkage analysis in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12186/abstract Plant Biotechnology Journal. 12:851-860]
# Ruperao P, Chan KCK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D. (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12182/abstract Plant Biotechnology Journal. 12:778-786]
# Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 [http://www.mdpi.com/2079-7737/2/4/1357/pdf Biology 2: 1357-1377]
# Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Long Y, Meng J, Batley J, Edwards D. (2013) Characterising diversity in the Brassica genomes. [http://www.actahort.org/books/1005/ Acta Horticulturae. 1005: 33-48]
# Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. [http://link.springer.com/article/10.1007%2Fs11105-013-0669-x Plant Molecular Biology Reporter. 1-14]
# Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X , Kahl G, Edwards D, Varshney RK. (2013) Functional genomics to study stress responses in crop legumes: Progress and prospects. [http://www.publish.csiro.au/paper/FP13191.htm Functional Plant Biology. 40(12) 1221-1233]
# Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MY, Campbell E, Hayward A, Edwards D, Raman H and Batley J. (2013) Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. [http://link.springer.com/article/10.1007%2Fs10142-013-0324-5 Functional and Integrative Genomics. 13: 295–308]
# Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. (2013) A consensus map of rapeseed (Brassica napus L) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits. [http://www.biomedcentral.com/1471-2164/14/277 BMC Genomics 14: 277]
# Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Tar'an B, Millan T, Zhang X, Rosen B, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Thudi M, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, SinghKB, Datta SK, Jackson SA, Wang J, Cook D. (2013) Draft genome sequence of kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. [http://www.nature.com/nbt/journal/v31/n3/full/nbt.2491.html Nature Biotechnology 31, 240–246]
# Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST-SSRs in silico. (2013) [http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12078/abstract Molecular Ecology Resources 13 (3): 538-45]
# Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12044/full Plant Biotechnology Journal 11 (5): 564-571]
# Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, Scott PT, Gresshoff PM. (2012) Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051687 PLOS ONE e51687]
# Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J,Luckett D, Wratten N, Dennis E. (2013) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.) [http://link.springer.com/article/10.1007/s00122-012-1966-8 Theoretical and Applied Genetics 126 (1): 119-132]
# Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. [http://link.springer.com/article/10.1007/s00122-012-1964-x Theoretical and Applied Genetics 126 (1): 1-11]
# Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. [http://www.mdpi.com/2079-7737/1/2/370 Biology 1(2): 370-38]
# Edwards D, Henry RJ and Edwards KJ. (2012) Advances in DNA sequencing accelerating plant biotechnology. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00724.x/full Plant Biotechnology Journal. 10 (6): 621–622]
# Hayashi S, Reid D, Lorenc M, Stiller J, Edwards D, Gresshoff PM and Ferguson BJ. (2012) Transient Nod-factor dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00729.x/abstract Plant Biotechnology Journal. 8: 995–1010]
# Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT and Gresshoff PM. (2012) Genetic, biochemical, and morphological diversity of the legume biofuel tree Pongamia pinnata. Journal of Plant Genome Sciences. 1 (3): 54-67
# Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00718.x/abstract Plant Biotechnology Journal. 10 (6): 743-749]
# Hayward A, Vighnesh G, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D and Batley J. (2012) Second Generation Sequencing for Gene Discovery in the Brassicaceae. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00719.x/abstract Plant Biotechnology Journal. 10 (6): 750-759]
# Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Edwards D and Batley J. (2012) Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00716.x/abstract Plant Biotechnology Journal. 10 (6): 709-715]
# Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00717.x/abstract Plant Biotechnology Journal. 10 (6): 703-708]
# Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. [http://www.amjbot.org/content/99/9/e369.short American Journal of Botany. 99 (9) e369-e371]
# Reid DE, Hayashi S, Lorenc M, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. (2012) Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00706.x/abstract Plant Biotechnology Journal. 10 (6): 680-689]
#Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D and Batley J. (2012) SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology. 39: 1-12
#Raman R, Taylor B, Marcroft S, Stiller J, Eckermann P, Coombes N, Rehman A, Lindbeck K, Luckett D, Wratten N, Batley J, Edwards D, Wang X, Raman H. Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.) [http://www.springerlink.com/content/a1h7t6648087735w/abstract/ Theoretical and Applied Genetics 125: 405-415]
#Lai K, Lorenc MT and Edwards D. (2012) Genomic databases for crop improvement. [http://www.mdpi.com/2073-4395/2/1/62/ Agronomy 2: 67-73]
#Azam S, Thakur V, Pradeep R, Shah T, Jayashree B, BhanuPrakash A, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG and Varshney R. (2012) Coverage based consensus calling (CBCC) of short sequence reads and comparison of CBCC-results for the identification of SNPs in chickpea, a crop species without the reference genome. [http://www.amjbot.org/content/early/2012/01/31/ajb.1100419 American Journal of Botany 99 (2): 186-192]
#Hayward A, McLanders J, Campbell E, Edwards D and Batley J. (2012) Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. [http://onlinelibrary.wiley.com/doi/10.1111/j.1438-8677.2011.00481.x/abstract Plant Biology 14 (1): 1-10]
#Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) [http://www.amjbot.org/content/99/2/365.short American Journal of Botany 99 (2): 365-371]
#Lee H, Lai K, Lorenc MT, Imelfort M, Duran C and Edwards D. (2012) Bioinformatics tools and databases for analysis of next generation sequence data. [http://bfg.oxfordjournals.org/content/early/2011/12/18/bfgp.elr037.abstract Briefings in Functional Genomics 11 (1), 12-24]
#Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.short Plant and Cell Physiology 53(2): e2(1–7)]
#Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. [http://www.springerlink.com/content/uk508r17832pkht8/ Theoretical and Applied Genetics 3: 423-432]
#Rosic N, Kaniewska P, Ling E, Edwards D, Dove S, Hoegh-Guldberg O. (2011) Transcriptomics of the Coral-Algal Symbiosis in Response to Environmental Stress. European Journal of Phycology 46, 97
#The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html Nature Genetics 43: 1035-1040]
#Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Plant Biotechnology Journal 9 (7): 768-775]
#Mun JH, Kwon SJ, Seol YJ, Kim JA, Jin M, Kim JS, Lim MH, Lee SI, Hong JK, Park TH, Lee SC, Kim BJ, Seo MS, Baek S, Lee MJ, Shin JY, Hahn JH, Hwang YJ, Lim KB, Park JY, Lee J, Yang TJ, Yu HJ, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Parkin IAP, Batley J, Edwards D and Park BS. (2010) Sequence and structure of Brassica rapa chromosome A3. [http://genomebiology.com/2010/11/9/R94 Genome Biology 11: R94]
#Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, PhD; Hur Y and Lim YP. (2010) Rapid Divergence of Repetitive DNAs in Brassica Relatives. [http://dx.doi.org/10.1016/j.ygeno.2010.12.002 Genomics 97(3): 173-185 ]
#Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman P, Clark T, McKenzie M, Appleby N, Batley J, Basford K, and Edwards D. (2010) Future tools for association mapping in crop plants. [http://rparticle.web-p.cisti.nrc.ca/rparticle/AbstractTemplateServlet?calyLang=eng&journal=gen&volume=53&year=2010&issue=11&msno=g10-057 Genome 53: 1017-1023]
#Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]
#Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. [http://bioinformatics.oxfordjournals.org/content/26/2/273.short Bioinformatics 26 (2): 273-274]
#Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00459.x/abstract Plant Biotechnology Journal 8: 2–9]
#Kaur S, Cogan N.O.I, Ye G, Baillie R.C, M. L. Hand M.L, Ling A.E., Mcgearey A.K., Kaur J, Hopkins C.J, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith K.F, Forster J.W, Spangenberg G.C. (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. [http://www.springerlink.com/content/lk759m559hl8quw2/ Theoretical and Applied Genetics 120 (1): 71-83]
#Imelfort M and Edwards D. (2009) De novo sequencing of plant genomes using second-generation technologies. [http://bib.oxfordjournals.org/content/10/6/609.abstract Briefings in Bioinformatics 10: 609-618]
#Batley J and Edwards D. (2009) Genome sequence data: management, storage, and visualization. [http://www.biotechniques.com/multimedia/archive/00044/BTN_A_000113134_O_44655a.pdf Biotechniques 46:333-336]
#Duran C, Appleby N, Vardy M, Imelfort M, Edwards D and Batley J. (2009) Single Nucleotide Polymorphism Discovery in Barley using AutoSNPdb. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00407.x/abstract Plant Biotechnology Journal 7 (4): 326 – 333]
#Imelfort M, Duran C, Batley J and Edwards D. (2009) Discovering genetic polymorphisms in next generation sequencing data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00406.x/abstract Plant Biotechnology Journal 7 (4): 312 – 317]
#Duran C, Appleby N,, Edwards D and Batley J. (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. [http://www.bentham.org/cbio/Samples/cbio%204-1/0003CBIO.pdf Current Bioinformatics 4: 16-27]
#Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J and Edwards D. (2009) AutoSNPdb: An Annotated Single Nucleotide Polymorphism Database for Crop Plants. [http://nar.oxfordjournals.org/content/37/suppl_1/D951.short Nucleic Acids Research 37: 951–953]
#Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS and Lim YP. (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. [http://www.springerlink.com/content/n6h2q013qn105667/ Theoretical and Applied Genetics 115 (6): 777-792]
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G and Edwards D. (2007) A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis. [http://www.biomedcentral.com/1471-2229/7/40 BMC Plant Biology 7: 40]
#Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, Hur YK, Bhak J, Edwards D and Lim YP. (2007) Genomic distribution of Simple Sequence Repeats in Brassica rapa. [http://molcells.inforang.com/article_pdf/Ksmcb/23/Ksmcb23-3-10.pdf Molecules and Cells 23 (3): 349-356]
#Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC and Edwards D. (2007) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Brassica napus expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01738.x/abstract Molecular Ecology Notes 7: 886–889.]
#Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D and Batley J. (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01681.x/abstract Molecular Ecology Notes 7: 697-700]
#Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiwiecz M, Spangenberg G, Edwards D and Batley J. (2007) Characterisation of Simple Sequence Repeat markers derived in silico from Brassica rapa Bacterial Artificial Chromosome sequences and their application in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01578.x/abstract Molecular Ecology Notes 7: 273-277]
#Erwin T, Jewell E, Love C, Lim G, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg G and Edwards D. (2007) BASC: an integrated bioinformatics system for Brassica research. [http://nar.oxfordjournals.org/content/35/suppl_1/D870.full Nucleic Acids Research 35: D870–D873]
#Donnison IS, Gay AP, Thomas H, Edwards KJ, Edwards D, James CL, Thomas AM, Ougham HJ. (2007) Modification of nitrogen remobilisation, grain fill and leaf senescence in maize (Zea mays L.) by transposon insertional mutagenesis. [http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2006.01928.x/abstract New Phytologist 173: 481-494]
#Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg G, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01488.x/abstract Molecular Ecology Notes 6: 1191-1194]
#Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Uhm T, Bang JW, Edwards D, Bancroft I, Park BS, Lee J, and Lim YP. (2006) A Survey of the Brassica rapa Genome through BAC-End Sequence Analysis, and Comparative Analysis with Arabidopsis thaliana. [http://molcells.inforang.com/article_pdf/Ksmcb/22/Ksmcb22-3-8.pdf Molecules and Cells 22: 300-307]
#Philippar K, Büchsenschütz K, Edwards D, Löffler J, Lüthen H, Kranz E, Edwards KJ and Hedrich R. (2006) The auxin-induced K+ channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development. [http://www.springerlink.com/content/aj37695670l2h21g/ Plant Molecular Biology 61: 757-768]
#Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC and Edwards D. (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. [http://nar.oxfordjournals.org/content/34/suppl_2/W656.abstract Nucleic Acids Research 34: W656–W659]
#Love C, Logan E, Erwin T, Spangenberg G and Edwards D. (2006) Analysis of the Brassica A and C Genomes and Comparison with the Genome of Arabidopsis thaliana. [http://www.actahort.org/books/706/706_9.htm Acta Horticulturae 706: 99-104]
#Love C, Logan E, Erwin T, Kaur J, Lim GAC, Hopkins C, Batley J, James N, May S, Spangenberg G and Edwards D. (2006) Integrating and interrogating diverse Brassica data within an EnsEMBL structured database. [http://www.actahort.org/books/706/706_7.htm Acta Horticulturae 706: 77-82]
#Hopkins C, Mogg R, Gororo N, Salisbury PA, Burton WA, Love C, Spangenberg GC, Edwards D and Batley J. (2006) An assessment of genetic diversity within and between Brassica napus and Brassica juncea lines from international germplasm collections. [http://www.actahort.org/books/706/706_11.htm Acta Horticulturae 706: 115-119]
#Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GS, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Fragaria x ananassa expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2005.01215.x/abstract Molecular Ecology Notes 6: 319-322]
#Felitti S, Shields K, Ramsperger M, Tian P, Sawbridge T, Webster T, Logan E, Erwin T, Forster J, Edwards D and Spangenberg G. (2006) Transcriptome analysis of Neotyphodium and Epichloë grass endophytes. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WFV-4JJ2BVB-1&_user=10&_coverDate=07%2F31%2F2006&_rdoc=2&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info%28%23toc%236804%232006%23999569992%23623142%23FLA%23display%23Volume%29&_cdi=6804&_sort=d&_docanchor=&_ct=6&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=946ca03d60d162de79d2b5c3c8079bdc&searchtype=a Fungal Genetics and Biology 43: 465-475]
#Sexton A, Cozijnsen A, Keniry A, Logan E, Love C, Batley J, Edwards D and Howlett B. (2006) Transcription profile of genes from three developmental stages of the plant pathogen Sclerotinia sclerotiorum. [http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00212.x/abstract FEMS Microbiology Letters 258: 150-160]
#Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker GLA, Spangenberg GC and Edwards D. (2005) SNPServer: A Realtime SNP Discovery tool. [http://nar.oxfordjournals.org/content/33/suppl_1/D656.abstract Nucleic Acids Research 33: D656-D659]
#Mortimer J, Batley J, Love C, Logan E and Edwards D. (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology 7: 17-25
#Love C, Robinson A, Lim G, Hopkins C, Batley J, Barker G, Spangenberg G and Edwards D. (2005) Brassica ASTRA: An Integrated Database for Brassica Genomic Research. [http://nar.oxfordjournals.org/content/33/suppl_2/W493.abstract Nucleic Acids Research 33: W493-W495]
#Robinson AJ, Love CG, Batley J, Barker G and Edwards D. (2004) Simple Sequence Repeat Marker Loci Discovery using SSR Primer. [http://bioinformatics.oxfordjournals.org/content/20/9/1475.abstract Bioinformatics 20: 1475-1476]
#Wilson ID, Barker GLA, Beswick RW, Shepherd SK, Lu C, Coghill JA, Edwards D, Owen P, Lyons R, Parker JS, Lenton JR, Holdsworth MJ, Shewry PR and Edwards KJ. (2004) A transcriptomics resource for wheat functional genomics. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2004.00096.x/abstract Plant Biotechnology Journal 2: 495-506]
#Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. [http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2804%2900076-9 Trends in Biotechnology 22: 232-237]
#Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, and Edwards D. (2004) New computational tools for Brassica genome research. [http://www.hindawi.com/journals/cfg/2004/160354.abs.html Comparative and Functional Genomics 5: 276-280]
#Love CG, Batley J and Edwards D. (2003) Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
#Batley J, Barker G, O'Sullivan H, Edwards KJ and Edwards D. (2003) Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. [http://www.plantphysiol.org/cgi/content/abstract/132/1/84 Plant Physiology 132: 84-91]
#Batley J, Mogg R, Edwards D, O’Sullivan H and Edwards KJ. (2003) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. [http://www.springerlink.com/content/q142t023674pl328/ Molecular Breeding 11: 111-120]
#Barker G, Batley J, O'Sullivan H, Edwards KJ and Edwards D. (2003) Redundancy Based Detection of Sequence Polymorphisms in Expressed Sequence Tag Data using AutoSNP. [http://bioinformatics.oxfordjournals.org/content/19/3/421.abstract Bioinformatics 19: 421-422]
#Edwards D, Coghill J, Batley J, Holdsworth M and Edwards KJ. (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. [http://www.biotechniques.com/multimedia/archive/00011/02325rr04_11101a.pdf Biotechniques 32: 1090-1097]
#Edwards D, Stevenson D, Forsyth A, Hegarty M, Batley J, Holdsworth M and Edwards KJ. (2002) Identification of transposon-tagged maize genes displaying homology to arrayed cDNA clones using Mutator insertion display. Genome letters 1: 48-55
#Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H and Edwards KJ. (2002) Characterisation of the flanking regions of Zea Mays microsatellites reveals a large number of useful sequence polymorphisms. [http://www.ingentaconnect.com/content/asp/glet/2002/00000001/00000001/art00006 Theoretical and Applied Genetics 105: 532-543]
#O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. [http://www.cabi.org/AgBioTechNet/ AgBiotechNet (2000) 2]
#Hanley S, Edwards D, Stevenson D, Haines S, Hegarty M, Schuch W, Edwards KJ. Identification of transposon tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.2000.00830.x/abstract Plant Journal (2000) 23 (4):557-566]
#Edwards D, Murray JAH, Smith AG. (1998) Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. [http://www.plantphysiol.org/cgi/content/abstract/117/3/1015 Plant Physiology 117 (3): 1015-1022]
#Edwards KJ, Thompson H, Edwards D, DeSaizeu A, Sparks C, Thompson JA, Greenland AJ, Eyers M and Schuch W. (1992) Construction and Characterisation of a Yeast Artificial Chromosome Library Containing 3 Haploid Maize Genome Equivalents. [http://www.springerlink.com/content/t44p88j375vr2522/ Plant Molecular Biology 19: (2) 299-308]

===CONFERENCE PAPERS: ===

#Batley J, Edwards D, Spangenberg G, Burgess BR, Burton W, Erwin T, Hand M, Hopkins C, Howlett B, Jewell E, Kaur J, Keniry A, Li X, Love CG, Marcroft S, Mountford H, Salisbury P and Walkiewicz M. (2005) Development of molecular markers for implementation in Australian Brassica Improvement. In: 14th Australian Research Assembly on Brassicas. of a conference, Port Lincoln 2005. Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 65-69
#Edwards D, Batley J, Spangenberg G, Burgess BR, Erwin T, Hand M, Hopkins C, Jewell E, Keniry A, Li X, Love CG, Mountford H and Walkiewicz M. (2005) The Multinational Brassica Genome Project. In: 14th Australian Research Assembly on Brassicas. Port Lincoln 2005, Proceedings Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 70-72
#Batley J and Edwards D. (2004) Molecular Tools for Plant Biology. In: Proceedings of Vision for Practical Use of Biotechnology. The Korean Society of Plant Biotechnology. Korea pp 19-24
#Batley J, Vecchies A, Mogg R, Bond J, Cogan N, Hopkins C, Gororo N, Marcroft S, Forster J, Spangenberg G and Edwards D. (2003) A study of genetic diversity among Brassica napus and Brassica juncea germplasm collections using Simple Sequence Repeat (SSR) markers. Thirteen Biennial Australian Research Assembly on Brassicas. Proceedings of a conference, Tamworth, New South Wales. pp 84-86
#Edwards D. (2003) Applied Computational Tools for Crop Genome Research. In: Proceedings of Development of Core Biotechnology for Next Generation. The Korean Society of Plant Biotechnology. Korea 33-34

===OTHER PUBLICATIONS:===

#Li X, Jewell E, Erwin TA, Lim GAC, Love CG, Batley J, Spangenberg GC and Edwards D. (2007) Brassica Bacterial Artificial Chromosome (BAC) and Gene Annotator. Cruciferae Newsletter 27
#Ling A, Hopkins C, Burton W, Hand M, Kaur S, McGearey A, Kaur J, Love C, Salisbury P, Todorovic M, Vardy M, Walkiewicz M, Spangenberg G, Edwards D and Batley J. (2007) Development of Molecular Markers for Implementation in the Australian National Brassica Improvement Program. Cruciferae Newsletter 27
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27
#Erwin TA, Jewell E, Love CG, Xi Li, Lim GAC, Chapman R, Spangenberg G, and Edwards D. (2007) Brassica BASC: An Integrated Bioinformatics System for Brassica Research. Cruciferae Newsletter 27
#Kaur J, Webster T, Chapman R, Batley J, Salisbury P, Spangenberg GC and Edwards D. (2007) Gene Expression Studies in Canola in Response to Blackleg (Leptosphaeria maculans) Infection. Cruciferae Newsletter 27
#Savage D, Logan E, Erwin T, Robinson A, Love CG, Barker G, Batley J and Edwards D. (2007) Real-time mining of maize genome data for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular genetic markers. Maize Newsletter 79
#Swarbreck D, O’Sullivan D, Ripoll PJ, Edwards D, Edwards KJ and Theodoulou F. (2002) Unravelling the MRP family in monocots. Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 32: S1

BOLPANGENOME

2017-05-01T08:22:27Z

Uqccha18: Replaced content with "This page has been moved to [http://brassicagenome.net/databases.php brassicagenome.net] which contains all our Brassica works."

This page has been moved to [http://brassicagenome.net/databases.php brassicagenome.net] which contains all our Brassica works.

Kenneth Chan

2017-03-31T02:59:41Z

Uqccha18:

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2015 - present University of Western Australia. Postdoctoral Bioinformatics Researcher
*2013 - 2014 University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ applied bioinformatics group in UQ. Since then, I have intensively worked with various NGS data. Following Dave's relocation to UWA in 2015, I have also moved from UQ to UWA.

My research interest is in NGS data management , analysis and visualisation, bioinformatics tool and pipeline development, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

===Contact:===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: kenneth.chan@uwa.edu.au

Kenneth Chan

2017-03-31T02:55:45Z

Uqccha18:

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2015 - present University of Western Australia. Postdoctoral Bioinformatics Researcher
*2013 - 2014 University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ applied bioinformatics group in UQ. Since then, I have intensively worked with various NGS data. Following Dave's relocation to UWA in 2015, I have also moved from UQ to UWA.

My research interest is in NGS data management , analysis and visualisation, bioinformatics tool and pipeline development, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

[[File:Kenneth_orcid_qrcode.png|frameless|100px|Kenneth ORCID QR Code]]

===Contact:===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: kenneth.chan@uwa.edu.au

Main Page

2017-01-31T03:51:32Z

Uqccha18: /* PhD students */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (HueyTyng) Lee]]

[[Juan Montenegro]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

[[Ricky Hu]]

Positions available, please contact David Edwards if interested

=== Interns ===

[[Oliver Schliebs]]

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2017-01-31T03:50:44Z

Uqccha18: /* Interns */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (HueyTyng) Lee]]

[[Juan Montenegro]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

[[Ricky Hu]]

Positions available, please contact David Edwards if interested

=== Interns ===

[[Oliver Schliebs]]

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2017-01-31T03:50:00Z

Uqccha18: /* Honours students */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (HueyTyng) Lee]]

[[Juan Montenegro]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

[[Ricky Hu]]

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2017-01-31T03:49:18Z

Uqccha18: /* PhD students */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Jenny (HueyTyng) Lee]]

[[Juan Montenegro]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Publications KC

2017-01-31T03:44:47Z

Uqccha18: /* JOURNAL ARTICLES: */

==Publications - Chon Kit Kenneth Chan==

===JOURNAL ARTICLES:===
# Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP et al: The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications 2016, 7:13390.
# Lee H, Golicz AA, Bayer PE, Jiao Y, Tang H, Paterson AH, Sablok G, Krishnaraj RR, Chan CK, Batley J et al: The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri). Plant Physiol 2016, 172(1):272-283.
# Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan C-KK, Staňková H et al: An efficient approach to BAC based assembly of complex genomes. Plant Methods 2016, 12:2.
# Kaniewska P, Chan C-KK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg O, Dove S: Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change. PLoS ONE 2015, 10(10):e0139223.
# Bayer P, Ruperao P, Mason A, Stiller J, Chan C-KK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P et al: High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 2015, 128(6):1039-1047.
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015, 66(5):1489-1498.
# Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
# Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
# Ruperao P, Chan C-KK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
# Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
# Chan C-KK, Halgamuge SK: [http://www.google.com.au/url?sa=t&source=web&cd=1&ved=0CBYQFjAA&url=http%3A%2F%2Fwww.sersc.org%2Fjournals%2FIJBSBT%2Fvol1_no1%2F1.pdf&ei=EXWdTeimL4LovQO-mcCsBA&usg=AFQjCNF1LEKGsSVzWZ5Em6TBRlHgG8TTXA&sig2=WyfI3Q4Zd6lZRmohmDNziA A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature] International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
# Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: [http://www.biomedcentral.com/1471-2105/9/215 Binning sequences using very sparse labels within a metagenome] BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: [http://www.hindawi.com/journals/jbb/2008/513701/ref/ Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing] Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.
# Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

===BOOK CHAPER:===
# Ghosh S, Chan C-KK: Analysis of RNA-Seq Data Using TopHat and Cufflinks. In: Plant Bioinformatics: Methods and Protocols. Edited by Edwards D. New York, NY: Springer New York; 2016: 339-361.
# Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Sequences Using Very Sparse Labels Within a Metagenome. In: Encyclopedia of Metagenomics. Edited by Nelson EK. New York, NY: Springer New York; 2013: 1-13.
# Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Metagenomic Sequences Using Seeded GSOM. In: Handbook of Molecular Microbial Ecology I. John Wiley & Sons, Inc.; 2011: 369-378.

===CONFERENCE PAPERS:===
# Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
# Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: [http://bric.postech.ac.kr/vod/vod_detail.php?nNum=3326 Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes] In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
# Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
# Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
# Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

===MONSANTO INTERNAL CONFERENCE POSTERS:===
# Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

[[Kenneth_Chan|Back to Kenneth's Profile]]

Publications KC

2016-04-13T12:57:34Z

Uqccha18:

==Publications - Chon Kit Kenneth Chan==

===JOURNAL ARTICLES:===
# Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan C-KK, Staňková H et al: An efficient approach to BAC based assembly of complex genomes. Plant Methods 2016, 12:2.
# Kaniewska P, Chan C-KK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg O, Dove S: Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change. PLoS ONE 2015, 10(10):e0139223.
# Bayer P, Ruperao P, Mason A, Stiller J, Chan C-KK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P et al: High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 2015, 128(6):1039-1047.
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015, 66(5):1489-1498.
# Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
# Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
# Ruperao P, Chan C-KK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
# Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
# Chan C-KK, Halgamuge SK: [http://www.google.com.au/url?sa=t&source=web&cd=1&ved=0CBYQFjAA&url=http%3A%2F%2Fwww.sersc.org%2Fjournals%2FIJBSBT%2Fvol1_no1%2F1.pdf&ei=EXWdTeimL4LovQO-mcCsBA&usg=AFQjCNF1LEKGsSVzWZ5Em6TBRlHgG8TTXA&sig2=WyfI3Q4Zd6lZRmohmDNziA A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature] International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
# Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: [http://www.biomedcentral.com/1471-2105/9/215 Binning sequences using very sparse labels within a metagenome] BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: [http://www.hindawi.com/journals/jbb/2008/513701/ref/ Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing] Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.
# Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

===BOOK CHAPER:===
# Ghosh S, Chan C-KK: Analysis of RNA-Seq Data Using TopHat and Cufflinks. In: Plant Bioinformatics: Methods and Protocols. Edited by Edwards D. New York, NY: Springer New York; 2016: 339-361.
# Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Sequences Using Very Sparse Labels Within a Metagenome. In: Encyclopedia of Metagenomics. Edited by Nelson EK. New York, NY: Springer New York; 2013: 1-13.
# Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Metagenomic Sequences Using Seeded GSOM. In: Handbook of Molecular Microbial Ecology I. John Wiley & Sons, Inc.; 2011: 369-378.

===CONFERENCE PAPERS:===
# Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
# Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: [http://bric.postech.ac.kr/vod/vod_detail.php?nNum=3326 Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes] In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
# Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
# Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
# Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

===MONSANTO INTERNAL CONFERENCE POSTERS:===
# Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

[[Kenneth_Chan|Back to Kenneth's Profile]]

Publications KC

2016-03-14T08:09:02Z

Uqccha18: /* Publications - Chon Kit Kenneth Chan */

==Publications - Chon Kit Kenneth Chan==

===JOURNAL ARTICLES:===
# Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan C-KK, Staňková H et al: An efficient approach to BAC based assembly of complex genomes. Plant Methods 2016, 12:2.
# Kaniewska P, Chan C-KK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg O, Dove S: Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change. PLoS ONE 2015, 10(10):e0139223.
# Bayer P, Ruperao P, Mason A, Stiller J, Chan C-KK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P et al: High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 2015, 128(6):1039-1047.
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015, 66(5):1489-1498.
# Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
# Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
# Ruperao P, Chan C-KK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
# Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
# Chan C-KK, Halgamuge SK: [http://www.google.com.au/url?sa=t&source=web&cd=1&ved=0CBYQFjAA&url=http%3A%2F%2Fwww.sersc.org%2Fjournals%2FIJBSBT%2Fvol1_no1%2F1.pdf&ei=EXWdTeimL4LovQO-mcCsBA&usg=AFQjCNF1LEKGsSVzWZ5Em6TBRlHgG8TTXA&sig2=WyfI3Q4Zd6lZRmohmDNziA A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature] International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
# Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: [http://www.biomedcentral.com/1471-2105/9/215 Binning sequences using very sparse labels within a metagenome] BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: [http://www.hindawi.com/journals/jbb/2008/513701/ref/ Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing] Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.
# Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

===BOOK CHAPER:===
# Ghosh S, Chan C-KK: Analysis of RNA-Seq Data Using TopHat and Cufflinks. In: Plant Bioinformatics: Methods and Protocols. Edited by Edwards D. New York, NY: Springer New York; 2016: 339-361.
# Tseng, C.-H., Chan, C.-K. K., Hsu, A. L., Halgamuge, S. K. and Tang, S.-L. (2011) Binning Metagenomic Sequences Using Seeded GSOM, in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (ed F. J. de Bruijn), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118010518.ch42

===CONFERENCE PAPERS:===
# Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
# Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: [http://bric.postech.ac.kr/vod/vod_detail.php?nNum=3326 Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes] In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
# Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
# Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
# Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

===MONSANTO INTERNAL CONFERENCE POSTERS:===
# Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

[[Kenneth_Chan|Back to Kenneth's Profile]]

A differential kmer analysis pipeline

2015-09-11T02:57:06Z

Uqccha18:

Most next generation transcriptome sequencing projects rely on either mapping sequenced reads to a reference of the assembly of the reads themselves to produce a reference for mapping.

As an alternative approach, we have established a non-mapping method where differential expressed reads are determined by examining kmer abundance. While computationally expensive, this approach has the advantage in that it works well for metagenomic samples and can differentiate between very similar genes from the same or related organisms.

This method has been successfully applied to identify differential genes in coral RNA-Seq data. The pipeline can be downloaded from [[DiffKAP]].

Back to [[Main_Page]]

DiffKAP

2015-09-11T02:53:48Z

Uqccha18:

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version 0.9 (23/09/2013):
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.zip DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

== Citation ==
* Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052

Back to [[Main_Page]]

Publications KC

2015-08-31T07:36:02Z

Uqccha18:

==Publications - Chon Kit Kenneth Chan==

===JOURNAL ARTICLES:===
# Bayer P, Ruperao P, Mason A, Stiller J, Chan C-KK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P et al: High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 2015, 128(6):1039-1047.
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015, 66(5):1489-1498.
# Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
# Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
# Ruperao P, Chan C-KK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
# Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
# Chan C-KK, Halgamuge SK: [http://www.google.com.au/url?sa=t&source=web&cd=1&ved=0CBYQFjAA&url=http%3A%2F%2Fwww.sersc.org%2Fjournals%2FIJBSBT%2Fvol1_no1%2F1.pdf&ei=EXWdTeimL4LovQO-mcCsBA&usg=AFQjCNF1LEKGsSVzWZ5Em6TBRlHgG8TTXA&sig2=WyfI3Q4Zd6lZRmohmDNziA A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature] International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
# Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: [http://www.biomedcentral.com/1471-2105/9/215 Binning sequences using very sparse labels within a metagenome] BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: [http://www.hindawi.com/journals/jbb/2008/513701/ref/ Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing] Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.
# Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

===BOOK CHAPER:===
# Tseng, C.-H., Chan, C.-K. K., Hsu, A. L., Halgamuge, S. K. and Tang, S.-L. (2011) Binning Metagenomic Sequences Using Seeded GSOM, in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (ed F. J. de Bruijn), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118010518.ch42

===CONFERENCE PAPERS:===
# Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
# Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: [http://bric.postech.ac.kr/vod/vod_detail.php?nNum=3326 Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes] In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
# Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
# Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
# Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

===MONSANTO INTERNAL CONFERENCE POSTERS:===
# Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

[[Kenneth_Chan|Back to Kenneth's Profile]]

Kenneth Chan

2015-01-19T07:28:06Z

Uqccha18: /* Posts held: */

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2015 - present University of Western Australia. Postdoctoral Bioinformatics Researcher
*2013 - 2014 University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ applied bioinformatics group in UQ. Since then, I have intensively worked with various NGS data. Following Dave's relocation to UWA in 2015, I have also moved from UQ to UWA.

My research interest is in NGS data management, analysis and visualisation, bioinformatics tool and pipeline development, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

===Contact:===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: kenneth.chan@uwa.edu.au

Kenneth Chan

2015-01-19T07:27:41Z

Uqccha18:

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2014 - present University of Western Australia. Postdoctoral Bioinformatics Researcher
*2013 - 2014 University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ applied bioinformatics group in UQ. Since then, I have intensively worked with various NGS data. Following Dave's relocation to UWA in 2015, I have also moved from UQ to UWA.

My research interest is in NGS data management, analysis and visualisation, bioinformatics tool and pipeline development, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

===Contact:===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: kenneth.chan@uwa.edu.au

Publications KC

2015-01-19T05:06:20Z

Uqccha18:

==Publications - Chon Kit Kenneth Chan==

===JOURNAL ARTICLES:===
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015.
# Rosic N, Kaniewska P, Chan C-K, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
# Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
# Ruperao P, Chan C-KK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
# Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
# Chan C-KK, Halgamuge SK: [http://www.google.com.au/url?sa=t&source=web&cd=1&ved=0CBYQFjAA&url=http%3A%2F%2Fwww.sersc.org%2Fjournals%2FIJBSBT%2Fvol1_no1%2F1.pdf&ei=EXWdTeimL4LovQO-mcCsBA&usg=AFQjCNF1LEKGsSVzWZ5Em6TBRlHgG8TTXA&sig2=WyfI3Q4Zd6lZRmohmDNziA A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature] International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
# Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: [http://www.biomedcentral.com/1471-2105/9/215 Binning sequences using very sparse labels within a metagenome] BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: [http://www.hindawi.com/journals/jbb/2008/513701/ref/ Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing] Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.
# Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

===BOOK CHAPER:===
# Tseng, C.-H., Chan, C.-K. K., Hsu, A. L., Halgamuge, S. K. and Tang, S.-L. (2011) Binning Metagenomic Sequences Using Seeded GSOM, in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (ed F. J. de Bruijn), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118010518.ch42

===CONFERENCE PAPERS:===
# Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
# Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
# Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: [http://bric.postech.ac.kr/vod/vod_detail.php?nNum=3326 Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes] In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
# Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
# Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
# Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

===MONSANTO INTERNAL CONFERENCE POSTERS:===
# Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
# Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

[[Kenneth_Chan|Back to Kenneth's Profile]]

Kenneth Chan

2015-01-14T04:02:58Z

Uqccha18: /* Contact: */

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2013 - present University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ group and currently working on several projects in sequence analysis that includes coral, wheat, chickpea, brassica and soybean genomic, transcriptomic and meta-transcriptomic NGS data.

My research interest is in bioinformatics tool development, NGS data management and analysis, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

===Contact:===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: kenneth.chan@uwa.edu.au

Main Page

2014-08-28T00:56:48Z

Uqccha18: /* Group members */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland to lead a Bioinformatics node for the Australian Centre for Plant Functional Genomics and establish independent research in applied bioinformatics. Since this time, the group has attracted more than 6.5 M AU$ in competitive funds and is a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex plant genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.acpfg.com.au/ Australian Centre for Plant Functional Genomics], the [http://www.uq.edu.au/ University of Queensland], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uq.edu.au David Edwards] for further information.

We are based at the University of Queensland's St Lucia campus in Brisbane, Australia.

==Publications==

A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:A differential kmer analysis pipeline

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Philipp Bayer]]

[[Agnieszka Golicz]]

[[Bhavna Hurgobin]]

[[Kaitao Lai]]

[[Jenny (Huey Tyng) Lee]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Fabian Inturrsis]]

[[Sarah Loberg]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

Positions available, please contact David Edwards if interested

=== Master students ===

[[Patricia Angelica Vera]]

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions availble at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uq.edu.au.

Main Page

2014-08-28T00:55:41Z

Uqccha18:

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland to lead a Bioinformatics node for the Australian Centre for Plant Functional Genomics and establish independent research in applied bioinformatics. Since this time, the group has attracted more than 6.5 M AU$ in competitive funds and is a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex plant genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.acpfg.com.au/ Australian Centre for Plant Functional Genomics], the [http://www.uq.edu.au/ University of Queensland], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uq.edu.au David Edwards] for further information.

We are based at the University of Queensland's St Lucia campus in Brisbane, Australia.

==Publications==

A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:A differential kmer analysis pipeline

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

Positions available, please contact David Edwards if interested

===Research Assistants===

[[Bhavna Hurgobin]]

===PhD students===

Primary supervisor:

[[Philipp Bayer]]

[[Agnieszka Golicz]]

[[Bhavna Hurgobin]]

[[Kaitao Lai]]

[[Jenny (Huey Tyng) Lee]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Fabian Inturrsis]]

[[Sarah Loberg]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

Positions available, please contact David Edwards if interested

=== Master students ===

[[Patricia Angelica Vera]]

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions availble at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uq.edu.au.

TAGdb

2014-08-07T00:56:23Z

Uqccha18:

'''TAGdb''' is a web-based query tool for aligning query sequences to an existing database of paired short read data. The system has been developed using Perl and MySQL and runs on a public web server [http://sequencetagdb.info TAGdb].

The interface allows researchers to upload or input a FASTA formatted nucleotide sequence up to 5000 base pairs long for comparison with one or more paired read sequence libraries. TAGdb is a public tool and we are happy to host public data. Pease contact [[David Edwards]] for details.

'''Further information on TAGdb can be found in the publication:'''

* Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]

Back to [[Main_Page]]

Barley

2014-08-07T00:55:57Z

Uqccha18:

The applied Bioinformatics group undertakes barley research to support ongoing projects within the [http://www.acpfg.com.au/ ACPFG]

As part of this research, we have produced Illumina paired read and mate paired whole genome sequence data. This is searchable at [http://sequencetagdb.info TAGdb].

All sequence data is freely available from [mailto:Dave.Edwards@uq.edu.au David Edwards] on request.

Back to [[Main_Page]]

Barley

2014-08-07T00:39:36Z

Uqccha18:

The applied Bioinformatics group undertakes barley research to support ongoing projects within the [http://www.acpfg.com.au/ ACPFG]

As part of this research, we have produced Illumina paired read and mate paired whole genome sequence data. This is searchable at [http://sequencetagdb.info/tagdb TAGdb].

All sequence data is freely available from [mailto:Dave.Edwards@uq.edu.au David Edwards] on request.

Back to [[Main_Page]]

TAGdb

2014-08-07T00:39:00Z

Uqccha18:

'''TAGdb''' is a web-based query tool for aligning query sequences to an existing database of paired short read data. The system has been developed using Perl and MySQL and runs on a public web server [http://sequencetagdb.info/tagdb TAGdb].

The interface allows researchers to upload or input a FASTA formatted nucleotide sequence up to 5000 base pairs long for comparison with one or more paired read sequence libraries. TAGdb is a public tool and we are happy to host public data. Pease contact [[David Edwards]] for details.

'''Further information on TAGdb can be found in the publication:'''

* Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]

Back to [[Main_Page]]

SSRPoly

2014-04-17T07:05:32Z

Uqccha18:

== SSRPoly: an efficient tool for polymorphic Simple Sequence Repeat identification ==

The public availability of large quantities of gene sequence data enables mining for Simple Sequence Repeats (SSRs), molecular genetic markers which may be applied for genetic and genomic analysis. However, laboratory assessment of the SSRs is still required to assess their polymorphic status and consequently their applicability to genetic studies. We have developed the tool SSRPoly for the identification of polymorphic SSRs from EST (Expressed Sequence Tag) data, removing the requirement for this expensive and time consuming laboratory assessment. Polymorphic SSRs are distinguished from monomorphic SSRs by the representation of varying motif lengths within an alignment of sequence reads. Additional value is gained by integrating polymorphic SSR data with other relevant biological information such as predicted gene function and comparative map position. This tool can be applied for any species for which EST sequences are available. The SSRs identified may be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies, and marker assisted selection.

This software may be [http://www.appliedbioinformatics.com.au/download/SSRPoly.zip downloaded] freely for academic use only. For commercial use, please contact David Edwards at Dave.Edwards@uq.edu.au to obtain a licence.

Back to [[Main_Page|main page]]

TAGdb

2013-10-30T00:18:37Z

Uqccha18:

'''TAGdb''' is a web-based query tool for aligning query sequences to an existing database of paired short read data. The system has been developed using Perl and MySQL and runs on a public web server [http://130.102.154.90/tagdb TAGdb].

The interface allows researchers to upload or input a FASTA formatted nucleotide sequence up to 5000 base pairs long for comparison with one or more paired read sequence libraries. TAGdb is a public tool and we are happy to host public data. Pease contact [[David Edwards]] for details.

'''Further information on TAGdb can be found in the publication:'''

* Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]

Back to [[Main_Page]]

Barley

2013-10-30T00:18:08Z

Uqccha18:

The applied Bioinformatics group undertakes barley research to support ongoing projects within the [http://www.acpfg.com.au/ ACPFG]

As part of this research, we have produced Illumina paired read and mate paired whole genome sequence data. This is searchable at [http://130.102.154.90/tagdb TAGdb].

All sequence data is freely available from [mailto:Dave.Edwards@uq.edu.au David Edwards] on request.

Back to [[Main_Page]]

TAGdb

2013-10-30T00:17:14Z

Uqccha18:

'''TAGdb''' is a web-based query tool for aligning query sequences to an existing database of paired short read data. The system has been developed using Perl and MySQL and runs on a public web server http://130.102.154.90/tagdb.

The interface allows researchers to upload or input a FASTA formatted nucleotide sequence up to 5000 base pairs long for comparison with one or more paired read sequence libraries. TAGdb is a public tool and we are happy to host public data. Pease contact [[David Edwards]] for details.

'''Further information on TAGdb can be found in the publication:'''

* Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]

Back to [[Main_Page]]

DiffKAP

2013-09-23T04:19:13Z

Uqccha18: /* Download */

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version 0.9 (23/09/2013):
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.zip DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

Back to [[Main_Page]]

DiffKAP

2013-09-23T04:18:23Z

Uqccha18: /* How to interpret the results? */

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version:
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.zip DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

Back to [[Main_Page]]

DiffKAP

2013-09-23T04:18:10Z

Uqccha18: /* How to install? */

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version:
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.zip DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

Back to [[Main_Page]]

DiffKAP

2013-09-23T04:15:56Z

Uqccha18:

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version:
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.zip DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

Back to [[Main_Page]]

DiffKAP

2013-09-23T03:42:17Z

Uqccha18:

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version:
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.gz DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz here].
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-centric summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A result summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

Back to [[Main_Page]]

DiffKAP

2013-09-23T02:41:37Z

Uqccha18:

Next generation DNA sequencing technologies such as RNA-Seq currently dominate genome wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences.

With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.

The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.

== What does DiffKAP depend on? ==
DiffKAP depends on the following things:
* [http://www.cbcb.umd.edu/software/jellyfish Jellyfish] for fast kmer counting
* blastx for sequence alignment
* Some non-standard Perl modules:
** bioperl
*** Bio::SeqIO
*** Bio::SearchIO
** Parallel::ForkManager
** Statistics::Descriptive
** Config::IniFiles
** GD::Graph::linespoints (for the script identifyKmerSize)

== Download ==
* Latest Version:
** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.gz DiffKAP package]
** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
* Archived Versions:
**

== How to install? ==
* Download the [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download DiffKAP package].
* Uncompress it into:
** a DiffKAP setup file
** a README file
** a VERSION file
** an example data folder containing a small subset of a metatranscriptomic data
* read the README
* Install the DiffKAP setup script by executing: DiffKAP_setup
* *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***

== How to run? ==
# Create your project configuration file by using the example config file in the sample data directory as a template.
# Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
* The processing log is stored in /tmp/DiffKAP.log by default.

== How to interpret the results? ==
* You can download the results of the sample data [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz here].
* The script "identifyKmerSize" generates 2 files in the [OUT_DIR]/identifyKmerSize folder:
*# a txt file: contains the uniqueness ratio (in %) for each kmer size.
*# a png file: the kmer size vs uniqueness ratio plot.
* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
*# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
*#* Median-T1: The median kmer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
*#* Median-T2: Similar to Median-T1 but for Treatment 2.
*#* Ratio of Median: The ratio of Median-T1 to Median-T2.
*#* CV-T1: The coefficient of variation of all kmer occurrence represented in Treatment 1 for all kmers in the read. To show how confident the Median-T1 representing all kmers in the read.
*#* CV-T2: Similar to CV-T1 but for Treatment 2.
*# 5 annotated DER files with the word 'AnnotatedDER' in the filenames. These files are similar to the 5 DER above but contain only the annotated DER.
*# A gene-based display summary with the word 'DEG' in the filename:
*#* In a tabular form showing the number of DER in the specific files (in columns 3-7) annotated to the specific gene.
*#* It shows the unique gene list.
*#* The 'Total' column is the total number of DER annotated to such gene.
*#* It is sorted by the 'Total' column in reversed order.
*# A data summary file with 'summary.log' in the filename.

== FAQ ==
*

== Reference ==
* Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.

Back to [[Main_Page]]

Kenneth Chan

2013-09-11T05:43:30Z

Uqccha18:

== Chon Kit Kenneth Chan ==

===Academic history:===

PhD The University of Melbourne 2008

BE (1st Class Hons) The University of Melbourne 2003

BCS The University of Melbourne 2003

===Posts held:===

*2013 - present University of Queensland. Senior Research Officer
*2011 – 2013 University of Queensland. Research Officer
*2010 - 2011 Monsanto Biotech Research Center, Beijing, China. Collaboration Data Manager
*2009 - 2010 Monsanto Biotech Research Center, Beijing, China. Bioinformatics Scientist
*2008 - 2009 Objectiva Software Solutions, Beijing, China. Business Analyst
*2008 - 2008 Microsoft China, Beijing, China. Software Development Engineer
*2003 - 2004 AJAX Engineered Fasteners, Victoria, Australial. Mechatronics Engineer

I finished my PhD in Bioinformatics at the University of Melbourne focusing on developing algorithms for metagenomic sequence analysis.

After my PhD, I spent a few years travelling around northern China and worked there before coming back to Australia. I took up a few positions during my time in Beijing China. I worked in Microsoft Beijing as a Software Development Engineer; in a software company as a Business Analyst; and my last job there was working in Monsanto as a Bioinformatics Scientist focusing on developing genomic visualisation tools and later as a Collaboration Data Manager to handle all sequences and phenotypic data generated by Monsanto’s collaborators in China.

Then in early 2011, I joined Dave Edwards’ group and currently working on several projects in sequence analysis that includes coral, wheat, chickpea, brassica and soybean genomic, transcriptomic and meta-transcriptomic NGS data.

My research interest is in bioinformatics tool development, NGS data management and analysis, and machine learning.

===[[publications_KC|Publications: (follow this link)]]===

===Contact:===

University of Queensland

St Lucia, Brisbane, Australia

Tel: +61 (0)7 3346 7083

email: c.chan10@uq.edu.au

Main Page

2013-08-01T08:16:35Z

Uqccha18: /* Group members */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland to lead a Bioinformatics node for the Australian Centre for Plant Functional Genomics and establish independent research in applied bioinformatics. Since this time, the group has attracted more than 6.5 M AU$ in competitive funds and is a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex plant genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.acpfg.com.au/ Australian Centre for Plant Functional Genomics], the [http://www.uq.edu.au/ University of Queensland], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uq.edu.au David Edwards] for further information.

We are based at the University of Queensland's St Lucia campus in Brisbane, Australia.

==Publications==

A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:A differential kmer analysis pipeline

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

Positions available, please contact David Edwards if interested

===Research Assistants===

[[Bhavna Hurgobin]]

===PhD students===

Primary supervisor:

[[Philipp Bayer]]

[[Agnieszka Golicz]]

[[Kaitao Lai]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Lars Smits]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

[[Tek-Jun Ling]]

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions availble at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uq.edu.au.