Applied Bioinformatics Group - New pages [en]

Shameela Mohamedikbal

2023-11-14T01:47:30Z

Dave: Created page with "'''Shameela Mohamedikbal''' My name is Shameela, and I am currently completing my Master’s in Biotechnology with a specialization in Genetics and Genomics at UWA. My disser..."

'''Shameela Mohamedikbal'''

My name is Shameela, and I am currently completing my Master’s in Biotechnology with a specialization in Genetics and Genomics at UWA. My dissertation project is on identifying the genomic regions and haplotype structures associated with flowering time variation in soybean using advanced bioinformatics approaches.

Areas of Interest:

Bioinformatics, Population Genomics, Agriculture, Data Science

Academic History:

2021 – present: Master of Biotechnology at the University of Western Australia (Australia), with dissertation project titled “Genome-Wide Association Study and Haplotype Analysis for Flowering Time in Soybean” supervised by Prof. Dave Edwards and Dr. Hawlader Al-Mamun

Bachelor of Technology (B.Tech) in Biotechnology and Biochemical Engineering, at the University of Kerala (India) with project titled “Isolation and Sequencing of an Unknown Gene from a c-DNA Library” supervised by Dr. Priya Srinivas at Rajiv Gandhi Centre for Biotechnology, Kerala, India

Contact:
23140255@student.uwa.edu.au

Michael Mckay

2023-11-03T00:44:43Z

Dave: Created page with "My name is Michael Mckay, I am currently completing my masters degree with dissertation at UWA. After completing my undergraduate degree at Curtin University, I wanted to get..."

My name is Michael Mckay, I am currently completing my masters degree with dissertation at UWA. After completing my undergraduate degree at Curtin University, I wanted to get into the field of Bioinformatics as it was an exciting new field of development particularly in my interest area of genetics. My dissertation project is training deep learning models to perform image segmentation to recognise agricultural crop species, in my case canola, in order to map weeds in fields. The project offered a unique approach as it targets crop structures rather than weed structures, increasing its versatility of application in precision agriculture technologies.

Areas of Interest: Genetics, Bioinformatics, Deep-learning, Data Science, Agriculture, Aquaculture

Academic history:

July 2021 to present: Master of Bioinformatics at the University of Western Australia (Australia). Supervised by Prof. David Edwards and Dr. Monica Danilevicz
January 2020 to November 2020: Honours in Biomedical Science in collaboration with CSIRO, Investigating Manganese oxidating organisms and their impact on desirable earth elements.
2017 to 2019: Molecular Genetics and Biotechnology at Curtin University

Publications:
N/A

Hawlader Al-Mamun

2023-01-25T02:48:58Z

Cassandria:

I’m a Research fellow at University of Western Australia, with a formal education in computer science, bioinformatics and quantitative genetics. My current research focuses on the development of machine learning methods to integrate high-dimensional multi-omic data to i) improve prediction accuracy of commercially important phenotype in both plants and animals and ii) understand the various factors determining biological outcomes.

==Areas of Interest==
• Artificial intelligence and machine learning for optimization of biological problems <br>
• Computational methods and statistical analysis of high-throughput genomic data<br>
• Use of functional knowledge in genomic selection<br>
• Functional integration of GWAS and gene expression data

==Academic History==

PhD in Quantitative Genetics (2015) from University of New England, Armidale, NSW, Australia. Title of PhD Thesis: ‘The Genetic Architecture of Complex Traits in Sheep’. Supervisors: Professor Paul Kwan, Professor Cedric Gondro and A/Professor Samuel Clark.

Masters in Bioinformatics (2007) from Chalmers University of Technology, Gothenburg, Sweden. Title of Masters Thesis: ‘Intelligent Searches: A better way to search in the ArrayExpress Data Warehouse’. Supervisors: Dr Ugis Sarkans (European Bioinformatics Institute, Cambridge, UK), and Professor Graham Kemp (Chalmers University of Technology, Gothenburg, Sweden).

Bachelor of Science in Computer Science and Engineering (2002) from Khulna University, Khulna, Bangladesh. Title of BSc. project: ‘An Approach to Define an Electronic Market place of Intelligent Agents Supporting Negotiations’.

==Publications==

Current list of publication is available at https://scholar.google.com.au/citations?user=14TEJEoAAAAJ&hl=en

==Contact==
hawlader.almamun@uwa.edu.au

Benjamin Nestor

2022-12-22T06:40:00Z

Cassandria: /* Academic History */

I am a PhD student in the Applied Bioinformatics group and Finnegan lab at the University of Western Australia. In my PhD, I have mainly been working on and analysing a transcriptome and genome assembly for a native Australian plant, Harsh hakea (Hakea prostrata). My research group is keenly interested in this species because of its high efficiency in taking up and using phosphorus from the soil.

Before starting my PhD, I completed a Bachelor’s degree in Botany and Conservation Biology followed by an Honours degree in Plant Biology at the University of Western Australia. Most of this work was lab-based, but during my Honours I began transitioning to bioinformatics and I am now continuing this work as part of my PhD.

==Areas of Interest==
Plant biology, Australian native plants, genome assembly, transcriptome assembly, annotation, gene family identification, phylogenetic trees, gene expression, 3D protein modelling.

==Publications==
Current record of publication is available at https://scholar.google.com.au/citations?user=saP73_MAAAAJ&hl=en&oi=ao

==Academic History==
2020 to present PhD in Biological Sciences at the University of Western Australia. Supervised by Assoc. Prof. Patrick Finnegan, Prof. David Edwards, Dr. Philipp Bayer, and Emer. Prof. Hans Lambers. Project title: “Genomic resources for studying high nutrient-use-efficiency traits in Australian plants”.

2019 – 2019 Honours in Plant Biology at the University of Western Australia. Supervised by Assoc. Prof. Patrick Finnegan, Dr. Philipp Bayer, and Dr. Kosala Ranathunge. Project title: “Low diversity of high-affinity NITRATE TRANSPORTER 2 (NRT2) genes likely underlies nitrate-influx restraint in the high phosphorus-use-efficient ''Hakea prostrata'' (Proteaceae)”.

2016 – 2018 Bachelor of Science, majoring in Botany and Conservation Biology at the University of Western Australia.

==Contact==
benjamin.nestor@research.uwa.edu.au

Shriprabha Upadhyaya

2022-12-22T06:22:54Z

Cassandria: Created page with "I am Shri, a PhD student at the Applied Bioinformatics Group, UWA. I joined Applied Bioinformatics Group as part of my master's dissertation in 2020 and continued on to my PhD..."

I am Shri, a PhD student at the Applied Bioinformatics Group, UWA. I joined Applied Bioinformatics Group as part of my master's dissertation in 2020 and continued on to my PhD. Most of my bachelor’s project was wet lab based and I slowly moved to bioinformatics during my Masters. My current project mainly focuses on using machine learning on plant datasets.
==Academic History==
2022 – Present PhD candidate at the University of Western Australia (Australia) supervised by Prof. David Edwards, Dr. Hawlader Al-Mamun and WProf. Mohammed Bennamoun.

2020-2021 Masters of Biotechnology (Genetics and Genomics) at the University of Western Australia (Australia) supervised by Prof. David Edwards, Dr. Philipp Bayer and Prof. Ian Small, project titled “Genetic Analysis of Crop – Assessing false positive gene models using machine learning”.

2014 – 2018 Bachelor of Engineering (Biotechnology) at Sapthagiri College of Engineering, affiliated to Visvesvaraya Technological University (India). Supervised by Dr. Rohit K.C, external supervisor Dr. M. Vasundara, project titled “Extraction, Chemo profiling and Pharmacological Activity of Clausena lansium (Lour.) Skeels Essential Oil and Development of Oral Hygiene Product”.

==Research Area==
Bioinformatics
Plant Genomics
Application of Machine learning on genome datasets
==Publication List==
Current publications available at - https://scholar.google.com.au/citations?user=-P5D8kwAAAAJ&hl=en
==Contact==
shriprabha.upadhyaya@research.uwa.edu.au

Tessa Macnish

2022-12-21T03:23:57Z

Cassandria: Created page with "My name is Tessa, I am a Masters student at the University of Western Australia. I am working on a graph pangenome of three Brassica species. I hope that this will be used to..."

My name is Tessa, I am a Masters student at the University of Western Australia. I am working on a graph pangenome of three Brassica species. I hope that this will be used to improve crops resistance to climate change.

== Areas of Interest ==
Bioinformatics, Genetics, Agriculture, Evolution, Zoology.
==Academic History==
2022 – present Master of Bioinformatics at the University of Western Australia (Australia), supervised by Prof. David Edwards and Dr. Hawlader Al-Mamun.
2019 – 2021 Bachelor of Science majoring in Genetics and Zoology at the University of Western Australia (Australia).
==Publications==
n/a
==Contact==
22724711@student.uwa.edu.au