Difference between revisions of "Andy Yuan"

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==Research area==
 
==Research area==
  
−
Previously, I was doing research in the human genome and cancer at the Institute for Molecular Bioscience (IMB), Univesity of Queensland.  
+
Previously, I was doing research in the human genome at the Institute for Molecular Bioscience (IMB), Univesity of Queensland.  
  
 
Now I'm applying the knowledge of bioinformatics and genomics to the study of plants at the University of Western Australia.
 
Now I'm applying the knowledge of bioinformatics and genomics to the study of plants at the University of Western Australia.
  
−
My research is using the improved long read sequencing and optical mapping to improve plant genome assembly and then performing structural variation detection. The major plants involved are ''Brassica napus'' and ''Trifolium subterraneum''.
+
My major research is using the improved long read sequencing and optical mapping to improve plant genome assemblies and then performing structural variation detection between different plant cultivars. The plants involved are ''Brassica napus'', ''Triticum aestivum'' and ''Trifolium subterraneum''.
 +
 
 +
==Awards and Prizes==
 +
2015: Scholarship for International Research Fees by the University of Western Austraila
 +
 
 +
2015: Postgraduate scholarship by the China Scholarship Council.
  
 
==Publications==
 
==Publications==
  
 
*Book chapters
 
*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)
+
#'''Yuan Y''', Scheben A, Batley J and Edwards D. (2019) Using genomics to adapt crops to climate change. In: Sarkar A., Sensarma S., vanLoon G. (eds) Sustainable Solutions for Food Security. ''Springer'', Cham, doi:10.1007/978-3-319-77878-5_5
 +
#'''Yuan Y''', Scheben A, Chan CKK and Edwards D. (2017) Databases for wheat genomics and crop improvement. Wheat Biotechnology: Methods and Protocols, ''Methods in Molecular Biology'', vol. 1679, doi: 10.1007/978-1-4939-7337-8_18, ''Springer''
  
 
*Papers
 
*Papers
−
#Scheben A, '''Yuan Y''', Edwards D. (2016) Advances in genomics for adapting crops to climate change. Current Plant Biology. 6: 2-10
+
#Valliyodan B, Cannon S, Bayer B, Shu S, Ren L, Jenkins J, Chung C, Chan T, Daum C, Plott C, Hastie A, Baruch K, Barry W, Huang W, Patil G, Varshney R, Hu H, Batley J, '''Yuan Y''', Song Q, Goodstein D, Stacey G, Lam H, Jackson S, Schmutz J, Grimwood J, Edwards D, Nguyen H (2019) Construction and comparison of three new reference-quality genome assemblies for soybean, ''the Plant Journal'', doi: 10.1111/tpj.14500
−
#Kaur P, Bayer P, 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)  
+
#'''Yuan Y''', Bayer P, Vrana, J, Dolezel J, Edwards D, Erskine W, Kaur P. (2018) Large-scale structural variation detection in subterranean clover subtypes using optical mapping, ''Frontiers in Plant Science'', 9, 971, doi: 10.3389/fpls.2018.00971
 +
#'''Yuan Y''', Lee H, Hu H, Scheben A, Edwards D. (2018) Single-cell genomic analysis in plants. ''Genes''. doi: 10.3390/genes9010050
 +
#'''Yuan Y''', Bayer P, Scheben A, Chan CKK, Edwards D. (2017) BioNanoAnalyst: A visualisation tool to assess genome assembly quality using BioNano data. ''BMC Bioinformatics''. doi: 10.1186/s12859-017-1735-4
 +
#'''Yuan Y''', Bayer P, Lee H, Edwards D. (2017) runBNG: A software package for BioNano genomic analysis on the command line. ''Bioinformatics''. doi: 10.1093/bioinformatics/btx366
 +
#Bayer P, Hurgobin B, Golicz A, Chan K, '''Yuan Y''', Lee H, 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 Biotechnology Journal''. doi:10.1111/pbi.12742
 +
#'''Yuan Y''', Bayer P, Batley J, Edwards D. (2017) Improvements in genomic technologies: application to crop genomics. ''Trends in Biotechnology''. doi: 10.1016/j.tibtech.2017.02.009
 +
#Kaur P, Bayer P, 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''. doi: 10.1111/pbi.12697
 +
#Scheben A, '''Yuan Y''', Edwards D. (2016) Advances in genomics for adapting crops to climate change. ''Current Plant Biology''. 6: 2-10. doi:10.1016/j.cpb.2016.09.001
 +
 
 +
*Preprints
 +
#'''Yuan Y''', Bayer P, Vrana, J, Dolezel J, Edwards D, Erskine W, Kaur P. (2017) Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level, ''bioRxiv'', 232132, doi: 10.1101/232132
 +
 
 +
*Conference proceedings
 +
#'''Yuan Y''', Bayer P, Edwards D. (2016) Improving crop genome assemblies using optical mapping and long read sequencing. ''Brassica'' Conference 2016 Melbourne, PO053
 +
#'''Yuan Y''', Anderson R, Bayer P, Lee H, Chan C, Edwards D (2019) A fast and efficient long-read genome assembly approach for large and complex genomes. ''The International Plant & Animal Genome XXVII'', San Diego, USA, PO0061
  
−
*Posters
+
*Conference presentations:
−
#'''Yuan Y''', Bayer P, Edwards D. (2016) Improving crop genome assemblies using optical mapping and long read sequencing. Brassica Conference 2016 Melbourne, PO053
+
#'''Yuan Y''', Bayer P, Lee H, Scheben A, Chan C, Edwards D (2019) Bionano data analysis on the command line and genome assembly quality assessment using a GUI. ''The International Plant & Animal Genome XXVII'', San Diego, USA, C01
  
 
==Contact==
 
==Contact==
Line 31: Line 51:
 
PhD candidate (Applied Bioinformatics)
 
PhD candidate (Applied Bioinformatics)
  
−
School of Plant Biology
+
School of Biological Sciences
  
 
University of Western Australia  
 
University of Western Australia  

Latest revision as of 09:14, 27 September 2019

Academic achievement

2015 - present PhD candidate. University of Western Australia (Australia)

2014 Master with Honours. University of Queensland (Australia)

Research area

Previously, I was doing research in the human genome at the Institute for Molecular Bioscience (IMB), Univesity of Queensland.

Now I'm applying the knowledge of bioinformatics and genomics to the study of plants at the University of Western Australia.

My major research is using the improved long read sequencing and optical mapping to improve plant genome assemblies and then performing structural variation detection between different plant cultivars. The plants involved are Brassica napus, Triticum aestivum and Trifolium subterraneum.

Awards and Prizes

2015: Scholarship for International Research Fees by the University of Western Austraila

2015: Postgraduate scholarship by the China Scholarship Council.

Publications

  • Book chapters
  1. Yuan Y, Scheben A, Batley J and Edwards D. (2019) Using genomics to adapt crops to climate change. In: Sarkar A., Sensarma S., vanLoon G. (eds) Sustainable Solutions for Food Security. Springer, Cham, doi:10.1007/978-3-319-77878-5_5
  2. Yuan Y, Scheben A, Chan CKK and Edwards D. (2017) Databases for wheat genomics and crop improvement. Wheat Biotechnology: Methods and Protocols, Methods in Molecular Biology, vol. 1679, doi: 10.1007/978-1-4939-7337-8_18, Springer
  • Papers
  1. Valliyodan B, Cannon S, Bayer B, Shu S, Ren L, Jenkins J, Chung C, Chan T, Daum C, Plott C, Hastie A, Baruch K, Barry W, Huang W, Patil G, Varshney R, Hu H, Batley J, Yuan Y, Song Q, Goodstein D, Stacey G, Lam H, Jackson S, Schmutz J, Grimwood J, Edwards D, Nguyen H (2019) Construction and comparison of three new reference-quality genome assemblies for soybean, the Plant Journal, doi: 10.1111/tpj.14500
  2. Yuan Y, Bayer P, Vrana, J, Dolezel J, Edwards D, Erskine W, Kaur P. (2018) Large-scale structural variation detection in subterranean clover subtypes using optical mapping, Frontiers in Plant Science, 9, 971, doi: 10.3389/fpls.2018.00971
  3. Yuan Y, Lee H, Hu H, Scheben A, Edwards D. (2018) Single-cell genomic analysis in plants. Genes. doi: 10.3390/genes9010050
  4. Yuan Y, Bayer P, Scheben A, Chan CKK, Edwards D. (2017) BioNanoAnalyst: A visualisation tool to assess genome assembly quality using BioNano data. BMC Bioinformatics. doi: 10.1186/s12859-017-1735-4
  5. Yuan Y, Bayer P, Lee H, Edwards D. (2017) runBNG: A software package for BioNano genomic analysis on the command line. Bioinformatics. doi: 10.1093/bioinformatics/btx366
  6. Bayer P, Hurgobin B, Golicz A, Chan K, Yuan Y, Lee H, 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 Biotechnology Journal. doi:10.1111/pbi.12742
  7. Yuan Y, Bayer P, Batley J, Edwards D. (2017) Improvements in genomic technologies: application to crop genomics. Trends in Biotechnology. doi: 10.1016/j.tibtech.2017.02.009
  8. Kaur P, Bayer P, 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. doi: 10.1111/pbi.12697
  9. Scheben A, Yuan Y, Edwards D. (2016) Advances in genomics for adapting crops to climate change. Current Plant Biology. 6: 2-10. doi:10.1016/j.cpb.2016.09.001
  • Preprints
  1. Yuan Y, Bayer P, Vrana, J, Dolezel J, Edwards D, Erskine W, Kaur P. (2017) Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level, bioRxiv, 232132, doi: 10.1101/232132
  • Conference proceedings
  1. Yuan Y, Bayer P, Edwards D. (2016) Improving crop genome assemblies using optical mapping and long read sequencing. Brassica Conference 2016 Melbourne, PO053
  2. Yuan Y, Anderson R, Bayer P, Lee H, Chan C, Edwards D (2019) A fast and efficient long-read genome assembly approach for large and complex genomes. The International Plant & Animal Genome XXVII, San Diego, USA, PO0061
  • Conference presentations:
  1. Yuan Y, Bayer P, Lee H, Scheben A, Chan C, Edwards D (2019) Bionano data analysis on the command line and genome assembly quality assessment using a GUI. The International Plant & Animal Genome XXVII, San Diego, USA, C01

Contact

Andy Yuan

PhD candidate (Applied Bioinformatics)

School of Biological Sciences

University of Western Australia

Perth, WA, 6009

Australia

yuxuan.yuan@outlook.com

https://github.com/AppliedBioinformatics

Retrieved from "https://appliedbioinformatics.com.au/Edwards/index.php?title=Andy_Yuan&oldid=1110"