Dr Paul Muhindira

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Chief Investigator

Doctor of Philosophy (University of Queensland)

Dr Paul Visendi Muhindira is a bioinformatician with extensive academic and commercial research experience focused on food security through application of bioinformatics and genomics for crop improvement. Improving the accuracy of gene identification saves tremendous amounts of time required for the development of resilient crop varieties with an ever-growing global food demand. Paul applies novel genomic approaches to better identify and characterise gene candidates that are most promising for banana disease resistance. His current research projects include the development of bioinformatic algorithms for the identification of Fusarium, Sigatoka and banana bunchy top virus resistance and susceptibility genes in bananas. PhD and Post-doctoral research project opportunities are available in the above general areas applying machine learning, metabolomics, structural bioinformatics and phylogenetics. Background Paul completed his PhD in Bioinformatics at the University of Queensland, developing efficient and cost-effective genome assembly approaches for large complex plant genome under the International Wheat Genome Sequencing Consortium (IWGSC), published in Science ((IWGSC) et al. 2018). He then undertook post-doctoral work at the Natural Resources Institute, UK as the lead bioinformatician on an International $US 16M Bill & Melinda Gates Foundation project, where he established core bioinformatics capacity while supporting 12 PI’s within the university and internationally, 8 PhD students and 3 postdocs in the project. In this role he assembled multiple chromosome level genomes of the highly heterozygous whitefly genome and identified potential candidate genes for gene drive applications for whitefly control in East Africa. Paul returned to Australia in 2018, joining the banana biotechnology program at QUT led by Distinguished Professor James Dale and Professor Rob Harding where he leads the genomics efforts of the program.

Additional information

Publications

  • Abrouk M, Fischer I, Uauy C, Borrill P, Ramirez-gonzalez R, Arnaud D, Chalabi S, Chalhoub B, Cory A, Datla R, Davey M, Jacobs J, Robinson S, Steuernagel B, Van Ex F, Wulff B, Benhamed M, Bendahmane A, Concia L, Latrasse D, Bartoš J, Bellec A, Berges H, Doležel J, Frenkel Z, Gill B, Korol A, Letellier T, Olsen O, Singh K, Valárik M, Van Der Vossen E, Vautrin S, Weining S, Fahima T, Glikson V, Raats D, Cíhalíková J, Toegelová H, Vrána J, Sourdille P, Darrier B, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Jones J, Gundlach H, Haberer G, Mayer K, Ormanbekova D, Prade V, Šimková H, Wicker T, Swarbreck D, Rimbert H, Felder M, Guilhot N, Kaithakottil G, Keilwagen J, Leroy P, Lux T, Twardziok S, Venturini L, Juhász A, Yu G, Small I, Melonek J, Zhou R, Belova T, Kanyuka K, King R, Nilsen K, Walkowiak S, Cuthbert R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Cížková J, Akpinar B, Biyiklioglu S, Gao L, N’daiye A, Kubaláková M, Šafár J, Alfama F, Adam-blondon A, Flores R, Guerche C, Loaec M, Quesneville H, Condie J, Ens J, Maclachlan R, Tan Y, Alberti A, Aury J, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Kaur G, Luo M, Sehgal S, Chhuneja P, Gupta O, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh N, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar R, Holušová K, Plíhal O, Clark M, Heavens D, Kettleborough G, Wright J, Balcárková B, Hu Y, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Cattonaro F, Jiumeng M, Kugler K, Pfeifer M, Sandve S, Xun X, Zhan B, Batley J, Bayer P, Edwards D, Hayashi S, Tulpová Z, Visendi P, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Appels R, Eversole K, Stein N, Feuillet C, Keller B, Rogers J, Pozniak C, Choulet F, Distelfeld A, Poland J, Ronen G, Sharpe A, Barad O, Baruch K, Keeble-gagnère G, Mascher M, Ben-zvi G, Josselin A, Himmelbach A, Balfourier F, Gutierrez-gonzalez J, Hayden M, Koh C, Muehlbauer G, Pasam R, Paux E, Rigault P, Tibbits J, Tiwari V, Spannagl M, Lang D, Witek K, (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome, Science, 361 (6403).
  • Chan C, Rosic N, Lorenc M, Visendi P, Lin M, Kaniewska P, Ferguson B, Gresshoff P, Batley J, Edwards D, (2019) A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference, Functional and Integrative Genomics, 19 (2), pp. 363-371.
  • Visendi P, Ng'ang'a W, Bulimo W, Bishop R, Ochanda J, De Villiers E, (2011) TparvaDB: A database to support Theileria parva vaccine development, Database, 2011, pp. 1-5.
  • Visendi P, Berkman P, Hayashi S, Golicz A, Bayer P, Ruperao P, Hurgobin B, Montenegro J, Chan C, Stankova H, Batley J, Simkova H, Dolezel J, Edwards D, (2016) An efficient approach to BAC based assembly of complex genomes, Plant Methods, 12 (1), pp. 1-9.
  • Visendi P, Batley J, Edwards D, (2014) Next generation sequencing and germplasm resources. In R Tuberosa, A Graner & E Frison, Genomics of Plant Genetic Resources: Volume 1. Managing, Sequencing and Mining Genetic Resources, Springer, pp. 369-390.
  • Berkman P, Visendi P, Lee H, Stiller J, Manoli S, Lorenc M, Lai K, Batley J, Fleury D, Simkova H, Kubalakova M, Weining S, Dolezel J, Edwards D, (2013) Dispersion and domestication shaped the genome of bread wheat, Plant Biotechnology Journal, 11 (5), pp. 564-571.
  • Visendi P, Batley J, Edwards D, (2013) Next generation characterisation of cereal genomes for marker discovery, Biology, 2 (4), pp. 1357-1377.
  • Tulpová Z, Luo M, Toegelová H, Visendi P, Hayashi S, Vojta P, Paux E, Kilian A, Abrouk M, Bartoš J, Hajdúch M, Batley J, Edwards D, Doležel J, Šimková H, (2019) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies, New Biotechnology, 48, pp. 12-19.

Current Supervisions