Knowledge for a sustainable world

PhD

Dr Paul Visendi completed his MSc in Bioinformatics at the University of Nairobi, Kenya in 2010, in collaboration with the Biosciences for Eastern Africa BeCA/ILRI Hub where he developed a Bioinformatics database, TparvaDB. TparvaDB is a database for the tick-borne pathogen, Theileria parva and functions as a resource to facilitate research in the development of an East Coast Fever (ECF) vaccine by providing a single user‐friendly database of all genomic sequences and related metadata for Theileria parva. The database was implemented on a Linux cluster, running PostgreSQL with the GMOD chado schema and a Gbrowse and Biomart font end at the BecA/ILRI Hub.

In 2011, Dr Visendi moved to the University of Queensland, Australia where he attained a PhD in Bioinformatics. During his PhD, Dr Visendi developed a novel cost effective and accurate method for the sequencing and assembly of complex polyploid genomes using a BAC-by-BAC approach, and demonstrated the applicability of this method in Saccharum hybrid (sugarcane) and Triticum aestivum (bread wheat) chromosome arm 7DS. The method is applicable for the sequencing and assembly of polyploid and highly repetitive genomes.

His PhD resulted in several publications and was selected by the Dean, UQ Graduate School, as a recipient of the 2016 Dean’s Award for Outstanding Higher Degrees by Research Theses. Fewer than 10% of PhD and MPhil graduates are recognised this way each year by the University of Queensland.

Undertaking several Bioinformatics projects has enabled Dr Visendi to develop core competencies in R programming, Linux cluster setup and administration, database management systems (PostgreSQL and MySQL), pipeline development in Perl and Python and working with large genomic datasets on a Linux batch environment running Torque, Slurm, LSF and PBS job schedulers.

Dr Visendi has experience collaborating and supporting a diverse international group of scientists. Currently at the Natural Resources Institute, he collaborates with the European Bioinformatics Institute (EBI, UK), and with research partners based in East Africa, China, Colombia, Israel and the USA. At the University of Queensland in Australia, he collaborated with scientists from Europe, China and the USA. His contributions to these research consortia resulted in joint publications and strengthened networks between institutions.

Dr Visendi currently works as a Bioinformatics Postdoctoral Fellow, at NRI under the Molecular Virology and Entomology group, headed by Prof Susan Seal.

He is currently assembling, annotating and comparing multiple genomes and transcriptomes of Bemisia tabaci (Hemiptera: Aleyrodidae) populations using Illumina, PacBio, MiniON and Hi-C sequencing platforms for the African cassava whitefly: outbreak causes and sustainable solutions project funded by a grant from the Bill & Melinda Gates Foundation.

Dr Visendi’s broad research interests are the application of statistically robust algorithms to the analysis of Next Generation Sequence (NGS) datasets in food crops with an aim of improving productivity, and food security. Dr Paul Visendi has a passion for working on African staple food crops such as cassava, yam and maize. Specific research interest include Machine Learning (ML), NGS design of experiments, phylogenetics, Near Infra-Red (NIR) spectroscopy, metabolic modelling of genome assemblies and structural bioinformatics.

Dr Visendi enjoys working on Linux High Performance Computing (HPC) clusters, programming in R, Perl and Python. Dr Visendi also undertakes bioinformatics capacity building focused on young African scientists under the AWCP project. He co-supervises several Bioinformatics PhD students, offers bioinformatics support to students and staff and also Lectures.

  • International Wheat Genome Sequencing Consortium (IWGSC), IWGSC RefSeq principal investigators:, Keller, B., Rogers, J., IWGSC whole-genome assembly principal investigators:, Distelfeld, A., Eversole, K., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., et al. (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 361, eaar7191.
  • .Tulpová, Z., Luo, M., Toegelová, H., Visendi, P., Hayashi, S., Vojta, P., Paux, E., Kilian, A., Abrouk, M., Bartos, J., et al. (2018). Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. N Biotechnol.
  • Bömer, M., Rathnayake, A.I., Visendi, P., Silva, G., Seal, S.E., 2017. Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Arch. Virol. 2, 305–6. doi:10.1007/s00705-017-3605-9
  • Montenegro, J.D., Golicz, A.A., Bayer, P.E., Hurgobin, B., Lee, H., Chan, C.-K.K., Visendi, P., Lai, K., Doležel, J., Batley, J., Edwards, D., 2017. The pangenome of hexaploid bread wheat. The Plant Journal. 90, 1007–1013. doi:10.1111/tpj.1351
  • Visendi, P., 2016. A novel approach for the assembly of complex genomic DNA cloned into bacterial artificial chromosome vectors: assembly and analysis of Triticum aestivum chromosome arm 7DS. doi:10.14264/uql.2016.521
  • Staňková, H., Hastie, A.R., Chan, S., Vrána, J., Tulpová, Z., Kubaláková, M., Visendi, P., Hayashi, S., Luo, M., Batley, J., Edwards, D., Doležel, J., Šimková, H., 2016. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal. 14, n/a–n/a. doi:10.1111/pbi.12513
  • Visendi, P., Berkman, P.J., Hayashi, S., Golicz, A.A., Bayer, P.E., Ruperao, P., Hurgobin, B., Montenegro, J., Chan, C.-K.K., Staňková, H., Batley, J., Šimková, H., Doležel, J., Edwards, D., 2016. An efficient approach to BAC based assembly of complex genomes. Plant Methods. 12, 778. doi:10.1186/s13007-016-0107-9
  • Gou, L., Hattori, J., Fedak, G., Balcerzak, M., Sharpe, A., Visendi, P., Edwards, D., Tinker, N., Wei, Y.-M., Chen, G.-Y., Ouellet, T., 2016. Development and validation of Thinopyrum elongatum expressed molecular markers specific for the long arm of chromosome 7E. Crop Science. 56, 354. doi:10.2135/cropsci2015.03.0184
  • Bayer, P.E., Ruperao, P., Mason, A.S., Stiller, J., Chan, C.-K.K., Hayashi, S., Long, Y., Meng, J., Sutton, T., Visendi, P., Varshney, R.K., 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, 1039–1047. doi:10.1007/s00122-015-2488-y
  • Golicz, A.A., Martinez, P.A., Zander, M., Patel, D.A., Van De Wouw, A.P., Visendi, P., Fitzgerald, T.L., Edwards, D., Batley, J., 2014. Gene loss in the fungal canola pathogen Leptosphaeria maculans. Functional & Integrative Genomics. 15, 189–196. doi:10.1007/s10142-014-0412-1
  • Lai, K., Lorenc, M.T., Lee, H.C., Berkman, P.J., Bayer, P.E., Visendi, P., Ruperao, P., Fitzgerald, T.L., Zander, M., Chan, C.-K.K., Manoli, S., Stiller, J., Batley, J., Edwards, D., 2014. Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal. 13, 97–104. doi:10.1111/pbi.12240
  • Ruperao, P., Chan, C.-K.K., Azam, S., Karafiátová, M., Hayashi, S., Čížková, J., Saxena, R.K., Šimková, H., Song, C., Vrána, J., Chitikineni, A., Visendi, P., Gaur, P.M., Millán, T., Singh, K.B., Taran, B., Wang, J., Batley, J., Doležel, J., Varshney, R.K., Edwards, D., 2014. A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal. 12, 778–786. doi:10.1111/pbi.12182
  • Visendi, P., Batley, J., Edwards, D., 2013a. Next generation characterisation of cereal genomes for marker discovery. Biology. 2, 1357–1377. doi:10.3390/biology2041357
  • Visendi, P., Batley, J., Edwards, D., 2013b. Next Generation Sequencing and Germplasm Resources, in: Genomics of Plant Genetic Resources. Springer Netherlands, Dordrecht, pp. 369–390. doi:10.1007/978-94-007-7572-5_15
  • 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., Edwards, D., 2013. Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal. 11, 564–571. doi:10.1111/pbi.12044
  • 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., Edwards, D., 2013. Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal. 11, 564–571. doi:10.1111/pbi.12044
  • Visendi, P., Ng'ang'a, W., Bulimo, W., Bishop, R., Ochanda, J., de Villiers, E.P., 2011. TparvaDB: a database to support Theileria parva vaccine development 2011, bar015–bar015. doi:10.1093/database/bar015
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