The University of Queensland

De Novo Assembly of Linked Reads Using Supernova 2.0

Visendi, Paul (2022). De Novo Assembly of Linked Reads Using Supernova 2.0. Plant Bioinformatics. (pp. 233-243) New York, NY: Springer US. doi: 10.1007/978-1-0716-2067-0_12

Trimming and validation of illumina short reads using trimmomatic, trinity assembly, and assessment of RNA-Seq data

Sewe, Steven O., Silva, Gonçalo, Sicat, Paulo, Seal, Susan E. and Visendi, Paul (2022). Trimming and validation of illumina short reads using trimmomatic, trinity assembly, and assessment of RNA-Seq data. Plant bioinformatics. (pp. 211-232) edited by David Edwards. New York, NY, United States: Springer US. doi: 10.1007/978-1-0716-2067-0_11

Next generation sequencing and germplasm resources

Visendi, Paul, Batley, Jacqueline and Edwards, David (2014). Next generation sequencing and germplasm resources. Genomics of plant genetic resources: volume 1: managing, sequencing and mining genetic resources. (pp. 369-390) edited by Roberto Tuberosa, Andreas Graner and Emile Frison. Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/978-94-007-7572-5_15

In silico prediction of candidate gene targets for the management of African cassava whitefly (Bemisia tabaci, SSA1-SG1), a key vector of viruses causing cassava brown streak disease

Kaweesi, Tadeo, Colvin, John, Campbell, Lahcen, Visendi, Paul, Maslen, Gareth, Alicai, Titus and Seal, Susan (2024). In silico prediction of candidate gene targets for the management of African cassava whitefly (Bemisia tabaci, SSA1-SG1), a key vector of viruses causing cassava brown streak disease. PeerJ, 12 e16949, e16949. doi: 10.7717/peerj.16949

Near-infrared spectroscopy and machine learning algorithms for rapid and non-invasive detection of Trichuris

Kariyawasam, Tharanga N., Ciocchetta, Silvia, Visendi, Paul, Soares Magalhães, Ricardo J., Smith, Maxine E., Giacomin, Paul R. and Sikulu-Lord, Maggy T. (2023). Near-infrared spectroscopy and machine learning algorithms for rapid and non-invasive detection of Trichuris. PLOS Neglected Tropical Diseases, 17 (11) e0011695, e0011695. doi: 10.1371/journal.pntd.0011695

Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors

Campbell, Lahcen I., Nwezeobi, Joachim, van Brunschot, Sharon L., Kaweesi, Tadeo, Seal, Susan E., Swamy, Rekha A. R., Namuddu, Annet, Maslen, Gareth L., Mugerwa, Habibu, Armean, Irina M., Haggerty, Leanne, Martin, Fergal J., Malka, Osnat, Santos-Garcia, Diego, Juravel, Ksenia, Morin, Shai, Stephens, Michael E., Muhindira, Paul Visendi, Kersey, Paul J., Maruthi, M. N., Omongo, Christopher A., Navas-Castillo, Jesús, Fiallo-Olivé, Elvira, Mohammed, Ibrahim Umar, Wang, Hua-Ling, Onyeka, Joseph, Alicai, Titus and Colvin, John (2023). Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors. BMC Genomics, 24 (1) 408, 1-36. doi: 10.1186/s12864-023-09474-3

Characterization of transposable elements within the Bemisia tabaci species complex

Sicat, Juan Paolo A., Visendi, Paul, Sewe, Steven O., Bouvaine, Sophie and Seal, Susan E. (2022). Characterization of transposable elements within the Bemisia tabaci species complex. Mobile DNA, 13 (1) 12. doi: 10.1186/s13100-022-00270-6

First report of the detection of DENV1 in human blood plasma with near-infrared spectroscopy

Goh, Brendon, Visendi, Paul, Lord, Anton R., Ciocchetta, Silvia, Liu, Wenjun and Sikulu-Lord, Maggy T. (2022). First report of the detection of DENV1 in human blood plasma with near-infrared spectroscopy. Viruses, 14 (10) 2248, 2248. doi: 10.3390/v14102248

Lysine provisioning by horizontally acquired genes promotes mutual dependence between whitefly and two intracellular symbionts

Bao, Xi-Yu, Yan, Jin-Yang, Yao, Ya-Lin, Wang, Yan-Bin, Visendi, Paul, Seal, Susan and Luan, Jun-Bo (2021). Lysine provisioning by horizontally acquired genes promotes mutual dependence between whitefly and two intracellular symbionts. PLoS Pathogens, 17 (11) e1010120, e1010120. doi: 10.1371/journal.ppat.1010120

Genetic diversity of whitefly (Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa

Mugerwa, Habibu, Colvin, John, Alicai, Titus, Omongo, Christopher A., Kabaalu, Richard, Visendi, Paul, Sseruwagi, Peter and Seal, Susan E. (2021). Genetic diversity of whitefly (Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa. Journal of Pest Science, 94 (4), 1307-1330. doi: 10.1007/s10340-021-01355-6

Molecular Evolution of the Glutathione S-Transferase Family in the Bemisia tabaci Species Complex

Aidlin Harari, Ofer, Santos-Garcia, Diego, Musseri, Mirit, Moshitzky, Pnina, Patel, Mitulkumar, Visendi, Paul, Seal, Susan, Sertchook, Rotem, Malka, Osnat and Morin, Shai (2020). Molecular Evolution of the Glutathione S-Transferase Family in the Bemisia tabaci Species Complex. Genome Biology and Evolution, 12 (2), 3857-3872. doi: 10.1093/gbe/evaa002

Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing

Silva, Gonçalo, Bömer, Moritz, Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. (2019). Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6) 167, 1-10. doi: 10.3390/plants8060167

Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses

Bömer, Moritz, Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo, Kumar, P. Lava and Seal, Susan E. (2019). Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology, 105, 54-66. doi: 10.1016/j.pmpp.2018.06.003

Species-complex diversification and host-plant associations in Bemisia tabaci: a plant-defence, detoxification perspective revealed by RNA-Seq analyses

Malka, Osnat, Santos-Garcia, Diego, Feldmesser, Ester, Sharon, Elad, Krause-Sakate, Renate, Delatte, Hélène, van Brunschot, Sharon, Patel, Mitulkumar, Visendi, Paul, Mugerwa, Habibu, Seal, Susan, Colvin, John and Morin, Shai (2018). Species-complex diversification and host-plant associations in Bemisia tabaci: a plant-defence, detoxification perspective revealed by RNA-Seq analyses. Molecular Ecology, 27 (21), 4241-4256. doi: 10.1111/mec.14865

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Appels, Rudi, Eversole, Kellye, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Stein, Nils, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Barad, Omer, Baruch, Kobi, Keeble-Gagnère, Gabriel, Mascher, Martin, Ben-Zvi, Gil, Josselin, Ambre-Aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-Gonzalez, Juan, Hayden, Matthew, Koh, Chu Shin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel ... Wang, Le (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361 (6403) eaar7191, 661-+. doi: 10.1126/science.aar7191

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

Bömer, Moritz, Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo and Seal, Susan E. (2018). 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. Archives of Virology, 163 (2), 533-538. doi: 10.1007/s00705-017-3605-9

A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference

Chan, Chon-Kit Kenneth, Rosic, Nedeljka, Lorenc, Michał T., Visendi, Paul, Lin, Meng, Kaniewska, Paulina, Ferguson, Brett J., Gresshoff, Peter M., Batley, Jacqueline and Edwards, David (2018). A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference. Functional and Integrative Genomics, 19 (2), 363-371. doi: 10.1007/s10142-018-0647-3

The pangenome of hexaploid bread wheat

Montenegro, Juan D. , Golicz, Agnieszka A. , Bayer, Philipp E. , Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Visendi, Paul, Lai, Kaitao, Dolezel, Jaroslav, Batley, Jacqueline and Edwards, David (2017). The pangenome of hexaploid bread wheat. Plant Journal, 90 (5), 1007-1013. doi: 10.1111/tpj.13515

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

Stankova, Helena, Hastie, Alex R., Chan, Saki, Vrana, Jan, Tulpova, Zuzana, Kubalakova, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Dolezel, Jaroslav and Simkova, Hana (2016). BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7), 1523-1531. doi: 10.1111/pbi.12513

An efficient approach to BAC based assembly of complex genomes

Visendi, Paul, Berkman, Paul J., Hayashi, Satomi, Golicz, Agnieszka A., Bayer, Philipp E., Ruperao, Pradeep, Hurgobin, Bhavna, Montenegro, Juan, Chan, Chon-Kit Kenneth, Stankova, Helena, Batley, Jacqueline, Simkova, Hana, Dolezel, Jaroslav and Edwards, David (2016). An efficient approach to BAC based assembly of complex genomes. Plant Methods, 12 (1) 2, 2. doi: 10.1186/s13007-016-0107-9

Development and validation of Thinopyrum elongatum–expressed molecular markers specific for the long arm of chromosome 7E

Gou, Lulu, Hattori, Jiro, Fedak, George, Balcerzak, Margaret, Sharpe, Andrew, Visendi, Paul, Edwards, David, Tinker, Nicholas, Wei, Yu-Ming, Chen, Guo-Yue and Ouellet, Thérèse (2016). Development and validation of Thinopyrum elongatum–expressed molecular markers specific for the long arm of chromosome 7E. Crop Science, 56 (1), 354-363. doi: 10.2135/cropsci2015.03.0184

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

Bayer, Philipp E, Ruperao, Pradeep, Mason, Annaliese S, Stiller, Jiri, Chan, Chon-Kit Kenneth, Hayashi, Satomi, Long, Yan, Meng, Jinling, Sutton, Tim, Visendi, Paul, Varshney, Rajeev K, Batley, Jacqueline and Edwards, David (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. doi: 10.1007/s00122-015-2488-y

Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat

Lai, Kaitao, Lorenc, Michael T., Lee, Hong Ching, Berkman, Paul J., Bayer, Philipp Emanuel, Visendi, Paul, Ruperao, Pradeep, Fitzgerald, Timothy L., Zander, Manuel, Chan, Chon-Kit Kenneth, Manoli, Sahana, Stiller, Jiri, Batley, Jacqueline and Edwards, David (2015). Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal, 13 (1), 97-104. doi: 10.1111/pbi.12240

Gene loss in the fungal canola pathogen Leptosphaeria maculans

Golicz, Agnieszka A., Martinez, Paula A., Zander, Manuel, Patel, Dhwani A., Van De Wouw, Angela P., Visendi, Paul, Fitzgerald, Timothy L., Edwards, David and Batley, Jacqueline (2014). Gene loss in the fungal canola pathogen Leptosphaeria maculans. Functional and Integrative Genomics, 15 (2), 189-196. doi: 10.1007/s10142-014-0412-1

A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies

Ruperao, Pradeep, Chan, Chon-Kit, Azam, Sarwar, Karafiatova, Miroslava, Hayashi, Satomi, Cizkova, Jana, Saxena, Rachit K., Simkova, Hana, Song, Chi, Vrana, Jan, Chitikineni, Annapurna, Visendi, Paul, Gaur, Pooran M., Millan, Teresa, Singh, Karam B., Taran, Bunyamin, Wang, Jun, Batley, Jacqueline, Dolezel, Jaroslav, Varshney, Rajeev K. and Edwards, David (2014). A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal, 12 (6), 778-786. doi: 10.1111/pbi.12182

Next generation characterisation of cereal genomes for marker discovery

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013). Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4), 1357-1377. doi: 10.3390/biology2041357

Dispersion and domestication shaped the genome of bread wheat

Berkman, Paul J., Visendi, Paul, Lee, Hong C., Stiller, Jiri, Manoli, Sahana, Lorenc, Michal T., Lai, Kaitao, Batley, Jacqueline, Fleury, Delphine, Simkova, Hana, Kubalakova, Marie, Weining, Song, Dolezel, Jaroslav and Edwards, David (2013). Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal, 11 (5), 564-571. doi: 10.1111/pbi.12044

Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP

Lorenc, Michal T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012). Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (2), 370-382. doi: 10.3390/biology1020370

TparvaDB: A database to support Theileria parva vaccine development

Visendi, Paul, Ng'ang'a, Wanjiku, Bulimo, Wallace, Bishop, Richard, Ochanda, James and De Villiers, Etienne P. (2011). TparvaDB: A database to support Theileria parva vaccine development. Database, 2011 bar015. doi: 10.1093/database/bar015

In vitro detection of dengue 1 virus in human whole blood, plasma, and serum with nearinfrared spectroscopy

Goh, Brendon, Visendi, Paul, Ciocchetta, Silvia, Soares, Ricardo, Liu, Wenjun and Lord, Maggy (2022). In vitro detection of dengue 1 virus in human whole blood, plasma, and serum with nearinfrared spectroscopy. American Society of Tropical Medicine and Hygiene 2022 Annual Meeting, Seattle, WA, United States, October 30 - November 3, 2022. Arlington, VA United States: American Society of Tropical Medicine and Hygiene.

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

Tulpova, Zuzana, Luo, Ming-Cheng, Toegelova, Helena, Visendi, Paul, Hayashi, Satomi, Vojta, Petr, Paux, Etienne, Kilian, Andrzej, Abrouk, Michael, Bartos, Jan, Hajduch, Marian, Batley, Jacqueline, Edwards, David, Dolezel, Jaroslav and Simkova, Hana (2019). Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. Conference on Biotechnology of Plant Products - Green for Good IV, Olomouc Czech Republic, 19 - 22 June 2017. Amsterdam, Netherlands: Elsevier BV. doi: 10.1016/j.nbt.2018.03.003

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

Muhindira, Paul Visendi (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. PhD Thesis, School of Agriculture and Food Sciences, The University of Queensland. doi: 10.14264/uql.2016.521