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ORCIDPaul J. Kersey
Paul Julian Kersey
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2020 – today
- 2023
[j31]Marcela Uliano-Silva
, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Mark L. Blaxter, Nova Mieszkowska, Neil Hall, Peter Holland, Richard Durbin, Thomas Richards, Paul J. Kersey, Peter Hollingsworth, Willie Wilson, Alex Twyford, Ester Gaya, Mara Lawniczak, Owen Lewis, Gavin Broad, Fergal Martin, Michelle Hart, Ian Barnes, Giulio Formenti, Linelle Abueg, James W. Torrance, Eugene W. Myers, Shane A. McCarthy:
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinform. 24(1): 288 (2023)- 2021
- [j30]Marcela K. Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari, Vivek Kumar, Bruno Contreras-Moreira, Guy Naamati, Nancy George, Justin Cook, Dan M. Bolser, Peter D'Eustachio, Lincoln D. Stein, Amit Gupta, Weijia Xu, Jennifer Regala, Irene Papatheodorou, Paul J. Kersey, Paul Flicek, Crispin Taylor, Pankaj Jaiswal, Doreen Ware:
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49(Database-Issue): D1452-D1463 (2021) - [i1]Hugh F. Williamson, Julia Brettschneider, Mario Cáccamo, Robert P. Davey, Carole A. Goble, Paul J. Kersey, Sean T. May, Richard J. Morris, Richard Ostler, Tony P. Pridmore, Christopher J. Rawlings, David J. Studholme, Sotirios A. Tsaftaris, Sabina Leonelli:
Data management challenges for artificial intelligence in plant and agricultural research. F1000Research 10: 324 (2021) - 2020
- [j29]Kevin L. Howe, Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu A. Akanni, James E. Allen, Jorge Álvarez-Jarreta, Matthieu Barba, Dan M. Bolser, Lahcen Cambell, Manuel Carbajo, Marc Chakiachvili, Mikkel B. Christensen, Carla A. Cummins, Alayne Cuzick, Paul Davis, Silvie Fexova, Astrid Gall, Nancy George, Laurent Gil, Parul Gupta, Kim E. Hammond-Kosack, Erin Haskell, Sarah E. Hunt, Pankaj Jaiswal, Sophie H. Janacek, Paul J. Kersey, Nick Langridge, Uma Maheswari, Thomas Maurel, Mark D. McDowall, Benjamin Moore, Matthieu Muffato, Guy Naamati, Sushma Naithani, Andrew Olson, Irene Papatheodorou, Mateus Patricio, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Marc Rosello, Matthew Russell, Vasily Sitnik, Daniel M. Staines, Joshua C. Stein, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Sharon Wei, Doreen Ware, Gary Williams, Andrew D. Yates, Paul Flicek:
Ensembl Genomes 2020 - enabling non-vertebrate genomic research. Nucleic Acids Res. 48(Database-Issue): D689-D695 (2020)
2010 – 2019
- 2018
- [j28]Marcela K. Tello-Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser, Guy Naamati, Electra Tapanari, Nuno A. Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Y. Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D. Stein, Robert Petryszak, Irene Papatheodorou, Paul J. Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware:
Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46(Database-Issue): D1181-D1189 (2018) - [j27]Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel, Benjamin Moore, Mark D. McDowall, Uma Maheswari, Guy Naamati, Victoria Newman, Chuang Kee Ong, Michael Paulini, Helder Pedro, Emily Perry, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor, Alessandro Vullo, Gareth Williams, Amonida Zadissa, Andrew Olson, Joshua C. Stein, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani, Simon C. Potter, Robert D. Finn, Martin Urban, Kim E. Hammond-Kosack, Dan M. Bolser, Nishadi De Silva, Kevin L. Howe, Nicholas Langridge, Gareth Maslen, Daniel Michael Staines, Andrew D. Yates:
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res. 46(Database-Issue): D802-D808 (2018) - [j26]Raymond Y. N. Lee, Kevin L. Howe, Todd W. Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, Sibyl Gao, Christian A. Grove, Ranjana Kishore, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini, Daniela Raciti, Faye Rodgers, Matthew Russell, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul J. Kersey, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase 2017: molting into a new stage. Nucleic Acids Res. 46(Database-Issue): D869-D874 (2018) - 2016
- [j25]Paul Julian Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K. Aranganathan, Nicholas Langridge, Ernesto Lowy-Gallego, Mark D. McDowall, Uma Maheswari, Michael Nuhn, Chuang Kee Ong, Bert Overduin, Michael Paulini, Helder Pedro, Emily Perry, Giulietta Spudich, Electra Tapanari, Brandon Walts, Gareth Williams, Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Doreen Ware, Daniel M. Bolser, Kevin L. Howe, Eugene Kulesha, Daniel Lawson, Gareth Maslen, Daniel M. Staines:
Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 44(Database-Issue): 574-580 (2016) - [j24]Helder Pedro, Uma Maheswari, Martin Urban, Alistair George Irvine, Alayne Cuzick, Mark D. McDowall, Daniel M. Staines, Eugene Kulesha, Kim Elizabeth Hammond-Kosack, Paul Julian Kersey:
PhytoPath: an integrative resource for plant pathogen genomics. Nucleic Acids Res. 44(Database-Issue): 688-693 (2016) - [j23]Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas A. Down, Sibyl Gao, Christian A. Grove, Todd W. Harris, Ranjana Kishore, Raymond Y. N. Lee, Jane Lomax, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini, Daniela Raciti, Gary Schindelman, Eleanor Stanley, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul J. Kersey, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 44(Database-Issue): 774-780 (2016) - [j22]Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura Huerta, Maria Keays, Y. Amy Tang, Helen E. Parkinson, Antonio Fabregat, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, Doreen Ware:
Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 44(Database-Issue): 1133-1140 (2016) - 2015
- [j21]Mark D. McDowall, Midori A. Harris, Antonia Lock, Kim Rutherford, Daniel M. Staines, Jürg Bähler, Paul J. Kersey, Stephen G. Oliver, Valerie Wood:
PomBase 2015: updates to the fission yeast database. Nucleic Acids Res. 43(Database-Issue): 656-661 (2015) - [c2]Felix Shaw, Anthony Etuk, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Paul J. Kersey, Ruth Bastow, Susanna-Assunta Sansone, Vicky Schneider, Robert P. Davey, David Johnson:
COPO - Linked Open Infrastructure for Plant Data. SWAT4LS 2015: 181-182 - 2014
- [j20]Paul Julian Kersey, James E. Allen, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall, Uma Maheswari, Gareth Maslen, Michael Nuhn, Chuang Kee Ong, Michael Paulini, Helder Pedro, Iliana Toneva, Mary Ann Tuli, Brandon Walts, Gareth Williams, Derek Wilson, Ken Youens-Clark, Marcela K. Monaco, Joshua C. Stein, Xuehong Wei, Doreen Ware, Daniel M. Bolser, Kevin Lee Howe, Eugene Kulesha, Daniel Lawson, Daniel Michael Staines:
Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 42(Database-Issue): 546-552 (2014) - [j19]Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian A. Grove, Kevin L. Howe, Ranjana Kishore, Raymond Y. N. Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Michael Paulini, Daniela Raciti, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, J. D. Wong, Karen Yook, Tim Schedl, Jonathan Hodgkin, Matthew Berriman, Paul J. Kersey, John Spieth, Lincoln Stein, Paul W. Sternberg:
WormBase 2014: new views of curated biology. Nucleic Acids Res. 42(Database-Issue): 789-793 (2014) - [j18]Marcela K. Monaco, Joshua C. Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson, Yinping Jiao, Zhenyuan Lu, Daniel M. Bolser, Arnaud Kerhornou, Daniel M. Staines, Brandon Walts, Guanming Wu, Peter D'Eustachio, Robin Haw, David Croft, Paul J. Kersey, Lincoln Stein, Pankaj Jaiswal, Doreen Ware:
Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. 42(Database-Issue): 1193-1199 (2014) - 2012
- [j17]Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul S. Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D. McDowall, Karine Megy, Uma Maheswari, Michael Nuhn, Michael Paulini, Helder Pedro, Iliana Toneva, Derek Wilson, Andrew D. Yates, Ewan Birney:
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 40(Database-Issue): 91-97 (2012) - [j16]Valerie Wood, Midori A. Harris, Mark D. McDowall, Kim Rutherford, Brendan W. Vaughan, Daniel M. Staines, Martin Aslett, Antonia Lock, Jürg Bähler, Paul J. Kersey, Stephen G. Oliver:
PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res. 40(Database-Issue): 695-699 (2012) - [j15]Karen Yook, Todd W. Harris, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, Norie De La Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian A. Grove, Kevin L. Howe, Snehalata Kadam, Ranjana Kishore, Raymond Y. N. Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini, Daniela Raciti, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M. Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman, Richard Durbin, Paul J. Kersey, John Spieth, Lincoln Stein, Paul W. Sternberg:
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 40(Database-Issue): 735-741 (2012) - 2011
- [j14]Rhoda Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, Glenn Proctor, Giulietta Spudich, Jeff Almeida-King, Daniel M. Staines, Paul S. Derwent, Arnaud Kerhornou, Paul J. Kersey, Paul Flicek:
Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database J. Biol. Databases Curation 2011 (2011) - [j13]Ken Youens-Clark, Edward S. Buckler, Terry M. Casstevens, Charles Chen, Genevieve DeClerck, Paul S. Derwent, Palitha Dharmawardhana, Pankaj Jaiswal, Paul J. Kersey, A. S. Karthikeyan, Jerry Lu, Susan McCouch, Liya Ren, William Spooner, Joshua C. Stein, Jim Thomason, Sharon Wei, Doreen Ware:
Gramene database in 2010: updates and extensions. Nucleic Acids Res. 39(Database-Issue): 1085-1094 (2011) - 2010
- [j12]Paul J. Kersey, Daniel Lawson, Ewan Birney, Paul S. Derwent, Matthias Haimel, Javier Herrero, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Andreas Kähäri, Rhoda Kinsella, Eugene Kulesha, Uma Maheswari, Karine Megy, Michael Nuhn, Glenn Proctor, Daniel M. Staines, Franck Valentin, Albert J. Vilella, Andy Yates:
Ensembl Genomes: Extending Ensembl across the taxonomic space. Nucleic Acids Res. 38(Database-Issue): 563-569 (2010)
2000 – 2009
- 2005
- [j11]Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul J. Kersey, Jorge Duarte, Cecilia Saccone, Graziano Pesole:
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 33(Database-Issue): 141-146 (2005) - [j10]Paul J. Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter McLaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler:
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 33(Database-Issue): 297-302 (2005) - [p1]Allyson L. Williams, Paul J. Kersey, Manuela Pruess, Rolf Apweiler:
Biological Databases: Infrastructure, Content and Integration. Data Analysis and Visualization in Genomics and Proteomics 2005: 11-28 - 2004
- [j9]Manuela Pruess, Paul J. Kersey, Rolf Apweiler:
The Integr8 project - a resource for genomic and proteomic data. Silico Biol. 5(2): 179-185 (2004) - [j8]Manuela Pruess, Paul J. Kersey, Rolf Apweiler:
Integrating Genomic and Proteomic Data: The Integr8 Project. J. Integr. Bioinform. 1(1) (2004) - 2003
- [j7]Alexandre Gattiker, Karine Michoud, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Tania Lima, Paul J. Kersey, Marco Pagni, Christian J. A. Sigrist, Corinne Lachaize, Anne-Lise Veuthey, Elisabeth Gasteiger, Amos Bairoch:
Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 27(1): 49-58 (2003) - [j6]Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler:
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31(1): 414-417 (2003) - 2002
- [j5]Margaret Biswas, Joseph F. O'Rourke, Evelyn Camon, Gillian Fraser, Alexander Kanapin, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler:
Applications of InterPro in Protein Annotation and Genome Analysis. Briefings Bioinform. 3(3): 285-295 (2002) - [j4]Alexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Florence Servant, Evgeni M. Zdobnov:
Interactive InterPro-based comparisons of proteins in whole genomes. Bioinform. 18(2): 374-375 (2002) - 2001
- [j3]Rolf Apweiler, Paul J. Kersey, Vivien Junker, Amos Bairoch:
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al. Bioinform. 17(6): 533-534 (2001) - [j2]Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Evgeni M. Zdobnov:
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. Nucleic Acids Res. 29(1): 44-48 (2001) - 2000
- [j1]Paul J. Kersey, Henning Hermjakob, Rolf Apweiler:
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. Bioinform. 16(11): 1048-1049 (2000) - [c1]Margaret Biswas, Rolf Apweiler, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Evgeni M. Zdobnov:
Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole Genomes. German Conference on Bioinformatics 2000: 149-158
Coauthor Index
Daniel M. Staines
aka: Daniel Michael Staines
aka: Daniel Michael Staines
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