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Paul J. Kersey
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Journal Articles
- 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) - 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) - 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) - 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) - 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) - 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)
Conference and Workshop Papers
- 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 - 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
Parts in Books or Collections
- 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
Informal and Other Publications
- 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)
Coauthor Index
aka: Daniel Michael Staines
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