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Journal Articles
- 2021
[j20]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
- [j19]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
- [j18]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) - [j17]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) - 2016
- [j16]Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - [j15]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) - [j14]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) - 2014
- [j13]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) - [j12]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) - 2013
- [j11]Jing-Woei Li, Dan M. Bolser, Magnus Manske, Federico Manuel Giorgi, Nikolay Vyahhi, Björn Usadel, Bernardo J. Clavijo, Ting-Fung Chan, Nathalie Wong, Daniel R. Zerbino, Maria Victoria Schneider:
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Briefings Bioinform. 14(5): 548-555 (2013) - [j10]Jon C. Ison, Matús Kalas, Inge Jonassen, Dan M. Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer, Peter M. Rice:
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinform. 29(10): 1325-1332 (2013) - 2012
- [j9]Dan M. Bolser, Pierre-Yves Chibon, Nicolas Palopoli, Sungsam Gong, Daniel Jacob, Victoria Dominguez Del Angel, Daniel Swan, Sebastian Bassi, Virginia González, Prashanth Suravajhala, Seungwoo Hwang, Paolo Romano, Rob Edwards, Bryan Bishop, John Eargle, Timur Shtatland, Nicholas J. Provart, Dave Clements, Daniel P. Renfro, Daeui Park, Jong Bhak:
MetaBase - the wiki-database of biological databases. Nucleic Acids Res. 40(Database-Issue): 1250-1254 (2012) - [j8]Jing-Woei Li, Keith Robison, Marcel Martin, Andreas Sjödin, Björn Usadel, Matthew Young, Eric C. Olivares, Dan M. Bolser:
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis. Nucleic Acids Res. 40(Database-Issue): 1313-1317 (2012) - 2010
- [j7]Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, Dan M. Bolser:
PDBWiki: added value through community annotation of the Protein Data Bank. Database J. Biol. Databases Curation 2010 (2010) - 2005
- [j6]Sungsam Gong, Giseok Yoon, Insoo Jang, Dan M. Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak:
PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinform. 21(10): 2541-2543 (2005) - [j5]Daeui Park, Semin Lee, Dan M. Bolser, Michael Schroeder, Michael Lappe, Donghoon Oh, Jong Bhak:
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinform. 21(15): 3234-3240 (2005) - [j4]Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M. Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak:
A protein domain interaction interface database: InterPare. BMC Bioinform. 6: 207 (2005) - 2004
- [j3]Wan Kyu Kim, Dan M. Bolser, Jong H. Park:
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinform. 20(7): 1138-1150 (2004) - [j2]Panos Dafas, Dan M. Bolser, Jacek Gomoluch, Jong-Chan Park, Michael Schroeder:
Using convex hulls to extract interaction interfaces from known structures. Bioinform. 20(10): 1486-1490 (2004) - 2003
- [j1]Dan M. Bolser, Panos Dafas, Richard Harrington, Jong-Chan Park, Michael Schroeder:
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. BMC Bioinform. 4: 45 (2003)
Conference and Workshop Papers
- 2003
- [c1]Panos Dafas, Dan M. Bolser, Jacek Gomoluch, Jong-Chan Park, Michael Schroeder:
Fast and efficient computation of domain-domaininteractions from known protein structures in the PDB. German Conference on Bioinformatics 2003: 27-32
Coauthor Index
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