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2020 – today
- 2024
[j105]Marija Orlic-Milacic
, Karen Rothfels, Lisa Matthews, Adam J. Wright, Bijay Jassal, Veronica Shamovsky, Quang M. Trinh, Marc Gillespie, Cristoffer Sevilla, Krishna Tiwari, Eliot Ragueneau, Chuqiao Gong, Ralf Stephan, Bruce May, Robin Haw, Joel Weiser, Deidre Beavers, Patrick Conley, Henning Hermjakob, Lincoln D. Stein, Peter D'Eustachio, Guanming Wu:
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database J. Biol. Databases Curation 2024 (2024)- [i2]Simha Sankar Baradwaj, Destiny Gilliland, Jack Rincon, Henning Hermjakob, Yu Yan, Irsyad Adam, Gwyneth Lemaster, Dean Wang, Karol Watson, Alex Bui, Wei Wang, Peipei Ping:
Building an Ethical and Trustworthy Biomedical AI Ecosystem for the Translational and Clinical Integration of Foundational Models. CoRR abs/2408.01431 (2024) - 2023
- [j104]Simona Panni, Kalpana Panneerselvam, Pablo Porras, Margaret J. Duesbury, Livia Perfetto, Luana Licata, Henning Hermjakob, Sandra E. Orchard:
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study. Database J. Biol. Databases Curation 2023 (2023) - [j103]Romain David, Audrey S. Richard, Claire Connellan, Katharina B. Lauer, Maria Luisa Chiusano, Carole A. Goble, Martin Houde, Isabel Kemmer, Antje Keppler, Philippe Lieutaud, Christian Ohmann, Maria Panagiotopoulou, Sara Raza Khan, Arina Rybina, Stian Soiland-Reyes, Charlotte Wit, Rudolf Wittner, Rafael Andrade Buono, Sarah Arnaud Marsh, Pauline Audergon, Dylan Bonfils, José María Carazo, Remi Charrel, Frederik Coppens, Wolfgang Fecke, Claudia Filippone, Eva G. Alvarez, Sheraz Gul, Henning Hermjakob, Katja Herzog, Petr Holub, Lukasz Kozera, Allyson L. Lister, José López-Coronado, Bénédicte Madon, Kurt Majcen, William Martin, Wolfgang Müller, Elli Papadopoulou, Christine M. A. Prat, Paolo Romano, Susanna-Assunta Sansone, Gary Saunders, Niklas Blomberg, Jonathan Ewbank:
Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. Data Sci. J. 22: 35 (2023) - 2022
- [j102]Anna Niarakis, Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j101]Barbara Füzi, Rahuman S. Malik-Sheriff, Emma J. Manners, Henning Hermjakob, Gerhard F. Ecker:
KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study. J. Cheminformatics 14(1): 37 (2022) - [j100]Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton I. Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna R. McEntyre:
The European Bioinformatics Institute (EMBL-EBI) in 2021. Nucleic Acids Res. 50(D1): 11-19 (2022) - [j99]Birgit H. M. Meldal, Livia Perfetto, Colin W. Combe, Tiago Lubiana, João Vitor Ferreira Cavalcante, Hema Bye-A-Jee, Andra Waagmeester, Noemi del-Toro, Anjali Shrivastava, Elisabet Barrera, Edith D. Wong, Bernhard Mlecnik, Gabriela Bindea, Kalpana Panneerselvam, Egon L. Willighagen, Juri Rappsilber, Pablo Porras, Henning Hermjakob, Sandra E. Orchard:
Complex Portal 2022: new curation frontiers. Nucleic Acids Res. 50(D1): 578-586 (2022) - [j98]Noemi del-Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin W. Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Bálint Mészáros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret J. Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwínski, Sandra E. Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob:
The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res. 50(D1): 648-653 (2022) - [j97]Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek M. Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary D. Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50(D1): 687-692 (2022) - [j96]Tao Chen, Jie Ma, Yi Liu, Zhiguang Chen, Nong Xiao, Yutong Lu, Yinjin Fu, Chunyuan Yang, Mansheng Li, Songfeng Wu, Xue Wang, Dongsheng Li, Fuchu He, Henning Hermjakob, Yunping Zhu:
iProX in 2021: connecting proteomics data sharing with big data. Nucleic Acids Res. 50(D1): 1522-1527 (2022) - [j95]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - 2021
- [j94]Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C. Lovering, Sandra E. Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper:
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36(24): 5712-5718 (2021) - [j93]Manuel Bernal Llinares, Javier Ferrer-Gómez, Nick S. Juty, Carole A. Goble, Sarala M. Wimalaratne, Henning Hermjakob:
Identifiers.org: Compact Identifier services in the cloud. Bioinform. 37(12): 1781-1782 (2021) - [j92]Eliot Ragueneau, Anjali Shrivastava, John H. Morris, Noemi del-Toro, Henning Hermjakob, Pablo Porras:
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis. Bioinform. 37(20): 3684-3685 (2021) - [j91]Momo Langenstein, Henning Hermjakob, Manuel Bernal Llinares:
A decoupled, modular and scriptable architecture for tools to curate data platforms. Bioinform. 37(20): 3693-3694 (2021) - 2020
- [j90]Livia Perfetto, Chiara Pastrello, Noemi del-Toro, Margaret J. Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, N. Rahimzadeh, Sylvie Ricard-Blum, Lukasz Salwínski, Anjali Shrivastava, Gianni Cesareni, Matteo Pellegrini, Sandra E. Orchard, Igor Jurisica, Henning Hermjakob, Pablo Porras:
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. Database J. Biol. Databases Curation 2020 (2020) - [j89]Mihai Glont, Chinmay Arankalle, Krishan K. Tiwari, Tung V. N. Nguyen, Henning Hermjakob, Rahuman S. Malik-Sheriff:
BioModels Parameters: a treasure trove of parameter values from published systems biology models. Bioinform. 36(17): 4649-4654 (2020) - [j88]Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers:
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17(2-3) (2020) - [j87]Eric W. Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Pérez-Riverol, Jeremy Carver, Deepti Jaiswal Kundu, David García-Seisdedos, Andrew F. Jarnuczak, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno:
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Res. 48(Database-Issue): D1145-D1152 (2020) - [j86]Kaiqiang You, Qi Huang, Chunyu Yu, Boyan Shen, Cristoffer Sevilla, Minglei Shi, Henning Hermjakob, Yang Chen, Tingting Li:
PhaSepDB: a database of liquid-liquid phase separation related proteins. Nucleic Acids Res. 48(Database-Issue): D354-D359 (2020) - [j85]Rahuman S. Malik-Sheriff, Mihai Glont, Tung V. N. Nguyen, Krishan K. Tiwari, Matthew G. Roberts, Ashley Xavier, Manh T. Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L. Fairbanks, Johannes P. Meyer, Chinmay Arankalle, Thawfeek M. Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M. Keating, Young Mi Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Hermjakob:
BioModels - 15 years of sharing computational models in life science. Nucleic Acids Res. 48(Database-Issue): D407-D415 (2020) - [j84]Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw, Fred Loney, Bruce May, Marija Milacic, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase. Nucleic Acids Res. 48(Database-Issue): D498-D503 (2020) - [j83]Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A. Grüning, Henning Hermjakob, Yasset Pérez-Riverol:
The omics discovery REST interface. Nucleic Acids Res. 48(Webserver-Issue): W380-W384 (2020)
2010 – 2019
- 2019
- [j82]Guilherme Viteri, Lisa Matthews, Thawfeek M. Varusai, Marc Gillespie, Marija Milacic, Justin Cook, Joel Weiser, Solomon Shorser, Konstantinos Sidiropoulos, Antonio Fabregat, Robin Haw, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
Reactome and ORCID - fine-grained credit attribution for community curation. Database J. Biol. Databases Curation 2019: baz123 (2019) - [j81]Livia Perfetto, Marcio Luis Acencio, Glyn Bradley, Gianni Cesareni, Noemi del-Toro, Dávid Fazekas, Henning Hermjakob, Tamás Korcsmáros, Martin Kuiper, Astrid Lægreid, Prisca Lo Surdo, Ruth C. Lovering, Sandra E. Orchard, Pablo Porras, Paul D. Thomas, Vasundra Touré, John Zobolas, Luana Licata:
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinform. 35(19): 3779-3785 (2019) - [j80]Jie Ma, Tao Chen, Songfeng Wu, Chunyuan Yang, Mingze Bai, Kunxian Shu, Kenli Li, Guoqing Zhang, Zhong Jin, Fuchu He, Henning Hermjakob, Yunping Zhu:
iProX: an integrated proteome resource. Nucleic Acids Res. 47(Database-Issue): D1211-D1217 (2019) - [j79]Birgit H. M. Meldal, Hema Bye-A-Jee, Lukás Gajdos, Zuzana Hammerová, Aneta Horácková, Filip Melicher, Livia Perfetto, Daniel Pokorný, Milagros Rodríguez-López, Alzbeta Türková, Edith D. Wong, Zengyan Xie, Elisabeth Barrera Casanova, Noemi del-Toro, Maximilian Koch, Pablo Porras, Henning Hermjakob, Sandra E. Orchard:
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Res. 47(Database-Issue): D550-D558 (2019) - 2018
- [j78]Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo Marín-García, Peipei Ping, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
Reactome diagram viewer: data structures and strategies to boost performance. Bioinform. 34(7): 1208-1214 (2018) - [j77]M. Sivade Dumousseau, Diego Alonso-López, Mais G. Ammari, Glyn Bradley, Nancy H. Campbell, Arnaud Céol, Gianni Cesareni, Colin W. Combe, Javier De Las Rivas, Noemi del-Toro, Joshua Heimbach, Henning Hermjakob, Igor Jurisica, Maximilian Koch, Luana Licata, Ruth C. Lovering, David J. Lynn, Birgit H. M. Meldal, Gos Micklem, Simona Panni, Pablo Porras, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwínski, Anjali Shrivastava, Julie M. Sullivan, Nicolas Thierry-Mieg, Yo Yehudi, Kim Van Roey, Sandra E. Orchard:
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinform. 19(1): 134:1-134:8 (2018) - [j76]Mingze Bai, Mingmin He, Qifeng Sun, Huadong Liao, Kunxian Shu, Henning Hermjakob:
A pipeline for identifying endogenous neuropeptides from spectral archives. Int. J. Data Min. Bioinform. 20(1): 12-35 (2018) - [j75]Mihai Glont, Tung V. N. Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M. Wimalaratne, Varun B. Kothamachu, Nicolas Rodriguez, Maciej J. Swat, Jurgen Eils, Roland Eils, Camille Laibe, Rahuman S. Malik-Sheriff, Vijayalakshmi Chelliah, Nicolas Le Novère, Henning Hermjakob:
BioModels: expanding horizons to include more modelling approaches and formats. Nucleic Acids Res. 46(Database-Issue): D1248-D1253 (2018) - [j74]Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani V. Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The Reactome Pathway Knowledgebase. Nucleic Acids Res. 46(Database-Issue): D649-D655 (2018) - [j73]Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marín-García, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
Reactome graph database: Efficient access to complex pathway data. PLoS Comput. Biol. 14(1) (2018) - 2017
- [j72]Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steven Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews, Heeyeon Song, Lincoln Stein, Robin Haw, Peter D'Eustachio, Peipei Ping, Henning Hermjakob, Antonio Fabregat:
Reactome enhanced pathway visualization. Bioinform. 33(21): 3461-3467 (2017) - [j71]Colin W. Combe, Marine Sivade, Henning Hermjakob, Joshua Heimbach, Birgit H. M. Meldal, Gos Micklem, Sandra E. Orchard, Juri Rappsilber:
ComplexViewer: visualization of curated macromolecular complexes. Bioinform. 33(22): 3673-3675 (2017) - [j70]Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner-Martinez, Pablo Marín-García, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob:
Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinform. 18(1): 142:1-142:9 (2017) - [j69]Eric W. Deutsch, Attila Csordas, Zhi Sun, Andrew F. Jarnuczak, Yasset Pérez-Riverol, Tobias Ternent, David S. Campbell, Manuel Bernal Llinares, Shujiro Okuda, Shin Kawano, Robert L. Moritz, Jeremy Carver, Mingxun Wang, Yasushi Ishihama, Nuno Bandeira, Henning Hermjakob, Juan Antonio Vizcaíno:
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 45(Database-Issue): D1100-D1106 (2017) - [j68]Dan Wang, Liuhui Yang, Ping Zhang, Joshua LaBaer, Henning Hermjakob, Dong Li, Xiaobo Yu:
AAgAtlas 1.0: a human autoantigen database. Nucleic Acids Res. 45(Database-Issue): D769-D776 (2017) - [j67]Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis, Michael Maguire, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham:
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45(Database-Issue): D985-D994 (2017) - 2016
- [j66]Sushil Tripathi, Steven Vercruysse, Konika Chawla, Karen R. Christie, Judith A. Blake, Rachael P. Huntley, Sandra E. Orchard, Henning Hermjakob, Liv Thommesen, Astrid Lægreid, Martin Kuiper:
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database J. Biol. Databases Curation 2016 (2016) - [j65]Enrique Audain, Yassel Ramos, Henning Hermjakob, Darren R. Flower, Yasset Pérez-Riverol:
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. Bioinform. 32(6): 821-827 (2016) - [j64]Aristotelis Kittas, Laura Bennett, Henning Hermjakob, Sophia Tsoka:
Organizational principles of the Reactome human BioPAX model using graph theory methods. J. Complex Networks 4(4): 604-615 (2016) - [j63]Juan Antonio Vizcaíno, Attila Csordas, Noemi del-Toro, José A. Dianes, Johannes Griss, Ilias Lavidas, Gerhard Mayer, Yasset Pérez-Riverol, Florian Reisinger, Tobias Ternent, Qing-Wei Xu, Rui Wang, Henning Hermjakob:
2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44(Database-Issue): 447-456 (2016) - [j62]Antonio Fabregat, Konstantinos Sidiropoulos, Phani V. Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon J. McKay, Lisa Matthews, Bruce May, Marija Milacic, Karen Rothfels, Veronica Shamovsky, Marissa Webber, Joel Weiser, Mark Williams, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The Reactome pathway Knowledgebase. Nucleic Acids Res. 44(Database-Issue): 481-487 (2016) - 2015
- [j61]Sandra E. Orchard, Henning Hermjakob:
Shared resources, shared costs - leveraging biocuration resources. Database J. Biol. Databases Curation 2015 (2015) - [j60]Jose M. Villaveces, Rafael C. Jiménez, Pablo Porras, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Sandra E. Orchard, H. Choi, Peipei Ping, N. C. Zong, Manor Askenazi, Bianca Habermann, Henning Hermjakob:
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database J. Biol. Databases Curation 2015 (2015) - [j59]Sarala M. Wimalaratne, Jerven T. Bolleman, Nick S. Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novère, Henning Hermjakob, Camille Laibe:
SPARQL-enabled identifier conversion with Identifiers.org. Bioinform. 31(11): 1875-1877 (2015) - [j58]Yasset Pérez-Riverol, Julian Uszkoreit, Aniel Sánchez, Tobias Ternent, Noemi del-Toro, Henning Hermjakob, Juan Antonio Vizcaíno, Rui Wang:
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. Bioinform. 31(17): 2903-2905 (2015) - [j57]Eric W. Deutsch, Juan P. Albar, Pierre-Alain Binz, Martin Eisenacher, Andrew R. Jones, Gerhard Mayer, Gilbert S. Omenn, Sandra E. Orchard, Juan Antonio Vizcaíno, Henning Hermjakob:
Development of data representation standards by the human proteome organization proteomics standards initiative. J. Am. Medical Informatics Assoc. 22(3): 495-506 (2015) - [j56]Birgit H. M. Meldal, Oscar Forner-Martinez, Maria C. Costanzo, Jose M. Dana, Janos Demeter, Marine Dumousseau, Selina S. Dwight, Anna Gaulton, Luana Licata, Anna N. Melidoni, Sylvie Ricard-Blum, Bernd Roechert, Marek S. Skrzypek, Manu Tiwari, Sameer Velankar, Edith D. Wong, Henning Hermjakob, Sandra E. Orchard:
The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database-Issue): 479-484 (2015) - [j55]Vijayalakshmi Chelliah, Nick S. Juty, Ishan Ajmera, Raza Ali, Marine Dumousseau, Mihai Glont, Michael Hucka, Gaël Jalowicki, Sarah M. Keating, Vincent Knight-Schrijver, Audald Lloret-Villas, Kedar Nath Natarajan, Jean-Baptiste Pettit, Nicolas Rodriguez, Michael Schubert, Sarala M. Wimalaratne, Yangyang Zhao, Henning Hermjakob, Nicolas Le Novère, Camille Laibe:
BioModels: ten-year anniversary. Nucleic Acids Res. 43(Database-Issue): 542-548 (2015) - [j54]Florian Reisinger, Noemi del-Toro, Tobias Ternent, Henning Hermjakob, Juan Antonio Vizcaíno:
Introducing the PRIDE Archive RESTful web services. Nucleic Acids Res. 43(Webserver-Issue): W599-W604 (2015) - 2014
- [j53]Sarala M. Wimalaratne, Pierre Grenon, Henning Hermjakob, Nicolas Le Novère, Camille Laibe:
BioModels linked dataset. BMC Syst. Biol. 8: 91 (2014) - [j52]Sandra E. Orchard, Mais G. Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Eugenia Galeota, Ursula Hinz, Marta Iannuccelli, Sruthi Jagannathan, Rafael C. Jiménez, Jyoti Khadake, Astrid Lægreid, Luana Licata, Ruth C. Lovering, Birgit Meldal, Anna N. Melidoni, Mila Milagros, Daniele Peluso, Livia Perfetto, Pablo Porras, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Andre Stutz, Michael Tognolli, Kim Van Roey, Gianni Cesareni, Henning Hermjakob:
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 42(Database-Issue): 358-363 (2014) - [j51]David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani V. Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob, Lincoln Stein, Peter D'Eustachio:
The Reactome pathway knowledgebase. Nucleic Acids Res. 42(Database-Issue): 472-477 (2014) - [r1]Vijayalakshmi Chelliah, Nick S. Juty, Camille Laibe, Henning Hermjakob, Nicolas Le Novère:
BioModels Database: a public repository for sharing models of biological processes. Encyclopedia of Computational Neuroscience 2014 - [i1]Manuel Corpas, Rafael C. Jiménez, Seth Carbon, Alexander García Castro, Leyla Jael Castro, Tatyana Goldberg, John Gómez, Alex Kalderimis, Suzanna E. Lewis, Ian Mulvany, Aleksandra Pawlik, Francis Rowland, Gustavo A. Salazar, Fabian Schreiber, Ian Sillitoe, William Spooner, Anil S. Thanki, Jose M. Villaveces, Guy Yachdav, Henning Hermjakob:
BioJS: an open source standard for biological visualisation - its status in 2014. F1000Research 3: 55 (2014) - 2013
- [j50]Nick S. Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe:
Towards the Collaborative Curation of the Registry underlying identifiers.org. Database J. Biol. Databases Curation 2013 (2013) - [j49]Gerhard Mayer, Luisa Montecchi-Palazzi, David Ovelleiro, Andrew R. Jones, Pierre-Alain Binz, Eric W. Deutsch, Matthew Chambers, Marius Kallhardt, Fredrik Levander, James Shofstahl, Sandra E. Orchard, Juan Antonio Vizcaíno, Henning Hermjakob, Christian Stephan, Helmut E. Meyer, Martin Eisenacher:
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database J. Biol. Databases Curation 2013 (2013) - [j48]Kim Van Roey, Sandra E. Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson:
Capturing cooperative interactions with the PSI-MI format. Database J. Biol. Databases Curation 2013 (2013) - [j47]John Gómez, Leyla J. García, Gustavo A. Salazar, Jose M. Villaveces, Swanand P. Gore, Alexander García Castro, Maria Jesus Martin, Guillaume Launay, Rafael Alcántara, Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Sameer Velankar, Henning Hermjakob, Chenggong Zong, Peipei Ping, Manuel Corpas, Rafael C. Jiménez:
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29(8): 1103-1104 (2013) - [j46]Rafael C. Jiménez, Juan P. Albar, Jong Bhak, Marie-Claude Blatter, Thomas Blicher, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Marc A. van Driel, Michael J. Dunn, Pedro L. Fernandes, Celia W. G. van Gelder, Henning Hermjakob, Vassilios Ioannidis, David Phillip Judge, Pascal Kahlem, Eija Korpelainen, Hans-Joachim Kraus, Jane E. Loveland, Christine Mayer, Jennifer McDowall, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Gustavo A. Salazar, Reinhard Schneider, Allegra Via, Jose M. Villaveces, Ping Yu, Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas:
iAnn: an event sharing platform for the life sciences. Bioinform. 29(15): 1919-1921 (2013) - [j45]Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère:
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7: 116 (2013) - [j44]Rafael Alcántara, Joseph Onwubiko, Hong Cao, Paula de Matos, Jennifer A. Cham, Julius O. B. Jacobsen, Gemma L. Holliday, Julia D. Fischer, Syed Asad Rahman, Bijay Jassal, Mickael Goujon, Francis Rowland, Sameer Velankar, Rodrigo Lopez, John P. Overington, Gerard J. Kleywegt, Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Janet M. Thornton, Christoph Steinbeck:
The EBI enzyme portal. Nucleic Acids Res. 41(Database-Issue): 773-780 (2013) - [j43]Juan Antonio Vizcaíno, Richard G. Côté, Attila Csordas, José A. Dianes, Antonio Fabregat, Joseph M. Foster, Johannes Griss, Emanuele Alpi, Melih Birim, Javier Contell, Gavin O'Kelly, Andreas Schoenegger, David Ovelleiro, Yasset Pérez-Riverol, Florian Reisinger, Daniel Rios, Rui Wang, Henning Hermjakob:
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41(Database-Issue): 1063-1069 (2013) - [j42]Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Rafael C. Jiménez, Eugenia Galeota, Guillaume Launay, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwínski, Henning Hermjakob:
A new reference implementation of the PSICQUIC web service. Nucleic Acids Res. 41(Webserver-Issue): 601-606 (2013) - [c12]Pablo Porras, Paola Roncaglia, Emily Dimmer, Jane Lomax, Rachael P. Huntley, Sandra E. Orchard, Marine Dumousseau, Samuel Kerrien, Henning Hermjakob:
The Apoptosis Gene Ontology project and the IntAct-Apoptosis dataset: updating the conceptual representation of apoptosis. IWBBIO 2013: 757-758 - 2012
- [j41]Attila Csordas, David Ovelleiro, Rui Wang, Joseph M. Foster, Daniel Rios, Juan Antonio Vizcaíno, Henning Hermjakob:
PRIDE: Quality control in a proteomics data repository. Database J. Biol. Databases Curation 2012 (2012) - [j40]Steven Lewis, Attila Csordas, Sarah A. Killcoyne, Henning Hermjakob, Michael R. Hoopmann, Robert L. Moritz, Eric W. Deutsch, John Boyle:
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC Bioinform. 13: 324 (2012) - [j39]Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan J. Bridge, Fiona Broackes-Carter, Carol Chen, Margaret J. Duesbury, Marine Dumousseau, Marc Feuermann, Ursula Hinz, Christine Jandrasits, Rafael C. Jiménez, Jyoti Khadake, Usha Mahadevan, Patrick Masson, Ivo Pedruzzi, Eric Pfeiffenberger, Pablo Porras, Arathi Raghunath, Bernd Roechert, Sandra E. Orchard, Henning Hermjakob:
The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40(Database-Issue): 841-846 (2012) - [j38]Samuel P. Wein, Richard G. Côté, Marine Dumousseau, Florian Reisinger, Henning Hermjakob, Juan Antonio Vizcaíno:
Improvements in the protein identifier cross-reference service. Nucleic Acids Res. 40(Web-Server-Issue): 276-280 (2012) - [c11]Nick S. Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe:
Delivering 'Cool URIs' That Do Not Change. SWAT4LS 2012 - 2011
- [j37]Robin Haw, David Croft, Christina K. Yung, Nelson Ndegwa, Peter D'Eustachio, Henning Hermjakob, Lincoln D. Stein:
The Reactome BioMart. Database J. Biol. Databases Curation 2011 (2011) - [j36]Nelson Ndegwa, Richard G. Côté, David Ovelleiro, Peter D'Eustachio, Henning Hermjakob, Juan Antonio Vizcaíno, David Croft:
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database J. Biol. Databases Curation 2011 (2011) - [j35]Jose M. Villaveces, Rafael C. Jiménez, Leyla J. García, Gustavo A. Salazar, Bernat Gel, Nicola J. Mulder, Maria Jesus Martin, Alexander García Castro, Henning Hermjakob:
Dasty3, a WEB framework for DAS. Bioinform. 27(18): 2616-2617 (2011) - [j34]Bernat Gel, Andrew M. Jenkinson, Rafael C. Jiménez, Xavier Messeguer Peypoch, Henning Hermjakob:
easyDAS: Automatic creation of DAS servers. BMC Bioinform. 12: 23 (2011) - [j33]Gustavo A. Salazar, Rafael C. Jiménez, Alexander García Castro, Henning Hermjakob, Nicola J. Mulder, Edwin H. Blake:
DAS Writeback: A Collaborative Annotation System. BMC Bioinform. 12: 143 (2011) - [j32]David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani V. Garapati, Gopal Gopinath, Bijay Jassal, Steven Jupe, Irina Kalatskaya, Shahana Mahajan, Bruce May, Nelson Ndegwa, Esther Schmidt, Veronica Shamovsky, Christina K. Yung, Ewan Birney, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein:
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 39(Database-Issue): 691-697 (2011) - 2010
- [j31]