Henning Hermjakob

ORCID

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 44

Top Venues

Nucleic Acids Res.

Bioinform.

Database J. Biol. Databases Curation

BMC Bioinform.

Publications

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)
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, Jose-Maria 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 (2023)
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)
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 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) (2022)
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) (2022)
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) (2022)
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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David 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) (2022)
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) (2022)
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) (2022)
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) (2022)
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone
. Briefings Bioinform. 23 (4) (2022)
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) (2021)
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) (2021)
Momo Langenstein, Henning Hermjakob, Manuel Bernal Llinares
A decoupled, modular and scriptable architecture for tools to curate data platforms. Bioinform. 37 (20) (2021)
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) (2021)
Rahuman S. Malik-Sheriff, Mihai Glont, Tung V. N. Nguyen, Krishna 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 M. 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) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
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)
Livia Perfetto, Chiara Pastrello, Noemi del-Toro, Margaret J. Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, K. Panneerselvam, Simona Panni, N. Rahimzadeh, Sylvie Ricard-Blum, Lukasz Salwínski, Anjali Shrivastava, Gianni Cesareni, M. 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)
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) (2019)
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 (2019)
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) (2019)
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) (2019)
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)
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) (2018)
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) (2018)
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) (2018)
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) (2018)
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) (2018)
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) (2017)
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) (2017)
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) (2017)
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) (2017)
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) (2017)
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) (2017)
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) (2016)
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) (2016)
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)
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) (2016)
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) (2016)
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) (2015)
Jose M. Villaveces, Rafael C. Jimenez, 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)
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) (2015)
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) (2015)
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) (2015)
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) (2015)
Sandra E. Orchard, Henning Hermjakob
Shared resources, shared costs - leveraging biocuration resources. Database J. Biol. Databases Curation 2015 (2015)
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) (2015)
Sarala M. Wimalaratne, Pierre Grenon, Henning Hermjakob, Nicolas Le Novère, Camille Laibe
BioModels linked dataset. BMC Syst. Biol. 8 (2014)
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. Jimenez, 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) (2014)
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 (2014)
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) (2014)
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) (2013)
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 (2013)
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) (2013)
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)
Rafael C. Jimenez, 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) (2013)
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. Jimenez
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29 (8) (2013)
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)
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)
Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Rafael C. Jimenez, 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) (2013)
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)
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 (2012)
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) (2012)
Nick S. Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe
Delivering 'Cool URIs' That Do Not Change. SWAT4LS (2012)
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)
Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan Bridge, Fiona Broackes-Carter, Carol Chen, Margaret J. Duesbury, Marine Dumousseau, Marc Feuermann, Ursula Hinz, Christine Jandrasits, Rafael C. Jimenez, 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) (2012)
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) (2011)
Bernat Gel, Andrew M. Jenkinson, Rafael C. Jimenez, Xavier Messeguer Peypoch, Henning Hermjakob
easyDAS: Automatic creation of DAS servers. BMC Bioinform. 12 (2011)
Gustavo A. Salazar, Rafael C. Jimenez, Alexander García Castro, Henning Hermjakob, Nicola J. Mulder, Edwin H. Blake
DAS Writeback: A Collaborative Annotation System. BMC Bioinform. 12 (2011)
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)
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)
Jose M. Villaveces, Rafael C. Jimenez, 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) (2011)
Alexey V. Antonov, Esther Schmidt, Sabine Dietmann, Maria Krestyaninova, Henning Hermjakob
spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Richard G. Côté, Florian Reisinger, Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, Henning Hermjakob
The Ontology Lookup Service: bigger and better. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Bruno Aranda, P. Achuthan, Yasmin Alam-Faruque, Irina M. Armean, Alan Bridge, C. Derow, Marc Feuermann, A. T. Ghanbarian, Samuel Kerrien, Jyoti Khadake, J. Kerssemakers, C. Leroy, M. Menden, Magali Michaut, Luisa Montecchi-Palazzi, S. N. Neuhauser, Sandra E. Orchard, V. Perreau, Bernd Roechert, K. van Eijk, Henning Hermjakob
The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38 (Database-Issue) (2010)
Bijay Jassal, Steven Jupe, Michael Caudy, Ewan Birney, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
The systematic annotation of the three main GPCR families in Reactome. Database J. Biol. Databases Curation 2010 (2010)
Juan Antonio Vizcaíno, Richard G. Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, Lennart Martens
The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 38 (Database-Issue) (2010)
Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani V. Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alexander Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, Peter D'Eustachio
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37 (Database-Issue) (2009)
Jennifer A. Siepen, Khalid Belhajjame, Julian N. Selley, Suzanne M. Embury, Norman W. Paton, Carole A. Goble, Stephen G. Oliver, Robert Stevens, Lucas Zamboulis, Nigel J. Martin, Alexandra Poulovassilis, Philip Jones, Richard G. Côté, Henning Hermjakob, Melissa M. Pentony, David T. Jones, Christine A. Orengo, Simon J. Hubbard
ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Corinne Cassier-Chauvat, Franck Chauvat, Jean-Christophe Aude, Pierre Legrain, Henning Hermjakob
InteroPORC: an automated tool to predict highly conserved protein interaction networks. BMC Bioinform. 9 (S-10) (2008)
Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic
Integrating biological data - the Distributed Annotation System. BMC Bioinform. 9 (S-8) (2008)
Sandra E. Orchard, Henning Hermjakob
The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world. Briefings Bioinform. 9 (2) (2008)
Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra E. Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, Janet M. Thornton
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinform. 24 (23) (2008)
Kieran O'Neill, Alexander García Castro, Anita Schwegmann, Rafael C. Jimenez, Dan Jacobson, Henning Hermjakob
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. BMC Bioinform. 9 (2008)
Philip Jones, Richard G. Côté, Sang Yun Cho, Sebastian Klie, Lennart Martens, Antony F. Quinn, David Thorneycroft, Henning Hermjakob
PRIDE: new developments and new datasets. Nucleic Acids Res. 36 (Database-Issue) (2008)
Tony Chiang, Nianhua Li, Sandra E. Orchard, Samuel Kerrien, Henning Hermjakob, Robert Gentleman, Wolfgang Huber
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinform. 24 (8) (2008)
Florian Reisinger, Manuel Corpas, John M. Hancock, Henning Hermjakob, Ewan Birney, Pascal Kahlem
ENFIN - An Integrative Structure for Systems Biology. DILS (2008)
Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe Aude, Pierre Legrain, Henning Hermjakob
InteroPORC: automated inference of highly conserved protein interaction networks. Bioinform. 24 (14) (2008)
Henning Hermjakob
EBI Proteomics Services. DILS (2008)
Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, Henning Hermjakob
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Rafael C. Jimenez, Antony F. Quinn, Alexander García Castro, Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A. Salazar, Henning Hermjakob
Dasty2, an Ajax protein DAS client. Bioinform. 24 (18) (2008)
Sebastian Klie, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Alexander Hinneburg, Henning Hermjakob
An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases. German Conference on Bioinformatics (2007)
Samuel Kerrien, Yasmin Alam-Faruque, Bruno Aranda, I. Bancarz, Alan Bridge, C. Derow, Emily Dimmer, Marc Feuermann, A. Friedrichsen, Rachael P. Huntley, C. Kohler, Jyoti Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard, Judith E. Risse, Karine Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob
IntAct - open source resource for molecular interaction data. Nucleic Acids Res. 35 (Database-Issue) (2007)
Sebastian Klie, Alexander Hinneburg, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob
Analysing latent topics in large-scale proteomics. LWA (2007)
Richard G. Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinform. 8 (2007)

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Henning Hermjakob