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Henning Hermjakob

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Yasset Perez-Riverol; Yassel Ramos; Aniel Sánchez; David L Tabb; Juan Antonio Vizcaino; Rui Wang; Lazaro Betancourt; Diogo Borges; Paulo Costa Carvalho; Gilberto B Domont; Gabriel Duarte; Luis Javier González; Henning Hermjakob; Jesus Noda; Fábio César Sousa Nogueira; Gabriel Padrón; Vladimir Besada
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
Johannes Griss; Henning Hermjakob; Joseph M Foster; Juan Antonio Vizcaino
PRIDE Cluster: building a consensus of proteomics data.
Joseph M Foster; Henning Hermjakob; Pablo Moreno; Christoph Steinbeck; Rolf Apweiler; Antonio Fabregat; Michael J O Wakelam; Juan Antonio Vizcaino
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics.

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2013: Yasset Perez-Riverol; Yassel Ramos; Aniel Sánchez; David L Tabb; Juan Antonio Vizcaino; Rui Wang; Lazaro Betancourt; Diogo Borges; Paulo Costa Carvalho; Gilberto B Domont; Gabriel Duarte; Luis Javier González; Henning Hermjakob; Jesus Noda; Fábio César Sousa Nogueira; Gabriel Padrón; Vladimir Besada
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
Analytical chemistry 2013;85(7):3515-20.
2013: Johannes Griss; Henning Hermjakob; Joseph M Foster; Juan Antonio Vizcaino
PRIDE Cluster: building a consensus of proteomics data.
Nature methods 2013;10(2):95-6.
2013: Joseph M Foster; Henning Hermjakob; Pablo Moreno; Christoph Steinbeck; Rolf Apweiler; Antonio Fabregat; Michael J O Wakelam; Juan Antonio Vizcaino
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics.
PloS one 2013;8(5):e61951.
2013: Nick Juty; Henning Hermjakob; Nicolas Le Novère; Camille Laibe
Towards the Collaborative Curation of the Registry underlying identifiers.org.
Database : the journal of biological databases and curation 2013;2013():bat017.
2013: Gerhard Mayer; Helmut E Meyer; Luisa Montecchi-Palazzi; Sandra Orchard; David Ovelleiro; James Shofstahl; Christian Stephan; Juan Antonio Vizcaíno; Pierre-Alain Binz; Matthew Chambers; Eric Deutsch; Martin Eisenacher; Henning Hermjakob; Andrew R Jones; Marius Kallhardt; Fredrik Levander
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Database : the journal of biological databases and curation 2013;2013(0):bat009.
2013: Juan Antonio Vizcaino; Rui Wang; Gavin O'Kelly; David Ovelleiro; Yasset Pérez-Riverol; Florian Reisinger; Daniel Ríos; Andreas Schoenegger; Emanuele Alpi; Melih Birim; Javier Contell; Richard G Côté; Attila Csordas; José A Dianes; Antonio Fabregat; Joseph M Foster; Johannes Griss; Henning Hermjakob
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Nucleic acids research 2013;41(Database issue):D1063-9.
2013: Rafael Alcántara; Hong Cao; Jennifer A Cham; Julia D Fischer; Mikael Goujon; Henning Hermjakob; Gemma L Holliday; Jules Jacobsen; Bijay Jassal; Gerard J Kleywegt; Rodrigo López; María Jesús Martín; Paula de Matos; Claire O'Donovan; Joseph Onwubiko; John Overington; Syed Asad Rahman; Francis Rowland; Janet M Thornton; Sameer Velankar; Christoph Steinbeck
The EBI enzyme portal.
Nucleic acids research 2013;41(Database issue):D773-80.
2012: Richard G Côté; Attila Csordas; José A Dianes; Johannes Griss; Albert J R Heck; Henning Hermjakob; Niels Hulstaert; Lennart Martens; David Ovelleiro; Yasset Perez-Rivevol; Florian Reisinger; Bas van Breukelen; Henk W P van den Toorn; Rui Wang; James C Wright; Harald Barsnes; Juan Antonio Vizcaino
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Molecular & cellular proteomics : MCP 2012;11(12):1682-9.
2012: Sandra Orchard; Juan Antonio Vizcaino; Andrew R Jones; George Nicola; Pierre-Alain Binz; Christoph Borchers; Eric Deutsch; Michael K Gilson; Henning Hermjakob
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.
Proteomics 2012;12(18):2767-72.
2012: Faviel F Gonzalez-Galarza; Henning Hermjakob; Simon Hubbard; Conrad Bessant; Jun Fan; Craig Lawless; Andrew R Jones
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Omics : a journal of integrative biology 2012;16(9):431-42.
2012: Samuel P Wein; Richard G Côté; Marine Dumousseau; Henning Hermjakob; Florian Reisinger; Juan Antonio Vizcaino
Improvements in the Protein Identifier Cross-Reference service.
Nucleic acids research 2012;40(Web Server issue):W276-80.
2012: Andrew R Jones; Randall Julian; Oliver Kohlbacher; Gerhard Mayer; Angel Pizarro; Florian Reisinger; Brian C Searle; Julian N Selley; Sean L Seymour; James Shofstahl; Jennifer Siepen; Juan Antonio Vizcaino; Eric Deutsch; Martin Eisenacher; Johannes Griss; Henning Hermjakob; Simon Hubbard; Pierre-Alain Binz; Matthew Chambers; David Creasy
The mzIdentML data standard for mass spectrometry-based proteomics results.
Molecular & cellular proteomics : MCP 2012;11(7):M111.014381.
2012: Gavin C K W Koh; Bruno Aranda; Henning Hermjakob; Pablo Porras; Sandra Orchard
Analyzing protein-protein interaction networks.
Journal of proteome research 2012;11(4):2014-31.
2012: Johannes Griss; Henning Hermjakob; Florian Reisinger; Juan Antonio Vizcaino
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Proteomics 2012;12(6):795-8.
2012: Florian Reisinger; Daniel Ríos; Juan Antonio Vizcaíno; Fawaz Ghali; Henning Hermjakob; Ritesh Krishna; Andrew R Jones
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
Proteomics 2012;12(6):790-4.
2012: Maggie P Y Lam; Arjen Scholten; Jennifer E Van Eyk; Fernando Vivanco; Henning Hermjakob; Peipei Ping
HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.
Proteomics 2012;12(6):749-51.
2012: Rui Wang; Richard G Côté; Attila Csordas; Antonio Fabregat; Joseph M Foster; Johannes Griss; Henning Hermjakob; Lennart Martens; David Ovelleiro; Yasset Perez-Riverol; Florian Reisinger; Daniel Ríos; Juan Antonio Vizcaino
PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Nature biotechnology 2012;30(2):135-7.
2012: Sandra Orchard; Juan Antonio Vizcaino; Salvador Martínez-Bartolomé; Juan Pablo Albar; Pierre-Alain Binz; Eric Deutsch; Martin Eisenacher; Henning Hermjakob
From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.
Proteomics 2012;12(3):351-5.
2012: Alexandra M E Jones; Marko Jovanovic; Craig Lawless; Günter Lochnit; Lennart Martens; Christian Ravnsborg; Sabine P Schrimpf; Yhong-Hee Shim; Deni Subasic; Andreas Tholey; Manuel Weiss; Ruedi Aebersold; Christian H Ahrens; Rolf Apweiler; Katja Baerenfaller; Mark Baker; Emøke Bendixen; Steve Briggs; Philip Brownridge; Erich Brunner; Michael Daube; Eric Deutsch; Ueli Grossniklaus; Joshua L Heazlewood; Michael O Hengartner; Henning Hermjakob; Christian von Mering; Klaas van Wijk; Xue Zheng
The HUPO initiative on Model Organism Proteomes, iMOP.
Proteomics 2012;12(3):340-5.
2012: Steven Lewis; Robert L Moritz; Attila Csordas; Eric Deutsch; Henning Hermjakob; Michael R Hoopmann; Sarah Killcoyne; John Boyle
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
BMC bioinformatics 2012;13():324.
2012: Gustavo A Salazar; Leyla J García; Sarah Hunter; Andrew M Jenkinson; Rafael C Jimenez; Philip Jones; Maria Martin; Nicola Mulder; Antony F Quinn; Henning Hermjakob
MyDas, an extensible Java DAS server.
PloS one 2012;7(9):e44180.
2012: Attila Csordas; Joseph M Foster; David Ovelleiro; Daniel Ríos; Juan Antonio Vizcaino; Rui Wang; Henning Hermjakob
PRIDE: quality control in a proteomics data repository.
Database : the journal of biological databases and curation 2012;2012():bas004.
2011: Sandra Orchard; Juan Antonio Vizcaino; Juan Pablo Albar; Eric Deutsch; Martin Eisenacher; Henning Hermjakob
Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.
Proteomics 2011;11(22):4284-90.
2011: Johannes Griss; Henning Hermjakob; María Martín; Claire O'Donovan; Rolf Apweiler; Juan Antonio Vizcaino
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Proteomics 2011;11(22):4434-8.
2011: Jose M Villaveces; Alexander Garcia; Leyla J Garcia; Bernat Gel; Rafael C Jimenez; Maria Martin; Nicola Mulder; Gustavo A Salazar; Henning Hermjakob
Dasty3, a WEB framework for DAS.
Bioinformatics (Oxford, England) 2011;27(18):2616-7.
2011: Sandra Orchard; John Overington; Christopher Southan; Christoph Steinbeck; David Wishart; Bissan Al-Lazikani; Steve Bryant; Elizabeth Calder; Dominic Clark; Ian Dix; Ola Engkvist; Mark Forster; Anna Gaulton; Michael Gilson; Robert C Glen; Martin Grigorov; Kim Hammond-Kosack; Lee Harland; Henning Hermjakob; Andrew Hopkins; Christopher Larminie; Elena Lo Piparo; Nick Lynch; Romeena K Mann; Peter Murray-Rust; Janet Thornton
Minimum information about a bioactive entity (MIABE).
Nature reviews. Drug discovery 2011;10(9):661-9.
2011: Robin Haw; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Reactome pathway analysis to enrich biological discovery in proteomics data sets.
Proteomics 2011;11(18):3598-613.
2011: Johannes Griss; Henning Hermjakob; Richard G Côté; Christopher Gerner; Juan Antonio Vizcaino
Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.
Molecular & cellular proteomics : MCP 2011;10(9):M111.008490.
2011: Nelson Ndegwa; David Ovelleiro; Juan Antonio Vizcaino; Richard G Côté; Peter D'Eustachio; Henning Hermjakob; 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 : the journal of biological databases and curation 2011;2011():bar047.
2011: Robin A Haw; Henning Hermjakob; Nelson Ndegwa; David Croft; Peter D'Eustachio; Christina K Yung; Lincoln D Stein
The Reactome BioMart.
Database : the journal of biological databases and curation 2011;2011():bar031.
2011: Gustavo A Salazar; Alexander Garcia; Henning Hermjakob; Rafael C Jimenez; Nicola Mulder; Edwin Blake
DAS writeback: a collaborative annotation system.
BMC bioinformatics 2011;12():143.
2011: Bernat Gel Moreno; Andrew M Jenkinson; Rafael C Jimenez; Xavier Messeguer Peypoch; Henning Hermjakob
easyDAS: automatic creation of DAS servers.
BMC bioinformatics 2011;12():23.
2011: Sandra Orchard; Henning Hermjakob
Preparing molecular interaction data for publication.
Methods in molecular biology (Clifton, N.J.) 2011;694():229-36.
2011: David Croft; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; Shahana Mahajan; Bruce May; Nelson Ndegwa; Esther Schmidt; Veronica Shamovsky; Christina Yung; Ewan Birney; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Reactome: a database of reactions, pathways and biological processes.
Nucleic acids research 2011;39(Database issue):D691-7.
2011: Sandra Orchard; Henning Hermjakob
Data standardization by the HUPO-PSI: how has the community benefitted?
Methods in molecular biology (Clifton, N.J.) 2011;696():149-60.
2011: Lennart Martens; Matthew Chambers; Marc Sturm; Darren Kessner; Fredrik Levander; Jim Shofstahl; Wilfred H Tang; Andreas Römpp; Steffen Neumann; Angel Pizarro; Luisa Montecchi-Palazzi; Natalie Tasman; Mike Coleman; Florian Reisinger; Puneet Souda; Henning Hermjakob; Pierre-Alain Binz; Eric Deutsch
mzML--a community standard for mass spectrometry data.
Molecular & cellular proteomics : MCP 2011;10(1):R110.000133.
2010: Laurent Gatto; Juan Antonio Vizcaíno; Henning Hermjakob; Wolfgang Huber; Kathryn S Lilley
Organelle proteomics experimental designs and analysis.
Proteomics 2010;10(22):3957-69.
2010: Sandra Orchard; Andrew Jones; Juan Pablo Albar; Sang Yun Cho; Kyung-Hoon Kwon; Cheolju Lee; Henning Hermjakob
Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea.
Proteomics 2010;10(17):3062-6.
2010: Frank Gibson; Christine Hoogland; Salvador Martínez-Bartolomé; Alberto Medina-Aunon; Juan Pablo Albar; Gyorgy Babnigg; Anil Wipat; Henning Hermjakob; Jonas Almeida; Romesh Stanislaus; Norman W Paton; Andrew R Jones
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.
Proteomics 2010;10(17):3073-81.
2010: Alexey V Antonov; Esther E Schmidt; Sabine Dietmann; Maria Krestyaninova; Henning Hermjakob
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.
Nucleic acids research 2010;38(Web Server issue):W78-83.
2010: Richard G Côté; Florian Reisinger; Lennart Martens; Harald Barsnes; Juan Antonio Vizcaino; Henning Hermjakob
The Ontology Lookup Service: bigger and better.
Nucleic acids research 2010;38(Web Server issue):W155-60.
2010: Victoria M Perreau; Sandra Orchard; Paul A Adlard; Shayne A Bellingham; Roberto Cappai; Giuseppe D Ciccotosto; Tiffany F Cowie; Peter J Crouch; James A Duce; Geneviève Evin; Noel G Faux; Andrew Hill; Ya Hui Hung; Simon A James; Qiao-Xin Li; Su San Mok; Deborah J Tew; Anthony R White; Ashley I Bush; Henning Hermjakob; Colin L Masters
A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease.
Proteomics 2010;10(12):2377-95.
2010: Sandra Orchard; Juan Pablo Albar; Eric Deutsch; Martin Eisenacher; Pierre-Alain Binz; Henning Hermjakob
implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada.
Proteomics 2010;10(10):1895-8.
2010: Sandra Orchard; Bruno Aranda; Henning Hermjakob
The publication and database deposition of molecular interaction data.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2010;Chapter 25():Unit 25.3.
2010: Kiyoung Lee; David Thorneycroft; Premanand Achuthan; Henning Hermjakob; Trey Ideker
Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.
The Plant cell 2010;22(4):997-1005.
2010: Carsten Kettner; Dawn Field; Susanna-Assunta Sansone; Chris Taylor; Jan Aerts; Nigel Binns; Andrew Blake; Cedrik Michael Britten; Ario de Marco; Jennifer Fostel; Pascale Gaudet; Alejandra González-Beltrán; Nigel Hardy; Jan Hellemans; Henning Hermjakob; Nick Juty; Jim Leebens-Mack; Eamonn Maguire; Steffen Neumann; Sandra Orchard; Helen Parkinson; William Piel; Shoba Ranganathan; Philippe Rocca-Serra; Annapaola Santarsiero; David Shotton; Peter Sterk; Andreas Untergasser; Patricia L Whetzel
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.
Standards in genomic sciences 2010;3(3):259-66.
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 : the journal of biological databases and curation 2010;2010():baq018.
2010: Juan Antonio Vizcaino; Richard Côté; Florian Reisinger; Harald Barsnes; Joseph M Foster; Jonathan Rameseder; Henning Hermjakob; Lennart Martens
The Proteomics Identifications database: 2010 update.
Nucleic acids research 2010;38(Database issue):D736-42.
2010: B Aranda; P Achuthan; Y Alam-Faruque; I Armean; A Bridge; C Derow; M Feuermann; A T Ghanbarian; Samuel Kerrien; Jyoti Khadake; J Kerssemakers; C Leroy; M Menden; M Michaut; Luisa Montecchi-Palazzi; S N Neuhauser; Sandra Orchard; V Perreau; Bernd Roechert; K van Eijk; Henning Hermjakob
The IntAct molecular interaction database in 2010.
Nucleic acids research 2010;38(Database issue):D525-31.
2009: Lukasz Salwinski; Luana Licata; Andrew Winter; David Thorneycroft; Jyoti Khadake; Arnaud Ceol; Andrew Chatr Aryamontri; Rose Oughtred; Michael Livstone; Lorrie Boucher; David Botstein; Kara Dolinski; Tanya Berardini; Eva Huala; Mike Tyers; David Eisenberg; Gianni Cesareni; Henning Hermjakob
Recurated protein interaction datasets.
Nature methods 2009;6(12):860-1.
2009: Pascal Kahlem; Andrew Clegg; Florian Reisinger; Ioannis Xenarios; Henning Hermjakob; Christine Orengo; Ewan Birney
ENFIN--A European network for integrative systems biology.
Comptes rendus biologies 2009;332(11):1050-8.
2009: Luisa Montecchi-Palazzi; Samuel Kerrien; Florian Reisinger; Bruno Aranda; Andrew R Jones; Lennart Martens; Henning Hermjakob
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
Proteomics 2009;9(22):5112-9.
2009: Sandra Orchard; Eric Deutsch; Pierre-Alain Binz; Andrew R Jones; David Creasy; Luisa Montechi-Palazzi; Garry Corthals; Henning Hermjakob
Annual spring meeting of the Proteomics Standards Initiative.
Proteomics 2009;9(19):4429-32.
2009: Sandra Orchard; Pierre-Alain Binz; Henning Hermjakob
Second Joint HUPO publication and Proteomics Standards Initiative workshop.
Proteomics 2009;9(19):4426-8.
2009: Juan Antonio Vizcaino; Richard Côté; Florian Reisinger; Joseph M Foster; Michael Mueller; Jonathan Rameseder; Henning Hermjakob; Lennart Martens
A guide to the Proteomics Identifications Database proteomics data repository.
Proteomics 2009;9(18):4276-83.
2009: Henry Rodriguez; Mike Snyder; Mathias Uhlén; Philip C Andrews; Ronald Beavis; Christoph Borchers; Robert J Chalkley; Sang Yun Cho; Katie Cottingham; Michael Dunn; Tomasz Dylag; Ron Edgar; Peter Hare; Albert J R Heck; Roland F Hirsch; Karen Kennedy; Patrik Kolar; Hans-Joachim Kraus; Parag Mallick; Alexey I Nesvizhskii; Peipei Ping; Fredrik Pontén; Liming Yang; John R Yates; Stephen E Stein; Henning Hermjakob; Christopher R Kinsinger; Rolf Apweiler
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Journal of proteome research 2009;8(7):3689-92.
2009: Juan Antonio Vizcaino; Michael Mueller; Henning Hermjakob; Lennart Martens
Charting online OMICS resources: A navigational chart for clinical researchers.
Proteomics. Clinical applications 2009;3(1):18-29.
2009: Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft; Bernard de Bono; Phani 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 research 2009;37(Database issue):D619-22.
2008: Gabrielle A Reeves; Karen Eilbeck; Michele Magrane; Claire O'Donovan; Luisa Montecchi-Palazzi; Midori A Harris; Sandra Orchard; Rafael C Jimenez; Andreas Prlic; Tim Hubbard; Henning Hermjakob; Janet M Thornton
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Bioinformatics (Oxford, England) 2008;24(23):2767-72.
2008: Sandra Orchard; Juan-Pablo Albar; Eric W Deutsch; Pierre-Alain Binz; Andrew R Jones; David Creasy; Henning Hermjakob
Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.
Proteomics 2008;8(20):4168-72.
2008: Rafael C Jimenez; Antony F Quinn; Alexander Garcia; Alberto Labarga; Kieran O'Neill; Fernando Martinez; Gustavo A Salazar; Henning Hermjakob
Dasty2, an Ajax protein DAS client.
Bioinformatics (Oxford, England) 2008;24(18):2119-21.
2008: Christopher Taylor; Dawn Field; Susanna-Assunta Sansone; Jan Aerts; Rolf Apweiler; Michael Ashburner; Catherine A Ball; Pierre-Alain Binz; Molly Bogue; Tim Booth; Alvis Brazma; Ryan R Brinkman; Adam Michael Clark; Eric W Deutsch; Oliver Fiehn; Jennifer Fostel; Peter Ghazal; Frank Gibson; Tanya Gray; Graeme Grimes; John M Hancock; Nigel W Hardy; Henning Hermjakob; Randall K Julian; Matthew Kane; Carsten Kettner; Christopher Kinsinger; Eugene Kolker; Martin Kuiper; Nicolas Le Novère; Jim Leebens-Mack; Suzanna E Lewis; Phillip Lord; Ann-Marie Mallon; Nishanth Marthandan; Hiroshi Masuya; ruth mcnally; Alexander Mehrle; Norman Morrison; Sandra Orchard; John Quackenbush; James Reecy; Donald G Robertson; Philippe Rocca-Serra; Henry Rodriguez; Heiko Rosenfelder; Javier Santoyo-Lopez; Richard Scheuermann; Daniel Schober; Barry Smith; Jason Snape; Christian J Stoeckert; Keith Tipton; Peter Sterk; Andreas Untergasser; Jo Vandesompele; Stefan Wiemann
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature biotechnology 2008;26(8):889-96.
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.
Bioinformatics (Oxford, England) 2008;24(14):1625-31.
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 research 2008;36(Web Server issue):W372-6.
2008: Jennifer A Siepen; Khalid Belhajjame; Julian N Selley; Suzanne M Embury; Norman W Paton; Carole Goble; Stephen G Oliver; Robert Stevens; Lucas Zamboulis; Nigel Martin; Alexandra Poulovassillis; Philip Jones; Richard Côté; Henning Hermjakob; Melissa M Pentony; David T Jones; Christine A Orengo; Simon Hubbard
ISPIDER Central: an integrated database web-server for proteomics.
Nucleic acids research 2008;36(Web Server issue):W485-90.
2008: Dawn Field; George M Garrity; Tanya Gray; Norman Morrison; Jeremy Selengut; Peter Sterk; Tatiana Tatusova; Nicholas Thomson; Michael Allen; Samuel V Angiuoli; Michael Ashburner; Nelson Axelrod; Sandra Baldauf; Stuart Ballard; Jeffrey Boore; Guy Cochrane; James Cole; Peter Dawyndt; Paul De Vos; Claude DePamphilis; Robert Edwards; Nadeem Faruque; Robert Feldman; Jack Gilbert; Paul Gilna; Frank Oliver Glöckner; Philip Goldstein; Robert Guralnick; Dan Haft; David Hancock; Henning Hermjakob; Christiane Hertz-Fowler; Phil Hugenholtz; Ian Joint; Leonid Kagan; Matthew Kane; Jessie Kennedy; George Kowalchuk; Renzo Kottmann; Eugene Kolker; Saul Kravitz; Nikos Kyrpides; Jim Leebens-Mack; Suzanna E Lewis; Kelvin Li; Allyson L Lister; Phillip Lord; Natalia Maltsev; Victor Markowitz; Jennifer Martiny; Barbara Methe; Ilene Mizrachi; Richard Moxon; Karen Nelson; Julian Parkhill; Lita Proctor; Owen R White; Susanna-Assunta Sansone; Andrew Spiers; Robert Stevens; Paul Swift; Chris Taylor; Yoshio Tateno; Adrian Tett; Sarah Turner; David Ussery; Bob Vaughan; Naomi Ward; Trish Whetzel; Ingio San Gil; Gareth Wilson; Anil Wipat
The minimum information about a genome sequence (MIGS) specification.
Nature biotechnology 2008;26(5):541-7.
2008: Tony Chiang; Nianhua Li; Sandra Orchard; Samuel Kerrien; Henning Hermjakob; Robert Gentleman; Wolfgang Huber
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
Bioinformatics (Oxford, England) 2008;24(8):1100-1.
2008: Sandra Orchard; Lennart Martens; Joshua Tasman; Pierre-Alain Binz; Juan Pablo Albar; Henning Hermjakob
6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.
Proteomics 2008;8(7):1331-3.
2008: Michael Mueller; Juan Antonio Vizcaino; Philip Jones; Richard Côté; David Thorneycroft; Rolf Apweiler; Henning Hermjakob; Lennart Martens
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Proteomics 2008;8(6):1138-48.
2008: Sandra Orchard; Henning Hermjakob
The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.
Briefings in bioinformatics 2008;9(2):166-73.
2008: Kieran O'Neill; Alexander Garcia; Anita Schwegmann; Rafael C Jimenez; Dan Jacobson; Henning Hermjakob
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
BMC bioinformatics 2008;9():437.
2008: Andrew Chatr-Aryamontri; Samuel Kerrien; Jyoti Khadake; Sandra Orchard; Arnaud CEOL; Luana Licata; Luisa Castagnoli; Stefano Costa; Cathy Derow; Rachael Huntley; Bruno Aranda; Catherine Leroy; Dave Thorneycroft; Rolf Apweiler; Gianni Cesareni; Henning Hermjakob
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Genome biology 2008;9 Suppl 2():S5.
2008: Andrew M Jenkinson; Mario Albrecht; Ewan Birney; Hagen Blankenburg; Thomas 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 Prlić
Integrating biological data--the Distributed Annotation System.
BMC bioinformatics 2008;9 Suppl 8():S3.
2008: Lennart Martens; Luisa Montecchi Palazzi; Henning Hermjakob
Data standards and controlled vocabularies for proteomics.
Methods in molecular biology (Clifton, N.J.) 2008;484():279-86.
2008: Barend Mons; Michael Ashburner; Christine Chichester; Erik van Mulligen; Marc Weeber; Johan T den Dunnen; Gert-Jan van Ommen; Mark Musen; Matthew Cockerill; Henning Hermjakob; Albert Mons; Abel L Packer; Roberto Pacheco; Suzanna Lewis; Alfred Berkeley; William Melton; Nickolas Barris; Jimmy Wales; Gerard Meijssen; Erik Moeller; Peter Jan Roes; Katy Börner; Amos Bairoch
Calling on a million minds for community annotation in WikiProteins.
Genome biology 2008;9(5):R89.
2008: Sebastian Klie; Lennart Martens; Juan Antonio Vizcaino; Richard Côté; Philip Jones; Rolf Apweiler; Alexander Hinneburg; Henning Hermjakob
Analyzing large-scale proteomics projects with latent semantic indexing.
Journal of proteome research 2008;7(1):182-91.
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 research 2008;36(Database issue):D878-83.
2007: Andrew R Jones; Michael Miller; Ruedi Aebersold; Rolf Apweiler; Catherine A Ball; Alvis Brazma; James Degreef; Nigel Hardy; Henning Hermjakob; Simon Hubbard; Peter Hussey; Mark Igra; Helen Jenkins; Randall K Julian; Kent Laursen; Stephen G Oliver; Norman W Paton; Susanna-Assunta Sansone; Ugis Sarkans; Christian J Stoeckert; Christopher Taylor; Patricia L Whetzel; Joseph A White; Paul Spellman; Angel Pizarro
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
2007: Sandra Orchard; Luisa Montechi-Palazzi; Eric Deutsch; Pierre-Alain Binz; Andrew R Jones; Norman Paton; Angel Pizarro; David M Creasy; Jérôme Wojcik; Henning Hermjakob
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.
Proteomics 2007;7(19):3436-40.
2007: Sandra Orchard; Samuel Kerrien; Philip Jones; Arnaud CEOL; Andrew Chatr-Aryamontri; Lukasz Salwinski; Jason Nerothin; Henning Hermjakob
Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.
Proteomics 2007;7 Suppl 1():28-34.
2007: Lennart Martens; Sandra Orchard; Rolf Apweiler; Henning Hermjakob
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Molecular & cellular proteomics : MCP 2007;6(9):1666-7.
2007: Sandra Orchard; Lukasz Salwinski; Samuel Kerrien; Luisa Montecchi-Palazzi; Matthias Oesterheld; Volker Stümpflen; Arnaud CEOL; Andrew Chatr-aryamontri; John Armstrong; Peter Woollard; John J Salama; Susan Moore; Jérôme Wojcik; Gary Bader; Marc Vidal; Michael E Cusick; Mark Gerstein; Anne-Claude Gavin; Giulio Superti-Furga; Jack Greenblatt; Joel Bader; Peter Uetz; Mike Tyers; Pierre Legrain; Stan Fields; Nicola Mulder; Michael K Gilson; Michael Niepmann; Lyle Burgoon; Javier De Las Rivas; Carlos Prieto; Victoria M Perreau; Chris Hogue; Hans-Werner Mewes; Rolf Apweiler; Ioannis Xenarios; David Eisenberg; Gianni Cesareni; Henning Hermjakob
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Nature biotechnology 2007;25(8):894-8.
2007: Christopher Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric Deutsch; Michael J Dunn; albert heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
The minimum information about a proteomics experiment (MIAPE).
Nature biotechnology 2007;25(8):887-93.
2007: Lennart Martens; Henning Hermjakob
Proteomics data validation: why all must provide data.
Molecular bioSystems 2007;3(8):518-22.
2007: Juan Antonio Vizcaino; Lennart Martens; Henning Hermjakob; Randall K Julian; Norman W Paton
The PSI formal document process and its implementation on the PSI website.
Proteomics 2007;7(14):2355-7.
2007: Michael L Tress; Pier Luigi Martelli; Adam Frankish; Gabrielle A Reeves; Jan Jaap Wesselink; Corin Yeats; Páll Isólfur Olason; Mario Albrecht; Hedi Hegyi; Alejandro Giorgetti; Domenico Raimondo; Julien Lagarde; Roman A Laskowski; Gonzalo López; Michael I Sadowski; James D Watson; Piero Fariselli; Ivan Rossi; Alinda Nagy; Wang Kai; Zenia Størling; Massimiliano Orsini; Yassen Assenov; Hagen Blankenburg; Carola Huthmacher; Fidel Ramírez; Andreas Schlicker; France Denoeud; Phil Jones; Samuel Kerrien; Sandra Orchard; Stylianos Antonarakis; Alexandre Reymond; Ewan Birney; Søren Brunak; Rita Casadio; Roderic Guigo; Jennifer Harrow; Henning Hermjakob; David T Jones; Thomas Lengauer; Christine A Orengo; László Patthy; Janet M Thornton; Anna Tramontano; Alfonso Valencia
The implications of alternative splicing in the ENCODE protein complement.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(13):5495-500.
2007: Mischak Harald; Rolf Apweiler; Rosamonde E Banks; Mark Conaway; Joshua Coon; Anna Dominiczak; Jochen H H Ehrich; Danilo Fliser; Mark Girolami; Henning Hermjakob; Denis Hochstrasser; Joachim Jankowski; Bruce A Julian; Walter Kolch; Ziad A Massy; Christian Neusuess; Jan Novak; Karlheinz Peter; Kasper Rossing; Joost Schanstra; O John Semmes; Dan Theodorescu; Visith Thongboonkerd; Eva M Weissinger; Jennifer E Van Eyk; Tadashi Yamamoto
Clinical proteomics: A need to define the field and to begin to set adequate standards.
Proteomics. Clinical applications 2007;1(2):148-56.
2007: Sandra Orchard; Christopher Taylor; Philip Jones; Luisa Montechi-Palazzo; Pierre-Alain Binz; Andrew R Jones; Angel Pizarro; Randall K Julian; Henning Hermjakob
Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
Proteomics 2007;7(3):337-9.
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 bioinformatics 2007;8():401.
2007: Samuel Kerrien; Sandra Orchard; Luisa Montecchi-Palazzi; Bruno Aranda; Antony F Quinn; Nisha Vinod; Gary Bader; Ioannis Xenarios; Jérôme Wojcik; David Sherman; Mike Tyers; John J Salama; Susan Moore; Arnaud CEOL; Andrew Chatr-Aryamontri; Matthias Oesterheld; Volker Stümpflen; Lukasz Salwinski; Jason Nerothin; Ethan Cerami; Michael E Cusick; Marc Vidal; Michael K Gilson; John Armstrong; Peter Woollard; Christopher Hogue; David Eisenberg; Gianni Cesareni; Rolf Apweiler; Henning Hermjakob
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
BMC biology 2007;5():44.
2007: Jennifer A Siepen; Neil Swainston; Andrew R Jones; Sarah Hart; Henning Hermjakob; Philip Jones; Simon Hubbard
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Proteome science 2007;5():4.
2007: Michael J Taussig; Oda Stoevesandt; Carl A K Borrebaeck; Andrew R Bradbury; Dolores Cahill; Christian Cambillau; Antoine de Daruvar; Stefan Dübel; Jutta Eichler; Ronald Frank; Toby J Gibson; David Gloriam; Larry Gold; Friedrich W Herberg; Henning Hermjakob; Jörg D Hoheisel; Thomas O Joos; Olli Kallioniemi; Manfred Koegl; Manfred Koegll; Zoltán Konthur; Bernhard Korn; Elisabeth Kremmer; Sylvia Krobitsch; Ulf Landegren; Silvère van der Maarel; John McCafferty; Serge Muyldermans; Per-Ake Nygren; sandrine palcy; Andreas Plückthun; Bojan Polic; Michael Przybylski; Petri Saviranta; Alan Sawyer; David Sherman; Arne Skerra; Markus Templin; Marius Ueffing; Mathias Uhlén
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Nature methods 2007;4(1):13-7.
2007: Sandra Orchard; Philip Jones; Chris Taylor; Weimin Zhu; Randall K Julian; Henning Hermjakob; Rolf Apweiler
Proteomic data exchange and storage: the need for common standards and public repositories.
Methods in molecular biology (Clifton, N.J.) 2007;367():261-70.
2007: Samuel Kerrien; Y Alam-Faruque; B Aranda; I Bancarz; A Bridge; C Derow; Emily Dimmer; M Feuermann; A Friedrichsen; R Huntley; C Kohler; Jyoti Khadake; C Leroy; A Liban; C Lieftink; Luisa Montecchi-Palazzi; Sandra Orchard; J Risse; K Robbe; Bernd Roechert; D Thorneycroft; Y Zhang; Rolf Apweiler; Henning Hermjakob
IntAct--open source resource for molecular interaction data.
Nucleic acids research 2007;35(Database issue):D561-5.
2007: L Miguel Camargo; V Collura; Jean-Christophe Rain; K Mizuguchi; Henning Hermjakob; Samuel Kerrien; Timothy P Bonnert; Paul J Whiting; Nicholas J Brandon
Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia.
Molecular psychiatry 2007;12(1):74-86.
2006: Brian B Haab; Amanda Paulovich; N Leigh Anderson; Adam M Clark; Gregory J Downing; Henning Hermjakob; Joshua LaBaer; Mathias Uhlen
A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report.
Molecular & cellular proteomics : MCP 2006;5(10):1996-2007.
2006: Henning Hermjakob
The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.
Proteomics 2006;6 Suppl 2():34-8.
2006: Sandra Orchard; Rolf Apweiler; Robert Barkovich; Dawn Field; John S Garavelli; David Horn; Andy Jones; Philip Jones; Randall K Julian; ruth mcnally; Jason Nerothin; Norman Paton; Angel Pizarro; Sean Seymour; Chris Taylor; Stefan Wiemann; Henning Hermjakob
Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Proteomics 2006;6(16):4439-43.
2006: Michael Hamacher; Christian Stephan; Martin Blüggel; Daniel C Chamrad; Gerhard Körting; Lennart Martens; Michael Müller; Henning Hermjakob; David Parkinson; Andrew W Dowsey; Kai A Reidegeld; Katrin Marcus; Michael J Dunn; Helmut E Meyer; Rolf Apweiler
The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
Proteomics 2006;6(6):1719-21.
2006: Henning Hermjakob; Rolf Apweiler
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Expert review of proteomics 2006;3(1):1-3.
2006: Sandra Orchard; Henning Hermjakob; Chris Taylor; Pierre-Alain Binz; Christine Hoogland; Randall K Julian; John S Garavelli; Ruedi Aebersold; Rolf Apweiler
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Proteomics 2006;6(3):738-41.
2006: Christopher Taylor; Henning Hermjakob; Randall K Julian; John S Garavelli; Ruedi Aebersold; Rolf Apweiler
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Omics : a journal of integrative biology 2006;10(2):145-51.
2006: Richard G Côté; Philip Jones; Rolf Apweiler; Henning Hermjakob
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
BMC bioinformatics 2006;7():97.
2006: Philip Jones; Richard G Côté; Lennart Martens; Antony F Quinn; Christopher Taylor; William Derache; Henning Hermjakob; Rolf Apweiler
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Nucleic acids research 2006;34(Database issue):D659-63.
2005: Sandra Orchard; Henning Hermjakob; Chris Taylor; Ruedi Aebersold; Rolf Apweiler
Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.
Proteomics 2005;5(18):4651-2.
2005: Sandra Orchard; Henning Hermjakob; Christopher Taylor; Frank Potthast; Philip Jones; Weimin Zhu; Randall K Julian; Rolf Apweiler
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).
Proteomics 2005;5(14):3552-5.
2005: Marcin Adamski; Thomas Blackwell; Rajasree Menon; Lennart Martens; Henning Hermjakob; Chris Taylor; Gilbert S Omenn; David States
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.
Proteomics 2005;5(13):3246-61.
2005: Gilbert S Omenn; David States; Marcin Adamski; Thomas W Blackwell; Rajasree Menon; Henning Hermjakob; Rolf Apweiler; Brian B Haab; Richard J Simpson; James S Eddes; Eugene A Kapp; Robert L Moritz; Daniel W Chan; Alex J Rai; Arie Admon; Ruedi Aebersold; Jimmy Eng; William S Hancock; Stanley A Hefta; Helmut Meyer; Young-Ki Paik; Jong-Shin Yoo; Peipei Ping; Joel G Pounds; Joshua Adkins; Xiaohong Qian; Rong Wang; Valerie Wasinger; Chi Yue Wu; Xiaohang Zhao; Rong Zeng; Alexander Archakov; Akira Tsugita; Ilan Beer; Akhilesh Pandey; Michael Pisano; Philip C Andrews; Harald Tammen; David W Speicher; Samir M Hanash
Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.
Proteomics 2005;5(13):3226-45.
2005: Lennart Martens; Henning Hermjakob; Philip Jones; Marcin Adamski; Chris Taylor; David States; Kris Gevaert; Joël Vandekerckhove; Rolf Apweiler
PRIDE: the proteomics identifications database.
Proteomics 2005;5(13):3537-45.
2005: Lennart Martens; Alexey I Nesvizhskii; Henning Hermjakob; Marcin Adamski; Gilbert S Omenn; Joël Vandekerckhove; Kris Gevaert
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.
Proteomics 2005;5(13):3501-5.
2005: Philip Jones; Nisha Vinod; Thomas A Down; Andre Hackmann; Andreas Kahari; Ernst Kretschmann; Antony Quinn; Daniela Wieser; Henning Hermjakob; Rolf Apweiler
Dasty and UniProt DAS: a perfect pair for protein feature visualization.
Bioinformatics (Oxford, England) 2005;21(14):3198-9.
2005: Sandra Orchard; Henning Hermjakob; Christopher Taylor; Frank Potthast; Philip Jones; Weimin Zhu; Randall K Julian; Rolf Apweiler
Second proteomics standards initiative spring workshop.
Expert review of proteomics 2005;2(3):287-9.
2005: Sandra Orchard; Henning Hermjakob; Rolf Apweiler
Annotating the human proteome.
Molecular & cellular proteomics : MCP 2005;4(4):435-40.
2005: Sandra Orchard; Henning Hermjakob; Pierre-Alain Binz; Christine Hoogland; Christopher Taylor; Weimin Zhu; Randall K Julian; Rolf Apweiler
Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.
Proteomics 2005;5(2):337-9.
2005: Sandra Orchard; Luisa Montecchi-Palazzi; Henning Hermjakob; Rolf Apweiler
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():186-96.
2004: Patrick G A Pedrioli; Jimmy K Eng; Robert Hubley; Mathijs Vogelzang; Eric Deutsch; Brian Raught; Brian Pratt; Erik Nilsson; Ruth Hogue Angeletti; Rolf Apweiler; Kei Cheung; Catherine E Costello; Henning Hermjakob; Sequin Huang; Randall K Julian; Eugene Kapp; Mark E McComb; Stephen G Oliver; Gilbert S Omenn; Norman W Paton; Richard Simpson; Richard Smith; Christopher Taylor; Weimin Zhu; Ruedi Aebersold
A common open representation of mass spectrometry data and its application to proteomics research.
Nature biotechnology 2004;22(11):1459-66.
2004: Sandra Orchard; Chris Taylor; Henning Hermjakob; Weimin Zhu; Randall K Julian; Rolf Apweiler
Current status of proteomic standards development.
Expert review of proteomics 2004;1(2):179-83.
2004: Sandra Orchard; Christopher Taylor; Henning Hermjakob; Randall K Julian; Rolf Apweiler
Advances in the development of common interchange standards for proteomic data.
Proteomics 2004;4(8):2363-5.
2004: Sandra Orchard; Henning Hermjakob; Randall K Julian; Kai Runte; David Sherman; Jérôme Wojcik; Weimin Zhu; Rolf Apweiler
Common interchange standards for proteomics data: Public availability of tools and schema.
Proteomics 2004;4(2):490-1.
2004: Henning Hermjakob; Luisa Montecchi-Palazzi; Gary Bader; Jérôme Wojcik; Lukasz Salwinski; Arnaud CEOL; Susan Moore; Sandra Orchard; Ugis Sarkans; Christian von Mering; Bernd Roechert; Sylvain Poux; Eva Jung; Henning Mersch; Paul Kersey; Michael Lappe; Yixue Li; Rong Zeng; Debashis Rana; Macha Nikolski; Holger Husi; Christine Brun; K Shanker; Seth G N Grant; Chris Sander; Peer Bork; Weimin Zhu; Akhilesh Pandey; Alvis Brazma; Bernard Jacq; Marc Vidal; David Sherman; Pierre Legrain; Gianni Cesareni; Ioannis Xenarios; David Eisenberg; Boris Steipe; Chris Hogue; Rolf Apweiler
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Nature biotechnology 2004;22(2):177-83.
2004: Pierre-Alain Binz; Henning Hermjakob; Paul van der Vet
The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'.
Comparative and functional genomics 2004;5(2):148-55.
2004: Henning Hermjakob; Luisa Montecchi-Palazzi; Chris Lewington; Sugath Mudali; Samuel Kerrien; Sandra Orchard; Martin Vingron; Bernd Roechert; Peter Roepstorff; Alfonso Valencia; Hanah Margalit; John Armstrong; Amos Bairoch; Gianni Cesareni; David Sherman; Rolf Apweiler
IntAct: an open source molecular interaction database.
Nucleic acids research 2004;32(Database issue):D452-5.
2003: Sandra Orchard; Weimin Zhu; Randall K Julian; Henning Hermjakob; Rolf Apweiler
Further advances in the development of a data interchange standard for proteomics data.
Proteomics 2003;3(10):2065-6.
2003: Sandra Orchard; Henning Hermjakob; Rolf Apweiler
The proteomics standards initiative.
Proteomics 2003;3(7):1374-6.
2003: Sandra Orchard; Paul Kersey; Weimin Zhu; Luisa Montecchi-Palazzi; Henning Hermjakob; Rolf Apweiler
Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Comparative and functional genomics 2003;4(2):203-6.
2003: Sandra Orchard; Paul Kersey; Henning Hermjakob; Rolf Apweiler
The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Comparative and functional genomics 2003;4(1):16-9.
2003: Paul Kersey; L Morris; Henning Hermjakob; Rolf Apweiler
Integr8: enhanced inter-operability of European molecular biology databases.
Methods of information in medicine 2003;42(2):154-60.
2002: Nicola J Mulder; Rolf Apweiler; Terri K Attwood; Amos Bairoch; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Phillip Bucher; Richard Copley; Emmanuel Courcelle; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Jerome Gouzy; Sam Griffith-Jones; Daniel Haft; Henning Hermjakob; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; Rodrigo Lopez; Ivica Letunic; Sandra Orchard; Marco Pagni; David Peyruc; Chris P Ponting; Florence Servant; Christian J A Sigrist
InterPro: an integrated documentation resource for protein families, domains and functional sites.
Briefings in bioinformatics 2002;3(3):225-35.
2002: Henning Hermjakob; Rolf Apweiler
TEMBLOR - Perspectives of EBI Database Services.
Comparative and functional genomics 2002;3(1):47-50.
2001: Latif Shooshtari Nasrin; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; N Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; John E Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; Andrew Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; Michael Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; Paul Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; John Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; Susan Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; Anna Pia Abola; M J Proctor; Richard Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; Roger A Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; Evan E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; Henning Hermjakob; K Hokamp; W Jang; L Steven Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W James Kent; P Kitts; E V Koonin; Ian F Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; John V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; Elia Stupka; J Szustakowski; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Initial sequencing and analysis of the human genome.
Nature 2001;409(6822):860-921.
2001: Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; F Corpet; Michael D R Croning; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Jérôme Gouzy; Henning Hermjakob; Nicolas Hulo; Inge Jonassen; Daniel Kahn; Alexander Kanapin; Youla Karavidopoulou; Rodrigo Lopez; B Marx; Nicola Mulder; Tom Oinn; Marco Pagni; Florence Servant; Christian J A Sigrist; Evgeny M Zdobnov
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic acids research 2001;29(1):37-40.
2000: Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; F Corpet; Michael D R Croning; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Jérôme Gouzy; Henning Hermjakob; Nicolas Hulo; Inge Jonassen; Daniel Kahn; Alexander Kanapin; Youla Karavidopoulou; Rodrigo Lopez; B Marx; Nicola Mulder; Tom Oinn; Marco Pagni; Florence Servant; Christian J A Sigrist; Evgeny M Zdobnov
InterPro--an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics (Oxford, England) 2000;16(12):1145-50.
2000: Paul Kersey; Henning Hermjakob; Rolf Apweiler
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Bioinformatics (Oxford, England) 2000;16(11):1048-9.
2000: K M Menne; Henning Hermjakob; Rolf Apweiler
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinformatics (Oxford, England) 2000;16(8):741-2.
2000: VL Junker; Sergio Contrino; Wolfgang Fleischmann; Henning Hermjakob; F Lang; Michele Magrane; Maria J Martin; N Mitaritonna; Claire O'Donovan; Rolf Apweiler
The role SWISS-PROT and TrEMBL play in the genome research environment.
Journal of biotechnology 2000;78(3):221-34.
1999: Rolf Apweiler; Henning Hermjakob; N Sharon
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Biochimica et biophysica acta 1999;1473(1):4-8.
1999: Henning Hermjakob; Wolfgang Fleischmann; Rolf Apweiler
Swissknife - 'lazy parsing' of SWISS-PROT entries.
Bioinformatics (Oxford, England) 1999;15(9):771-2.
1998: T Heinemeyer; Edgar Wingender; Ingmar Reuter; Henning Hermjakob; Alexander Kel; OV Kel; Elena V Ignatieva; Elena A Ananko; Olga A Podkolodnaya; Fedor Kolpakov; Nikolay L Podkolodny; Nikolay A Kolchanov
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Nucleic acids research 1998;26(1):362-7.
1997: Henning Hermjakob; R Giegerich; W Arnold
RIFLE: rapid identification of microorganisms by fragment length evaluation.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():131-9.