Henning Hermjakob

Henning Hermjakob

Team Leader Proteomics Services - Hermjakob team: Proteomics

MSc Bioinformatics University of Bielefeld, Germany, 1995. Research assistent at German National Centre for Biotechnology (GBF) 1996. At EMBL-EBI since 1997.

Tel:+44 (0)1223 494 671 / Fax:+44 (0)1223 494 468

http://www.ebi.ac.uk/~hhe (personal homepage)

Hermjakob team

The Proteomics Services Team, led by Henning Hermjakob, develops tools and resources for the representation, deposition, distribution and analysis of proteomics and systems biology data. The team follows an open-source, open-data approach and is a major contributor to community standards, in particular the Proteomics Standards Initiative (PSI) of the international Human Proteome Organization (HUPO), and COMBINE systems biology standards.

As a result of long-term engagement with the community, journal editors and funding organisations, data deposition in standards-compliant data resources such as IntAct, PRIDE, and BioModels is becoming a strongly recommended part of the publishing process. This has resulted in a rapid increase in the data content of EMBL-EBI's proteomics resources. In addition, the curation teams ensure consistency and appropriate annotation of all data, whether from direct depositions or literature curation, to provide the community with high-quality reference datasets.

The team also contributes to the development of data integration technologies using protocols like Distributed Annotation System (DAS) and semantic web technologies, and providing stable identifiers for biomolecular entities through identifiers.org.

The Proteomics Services Team offers a range of projects for interested Master's students. Please send a covering letter and CV to hhe [at] ebi.ac.uk.

Publications

2013

From Peptidome to PRIDE: Public proteomics data migration at a large scale
Csordas, A., Wang R., Rios D., Reisinger F., Foster J. M., Slotta D. J., Vizcaino J. A., and Hermjakob H.
Proteomics. Volume 13, Number 10-11, (2013), p.1692-5 doi:
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics
Walzer, M., Qi D., Mayer G., Uszkoreit J., Eisenacher M., Sachsenberg T., Gonzalez-Galarza F. F., Fan J., Bessant C., Deutsch E. W., et al.
Mol Cell Proteomics. (2013),
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics
Foster, J. M., Moreno P., Fabregat A., Hermjakob H., Steinbeck C., Apweiler R., Wakelam M. J., and Vizcaino J. A.
PLoS One. Volume 8, Number 5, (2013), p.e61951
PRIDE Cluster: building a consensus of proteomics data
Griss, J., Foster J. M., Hermjakob H., and Vizcaino J. A.
Nat Methods. Volume 10, Number 2, (2013), p.95-6
Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra
Hulstaert, N., Reisinger F., Rameseder J., Barsnes H., Vizcaino J. A., and Martens L.
J Proteomics. (2013),
Proteomics data exchange and storage: the need for common standards and public repositories
Jimenez, R. C., and Vizcaino J. A.
Methods Mol Biol. Volume 1007, (2013), p.317-33
Shorthand notation for lipid structures derived from mass spectrometry
Liebisch, G., Vizcaino J. A., Kofeler H., Trotzmuller M., Griffiths W. J., Schmitz G., Spener F., and Wakelam M. J.
J Lipid Res. Volume 54, Number 6, (2013), p.1523-30
Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
Mayer, G., Jones A. R., Binz P. A., Deutsch E. W., Orchard S., Montecchi-Palazzi L., Vizcaino J. A., Hermjakob H., Oveillero D., Julian R., et al.
Biochim Biophys Acta. (2013),
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions
Perez-Riverol, Y., Sanchez A., Noda J., Borges D., Carvalho P. C., Wang R., Vizcaino J. A., Betancourt L., Ramos Y., Duarte G., et al.
Anal Chem. Volume 85, Number 7, (2013), p.3515-20
Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
Perez-Riverol, Y., Wang R., Hermjakob H., Müller M., Vesada V., and Vizcaino J. A.
Biochim Biophys Acta. (2013),
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
Vizcaino, J. A., Cote R. G., Csordas A., Dianes J. A., Fabregat A., Foster J. M., Griss J., Alpi E., Birim M., Contell J., et al.
Nucleic Acids Res. Volume 41, Number Database issue, (2013), p.D1063-9
Update on activities at the Universal Protein Resource (UniProt) in 2013
Apweiler, Rolf, Martin Maria Jesus, O'Donovan Claire, Magrane Michele, Alam-Faruque Yasmin, Alpi Emanuele, Antunes Ricardo, Arganiska Joanna, Casanova Elisabet Barrera, Bely Benoit, et al.
NUCLEIC ACIDS RESEARCH. Volume 41, Number D 1, (2013), p.D43–D47 doi:

2012

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
Griss, J., Reisinger F., Hermjakob H., and Vizcaino J.A.
Proteomics. Volume 12, Number 6, (2012), p.795–798
PRIDE Inspector: a tool to visualize and validate MS proteomics data
Wang, R., Fabregat A., R{\'ıos D., Ovelleiro D., Foster J.M., Côté R.G., Griss J., Csordas A., Perez-Riverol Y., Reisinger F., et al.
Nature biotechnology. Volume 30, Number 2, (2012), p.135–137
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data
Reisinger, F., Krishna R., Ghali F., R{\'ıos D., Hermjakob H., Antonio Vizcaino J., and Jones A. R.
Proteomics. Volume 12, Number 6, (2012), p.790–794
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
Orchard, S., Kerrien S., Abbani S., Aranda B., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F., Cesareni G., et al.
Nature Methods. Volume 9, Number 4, (2012), p.345–350
Toward interoperable bioscience data
Sansone, S.A., Rocca-Serra P., Field D., Maguire E., Taylor C., Hofmann O., Fang H., Neumann S., Tong W., Amaral-Zettler L., et al.
Nature genetics. Volume 44, Number 2, (2012), p.121–126
The mzIdentML data standard for mass spectrometry-based proteomics results
Jones, A. R., Eisenacher M., Mayer G., Kohlbacher O., Siepen J., Hubbard S. J., Selley J.N., Searle B. C., Shofstahl J., Seymour S.L., et al.
Molecular & Cellular Proteomics. Volume 11, Number 7, (2012),
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
Lewis, S., Csordas A., Killcoyne S., Hermjakob H., Hoopmann M. R., Moritz R.L., Deutsch E.W., and Boyle J.
BMC bioinformatics. Volume 13, Number 1, (2012), p.324
From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland
Orchard, S., Albar J.P., Deutsch E.W., Eisenacher M., Binz P.A., Martinez-Bartolomé S., Vizcaino J.A., and Hermjakob H.
Proteomics. Volume 12, Number 3, (2012), p.351–355
A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis
Gonzalez-Galarza, F. F., Lawless C., Hubbard S. J., Fan J., Bessant C., Hermjakob H., and Jones A. R.
OMICS: A Journal of Integrative Biology. (2012),
The HUPO initiative on Model Organism Proteomes, iMOP| Macquarie University ResearchOnline
Jones, A. M. E., Aebersold R., Daube M., Deutsch E.W., Grossniklaus U., Heazlewood J., Hengartner M. O., Hermjakob H., Jovanovic M., Lawless C., et al.
(2012),
The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
Côté, R.G., Griss J., Dianes J.A., Wang R., Wright J.C., van den Toorn H. W. P., van Breukelen B., Heck A.J.R., Hulstaert N., Martens L., et al.
Molecular & Cellular Proteomics. Volume 11, Number 12, (2012), p.1682–1689
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Vizcaino, J.A., Côté R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., Griss J., Alpi E., Birim M., Contell J., et al.
Nucleic Acids Research. (2012),
The EBI enzyme portal
Alcántara, R., Onwubiko J., Cao H., De Matos P., Cham J.A., Jacobsen J., Holliday G.L., Fischer J.D., Rahman S.A., Jassal B., et al.
Nucleic Acids Research. (2012),
Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
Milacic, M., Haw R., Rothfels K., Wu G., Croft D., Hermjakob H., D'Eustachio P., and Stein L.
Cancers. Volume 4, Number 4, (2012), p.1180–1211
Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop
Orchard, S., Binz P.A., Borchers C., Gilson M. K., Jones A. R., Nicola G., Vizcaino J.A., Deutsch E.W., and Hermjakob H.
Proteomics. Volume 12, Number 18, (2012), p.2767–2772
MyDas, an Extensible Java DAS Server
Salazar, G. A., Garc{\'ıa L. J., Jones P., Jimenez R.C., Quinn A. F., Jenkinson A.M., Mulder N., Martin M., Hunter S., and Hermjakob H.
PLOS ONE. Volume 7, Number 9, (2012), p.e44180
The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
Côté, R.G., Griss J., Dianes J.A., Wang R., Wright J.C., van den Toorn H. W. P., van Breukelen B., Heck A.J.R., Hulstaert N., Martens L., et al.
Molecular & Cellular Proteomics. (2012),
HUPO 2011: The New Cardiovascular Initiative-Integrating Proteomics and Cardiovascular Biology in Health and Disease
Lam, M. P. Y., Vivanco F., Scholten A., Hermjakob H., Van Eyk J., and Ping P.
Proteomics. Volume 12, Number 6, (2012), p.749–751
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)| Macquarie University ResearchOnline
Kinsinger, C. R., Apffel J., Gorman J., Grimm R., Hancock W., Hermjakob H., Horn D., Hunter C., Kolar P., Kraus H.J., et al.
(2012),
Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
Orchard, S., Kerrien S., Abbani S., Aranda B., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F., Cesareni G., et al.
Nature Methods. Volume 9, Number 6, (2012), p.626–626
Analyzing Protein–Protein Interaction Networks†
Koh, G. C. K. W., Porras P., Aranda B., Hermjakob H., and Orchard S. E.
Journal of proteome research. Volume 11, Number 4, (2012), p.2014–2031
PRIDE: Quality control in a proteomics data repository
Csordas, A., Ovelleiro D., Wang R., Foster J.M., R{\'ıos D., Vizcaino J.A., and Hermjakob H.
Database: The Journal of Biological Databases and Curation. Volume 2012, (2012),
Improvements in the protein identifier cross-reference service
Wein, S. P., Côté R.G., Dumousseau M., Reisinger F., Hermjakob H., and Vizcaino J.A.
Nucleic acids research. Volume 40, Number W1, (2012), p.W276–W280
The HUPO initiative on Model Organism Proteomes, iMOP
Jones, A. M. E., Aebersold R., Ahrens C. H., Apweiler R., Baerenfaller K., Baker M., Bendixen E., Briggs S., Brownridge P., Brunner E., et al.
Proteomics. Volume 12, Number 3, (2012), p.340–345
Reactome-a curated knowledgebase of biological pathways: megakaryocytes and platelets
Jupe, S., Akkerman J. W., Soranzo N., and Ouwehand W.H.
Journal of Thrombosis and Haemostasis. (2012),
Integrating knowledge representation and quantitative modelling in physiology
de Bono, B., and Hunter P.
Biotechnology Journal. Volume 7, Number 8, (2012), p.958–972
Proteome signatures of inflammatory activated primary human peripheral blood mononuclear cells
Haudek-Prinz, V., Klepeisz P., Slany A., Griss J., Meshcheryakova A., Paulitschke V., Mitulovic G., Stöckl J., and Gerner C.
Journal of Proteomics. (2012),
Molecular interaction databases
Orchard, S.
Proteomics. Volume 12, Number 10, (2012), p.1656–1662
TraML a standard format for exchange of selected reaction monitoring transition lists
Deutsch, E.W., Chambers M., Neumann S., Levander F., Binz P.A., Shofstahl J., Campbell D.S., Mendoza L., Ovelleiro D., Helsens K., et al.
Molecular & Cellular Proteomics. Volume 11, Number 4, (2012),
Isoelectric point optimization using peptide descriptors and support vector machines
Perez-Riverol, Y., Audain E., Millan A., Ramos Y., Sanchez A., Vizcaino J.A., Wang R., Müller M., Machado Y. J., Betancourt L. H., et al.
Journal of proteomics. (2012),
ApiNATOMY: A novel toolkit for visualizing multiscale anatomy schematics with phenotype-related information
de Bono, B., Grenon P., and Sammut S.J.
Human Mutation. (2012),
The IntAct molecular interaction database in 2012
Kerrien, S., Aranda B., Breuza L., Bridge A., Broackes-Carter F., Chen C., Duesbury M., Dumousseau M., Feuermann M., Hinz U., et al.
Nucleic acids research. Volume 40, Number D1, (2012), p.D841–D846

2011

Dasty3, a WEB Framework for DAS
Villaveces, J. M., Jimenez R.C., Garcia L. J., Salazar G. A., Gel B., Mulder N., Martin M., Garcia A., and Hermjakob H.
Bioinformatics. Volume 27, Number 18, (2011), p.2616–2617
easyDAS: Automatic creation of DAS servers
Moreno, B. G., Jenkinson A.M., Jimenez R.C., Peypoch X. M., and Hermjakob H.
BMC bioinformatics. Volume 12, Number 1, (2011), p.23
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Kinsinger, C. R., Apffel J., Baker M., Bian X., Borchers C.H., Bradshaw R., Brusniak M.Y., Chan D. W., Deutsch E.W., Domon B., et al.
PROTEOMICS-Clinical Applications. Volume 5, Number 11-12, (2011), p.580–589
Data standardization by the HUPO-PSI: how has the community benefitted
Orchard, S., and Hermjakob H.
Methods in molecular biology (Clifton, NJ). Volume 696, (2011), p.149–160
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets
Griss, J., Mart{\'ın M., O'Donovan C., Apweiler R., Hermjakob H., and Vizcaino J.A.
Proteomics. (2011),
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations
Ndegwa, N., Côté R.G., Ovelleiro D., D'Eustachio P., Hermjakob H., Vizcaino J.A., and Croft D.
Database: the journal of biological databases and curation. Volume 2011, (2011),
Reactome pathway analysis to enrich biological discovery in proteomics data sets
Haw, R., Hermjakob H., D'Eustachio P., and Stein L.
Proteomics. Volume 11, Number 18, (2011), p.3598–3613
The Reactome BioMart
Haw, R. A., Croft D., Yung C. K., Ndegwa N., D'Eustachio P., Hermjakob H., and Stein L. D.
Database: the journal of biological databases and curation. Volume 2011, (2011),
Published and perished? The influence of the searched protein database on the long-term storage of proteomics data
Griss, J., Côté R.G., Gerner C., Hermjakob H., and Vizcaino J.A.
Molecular & Cellular Proteomics. Volume 10, Number 9, (2011),
Enabling BioSharing–a report on the Annual Spring Workshop of the HUPO-PSI April 11–13, 2011, EMBL-Heidelberg, Germany
Orchard, S., Albar J.P., Deutsch E.W., Eisenacher M., Vizcaino J.A., and Hermjakob H.
Proteomics. Volume 11, Number 22, (2011), p.4284–4290
Preparing molecular interaction data for publication.
Orchard, S., and Hermjakob H.
Methods in molecular biology (Clifton, NJ). Volume 694, (2011), p.229–236
DAS Writeback: a collaborative annotation system
Salazar, G. A., Jimenez R.C., Garcia A., Hermjakob H., Mulder N., and Blake E.
BMC bioinformatics. Volume 12, Number 1, (2011), p.143
Reactome: a database of reactions, pathways and biological processes
Croft, D., O’Kelly G., Wu G., Haw R., Gillespie M., Matthews L., Caudy M., Garapati P., Gopinath G., Jassal B., et al.
Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D691–D697
mzML—a community standard for mass spectrometry data
Martens, L., Chambers M., Sturm M., Kessner D., Levander F., Shofstahl J., Tang W. H., Römpp A., Neumann S., Pizarro A. D., et al.
Molecular & Cellular Proteomics. Volume 10, Number 1, (2011),

2010

Organelle proteomics experimental designs and analysis
Gatto, L., Vizcaino J.A., Hermjakob H., Huber W., and Lilley K. S.
Proteomics. Volume 10, Number 22, (2010), p.3957–3969
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative
Gibson, F., Hoogland C., Martinez-Bartolomé S., Medina-Aunon J. A., Albar J.P., Babnigg G., Wipat A., Hermjakob H., Almeida J. S., Stanislaus R., et al.
Proteomics. Volume 10, Number 17, (2010), p.3073–3081
Minimum information about a protein affinity reagent (MIAPAR)
Bourbeillon, J., Orchard S., Benhar I., Borrebaeck C., De Daruvar A., Dübel S., Frank R., Gibson F., Gloriam D., Haslam N., et al.
Nature biotechnology. Volume 28, Number 7, (2010), p.650–653
implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada
Orchard, S., Albar J.P., Deutsch E.W., Eisenacher M., Binz P.A., and Hermjakob H.
Proteomics. Volume 10, Number 10, (2010), p.1895–1898
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
Antonov, A.V., Schmidt E. E., Dietmann S., Krestyaninova M., and Hermjakob H.
Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W78–W83
Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO-PSI 28–30 March 2010, Seoul, South Korea
Orchard, S., Jones A., Albar J.P., Cho S.Y., Kwon K. H., Lee C., and Hermjakob H.
Proteomics. Volume 10, Number 17, (2010), p.3062–3066
The publication and database deposition of molecular interaction data
Orchard, S., Aranda B., and Hermjakob H.
Current Protocols in Protein Science. (2010), p.25–3
Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations”(MIBBI) workshop
Kettner, C., Field D., Sansone S.A., Taylor C., Aerts J., Binns N., Blake A., Britten C. M., de Marco A., Fostel J., et al.
Standards in genomic sciences. Volume 3, Number 3, (2010), p.259
High-throughput proteomics and bioinformatics: joined at the hip
Martens, L., and Hermjakob H.
Proteomics. (2010),
Mapping plant interactomes using literature curated and predicted protein–protein interaction data sets
Lee, K. Y., Thorneycroft D., Achuthan P., Hermjakob H., and Ideker T.
The Plant Cell Online. Volume 22, Number 4, (2010), p.997–1005
The proteomics identifications database: 2010 update
Vizcaino, J.A., Côté R., Reisinger F., Barsnes H., Foster J.M., Rameseder J., Hermjakob H., and Martens L.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D736–D742
The IntAct molecular interaction database in 2010
Aranda, B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A., Derow C., Feuermann M., Ghanbarian AT, Kerrien S., Khadake J., et al.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D525–D531
A community standard format for the representation of protein affinity reagents
Gloriam, D.E., Orchard S., Bertinetti D., Björling E., Bongcam-Rudloff E., Borrebaeck C. A. K., Bourbeillon J., Bradbury A. R. M., De Daruvar A., Dübel S., et al.
Molecular & Cellular Proteomics. Volume 9, Number 1, (2010), p.1–10
The Ontology Lookup Service: bigger and better
Côté, R., Reisinger F., Martens L., Barsnes H., Vizcaino J.A., and Hermjakob H.
Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W155–W160
A domain level interaction network of amyloid precursor protein and A$\beta$ of Alzheimer's disease
Perreau, V. M., Orchard S., Adlard P. A., Bellingham S. A., Cappai R., Ciccotosto G. D., Cowie T. F., Crouch P. J., Duce J. A., Evin G., et al.
Proteomics. Volume 10, Number 12, (2010), p.2377–2395

2009

Annual spring meeting of the Proteomics Standards Initiative
Orchard, S., Deutsch E.W., Binz P.A., Jones A. R., Creasy D., Montechi-Palazzi L., Corthals G., and Hermjakob H.
Proteomics. Volume 9, Number 19, (2009), p.4429–4432
Charting online OMICS resources: a navigational chart for clinical researchers
Vizcaino, J.A., Mueller M., Hermjakob H., and Martens L.
Proteomics Clinical Applications. Volume 3, Number 1, (2009), p.18–29
Second Joint HUPO Publication and Proteomics Standards Initiative Workshop
Orchard, S., Binz P.A., and Hermjakob H.
Proteomics. Volume 9, Number 19, (2009), p.4426–4428
Protein-protein interactions: analysis and prediction
Frishman, D., Albrecht M., Blankenburg H., Bork P., Harrington E. D., Hermjakob H., Jensen L.J., Juan D. A., Lengauer T., Pagel P., et al.
Modern genome annotation: The biosapiens network. (2009), p.353–410
2nd Joint Publication-PSI Workshop 24th April 2009, Turku Finland
Orchard, S., Binz PA, and Hermjakob H.
Proteomics. (2009),
New open drug activity data at EBI
Steinbeck, C., Al-Lazikani B., Hermjakob H., Overington J., and Thornton J.
Chemistry Central Journal. Volume 3, (2009), p.1–1
Present and future of proteomics data curation at the PRIDE database
Vizcaino, J.A., Hermjakob H., and Martens L.
(2009),
A guide to the Proteomics Identifications Database proteomics data repository
Vizcaino, J.A., Côté R., Reisinger F., Foster J. M., Mueller M., Rameseder J., Hermjakob H., and Martens L.
Proteomics. Volume 9, Number 18, (2009), p.4276–4283
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data
Montecchi-Palazzi, L., Kerrien S., Reisinger F., Aranda B., Jones A. R., Martens L., and Hermjakob H.
Proteomics. Volume 9, Number 22, (2009), p.5112–5119
Recurated protein interaction datasets
Salwinski, L., Licata L., Winter A., Thorneycroft D., Khadake J., Ceol A., Aryamontri A. C., Oughtred R., Livstone M., Boucher L., et al.
Nature methods. Volume 6, Number 12, (2009), p.860–861
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy-The Amsterdam Principles
Rodriguez, H., Snyder M., Uhlén M., Andrews P., Beavis R., Borchers C., Chalkley R. J., Cho S.Y., Cottingham K., Dunn M., et al.
Journal of proteome research. Volume 8, Number 7, (2009), p.3689

2008

Standardising Proteomics Data–the work of the HUPO Proteomics Standards Initiative
Sandra, O., and Henning H.
J Proteomics Bioinform. Volume 1, (2008), p.003–005
InteroPORC: an automated tool to predict highly conserved protein interaction networks
Michaut, M., Kerrien S., Montecchi-Palazzi L., Cassier-Chauvat C., Chauvat F., Aude J. C., Legrain P., and Hermjakob H.
BMC Bioinformatics. Volume 9, (2008), p.1–2
OntoDas–a tool for facilitating the construction of complex queries to the Gene Ontology
O'Neill, K., Garcia A., Schwegmann A., Jimenez R.C., Jacobson D., and Hermjakob H.
BMC bioinformatics. Volume 9, Number 1, (2008), p.437
Annual spring meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain
Orchard, S., Albar J.P., Deutsch E.W., Binz P.A., Jones A. R., Creasy D., and Hermjakob H.
Proteomics. Volume 8, Number 20, (2008), p.4168–4172
Data standards and controlled vocabularies for proteomics
Martens, L., Palazzi L. M., and Hermjakob H.
Methods Mol Biol. Volume 484, (2008), p.279–286
6th HUPO Annual World Congress–Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, Korea
Orchard, S., Martens L., Tasman J., Binz P.A., Albar J.P., and Hermjakob H.
Proteomics. Volume 8, Number 7, (2008), p.1331–1333
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository
Chiang, T., Li N., Orchard S., Kerrien S., Hermjakob H., Gentleman R., and Huber W.
Bioinformatics. Volume 24, Number 8, (2008), p.1100–1101
Inference of Synechocystis protein interaction network
Michaut, M., Kerrien S., Montecchi-Palazzi L., Cassier-Chauvat C., Chauvat F., Aude J. C., Legrain P., and Hermjakob H.
JOBIM proceedings. (2008), p.99–104
EBI Proteomics Services
Hermjakob, H.
Data Integration in the Life Sciences. (2008), p.207–207
Infrastructure for distributed protein annotation
Reeves, GA, Prlić A., Jimenez RC, Kulesha E., and Hermjakob H.
Modern Genome Annotation: The Biosapiens Network. (2008), p.413
PRIDE: new developments and new datasets
Jones, P., Côté R.G., Cho S.Y., Klie S., Martens L., Quinn A. F., Thorneycroft D., and Hermjakob H.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D878–D883
Calling on a million minds for community annotation in WikiProteins
Mons, B., Ashburner M., Chichester C., Van Mulligen E., Weeber M., Den Dunnen J., Van Ommen G. J., Musen M., Cockerill M., Hermjakob H., et al.
Genome biology. Volume 9, Number 5, (2008), p.R89
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
Côté, R.G., Jones P., Martens L., Apweiler R., and Hermjakob H.
Nucleic acids research. Volume 36, Number suppl 2, (2008), p.W372–W376
Integrating biological data–the distributed annotation system
Jenkinson, A.M., Albrecht M., Birney E., Blankenburg H., Down T., Finn R. D., Hermjakob H., Hubbard T. J. P., Jimenez R.C., Jones P., et al.
BMC bioinformatics. Volume 9, Number Suppl 8, (2008), p.S3
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
Taylor, C.F., Field D., Sansone S.A., Aerts J., Apweiler R., Ashburner M., Ball C.A., Binz P.A., Bogue M., Booth T., et al.
Nature biotechnology. Volume 26, Number 8, (2008), p.889–896
ISPIDER Central: an integrated database web-server for proteomics
Siepen, J.A., Belhajjame K., Selley J.N., Embury S.M., Paton N.W., Goble C.A., Oliver S. G., Stevens R., Zamboulis L., Martin N., et al.
Nucleic acids research. Volume 36, Number suppl 2, (2008), p.W485–W490
The Protein Feature Ontology: a tool for the unification of protein feature annotations
Reeves, G. A., Eilbeck K., Magrane M., O'Donovan C., Montecchi-Palazzi L., Harris M. A., Orchard S., Jimenez R.C., Prlić A., Hubbard T. J. P., et al.
Bioinformatics. Volume 24, Number 23, (2008), p.2767–2772 doi:
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
Chatr-aryamontri, A., Kerrien S., Khadake J., Orchard S., Ceol A., Licata L., Castagnoli L., Costa S., Derow C., Huntley R., et al.
Genome Biol. Volume 9, Number Suppl 2, (2008), p.S5
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
Mueller, M., Vizcaino J.A., Jones P., Côté R., Thorneycroft D., Apweiler R., Hermjakob H., and Martens L.
Proteomics. Volume 8, Number 6, (2008), p.1138–1148
InteroPORC: automated inference of highly conserved protein interaction networks
Michaut, M., Kerrien S., Montecchi-Palazzi L., Chauvat F., Cassier-Chauvat C., Aude J. C., Legrain P., and Hermjakob H.
Bioinformatics. Volume 24, Number 14, (2008), p.1625–1631
Dasty2, an Ajax protein DAS client
Jimenez, R.C., Quinn A. F., Garcia A., Labarga A., O'Neill K., Martinez F., Salazar G. A., and Hermjakob H.
Bioinformatics. (2008),
The HUPO proteomics standards initiative—easing communication and minimizing data loss in a changing world
Orchard, S., and Hermjakob H.
Briefings in Bioinformatics. Volume 9, Number 2, (2008), p.166–173

2007

MIACA–Minimum Information About a Cellular Assay, and the Cellular Assay Object Model
Wiemann, S., Mehrle E., Hahne F., Hermjakob H., Apweiler R., Arlt D., Bechtel S., Bielke W., Birmingham A., Boese Q., et al.
(2007),
Pride Wizard: generation of standards compliant quantitative proteomics data
Swainston, N., Siepen J.A., Jones A. R., Hart S. R., Hermjakob H., Jones P., and Hubbard S. J.
BMC Systems Biology. Volume 1, Number Suppl 1, (2007), p.P27
Corrigendum: ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome
Taussig, M.J., Stoevesandt O., Borrebaeck C. A. K., Bradbury A. R., Cahill D., Cambillau C., De Daruvar A., Dübel S., Eichler J., Frank R., et al.
Nature Methods. Volume 4, Number 2, (2007), p.187–187
An application of latent topic document analysis to large-scale proteomics databases
Klie, S., Martens L., Vizcaino J.A., Côté R., Jones P., Apweiler R., Hinneburg A., Hermjakob H., and Outstation E.
German Bioinformatics Conference. (2007),
Inference and validation of Synechocystis protein interaction network using orthology
Michaut, M., Kerrien S., Montecchi-Palazzi L., Chauvat F., Cassier-Chauvat C., Aude J. C., Legrain P., and Hermjakob H.
JOBIM proceedings. (2007), p.229–234
Broadening the horizon–level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, S., Orchard S., Montecchi-Palazzi L., Aranda B., Quinn A. F., Vinod N., Bader G.D., Xenarios I., Wojcik J., Sherman D., et al.
BMC biology. Volume 5, Number 1, (2007), p.44
The implications of alternative splicing in the ENCODE protein complement
Tress, M. L., Martelli P. L., Frankish A., Reeves G. A., Wesselink J. J., Yeats C., Albrecht M., Hegyi H., Giorgetti A., Raimondo D., et al.
Proceedings of the National Academy of Sciences. Volume 104, Number 13, (2007), p.5495–5500
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
Jones, A. R., Miller M., Aebersold R., Apweiler R., Ball C.A., Brazma A., DeGreef J., Hardy N., Hermjakob H., Hubbard S. J., et al.
Nature biotechnology. Volume 25, Number 10, (2007), p.1127–1133
Submit your interaction data the IMEx way
Orchard, S., Kerrien S., Jones P., Ceol A., Chatr-aryamontri A., Salwinski L., Nerothin J., and Hermjakob H.
Proteomics. Volume 7, Number S1, (2007), p.28–34
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Côté, R.G., Jones P., Martens L., Kerrien S., Reisinger F., Lin Q., Leinonen R., Apweiler R., and Hermjakob H.
BMC bioinformatics. Volume 8, Number 1, (2007), p.401
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome
Taussig, M.J., Stoevesandt O., Borrebaeck C. A. K., Bradbury A. R., Cahill D., Cambillau C., De Daruvar A., Dübel S., Eichler J., Frank R., et al.
Nature Methods. Volume 4, Number 1, (2007), p.13–17
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Orchard, S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., et al.
Nature biotechnology. Volume 25, Number 8, (2007), p.894–898
IntAct—open source resource for molecular interaction data
Kerrien, S., Alam-Faruque Y., Aranda B., Bancarz I., Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D561–D565
Clinical proteomics: a need to define the field and to begin to set adequate standards
Mischak, H., Apweiler R., Banks R. E., Conaway M., Coon J., Dominiczak A., Ehrich J. H. H., Fliser D., Girolami M., Hermjakob H., et al.
PROTEOMICS-Clinical Applications. Volume 1, Number 2, (2007), p.148–156
The minimum information about a proteomics experiment (MIAPE)
Taylor, C.F., Paton N.W., Lilley K. S., Binz P.A., Julian R. K., Jones A. R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., et al.
Nature biotechnology. Volume 25, Number 8, (2007), p.887–893
Proteomics data validation: why all must provide data
Martens, L., and Hermjakob H.
Mol. BioSyst.. Volume 3, Number 8, (2007), p.518–522
Entering the Implementation Era A report on the HUPO-PSI Fall workshop 25–27 September 2006, Washington DC, USA
Orchard, S., Taylor C.F., Jones P., Montechi-Palazzo L., Binz P.A., Jones A. R., Pizarro A., Julian Jr R. K., and Hermjakob H.
Proteomics. Volume 7, Number 3, (2007), p.337–339
Human Proteome Organization Proteomics Standards Initiative Data Standardization, a View on Developments and Policy
Martens, L., Orchard S., Apweiler R., and Hermjakob H.
Molecular & Cellular Proteomics. Volume 6, Number 9, (2007), p.1666–1667
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQTM
Siepen, J.A., Swainston N., Jones A. R., Hart S. R., Hermjakob H., Jones P., and Hubbard S. J.
Proteome science. Volume 5, Number 1, (2007), p.4
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
Orchard, S., Montechi-Palazzi L., Deutsch E.W., Binz P.A., Jones A. R., Paton N., Pizarro A., Creasy D. M., Wojcik J., and Hermjakob H.
Proteomics. Volume 7, Number 19, (2007), p.3436–3440
The PSI formal document process and its implementation on the PSI website
Vizcaino, J.A., Martens L., Hermjakob H., Julian R. K., and Paton N.W.
Proteomics. Volume 7, Number 14, (2007), p.2355–2357
Analyzing large-scale proteomics projects with latent semantic indexing
Klie, S., Martens L., Vizcaino J.A., Côté R., Jones P., Apweiler R., Hinneburg A., and Hermjakob H.
Journal of proteome research. Volume 7, Number 01, (2007), p.182–191

2006

Development and implementation of the PSI MI standard for molecular interaction
Kerrien, S., and Hermjakob H.
Simulation Conference, 2006. WSC 06. Proceedings of the Winter. (2006), p.1587–1594
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
Adamski, M., Blackwell T., Menon R., Martens L., Hermjakob H., Taylor C., Omenn G.S., and others
Exploring the Human Plasma Proteome. (2006), p.37–61
The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies
Hamacher, M., Stephan C., Blüggel M., Chamrad D., Körting G., Martens L., Müller M., Hermjakob H., Parkinson D., Dowsey A., et al.
Proteomics. Volume 6, Number 6, (2006), p.1719–1721
Call for Papers–Dataset Briefs
Hermjakob, H.
Proteomics. Volume 6, Number 9, (2006), p.2633–2633
TEMBLOR Ã{¢} €  “Perspectives of EBI Database Services
Hermjakob, H., and Apweiler R.
Comparative and functional genomics.. Volume 3, (2006),
The ESF Programme on Functional Genomics Workshop on Ã{¢} € ÂData Integration in Functional Genomics: Application to Biological PathwaysÃ{¢} € ™
Binz, P.A., Hermjakob H., and Van Der Vet P.
Comparative and functional genomics.. Volume 5, (2006),
In: In Silico Genomics and Proteomics ISBN 1-59454-995-8 Editors: N. Mulder and R. Apweiler, pp. 79-88{\copyright} 2006 Nova Science Publishers, Inc.
Orchard, S., and Hermjakob H.
In silico genomics and proteomics: functional annotation of genomes and proteins. (2006), p.79
Proteomic Data Standardization, Deposition and Exchange
Orchard, S., Hermjakob H., Pruess M., and Apweiler R.
Methods and Principles in Medicinal Chemistry. Volume 28, (2006), p.19
Marcin Adamski, Thomas Blackwell, Rajasree Menon, Lennart Martens
Hermjakob, H., Taylor C., Omenn G.S., and others
Exploring the Human Plasma Proteome. (2006),
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
Côté, R.G., Jones P., Apweiler R., and Hermjakob H.
Bmc Bioinformatics. Volume 7, Number 1, (2006), p.97
A Reagent Resource to Identify Proteins and Peptides of Interest for the Cancer Community A WORKSHOP REPORT
Haab, B. B., Paulovich A. G., Anderson N. L., Clark A. M., Downing G. J., Hermjakob H., LaBaer J., and Uhlén M.
Molecular & Cellular Proteomics. Volume 5, Number 10, (2006), p.1996–2007
The work of the human proteome organisation's proteomics standards initiative (HUPO PSI)
Taylor, C.F., Hermjakob H., Julian Jr R. K., Garavelli J.S., Aebersold R., and Apweiler R.
Omics: a journal of integrative biology. Volume 10, Number 2, (2006), p.145–151
PRIDE: a public repository of protein and peptide identifications for the proteomics community
Jones, P., Côté R.G., Martens L., Quinn A. F., Taylor C.F., Derache W., Hermjakob H., and Apweiler R.
Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D659–D663
Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia
Camargo, LM, Collura V., Rain JC, Mizuguchi K., Hermjakob H., Kerrien S., Bonnert TP, Whiting PJ, and Brandon NJ
Molecular psychiatry. Volume 12, Number 1, (2006), p.74–86
Proteomics and Beyond A report on the 3rd Annual Spring Workshop of the HUPO-PSI 21–23 April 2006, San Francisco, CA, USA
Orchard, S., Apweiler R., Barkovich R., Field D., Garavelli J.S., Horn D., Jones A., Jones P., Julian R., McNally R., et al.
Proteomics. Volume 6, Number 16, (2006), p.4439–4443
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4–6, 2005
Orchard, S., Hermjakob H., Taylor C., Binz P.A., Hoogland C., Julian R., Garavelli J.S., Aebersold R., and Apweiler R.
Proteomics. Volume 6, Number 3, (2006), p.738–741
Proteomic Data Exchange and Storage
Orchard, S., Jones P., Taylor C., Zhu W., Julian Jr R. K., Hermjakob H., and Apweiler R.
Mass Spectrometry Data Analysis in Proteomics. Volume 367, (2006), p.261
The HUPO proteomics standards initiative–overcoming the fragmentation of proteomics data
Hermjakob, H.
Proteomics. Volume 6, Number S2, (2006), p.34–38
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob, H., Apweiler R., and others
Expert review of proteomics. Volume 3, Number 1, (2006), p.1

2005

Human Proteome Organisation Proteomics Standards Initiative Pre-Congress Initiative
Orchard, S., Hermjakob H., Taylor C., Aebersold R., and Apweiler R.
Proteomics. Volume 5, Number 18, (2005), p.4651–4652
Further steps towards data standardisation: The Proteomic Standards Initiative HUPO 3rd annual congress, Beijing 25–27th October, 2004
Orchard, S., Hermjakob H., Binz P.A., Hoogland C., Taylor C.F., Zhu W., Julian R. K., and Apweiler R.
Proteomics. Volume 5, Number 2, (2005), p.337–339
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
Adamski, M., Blackwell T., Menon R., Martens L., Hermjakob H., Taylor C., Omenn G.S., and others
Proteomics. Volume 5, Number 13, (2005), p.3246–3261
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
Omenn, G.S., Adamski M., Blackwell T. W., Menon R., Hermjakob H., Apweiler R., Haab B. B., Simpson R. J., Eddes J. S., Kapp E. A., et al.
Proteomics. Volume 5, Number 13, (2005), p.3226–3245
PRIDE: the proteomics identifications database
Martens, L., Hermjakob H., Jones P., Adamski M., Taylor C., Gevaert K., Vandekerckhove J., Apweiler R., and others
Proteomics. Volume 5, Number 13, (2005), p.3537–3545
Proteome data integration: Characteristics and challenges
Belhajjame, K., Embury SM, Fan H., Goble CA, Hermjakob H., Hubbard SJ, Jones D., Jones P., Martin N., Oliver S., et al.
UK All Hands Meeting. (2005),
Second proteomics standards initiative spring workshop.
Orchard, S., Hermjakob H., Taylor C.F., Potthast F., Jones P., Zhu W., Julian Jr R. K., and Apweiler R.
Expert review of proteomics. Volume 2, Number 3, (2005), p.287
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
Orchard, S., Montecchi-Palazzi L., Hermjakob H., and Apweiler R.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. (2005), p.186
Further Steps in Standardisation Report of the Second Annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17–20th April 2005)
Orchard, S., Hermjakob H., Taylor C.F., Potthast F., Jones P., Zhu W., Julian R. K., and Apweiler R.
Proteomics. Volume 5, Number 14, (2005), p.3552–3555
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
Martens, L., Nesvizhskii A. I., Hermjakob H., Adamski M., Omenn G.S., Vandekerckhove J., and Gevaert K.
Proteomics. Volume 5, Number 13, (2005), p.3501–3505
Annotating the human proteome
Orchard, S., Hermjakob H., and Apweiler R.
Molecular & Cellular Proteomics. Volume 4, Number 4, (2005), p.435–440
Dasty and UniProt DAS: a perfect pair for protein feature visualization
Jones, P., Vinod N., Down T., Hackmann A., Kähäri A., Kretschmann E., Quinn A., Wieser D., Hermjakob H., and Apweiler R.
Bioinformatics. Volume 21, Number 14, (2005), p.3198–3199

2004

The HUPO plasma proteome project pilot phase: Reference specimens, technology platform comparisons, and standardized data analyses
Omenn, G.S., Chan D. W., Simpson R. J., Hermjakob H., and others
Proceedings of the American Association for Cancer Research. Volume 2004, Number 1, (2004), p.1104
Proteomics and data standardisation
Orchard, S., Hermjakob H., and Apweiler R.
Drug Discovery Today: Biosilico. Volume 2, Number 3, (2004), p.91–93
Maximising proteomics data for the scientific community
Hermjakob, H., and Apweiler R.
EUROPEAN PHARMACEUTICAL REVIEW. Volume 9, (2004), p.23–29
The ESF Programme on Functional Genomics Workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’
Binz, P.A., Hermjakob H., and Van Der Vet P.
Comparative and functional genomics. Volume 5, Number 2, (2004), p.148–155
Common interchange standards for proteomics data: Public availability of tools and schema. Report on the Proteomic Standards Initiative Workshop, 2nd Annual HUPO Congress, Montreal, Canada, 8–11th October 2003
Orchard, S., Hermjakob H., Julian Jr R. K., Runte K., Sherman D., Wojcik J., Zhu W., and Apweiler R.
Proteomics. Volume 4, Number 2, (2004), p.490–491
IntAct: an open source molecular interaction database
Hermjakob, H., Montecchi-Palazzi L., Lewington C., Mudali S., Kerrien S., Orchard S., Vingron M., Roechert B., Roepstorff P., Valencia A., et al.
Nucleic acids research. Volume 32, Number suppl 1, (2004), p.D452–D455
The HUPO PSI's molecular interaction format—a community standard for the representation of protein interaction data
Hermjakob, H., Montecchi-Palazzi L., Bader G., Wojcik J., Salwinski L., Ceol A., Moore S., Orchard S., Sarkans U., von Mering C., et al.
Nature biotechnology. Volume 22, Number 2, (2004), p.177–183 doi:
A common open representation of mass spectrometry data and its application to proteomics research
Pedrioli, P. G. A., Eng J. K., Hubley R., Vogelzang M., Deutsch E.W., Raught B., Pratt B., Nilsson E., Angeletti R. H., Apweiler R., et al.
Nature biotechnology. Volume 22, Number 11, (2004), p.1459–1466
Current status of proteomic standards development
Orchard, S., Taylor C., Hermjakob H., Zhu W., Julian R., and Apweiler R.
Expert review of proteomics. Volume 1, Number 2, (2004), p.179–183
Advances in the development of common interchange standards for proteomic data
Orchard, S., Taylor C.F., Hermjakob H., Julian R. K., Apweiler R., and others
Proteomics. Volume 4, Number 8, (2004), p.2363–2365

2003

Special Topic on Synergy between Research in Medical Informatics, Bio-Informatics and Neuro-Informatics-Integr8: Enhanced Inter-Operability of European Molecular Biology Databases
Kersey, PJ, Morris L., Hermjakob H., and Apweiler R.
Methods of Information in Medicine-Methodik der Information in der Medizin. Volume 42, Number 2, (2003), p.154–160
The proteomics standards initiative
Orchard, S., Hermjakob H., and Apweiler R.
Proteomics. Volume 3, Number 7, (2003), p.1374–1376
Progress in establishing common standards for exchanging proteomics data
Orchard, S., Kersey P., Zhu W., Montecchi-Palazzi L., Hermjakob H., and Apweiler R.
Comparative and functional genomics. Volume 4, Number 2, (2003), p.203–206 doi:
Integr8: enhanced inter-operability of European molecular biology databases
Kersey, PJ, Morris L., Hermjakob H., and Apweiler R.
Methods of information in medicine. Volume 42, Number 2, (2003), p.154–160 doi:
The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data
Orchard, S., Kersey P., Hermjakob H., and Apweiler R.
Comparative and functional genomics. Volume 4, Number 1, (2003), p.16–19
Further advances in the development of a data interchange standard for proteomics data
Orchard, S., Zhu W., Julian R. K., Hermjakob H., and Apweiler R.
Proteomics. Volume 3, Number 10, (2003), p.2065–2066

2002

TEMBLOR Perspectives of EBI database services
Hermjakob, H., and Apweiler R.
Comparative and functional genomics. Volume 3, Number 1, (2002), p.47–50
Data integration in functional genomics and proteomics: TEMBLOR: Perspectives of EBI database services: A presentation for the ESF workshop'Data integration in functional genomics and proteomics'
Hermjakob, H., and Apweiler R.
Comparative and functional genomics. Volume 3, Number 1, (2002), p.47–50

2001

Initial sequencing and analysis of the human genome
Lander, E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al.
Nature. Volume 409, Number 6822, (2001), p.860–921

2000

A comparison of signal sequence prediction methods using a test set of signal peptides
Menne, K. M. L., Hermjakob H., and Apweiler R.
Bioinformatics. Volume 16, Number 8, (2000), p.741–742
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL
Kersey, P., Hermjakob H., and Apweiler R.
Bioinformatics. Volume 16, Number 11, (2000), p.1048–1049 doi:
The role SWISS-PROT and TrEMBL play in the genome research environment
Junker, V., Contrino S., Fleischmann W., Hermjakob H., Lang F., Magrane M., Jesus Martin M., Mitaritonna N., O’Donovan C., and Apweiler R.
Journal of biotechnology. Volume 78, Number 3, (2000), p.221–234 doi:

1999

Feature Propagation Semi Automatic transfer of position dependent SWISSPROT annotation
Velds, A., Hermjakob H., and Apweiler R.
German Conference on Bioinformatics. (1999), p.229–230
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
Apweiler, R., Hermjakob H., and Sharon N.
Biochimica et Biophysica Acta (BBA)-General Subjects. Volume 1473, Number 1, (1999), p.4–8
Swissknife-'lazy parsing'of SWISS-PROT entries.
Hermjakob, H., Fleischmann W., and Apweiler R.
Bioinformatics. Volume 15, Number 9, (1999), p.771–772

1998

SPTR—a comprehensive, non-redundant and up-to-date protein sequence database
Hermjakob, H., Lang F., Apweiler R., Hinxton E. O., and Hinxton C. C. B.
The Bioinformer issue. Volume 4, (1998),
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL
Heinemeyer, T., Wingender E., Reuter I., Hermjakob H., Kel A. E., Kel OV, Ignatieva E. V., Ananko E. A., Podkolodnaya O. A., Kolpakov FA, et al.
Nucleic acids research. Volume 26, Number 1, (1998), p.362–367

Services

BioJS
BioModels
IntAct
OLS
PICR
PRIDE
Protein DAS
Reactome
SBO

Team members

Raza Ali
Alejandro Barrera
Vijayalakshmi Chelliah
David Croft
Attila Csordas
Noemi Del Toro Ayllon
Jose Dianes
Margaret Duesbury
Marine Dumousseau
Antonio Fabregat Mundo
Phani Garapati
Laurent Gatto
Mihai Glont
Kathryn Holmes
Bijay Jassal
Rafael Jimenez
Steven Jupe
Nick Juty
Sarah Keating
Camille Laibe
Steve Lewis
Oscar Forner Martinez
Birgit Meldal
Stuart Moodie
Sandra Orchard
Pablo Porras Millan
Florian Reisinger
Nicolas Rodriguez
Pau Ruiz Safont
Maciej Swat
Tobias Ternent
Ksenia Titorenko
Juan A Vizcaino
Rui Wang
Mark Williams
Sarala Wimalaratne
Qingwei Xu