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EBIGroupsProteomics Services TeamPublications

Proteomics Services Publications

The following is a list of publications for the Proteomic Services Team.

2008

Braconi Quintaje S., Orchard S. (2008)
Completion of the annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: One small step in manual annotation, one giant step for full comprehension of genomes.
Molecular and Cellular Proteomics 7(8): 1409-1419.
abstract full-text PDF

Côté R.G., Jones P., Martens L., Apweiler R., Hermjakob H. (2008)
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Nucleic Acids Research 36: W372-W376.
abstract full-text PDF

Eisenacher M., Hardt T., Martens L., Häkkinen J., Apweiler R., Hamacher M., Meyer H.E., Stephan C. (2008)
Proteomics Data Collection - 3(rd) ProDaC Workshop April 22(nd) 2008, Toledo, Spain.
Proteomics 8(20): 4163-4167.
abstract full-text PDF

Field D., Hermjakob H., Taylor C., Vaughan B., Wipat A. (2008)
The minimum information about a genome sequence (MIGS) specification.
Nature Biotechnology 26(5): 541-547.
abstract full-text PDF

Jenkinson A.M., Albrecht M., Birney E., Blankenburg H., Down T., Finn R.D., Hermjakob H., Hubbard T.J., Jimenez R.C., Jones P., Kähäri A., Kulesha E., Macías J.R., Reeves G.A., Prlic A. (2008)
Integrating biological data - the Distributed Annotation System.
BMC Bioinformatics 9(8): S3.
abstract full-text PDF

Jimenez R.C., Quinn A.F., Garcia A., Labarga A., O'Neill K., Martinez F., Salazar G.A., Hermjakob H. (2008)
Dasty2, an Ajax protein DAS client.
Bioinformatics 24(18): 2119-2121.
abstract full-text PDF

Hermjakob H. (2008)
EBI proteomics services.
In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 207
abstract full-text PDF [Subscription Required]

Martens L., Palazzi L.M., Hermjakob H. (2008)
Data standards and controlled vocabularies for proteomics.
Methods in Molecular Biology 484: 279-286.
abstract full-text PDF

Matthews L., D'Eustachio P., Gillespie M., Croft D., de Bono B., Gopinath G., Jassal B., Lewis S., Schmidt E., Vastrik I., Wu G., Birney E., Stein L. (2008)
An introduction to the Reactome Knowledgebase of human biological pathways and processes.
Bioinformatics Primer, NCI/Nature Pathway Interaction Database doi:10.1038/pid.2007.3.

Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. (2008)
InteroPORC: automated inference of highly conserved protein interaction networks.
Bioinformatics 24(14): 1625-1631.
abstract

Morsy M., Orchard S., Thorneycroft D., Cushman J.C. (2008)
Charting plant interactomes: possibilities and challenges.
Trends in Plant Science 13(4): 183-191.
abstract full-text HTML

Mons B., Hermjakob H., Bairoch A. (2008)
Calling on a million minds for community annotation in WikiProteins.
Genome Biology 9(5): R89.
abstract full-text HTML

Montecchi-Palazzi L., Beavis R., Binz P.A., Chalkley R.J., Cottrell J., Creasy D., Shofstahl J., Seymour S.L., Garavelli J.S. (2008)
The PSI-MOD community standard for representation of protein modification data.
Nature Biotechnology 26(8): 864-866.
abstract full-text HTML

Mueller M., Vizcaíno J.A., Jones P., Côté R., Thorneycroft D., Apweiler R., Hermjakob H., Martens L. (2008)
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Proteomics 8(6): 1138-1148.
abstract full-text PDF

Orchard S., Albar J.P., Deutsch E.W., Binz P.A., Jones A.R., Creasy D., Hermjakob H. (2008)
Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.
Proteomics 8(20): 4168-41.
abstract full-text PDF

Orchard S., Martens L., Hermjakob H. (2008)
6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.
Proteomics 8(7): 1331-133.
abstract full-text PDF

Reisinger F., Corpas M., Hancock J., Hermjakob H., Birney E. and Kahlem P. (2008)
ENFIN - An integrative structure for systems biology.
In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 132-143
abstract full-text PDF [Subscription Required]

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., Poulovassillis A., Jones P., Côté R., Hermjakob H., Pentony M.M., Jones D.T., Orengo C.A., Hubbard S.J. (2008)
ISPIDER Central: an integrated database web-server for proteomics.
Nucleic Acids Research 36: W485-W490.
abstract full-text PDF

Siepen J.A., Jones P., Côté R., Hermjakob H., Hubbard S.J. (2008)
ISPIDER Central: an integrated database web-server for proteomics.
Nucleic Acids Research 36: W485-W490.
abstract full-text PDF

Taylor C.F., Field D., Sansone S.A., Aerts J., Apweiler R., Ashburner M., Ball C.A., Binz P.A., Bogue M., Booth T., Brazma A., Brinkman R.R., Michael Clark A., Deutsch E.W., Fiehn O., Fostel J., Ghazal P., Gibson F., Gray T., Grimes G., Hancock J.M., Hardy N.W., Hermjakob H., Julian R.K. Jr, Kane M., Kettner C., Kinsinger C., Kolker E., Kuiper M., Novère N.L., Leebens-Mack J., Lewis S.E., Lord P., Mallon A.M., Marthandan N., Masuya H., McNally R., Mehrle A., Morrison N., Orchard S., Quackenbush J., Reecy J.M., Robertson D.G., Rocca-Serra P., Rodriguez H., Rosenfelder H., Santoyo-Lopez J., Scheuermann R.H., Schober D., Smith B., Snape J., Stoeckert C.J. Jr, Tipton K., Sterk P., Untergasser A., Vandesompele J., Wiemann S. (2008)
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature Biotechnology 26(8): 889-896.
abstract full-text PDF

Tsesmetzis N., Couchman M., Higgins J., Smith A., Doonan J.H., Seifert G.J., Schmidt E., Vastrik I., Birney E., Wu G., D'Eustachio P., Stein L., Morris R.J., Bevan M.W., Walsh S.V. (2008)
Arabidopsis Reactome: a foundation knowledgebase for systems biology in plants.
The Plant Cell 20: 1426-1436.
abstract full-text PDF

Vastrik, I. (2008)
Installing a local copy of the Reactome Web site and database.
Current Protocols in Bioinformatics 9: Unit 9.10.
abstract

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2007

Camargo L.M., Collura V., Rain J.C., Mizuguchi K., Hermjakob H., Kerrien S., Bonnert T.P., Whiting P.J., Brandon N.J. (2006)
Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia.
Molecular Psychiatry 12: 74–86.
abstract full-text PDF

de Bono B., Vastrik I., DEustachio P., Schmidt E., Gopinath G., Croft D., Gillespie M., Jassal B., Lewis S., Matthews L., Wu G., Birney E., Stein L. (2007)
Reactome: An integrated expert model of human molecular processes and access toolkit.
Journal of Integrative Bioinformatics 4: 84.


Eisenacher M., Hardt T., Hamacher M., Martens L., Häkkinen J., Levander F., Apweiler R., Meyer H.E., Stephan C. (2007)
Proteomics Data Collection - The 1(st) ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France.
Proteomics 17: 3034-3037.
abstract full-text PDF

Hamacher M., Stephan C., Eisenacher M., Lewczuk P., Wiltfang J., Martens L., Vizcaíno J.A., Kwon K.H., Yoo J.S., Park Y.M., Beckers J., Horsch M., de Angelis M.H., Cho Z.H., Apweiler R., Meyer H.E. (2007)
High Performance Proteomics: 7(th) HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Proteomics 15: 2490-2496.
abstract full-text PDF

Helsens K., Martens L., Vandekerckhove J., Gevaert K. (2007)
MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results.
Proteomics 7(3): 364-366.
[abstract] [full-text PDF]

Kerrien S., Alam-Faruque Y., Aranda B., Bancarz I, Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., Kohler C., Khadake J., Leroy C., Liban A., Lieftink C., Montecchi-Palazzi L., Orchard S., Risse J., Robbe K., Roechert B., Thorneycroft D., Zhang Y, Apweiler R., Hermjakob H. (2007)
IntAct--open source resource for molecular interaction data.
Nucleic Acids Research 35: D561-D565.
abstract full-text PDF

Orchard S. & Hermjakob, H. (2007)
Bioinformatics approaches in proteomics.
In: O'Connor, C.D. & Hames, B.D. Eds. Proteomics. Scion Press.
[More Info]

Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-Aryamontri A., Armstrong J., Woollard P., Salama J.J., Moore S., Wojcik J., Bader,G.D., Vidal M., Cusick M.E., Gerstein M., Gavin A.C., Superti-Furga G., Greenblatt J., Bader J., Uetz P., Tyers M., Legrain P., Fields S., Mulder N., Gilson M., Niepmann M., Burgoon L., Rivas J. de L., Prieto C., Perreau V.M., Hogue C., Mewes H.W., Apweiler R., Xenarios I., Eisenberg D., Cesareni G., Hermjakob H. (2007)
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Nature Biotechnology 25: 894-898.
abstract full-text PDF

Orchard S., Taylor C.F., Jones P., Montechi-Palazzo L., Binz P.A., Jones A.R., Pizarro A., Julian R.K. Jr., Hermjakob H. (2007)
Entering the Implementation Era A report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
Proteomics 7(3): 337-339.
[abstract] [full-text PDF]

Taussig M.J., O. Stoevesandt, C.A.K. Borrebaeck, A.R. Bradbury, D. Cahill, C. Cambillau, A. de Daruvar, S. Dubel, J. Eichler, R. Frank, T.J. Gibson, D. Gloriam, L. Gold, F.W. Herberg, H. Hermjakob, J.D. Hoheisel, T.O. Joos, O. Kallioniemi, M. Koegll, Z. Konthur, B. Korn, E. Kremmer, S. Krobitsch, U. Landegren, S. van der Maarel, J. McCafferty,(SANGER) S. Muyldermans, P.-A. Nygren, S. Palcy, A. Pluckthun, B. Polic, M. Przybylski, P. Saviranta, A. Sawyer, D.J. Sherman, A. Skerra, M. Templin, M. Ueffing & M. Uhlen (2007)
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Nature Methods 4: 13-17.
abstract full-text PDF

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., Dunn M.J., Heck A.J., Leitner A., Macht M., Mann M., Martens L., Neubert T.A., Patterson S.D., Ping P., Seymour S.L., Souda P., Tsugita A., Vandekerckhove J., Vondriska T.M., Whitelegge J.P., Wilkins M.R., Xenarios I., Yates J.R., Hermjakob H. (2007)
The minimum information about a proteomics experiment (MIAPE).
Nature Biotechnology 25: 887-893.
abstract full-text PDF

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2006

Cote R.G., Jones P., Apweiler R., Hermjakob H. (2006)
The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries.
BMC Bioinformatics 7: 97.
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Fiehn O., Kristal B., Ommen B.V., Sumner L.W., Sansone S.A., Taylor C., Hardy N., Kaddurah-Daouk R. (2006)
Establishing reporting standards for metabolomic and metabonomic studies: a call for participation.
OMICS 10(2): 158-163.
abstract full-text PDF

Hamacher M., Apweiler R., Arnold G., Becker A., Blueggel M., Carrette O., Colvis C., Dunn M.J., Froehlich T., Fountoulakis M., van Hall A., Herberg F., Ji J., Kretzschmar H., Lewczuk P., Lubec G., Marcus K., Martens L., Palacios Bustamante N., Park Y.M., Pennington S.R., Robben J., Stuehler K., Reidegeld K.A., Riederer P., Rossier J., Sanchez J.C., Schrader M., Stephan C., Tagle D., Thiele H., Wang J., Wiltfang J., Yoo J.S., Zhang C., Klose J., Meyer H.E. (2006)
HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.
Proteomics 6: 4890-4898.
abstract

Hamacher M., Stephan C., Blueggel M., Chamrad D., Koerting G., Martens L., Mueller M., Hermjakob H., Parkinson D., Dowsey A., Reidegeld K.A., Marcus K., Dunn M.J., Meyer H.E., Apweiler R. (2006)
The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studies.
Proteomics 6: 1719-1721.
abstract full-text PDF

Hermjakob H. (2006)
The HUPO Proteomics Standards Initiative - Overcoming the Fragmentation of Proteomics Data.
Proteomics 6: 34-38.
abstract full-text PDF

Hermjakob H., Apweiler R. (2006)
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Expert Reviews in Proteomics 3: 1-3.
abstract full-text PDF

Jones P., Côté R.G., Martens L., Quinn A.F., Taylor C.F., Derache W., Hermjakob H., and Apweiler R. (2006)
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Nucleic Acids Research 34: D659-D663.
abstract full-text HTML full-text PDF

Martens L., Mueller M., Stephan C., Hamacher M., Reidegeld K.A., Meyer H.E., Blueggel M., Vandekerckhove J., Gevaert K., Apweiler R. (2006)
A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.
Proteomics 6: 5076-5086.
abstract

Orchard S., Apweiler R., Barkovich R., Field D., Garavelli J.S., Horn D., Jones A., Jones P., Julian R., McNally R., Nerothin J., Paton N., Pizarro A., Seymour S., Taylor C., Wiemann S., Hermjakob H. (2006)
Proteomics and Beyond A report on the 3(rd) Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Proteomics 6(16): 4439-4443.
abstract full-text PDF

Orchard S., Hermjakob H. (2006)
Guilt by Association: Using Protein Interactions and Expression Patterns to Predict Protein Function.
In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder N., and Apweiler R. (eds); pp 79-88, Nova Science Publishers, Inc, New York.
[more info]

Orchard S., Hermjakob H., Pruess M., Apweiler R. (2006)
Proteomic Data Standardization, Deposition and Exchange.
In: Proteomics in Drug Research, Hamacher M., Marcus K., Stühler K., van Hall A., Warscheid B., Meyer H.E. (eds), John Wiley & Sons, Inc.
[Buy Book]

Orchard S., Hermjakob H., Taylor C., Binz P.A., Hoogland C., Julian R., Garavelli J.S., Aebersold R., Apweiler R. (2006)
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Proteomics 6: 738-741.
abstract full-text PDF

Orchard S., Ping P. (2006)
HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA.
Proteomics 6: 4436-4438.
abstract full-text PDF

Orchard S., Salwinski L., Kerrien S., Montecchi- Palazzi L., Oesterheld M., Stuempflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., Salama J., Moore S., Wojcik J., Bader G.D., Vidal M., Cusick M., Gerstein M., Gavin A.C, Superti-Furga G., Greenblatt J., Bader J., Uetz P., Tyers M., Legrain P., Fields S., The GO Consortium, Gilson M., Hogue C., Mewes H.W., Apweiler R., Xenarios I., Eisenberg D., Cesareni G., Hermjakob H (2006)
The Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx).
Nature Biotechnology, in press.

Pruess M., Kersey P., Kulikova T., Apweiler R. (2006)
Databases and resources for in silico proteome analysis.
Methods of Biochemical Analysis 49: 397-414.
[more info]

Reidegeld K.A., Hamacher M., Meyer H.E., Stephan C., Blueggel M., Koerting G., Chamrad D., Scheer C., Thiele H., Taylor C.F., Mueller M., Apweiler R., Jones P., Martens L. (2006)
The HUPO Brain Proteome Project.
European Pharmaceutical Review 33-38.
[Subscription Required]

Reidegeld K.A., Mueller M., Stephan C., Blueggel M., Hamacher M., Martens L., Koerting G, Chamrad D.C., Parkinson D., Apweiler R., Meyer H.E., Marcus K. (2006)
The power of cooperative investigation: Summary and comparison of the HUPO Brain Proteome Project pilot study results.
Proteomics 6: 4997-5014.
abstract

Stephan C., Reidegeld K.A., Hamacher M., van Hall A., Marcus K., Taylor C., Jones P., Muller M., Apweiler R., Martens L., Korting G., Chamrad D.C., Thiele H., Blueggel M., Parkinson D., Binz P.A., Lyall A., Meyer H.E. (2006)
Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
Proteomics 6: 5015-5029.
abstract

Taylor C.F. (2006)
Minimum Reporting Requirements for Proteomics: A MIAPE Primer.
Proteomics 6: 39-44.
abstract full-text PDF

Taylor C.F., Hermjakob H., Julian R.K., Garavelli J.S., Aebersold R., Apweiler R. (2006)
The Work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
OMICS 10(2): 145-151.
abstract full-text PDF

Whetzel P.L., Brinkman R.R., Causton H.C., Fan L., Field D., Fostel J., Fragoso G., Gray T., Heiskanen M., Hernandez-Boussard T., Morrison N., Parkinson H., Rocca-Serra P., Sansone S.A., Schober D., Smith B., Stevens R., Stoeckert C.J., Taylor C., White J., Wood A. (2006)
Development of FuGO: An Ontology for Functional Genomics Investigations.
OMICS 10(2): 199-204.
abstractfull-text PDF

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2005

Hermjakob H., Apweiler R. (2005)
Protein interaction databases.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde L.B., Little P.F.R., Dunn M.J., Subramanian S. (eds.), pp 2079-2089, John Wiley & Sons, Inc.
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Jones P., Vinod N., Down T., Hackmann A., Kahari A., Kretschmann E., Quinn A., Wieser D., Hermjakob H., Apweiler R. (2005)
Dasty and UniProt DAS: a perfect pair for protein feature visualization.
Bioinformatics 21(14): 3198-3199 (2005).
abstract full-text PDF

Orchard S., Hermjakob H., Taylor C., Aebersold R., Apweiler R. (2005)
Human proteome organisation proteomics standards initiative pre-congress initiative.
Proteomics 5: 4651-4652.
abstract full-text PDF

Orchard S., Hermjakob H., Taylor C.F., Potthast F., Jones P., Zhu W., Julian R.K. Jr., Apweiler R. (2005)
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).
Proteomics 5: 3552-3555.
abstract full-text PDF

Stephan C., Hamacher M., Blueggel M., Korting G., Chamrad D., Scheer C., Marcus K., Reidegeld K.A., Lohaus C., Schaefer H., Martens L., Jones P., Mueller M., Auyeung K., Taylor C., Binz P.A., Thiele H., Parkinson D., Meyer H.E., Apweiler R. (2005)
5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK-Setting the analysis frame.
Proteomics 5: 3560-3562.
abstract full-text PDF

Taylor C., Hermjakob H., Apweiler R., Orchard S., Zhu W. (2005)
Data standardization and the HUPO proteomics standards initiative.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde L.B., Little P.F.R., Dunn M.J., Subramanian S. (eds.), pp 3229-3233, John Wiley & Sons, Inc.
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2004



Pedrioli P. G. et al. (2004)
A common open representation of mass spectrometry data and its application to proteomics research.
Nature Biotechnology 22: 1459-1466.
abstract full-text PDF

Orchard S. et al. (2004)
Common interchange standards for proteomics data: Public availability of tools and schema.
Proteomics 4: 490-491.
abstract

Orchard S. Hermjakob H. & Apweiler R. (2004)
Proteomics and Data Standardisation.
Drug Discovery Today: BIOSILICO 2: 91-93.

Orchard S., Hermjakob H., Binz P.A., Hoogland C., Taylor C.F., Zhu W., Julian R.K. Jr., Apweiler R. (2004)
Further steps towards data standardisation: The Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.
Proteomics 5(2): 337-339.
abstract full-text PDF

Hermjakob H. & Apweiler R. (2004)
Maximising proteomics data for the scientific community.
European Pharmaceutical Review 9: 23-28.

Hermjakob H. et al. (2004)
IntAct: an open source molecular interaction database.
Nucleic Acids Research 32: D452-D455.
abstract full-text HTML

Hermjakob H. et al. (2004)
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Nature Biotechnology 22: 177-183.
abstract

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2003


Orchard S., Zhu W., Julian R. K. Jr., Hermjakob H. & Apweiler R. (2003)
Further advances in the development of a data interchange standard for proteomics data.
Proteomics 3: 2065-2066.
abstract full-text PDF

Orchard S. et al. (2003)
Progress in establishing common standards for exchanging proteomics data. The second meeting of the HUPO Proteomics Standards Initiative.
Comparative and Functional Genomics 4: 203-206 (2003).

Orchard S., Kersey P., Hermjakob H. & Apweiler R. (2003)
The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data.
Comparative and Functional Genomics 4: 16-19.

Orchard S., Hermjakob H. & Apweiler R. (2003)
The proteomics standards initiative.
Proteomics 3: 1374-1376.
abstract full-text PDF

Kersey P. J., Morris L., Hermjakob H. & Apweiler R. (2003)
Integr8: enhanced inter-operability of European molecular biology databases.
Methods Inf Med 42, 154-60.
abstract

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2002


Mulder N. J. et al. (2002)
InterPro: an integrated documentation resource for protein families, domains and functional sites.
Brief Bioinform 3: 225-235.
abstract full-text PDF

Hermjakob H. & Apweiler R. (2002)
TEMBLOR - Perspectives of EBI database services. A presentation for the ESF workshop Data integration in functional genomics and proteomics.
Comparative and Functional Genomics 3: 47-50.


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2001


Zdobnov E. M., Hermjakob H. & Apweiler R. (2001)
in RECOMB 2001: Annual Conference on Research in Computational Molecular Biology (ed. El-Mabrouk N., L. T., and Sankoff D.) 41-42 (Montreal, 2001).

Lander E. S. et al. (2001)
Initial sequencing and analysis of the human genome.
Nature 409: 860-921.
abstract full-text PDF

Apweiler R. et al. (2001)
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic Acids Res 29: 37-40.
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2000


Menne K. M., Hermjakob H. & Apweiler R. (2000)
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinformatics 16: 741-742.
abstract full-text PDF

Kersey P., Hermjakob H. & Apweiler R. (2000)
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Bioinformatics 16: 1048-1049.
abstract full-text PDF

Junker V. et al. (2000)
The role SWISS-PROT and TrEMBL play in the genome research environment.
J Biotechnol 78: 221-234.
abstract full-text PDF

Apweiler R. et al. (2000)
InterPro - An integrated documentation resource for protein families, domains and functional sites.
CCP11 Newsletter.

Apweiler R. et al. (2000)
InterPro--an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics 16: 1145-1150.
abstract full-text PDF

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1999


Hermjakob H., Fleischmann W. & Apweiler R. (1999)
Swissknife - 'lazy parsing' of SWISS-PROT entries.
Bioinformatics 15: 771-772.
abstract full-text PDF

Apweiler R., Hermjakob H. & Sharon N. (1999)
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Biochim Biophys Acta 1473: 4-8.
abstract full-text PDF

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1998


Heinemeyer T. et al. (1998)
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Nucleic Acids Res 26, 362-7.
abstract full-text HTML

Apweiler R. et al. (1998)
in The World Multiconference on Systemics, Cybernetics and Informatics (SCI '98 / ISAS '98) (ed. Callaos N., H. L., Osers R.) 184-191 (Orlando, Florida, USA, 1998).


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1997


Hermjakob H., Giegerich R. & Arnold W. (1997)
RIFLE: rapid identification of microorganisms by fragment length evaluation.
Proc Int Conf Intell Syst Mol Biol 5, 131-9.
abstract

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