spacer
  spacer
EBI Groups PANDA Group Publications Other

PANDA Group Publications

Reference Search

All References
European Nucleotide Archive
Ensembl
GOA
InterPro
Proteome Analysis
UniProt
VectorBase
Other


Other References


Aranda B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A, Derow C, Feuermann M, Ghanbarian A.T., Kerrien S., Khadake J., Kerssemakers J., Leroy C, Menden M., Michaut M., Montecchi-Palazzi L., Neuhauser S.N., Orchard S., Perreau V., Roechert B., van Eijk K., Hermjakob H. (2010)
The IntAct molecular interaction database in 2010.
Nucleic Acids Research 38: D525-D531.
abstract full-text PDF

Vizcaíno J.A., Côté R., Reisinger F., Barsnes H., Foster J.M., Rameseder J., Hermjakob H., Martens L. (2010)
The Proteomics Identifications database: 2010 update.
Nucleic Acids Research 38: D736-D742.
abstract full-text PDF

de Matos P., Alcántara R., Dekker A., Ennis M., Hastings J., Haug K., Spiteri I., Turner S., Steinbeck C. (2010)
Chemical Entities of Biological Interest: an update.
Nucleic Acids Research 38: D249-D254.
abstract full-text PDF

Robinson J., Mistry K., McWilliam H., Lopez R., Marsh S.G. (2010)
IPD--the Immuno Polymorphism Database.
Nucleic Acids Research 38: D863-D869.
abstract full-text PDF

Ilsley G.R., Luscombe N.M., Apweiler R. (2009)
Know Your Limits: Assumptions, Constraints and Interpretation in Systems Biology.
Biochimica et Biophysica Acta 2009 May 8
abstract

Degtyarenko K., Matos P.D., Ennis M., Hastings J., Zbinden M., McNaught A., Alcántara R., Darsow M., Guedj M., Ashburner M. (2008)
ChEBI: a database and ontology for chemical entities of biological interest.
Nucleic Acids Research 36: D344-D350.
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]

Jones P., Côté R.G., Cho S.Y., Klie S., Martens L., Quinn A.F., Thorneycroft D., Hermjakob H. (2008)
PRIDE: new developments and new datasets.
Nucleic Acids Research 36: D878-D883.
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]

Camargo L.M., Collura V., Rain J.C., Mizuguchi K., Hermjakob H., Kerrien S., Bonnert T.P., Whiting P.J., Brandon N.J. (2007)
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

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 7(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

Itoh T., Tanaka T., Barrero RA., Yamasaki C., Fujii Y., Hilton PB., Antonio BA., Aono H., Apweiler R., Bruskiewich R., Bureau T., Burr F., Costa de Oliveira A., Fuks G., Habara T., Haberer G., Han B., Harada E., Hiraki AT., Hirochika H., Hoen D., Hokari H., Hosokawa S., Hsing Y., Ikawa H., Ikeo K., Imanishi T., Ito Y., Jaiswal P., Kanno M., Kawahara Y., Kawamura T., Kawashima H., Khurana JP., Kikuchi S., Komatsu S., Koyanagi KO., Kubooka H., Lieberherr D., Lin YC., Lonsdale D., Matsumoto T., Matsuya A., McCombie WR., Messing J., Miyao A., Mulder N., Nagamura Y., Nam J., Namiki N., Numa H., Nurimoto S., O'donovan C., Ohyanagi H., Okido T., Oota S., Osato N., Palmer LE., Quetier F., Raghuvanshi S., Saichi N., Sakai H., Sakai Y., Sakata K., Sakurai T., Sato F., Sato Y., Schoof H., Seki M., Shibata M., Shimizu Y., Shinozaki K., Shinso Y., Singh NK., Smith-White B., Takeda JI., Tanino M., Tatusova T., Thongjuea S., Todokoro F., Tsugane M., Tyagi AK., Vanavichit A., Wang A., Wing RA., Yamaguchi K., Yamamoto M., Yamamoto N., Yu Y., Zhang H., Zhao Q., Higo K., Burr B., Gojobori T., Sasaki T. (2007)
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Genome Research 17(2): 175-83.
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

Martin M., Kulikova T., Pruess M., Apweiler R. (2007)
Gene and Protein Sequence Databases.
In: Comprehensive Medicinal Chemistry II, Triggle D.J, and Taylor J.B. (eds); Volume 3 – Drug Discovery Technologies, pp 349-372, Elsevier, Oxford (2007).
more info

Mischak H., Apweiler R., Banks R.E., Conaway M., Coon J., Dominiczak A., Ehrich J.H.H., Fliser D., Girolami M., Hermjakob H., Hochstrasser D., Jankowski J., Julian B.A., Kolch W., Massy Z.A., Neusuess C., Novak J., Peter K., Rossing K., Schanstra J., Semmes O.J., Theodorescu D., Thongboonkerd V., Weissinger E.M., Van Eyk J.E., and Yamamoto T. (2007)
Clinical proteomics: A need to define the field and to begin to set adequate standards.
Proteomics Clinical Applications 1: 148–156.
abstract full-text PDF

Mueller M., Martens L., and Apweiler R. (2007)
Annotating the human proteome: Beyond establishing a parts list.
Biochimica et Biophysica Acta 1774: 175-191.
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

Ping P., Apweiler R., Bergeron J. (2007)
MCP and HUPO: An Era of New Partnership.
Molecular and Cellular Proteomics 6(6): 951-952.
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

Brecher, J., Degtyarenko, K.N., Gottlieb, H., Hartshorn, R.M., Moss, G.P., Murray-Rust, P., Nyitrai, J., Powell, W., Smith, A., Stein, S., Taylor, K., Town, W., Williams, A. and Yerin, A. (2006)
Graphical representation of stereochemical configuration (IUPAC Recommendations 2006).
Pure and Applied Chemistry 78(10): 1897-1970.
abstract full-text PDF

Chamrad D.C., Körting, G., Schaefer H., Stephan C., Thiele H., Apweiler R., Meyer H.E., Marcus K., Blueggel M. (2006)
Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.
Proteomics 6: 5048-5058.
abstract

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.
abstract full-text HTML

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 HTMLfull-text PDF

Jones, P. and Brooksbank, C. (2006)
A Quick Guide to PRIDE: The PRoteomics IDentifications Database.
OBBeC Life. Science and Bioinformatics June, 24-26 (2006)
full-text HTML

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

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., Pruess M., Apweiler R. (2006)
Proteomic Data Standardization, Deposition and Exchange.
In: Proteomics in Drug Research, Hamacher M., Marcus K., Sthler K., van Hall A., Warscheid B., Meyer H.E. (eds), John Wiley & Sons, Inc (2006).
buy book

Orchard, S. and Brooksbank, C. (2006)
A Quick Guide to IntAct.
OBBeC Life. Science and Bioinformatics June, 24-26 (2006)
full-text HTML

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 (2006).
more info

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 HTML 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 HTML 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


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

Pruess M., Apweiler R. (2006).
Bioinformatics Resources for /in Silico/ Proteome Analysis.
In: Cell Biology. A Laboratory Handbook. Third Edition, Celis J.E.. (ed.); Volume 4 pp 469-475, Elsevier Academic Press (2006).
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 full-text HTML

Reidegeld K.A., Hamacher M., Meyer H.E., Stephan C., Blueggel M., Körting, 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 full-text HTML

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., Körting, 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.
abstract full-text PDF

Whitfield E.J., Pruess M., Apweiler R. (2006)
Bioinformatics database infrastructure for biotechnology research.
Journal of Biotechnology 124: 629-639.
abstract full-text HTML

Apweiler R. (2005)
Sequence databases.
In: Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd edition, Baxevanis A.D., Oullette B.F.F. (eds.); pp.3-54, John Wiley & Sons, Inc (2005).
more info

Apweiler R., Cornish-Bowden A., Hofmeyr J.-H.S., Kettner C., Leyh T.S., Schomburg D., Tipton K. (2005)
The importance of uniformity in reporting protein-function data.
Trends in Biochemical Sciences 30: 11-12.
abstract full-text HTML full-text PDF

Blaschke C., Yeh A., Camon E., Colosimo M., Apweiler R., Hirschman L., Valencia A. (2005)
Do you do text?
Bioinformatics 21: 4199-4200.
abstract full-text HTML full-text PDF

Degtyarenko K. (2005)
Metalloproteins.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde L.B., Little P.F.R., Dunn M.J., Subramanian S. (eds.), pp 2359-2387, John Wiley & Sons, Inc (2005).
more info

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.
abstract full-text HTML full-text PDF

Orchard S., Hermjakob H., Apweiler R. (2005)
Annotating the human proteome.
Molecular and Cellular Proteomics 4: 435-440.
abstract full-text PDF

Orchard S., Hermjakob H., Binz P.A., Hoogland C., Taylor C.F., Zhu W., Julian R.K. Jr., Apweiler R. (2005)
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

Orchard S., Hermjakob H., Taylor C.F., Potthast F., Jones P., Zhu W., Julian R.K. Jr., Apweiler R. (2005)
Second Proteomics Standards Initiative Spring Workshop Siena, Italy 17-20th April 2005.
Expert Review of Proteomics 2(3): 287-289.
abstract full-text PDF

Orchard S., Montecchi-Palazzi L., Hermjakob H., Apweiler R. (2005)
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
Pacific Symposium on Biocomputing 2005: 186-196.
abstract

Mignone F., Grillo G., Licciulli F., Iacono M., Liuni S., Kersey P.J., Duarte J., Saccone C., Pesole G. (2005)
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucleic Acids Research 33: D141-D146.
abstract full-text HTML full-text PDF

Pruess M., Whitfield E., Apweiler R. (2005)
Bioinformatics Databases for Biotechnology Research.
BIOforum Europe 9: 42-44.

Velankar S., McNeil P., Mittard-Runte V., Suarez A., Barrell D., Apweiler R., and Henrick K. (2005)
E-MSD: an integrated data resource for bioinformatics
Nucleic Acids Research 33: D262-D265.
abstract full-text HTML full-text PDF

Williams A.L., Kersey P.J., Pruess M., Apweiler R. (2005)
Biological Databases: Infrastructure, Content and Integration.
In: Data Analysis and Visualization in Genomics and Proteomics, Azuaje F.,
Dopazo J. (eds.); John Wiley & Sons, Inc (2005). pp. 11-28.
buy book

Apweiler R., Lopez R. (2004)
Sequence databases and analysis sites.
In: The Internet for Molecular Biologists, Samson C.E., Horton R.M. (eds.); pp.17-37, Oxford University Press (2004).
review sample pdf buy book

Bluggel M., Bailey S., Körting, G., Stephan C., Reidegeld K.A., Thiele H., Apweiler R., Hamacher M., Meyer H.E. (2004)
Towards data management of the HUPO Human Brain Proteome Project pilot phase.
Proteomics 4(8): 2361-2362.
abstract full-text PDF

Degtyarenko, K. and Contrino, S. (2004)
COMe: the ontology of bioinorganic proteins.
BMC Structural Biology 4(3).
full-text HTML full-text PDF

Farriol-Mathis, N., Garavelli, J.S., Boeckmann, B., Duvaud, S., Gasteiger, E., Gateau, A., Veuthey, A., Bairoch, A. (2004)
Annotation of post-translational modifications in the Swiss-Prot knowledge base.
Proteomics 4(6): 1537-1550.
abstract full-text PDF

Fleischmann, A., Darsow, M., Degtyarenko, K., Fleischmann, W., Boyce, S., Axelsen, KB., Bairoch, A., Schomburg, D., Tipton, K.F., Apweiler, R. (2004)
IntEnz, the integrated relational enzyme database.
Nucleic Acids Research 32(1): D434-D437.
abstract full-text HTML

Garavelli, J.S. (2004)
The RESID Database of Protein Modifications as a resource and annotation tool.
Proteomics 4: 1527-1533.
abstract full-text PDF

Garwood K., T. McLaughlin C., Garwood S., Joens N., Morrison C.F., Taylor K., Carroll C., Evans A.D., Whetton, S., Hart, D., Stead, Z., Yin, A.J., Brown A., Hesketh K., Chater L., Hansson, M. Mewissen P., Ghazal J., Howard K.S., Lilley S.J., Gaskell A., Brass S.J., Hubbard S.G., Oliver S.G. and Paton N.W. (2004)
PEDRo: a database for storing, searching and disseminating experimental proteomics data.
BioMed Central Genomics 5: 68-79.
abstract full-text PDF

Garwood K.L., Taylor C.F., Runte K.J., Brass A., Oliver S.G., Paton N.W. (2004)
Pedro: a configurable data entry tool for XML.
Bioinformatics 15: 2463-2465.
abstract full-text HTML

Harte N., Silventoinen V., Quevillon E., Robinson S., Kallio K., Fustero X., Patel P., Jokinen P. and Lopez R. (2004)
Public web-based services from the European Bioinformatics Institute
Nucleic Acids Research 32: W3-W9.
abstract full-text HTML

Hermjakob H. and Apweiler R. (2004)
Maximising proteomics data for the scientific community
European Pharmaceutical Review 9(3): 23-28.
abstract full-text HTML full-text PDF

Hermjakob H.,** Montecchi-Palazz L.,** Bader G., Wojcik J., Salwinski L., Ceol A., Moore S., Orchard S., Sarkans U., von Mering C., Roechert B., Poux S., Jung E., Mersch H., Kersey P., Lappe M., Li Y., Zeng R., Rana D., Nikolski M., Husi H., Brun C., Shanker K., Grant S. G. N., Sander C., Bork P., Zhu W., Pandey A., Brazma A., Jacq B., Vidal M., Sherman D., Legrain P., Cesareni G., Xenarios I., Eisenberg D., Steipe B., Hogue C. and Apweiler R. (2004)
The HUPO PSI's Molecular Interaction format-a community standard for the representation of protein interaction data
Nature Biotechnology 22(2): 177-183.
abstract full-text HTML full-text PDF

Imanishi T. et al (2004)
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones.
PLoS Biology 2(6): E162.
abstract full-text HTML

Kersey P.J, Duarte J., Williams A., Karavidopoulou Y., Birney E. and Apweiler R. (2004)
The International Protein Index: An integrated database for proteomics experiments
Proteomics 4(7): 1985-1988.
abstract full-text PDF

LeDuc R.D., Taylor G.K., Kim Y.B., Januszyk T.E., Bynum L.H., Sola J.V., Garavelli J.S., Kelleher N.L. (2004)
ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry.
Nucleic Acids Research 32: W340-W345.
abstract full-text HTML

Magrane M., Garcia-Pastor M., Apweiler R. (2004)
Survey of sequence databases: Archival projects.
In: Database Annotation in Molecular Biology, Lesk A.M. (ed.); pp.25-44, John Wiley & Sons, Ltd (2004).
more info

Martin-Sanchez F., Iakovidis I., Norager S., Maojo V., de Groen P., van der Lei J., Jones T., Abraham-Fuchs K., Apweiler R., Babic A., Baud R., Breton V., Cinquin P., Doupi P., Dugas M., Eils R., Engelbrecht R., Ghazal P., Jehenson P., Kulikowski C., Lampe K., De Moor G., Orphanoudakis S., Rossing N., Sarachan B., Sousa A., Spekowius G., Thireos G., Zahlmann G., Zvarova J., Hermosilla I., Vicente F.J. (2004)
Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care.
Journal of Biomedical Informatics 37(1): 30-42.
abstract full-text HTML full-text PDF

Pruess M. (2004)
Biological Databases - Insights and Trends.
In: The New Avenues in Bioinformatics. Series: Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 8., Seckbach J., Rubin E. (eds.); pp. 41-55, Kluwer Academic Publishers (2004).
more info

Orchard S., Hermjakob H., Apweiler R. (2004)
Proteomics and data standardisation.
Drug Discovery Today BIOSILICO 2: 91-93.
subscription required

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

Orchard S., Hermjakob H., Julian R.K. Jr., Runte K., Sherman D., Wojcik J., Zhu W., Apweiler R. (2004)
Common interchange standards for proteomics data: Public availability of tools and schema.
Proteomics 4: 490-491.
abstract full-text PDF

Orchard S., Taylor C., Hermjakob H., Zhu W., Julian R. and Apweiler R. (2004)
Current status of proteomic standards development.
Expert Review of Proteomics 1(2): 179–183.
abstract order hard copy

Orchard S., Taylor C.F., Hermjakob H., Zhu, W., Julian R.K. Jr, Apweiler R. (2004)
Advances in the development of common interchange standards for proteomic data.
Proteomics 4(8): 2363-2365.
abstract full-text PDF

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., Cheung K., Costello C.E., Hermjakob H., Huang S., Julian R.K., Kapp E., McComb M.E., Oliver S.G., Omenn G., Paton N.W., Simpson R., Smith R., Taylor C.F., Zhu W., Aebersold R. (2004)
A common open representation of mass spectrometry data and its application to proteomics research.
Nature Biotechnology 22: 1459-1466.
abstract full-text HTML full-text PDF

Pruess, M. (2004)
Tools fuer die Proteom-Analyse in silico.
Information Technology 1: 20-25.
abstract full text PDF- subscription required

Pruess M., Mulder N., Apweiler R. (2004)
Survey of sequence databases: Derived Databases.
In: Database Annotation in Molecular Biology, Lesk A.M. (ed.); pp.45-62, John Wiley & Sons, Ltd (2004).
more info

Ruau D., Duarte J., Ourjdal T., Perrière G., Laudet V. and Robinson-Rechavi M. (2004)
Update of NUREBASE: nuclear hormone receptor functional genomics
Nucleic Acids Research 32: D165-D167.
abstract full-text HTML

Apweiler R. (2003)
The rise of computational drug discovery?
BIOSILICO 1: 5-6.
subscription required

Apweiler R., Martin M.J., O'Donovan C., Pruess M. (2003)
Managing core resources for genomics and proteomics.
Pharmacogenomics 4: 343-350.
abstract full-text PDF

Brooksbank C., Camon E., Harris M. A., Magrane M., Martin M., Mulder N., O'Donovan C., Parkinson H., Tuli M., Apweiler R., Birney E., Brazma A., Henrick K., Lopez R. , Stoesser G., Stoehr P., and Cameron G. (2003)
The European Bioinformatics Institute's data resources.
Nucleic Acids Research 31: 43-50.
abstract full-text HTML

Garavelli J. S. (2003)
The RESID Database of Protein Modifications: 2003 developments.
Nucleic Acids Research 31: 499-501.
abstract full-text HTML

Gattiker A., Michoud K., Rivoire C., Auchincloss A.H., Coudert E., Lima T., Kersey P., Pagni M., Sigrist C.J.A., Lachaize C., Veuthey A.-L., Gasteiger E., Bairoch A. (2003)
Automated annotation of microbial proteomes in SWISS-PROT.
Computational Biology and Chemistry 27: 49-58.
abstract full-text PDF

Kanapin A., Batalov S., Davis M.J., Gough J., Grimmond S., Kawaji H., Magrane M., Matsuda H., Schonbach C., Teasdale R.D., Yuan Z., (2003)
Mouse proteome analysis.
Genome Research 13: 1335-1344.
abstract full-text PDF

Kasukawa T., Furuno M., Nikaido I., Bono H., Hume D.A., Bult C., Hill D.P., Baldarelli R., Gough J., Kanapin A., Matsuda H., Schriml L.M., Hayashizaki Y., Okazaki Y., Quackenbush J. (2003)
Development and evaluation of an automated annotation pipeline and cDNA annotation system.
Genome Research 13: 1542-1551.
abstract full-text PDF

Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., Kanapin A., Le Bot N., Moreno S., Sohrmann M., Welchman D.P., Zipperlen P., Ahringer J. (2003)
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi.
Nature 421(6920): 231-237.
abstract full-text PDF

Kriventseva E.V., Koch I., Apweiler R., Vingron M., Bork P., Gelfand M.S., Sunyaev S. (2003)
Increase of functional diversity by alternative splicing.
Trends in Genetics 19: 124-128.
abstract full-text PDF

Lopez R., Duggan K., Harte N., Kibria A. (2003)
Public services from the European Bioinformatics Institute.
Briefings in Bioinformatics 4(4): 332-340.
abstract full-text PDF

Lopez R., Silventoinen V., Robinson S., Kibria A., Gish W. (2003)
WU-BLAST2 server at the European Bioinformatics Institute
Nucleic Acids. Research 31: 3795-3798.
abstract   full-text PDF

Lopez R., Robinson S., Kibria A., Harte N., Patel G., Harper R., Quevillon E., Silventoinen V., Kallio K., Jokinen P. (2003)
The European Bioinformatics Institute web site: a new view
Bioinformatics 19: 546-547.
abstract   full-text PDF

Martin M.J., Herrero J., Mateos A., Dopazo J. (2003)
Comparing bacterial genomes through conservation profiles.
Genome Research 213(5): 991-998.
abstract full-text HTML

Orchard S., Hermjakob H., Apweiler R. (2003)
The proteomics standards initiative.
Proteomics 3(7): 1374-1376.
abstract   full-text PDF

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.
abstract full-text HTML full-text PDF

Orchard S., Kersey P., Zhu W., Montecchi-Palazzi L., Hermjakob H., Apweiler R. (2003)
Progress in establishing common standards for exchanging proteomics data. The second meeting of the HUPO Proteomics Standards Initiative
Comparative and Functional Genomics 4(2): 203-206.
abstract full-text HTML full-text PDF

Orchard S., Zhu W., Julian R.K.Jnr., Hermjakob H., Apweiler R. (2003)
Further advances in the development of a data interchange standard for proteomics data.
Proteomics 3: 2965-2066.
abstract

Phan I. Q. H., Pilbout S. F., Fleischmann W., Bairoch A. (2003)
NEWT, a new taxonomy portal.
Nucleic Acids Research 31: 3822-3823.
abstract full-text PDF

Pruess M., Apweiler R. (2003)
Bioinformatics Resources for In Silico Proteome Analysis.
Journal of Biomedicine and Biotechnology 2003(4): 231-236.
abstract

Robinson J., Waller M.J., Parham P., de Groot N., Bontrop R., Kennedy L.J., Stoehr P., Marsh S.G.E. (2003)
IMGT/hLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.
Nucleic Acids Research 31(1): 311-314.
abstract full-text HTML

Soinov L.A., Krestyaninova M.A., Brazma A. (2003)
Towards reconstruction of gene networks from expression data by supervised learning.
Genome Biology 4(1): R6 (2003).
full-text HTML 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.
full-text PDF

Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M. and Lewis S.E. (2002)
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Genome Biology 3(12): research0083.1-0083.22.
full-text HTML full-text PDF

Servant F., Bru C., Carrere S., Courcelle E., Gouzy J., Peyruc D., Kahn D. (2002)
ProDom: Automated clustering of homologous domains.
Briefings in Bioinformatics 3(3): 246-251.
full-text PDF

The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team. (2002)
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Nature 420: 563-573.
full-text HTML full-text PDF

Zdobnov E.M., Lopez R., Apweiler R, Etzold T. (2002)
The EBI SRS server - new features.
Bioinformatics 18(8): 1149-1150.
abstract full-text PDF

Zdobnov E. M., Lopez R., Apweiler R., Etzold T. (2002)
The EBI SRS server - recent developments
Bioinformatics 18: 368-373.
abstract full-text PDF

Carlton J.M.-R., Muller R., Yowell C.A., Fluegge M.R., Sturrock K.A., Pritt J.R., Vargas-Serrato E., Galinski M.R., Barnwell J.W., Mulder N., Kanapin A., Cawley S.E., Hide W.A., Dame J.B. (2001)
Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species.
Molecular and Biochemical Parasitology 118: 201-210.
abstract

Degtyarenko K.N., Kulikova T.A. (2001)
Evolution of bioinorganic motifs in P450-containing systems.
Biochemical Society Transactions 29: 139-147.
full-text HTML full-text PDF

International Human Genome Sequencing Consortium. (2001)
Initial sequencing and analysis of the human genome.
Nature 409: 860-921.
full-text HTML full-text PDF

Kawai J., Shinagawa A., Shibata K., Yoshino M., Itoh M., Ishii Y., Arakawa T., Hara A., Fukunishi Y., Konno H., Adachi J., Fukuda S., Aizawa K., Izawa M., Nishi K., Kiyosawa H., Kondo S., Yamanaka I., Saito T., Okazaki Y., Gojobori T., Bono H., Kasukawa T., Saito R., Kadota K., Matsuda H., Ashburner M., Batalov S., Casavant T., Fleischmann W., Gaasterland T., Gissi C., King B., Kochiwa H., Kuehl P., Lewis S., Matsuo Y., Nikaido I., Pesole G., Quackenbush J., Schriml L. M., Staubli F., Suzuki R., Tomita M., Wagner L., Washio T., Sakai K., Okido T., Furuno M., Aono H., Baldarelli R., Barsh G., Blake J., Boffelli D., Bojunga N., Carninci P., de Bonaldo M. F., Brownstein M. J., Bult C., Fletcher C., Fujita M., Gariboldi M., Gustincich S., Hill D., Hofmann M., Hume D. A, Kamiya M., Lee N. H., Lyons P., Marchionni L., Mashima J., Mazzarelli J., Mombaerts P., Nordone P., Ring B., Ringwald M., Rodriguez I., Sakamoto N., Sasaki H., Sato K., Schonbach C., Seya T., Shibata Y., Storch K.-F., Suzuki H., Toyo-O a K., Wang K. H., Weitz C., Whittaker C., Wilming L., Wynshaw-Boris A., Yoshida K., Hasegawa Y., Kawaji H., Kohtsuki S. (2001)
Functional annotation of a full-length mouse cDNA collection.
Nature 409: 685-690.
full-text HTML full-text PDF

Moller S., Croning M.D.R., Apweiler R. (2001)
Evaluation of methods for the prediction of membrane spanning regions.
Bioinformatics 17(7): 646-653.
abstract full-text PDF

Moller S., Schroeder M., Apweiler R. (2001)
Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins.
Journal of Computational Chemistry 26(1): 41-49.
abstract full-text PDF

Mulder N.J., Apweiler R. (2001)
Tools and resources for identifying protein families, domains and motifs.
Genome Biology 3(1): reviews2001.1-2001.8 .
abstract full-text PDF

Sudbrack R., Wieczorek G., Nuber U.A., W., Kirchner R., Erdogan F., Brown C.J., Woehrle D., Sterk P., Kalscheuer V.M., Berger W., Lehrach H. and Roper H. (2001)
X chromosome-specific cDNA arrays: identification of genes that escape from X-inactivation and other applications.
Human Molecular Genetics 10(1): 77-83 .
abstract

Zdobnov E.M., Lopez R., Apweiler R., Etzold T. (2001)
Using the Molecular Biology Data.
In: Biotechnology, vol. 5b: Genomics and Bioinformatics, C.W. Sernsen (eds); pp. 281-300, Wiley-VCH (2001).
full-text PDF

Abola E.E., Bairoch A., Barker W.C., Beck S., Benson D.A., Berman H., Cameron G., Cantor C., Doubet S., Hubbard T.J.P., Jones T.A., Kleywegt G.J., Kolaskar A.S., Van Kuik A., Lesk A.M., Mewes H.W., Neuhaus D., Pfeiffer F., TenEyck L.F., Simpson R.J., Stoesser G., Sussman J.L., Tateno Y., Tsugita A., Ulrich E.L., Vliegenthart J.F.G. (2000)
Quality Control In Databanks For Molecular Biology
BioEssays 22: 1024-1034.
abstract full-text PDF

Apweiler, R. (2000)
Protein sequence databases.
In: Advances in Protein Chemistry, Richards F.M., Eisenberg D.S., Kim P.S.(eds.); pp. 54:31-71, Academic Press, New York (2000).
abstract

Cameron G., Rodriguez-Tome P., Apweiler R. (2000)
Electronic Collaboration in Molecular Biology.
In: Electronic Collaboration in Science, Koslow S.H., Huerta M.F. (eds.); pp.73-87, Lawrence Erlbaum Associates (2000).
full-text HTML

Degtyarenko K. (2000)
Bioinorganic motifs: towards functional classification of metalloproteins.
Bioinformatics 16(10): 851-864.
abstract full-text PDF

Menne K.M.L., Hermjakob H., Apweiler R. (2000)
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinformatics 16(8): 741-742.
abstract full-text PDF

Moller S., Kriventseva E.V., Apweiler R. (2000)
A collection of well characterised integral membrane proteins.
Bioinformatics 16(12): 1159-1160.
abstract full-text PDF

Rubin G.M., Yandell M.D., Wortman J.R., Miklos G.L.G., Nelson C.R., Hariharan I.K., Fortini M.E., Li P.W, Apweiler R., Fleischmann W., Cherry J.M., Henikoff S., Skupski M.P., Misra S., Ashburner M., Birney E., Boguski M.S., Brody T., Brokstein P., Celniker S.E., Chervitz S.A,. Coates D., Cravchik A., Gabrielian A., Galle R.F., Gelbart W.M., George R.A., Goldstein L.S.B., Gong F., Guan P., Harris N.L., Hay B.A., Hoskins R.A., Li J., Li Z., Hynes R.O., Jones S.J.M., Kuehl P.M., Lemaitre B., Littleton J.T., Morrison D.K., Mungall C., O'Farrell P.H., Pickeral O.K., Shue C., Vosshall L.B., Zhang J., Zhao Q., Zheng X.H., Zhong F., Zhong W., Gibbs R., Venter J.G., Adams M.D., Lewis S. (2000)
Comparative Genomics of the Eukaryotes.
Science 287: 2204-2215 (2000).
full-text HTML full-text PDF

Zdobnov E., Lopez R., Apweiler R., Etzold T. (2000)
The EBI SRS server- recent developments.
In: Proceedings of the German Conference on Bioinformatics (GCB'00), Bornberg-Bauer E., Rost U., Stoye J., Vingron M. (eds.), pp. 139-147, Logos Verlag, Berlin, Germany (2000).
full-text PDF

Apweiler R. (1999)
Introduction to Molecular Biology Databases.
In: The EBI Online Manual on Molecular Biology Databases, Apweiler R., Lopez R., Marx B. (1999).
word doc full-text HTML

Lopez, R., Stoesser, G., and Harper, H. (1999)
Vector Sequence contamination in the public sequence databases.
EMBNET NEWS 5(3).
full-text HTML

Marx B. (1999)
Introduction to Database Modeling in Bioinformatics.
In: The EBI Online Manual on Molecular Biology Databases, Apweiler R., Lopez R., Marx B. (1999).
word doc full-text HTML

White J.A., Apweiler R., Blake J.A., Eppig J.T., Maltais L.J., Povey S. (1999)
Report of the Second International Nomenclature Workshop.
Genomics 62: 320-323.
abstract full-text PDF

Sterk, P., and Beck, S. (1998)
Monitoring the Progress of Major Genome Sequencing Projects: The Genome MOT
The Bioinformer 3 (1998).
full-text HTML

Sterk, P., and Beck, S. (1998)
Genome-Scale DNA sequencing where are we?
Current Opinion in Biotechnology 9: 116-121.


Junker V., Apweiler R. (1996)
Introduction: Internet resources for biologists.
In: Perspectives on Protein Engineering 3, CD-ROM edition, Geisow M.J. (eds.), BIODIGM Ltd, Nottingham, UK (1996)


Emmert D.B., Stoehr P.J., Stoesser G., Cameron G.N. (1994)
The European Bioinformatics Institute (EBI) databases.
Nucleic Acids Research 26(1): 3445-3449.
abstract

N.B. ** denotes equal contribution.



Top


spacer
spacer