| Year |
Citation |
Score |
| 2022 |
Cantelli G, Bateman A, Brooksbank C, Petrov AI, Malik-Sheriff RS, Ide-Smith M, Hermjakob H, Flicek P, Apweiler R, Birney E, McEntyre J. The European Bioinformatics Institute (EMBL-EBI) in 2021. Nucleic Acids Research. 50: D11-D19. PMID 34850134 DOI: 10.1093/nar/gkab1127 |
0.313 |
|
| 2019 |
Cook CE, Stroe O, Cochrane G, Birney E, Apweiler R. The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. Nucleic Acids Research. PMID 31701143 DOI: 10.1093/Nar/Gkz1033 |
0.428 |
|
| 2019 |
Pruess M, Apweiler R. Bioinformatics Resources for In Silico Proteome Analysis. Journal of Biomedicine & Biotechnology. 2003: 231-236. PMID 14615630 DOI: 10.1155/S1110724303209219 |
0.431 |
|
| 2019 |
Pruess M, Apweiler R. Bioinformatics Resources for In Silico Proteome Analysis. Journal of Biomedicine & Biotechnology. 2003: 231-236. PMID 14615630 DOI: 10.1155/S1110724303209219 |
0.431 |
|
| 2018 |
Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. The European Bioinformatics Institute in 2018: tools, infrastructure and training. Nucleic Acids Research. PMID 30445657 DOI: 10.1093/Nar/Gky1124 |
0.443 |
|
| 2018 |
Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, et al. Whither systems medicine? Experimental & Molecular Medicine. 50: e453. PMID 29497170 DOI: 10.1038/Emm.2017.290 |
0.346 |
|
| 2017 |
Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E. The European Bioinformatics Institute in 2017: data coordination and integration. Nucleic Acids Research. PMID 29186510 DOI: 10.1093/Nar/Gkx1154 |
0.444 |
|
| 2016 |
Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. Identifying ELIXIR Core Data Resources. F1000research. 5. PMID 27803796 DOI: 10.12688/F1000Research.9656.1 |
0.379 |
|
| 2015 |
Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R. The European Bioinformatics Institute in 2016: Data growth and integration. Nucleic Acids Research. PMID 26673705 DOI: 10.1093/Nar/Gkv1352 |
0.393 |
|
| 2014 |
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, et al. Representing kidney development using the gene ontology. Plos One. 9: e99864. PMID 24941002 DOI: 10.1371/Journal.Pone.0099864 |
0.307 |
|
| 2014 |
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, ... ... Apweiler R, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology. 32: 223-6. PMID 24727771 DOI: 10.1038/Nbt.2839 |
0.409 |
|
| 2014 |
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. The European Bioinformatics Institute's data resources 2014. Nucleic Acids Research. 42: D18-25. PMID 24271396 DOI: 10.1093/nar/gkt1206 |
0.392 |
|
| 2014 |
Apweiler R, Bateman A, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Alpi E, Antunes R, Arganiska J, Casanova EB, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, et al. Activities at the Universal Protein Resource (UniProt) Nucleic Acids Research. 42: D191-D198. PMID 24253303 DOI: 10.1093/Nar/Gkt1140 |
0.489 |
|
| 2013 |
Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, ... ... Apweiler R, et al. Integration of cardiac proteome biology and medicine by a specialized knowledgebase. Circulation Research. 113: 1043-53. PMID 23965338 DOI: 10.1161/Circresaha.113.301151 |
0.459 |
|
| 2013 |
Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, VizcaÃno JA. LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. Plos One. 8: e61951. PMID 23667450 DOI: 10.1371/Journal.Pone.0061951 |
0.404 |
|
| 2013 |
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database : the Journal of Biological Databases and Curation. 2013: bas062. PMID 23327938 DOI: 10.1093/Database/Bas062 |
0.468 |
|
| 2012 |
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, et al. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics. 12: 340-5. PMID 22290800 DOI: 10.1002/Pmic.201290014 |
0.363 |
|
| 2012 |
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, ... ... Apweiler R, et al. The UniProt-GO Annotation database in 2011. Nucleic Acids Research. 40: D565-70. PMID 22123736 DOI: 10.1093/Nar/Gkr1048 |
0.523 |
|
| 2012 |
Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Lewis SE, Mungall CJ, ... ... Apweiler R, et al. The Gene Ontology: Enhancements for 2011 Nucleic Acids Research. 40: D559-D564. PMID 22102568 DOI: 10.1093/Nar/Gkr1028 |
0.363 |
|
| 2012 |
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research. 40: D306-12. PMID 22096229 DOI: 10.1093/Nar/Gkr948 |
0.507 |
|
| 2011 |
Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. The impact of focused Gene Ontology curation of specific mammalian systems. Plos One. 6: e27541. PMID 22174742 DOI: 10.1371/Journal.Pone.0027541 |
0.457 |
|
| 2011 |
Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA. Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. Proteomics. 11: 4434-8. PMID 21932440 DOI: 10.1002/Pmic.201100363 |
0.455 |
|
| 2011 |
Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, Apweiler R, Martens L. A posteriori quality control for the curation and reuse of public proteomics data. Proteomics. 11: 2182-94. PMID 21538885 DOI: 10.1002/Pmic.201000602 |
0.455 |
|
| 2011 |
O'Donovan C, Apweiler R. A guide to UniProt for protein scientists. Methods in Molecular Biology (Clifton, N.J.). 694: 25-35. PMID 21082425 DOI: 10.1007/978-1-60761-977-2_2 |
0.45 |
|
| 2011 |
Apweiler R, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Antunes R, Barrell D, Bely B, Bingley M, Binns D, Bower L, Browne P, Chan WM, Dimmer E, Eberhardt R, et al. Ongoing and future developments at the Universal Protein Resource Nucleic Acids Research. 39: D214-D219. PMID 21051339 DOI: 10.1093/Nar/Gkq1020 |
0.494 |
|
| 2011 |
Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyl?g T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, et al. "4D Biology for health and disease" workshop report. New Biotechnology. 28: 291-3. PMID 20951846 DOI: 10.1016/J.Nbt.2010.10.003 |
0.398 |
|
| 2010 |
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R. Mining Unique- Substrings from Genomes. Journal of Proteomics & Bioinformatics. 3: 099-103. PMID 29657484 DOI: 10.4172/Jpb.1000127 |
0.366 |
|
| 2010 |
Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K. A large-scale protein-function database. Nature Chemical Biology. 6: 785. PMID 20956966 DOI: 10.1038/Nchembio.460 |
0.444 |
|
| 2010 |
Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. The Renal Gene Ontology Annotation Initiative. Organogenesis. 6: 71-5. PMID 20885853 DOI: 10.4161/Org.6.2.11294 |
0.342 |
|
| 2010 |
Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF, Dakna M, Dihazi H, et al. Recommendations for biomarker identification and qualification in clinical proteomics. Science Translational Medicine. 2: 46ps42. PMID 20739680 DOI: 10.1126/Scitranslmed.3001249 |
0.333 |
|
| 2010 |
Freitas AA, Wieser DC, Apweiler R. On the importance of comprehensible classification models for protein function prediction. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 172-82. PMID 20150679 DOI: 10.1109/Tcbb.2008.47 |
0.39 |
|
| 2009 |
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R. QuickGO: a user tutorial for the web-based Gene Ontology browser. Database : the Journal of Biological Databases and Curation. 2009: bap010. PMID 20157483 DOI: 10.1093/Database/Bap010 |
0.406 |
|
| 2009 |
Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, et al. Systematic comparison of the human saliva and plasma proteomes. Proteomics. Clinical Applications. 3: 116-134. PMID 19898684 DOI: 10.1002/Prca.200800140 |
0.408 |
|
| 2009 |
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics (Oxford, England). 25: 3045-6. PMID 19744993 DOI: 10.1093/Bioinformatics/Btp536 |
0.4 |
|
| 2009 |
Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, et al. Prepublication data sharing. Nature. 461: 168-70. PMID 19741685 DOI: 10.1038/461168A |
0.395 |
|
| 2009 |
Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR. Finding one's way in proteomics: a protein species nomenclature. Chemistry Central Journal. 3: 11. PMID 19740416 DOI: 10.1186/1752-153X-3-11 |
0.383 |
|
| 2009 |
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, et al. Approaching clinical proteomics: current state and future fields of application in cellular proteomics. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 75: 816-32. PMID 19739086 DOI: 10.1002/Cyto.A.20779 |
0.376 |
|
| 2009 |
Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece. Proteomics. 9: 3626-9. PMID 19639582 DOI: 10.1002/Pmic.200900205 |
0.432 |
|
| 2009 |
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, ... ... Apweiler R, et al. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9: 3928-33. PMID 19637238 DOI: 10.1002/Pmic.200900247 |
0.436 |
|
| 2009 |
Furnham N, Garavelli JS, Apweiler R, Thornton JM. Missing in action: enzyme functional annotations in biological databases. Nature Chemical Biology. 5: 521-5. PMID 19620987 DOI: 10.1038/Nchembio0809-521 |
0.4 |
|
| 2009 |
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (Oxford, England). 25: 2865-71. PMID 19561018 DOI: 10.1093/Bioinformatics/Btp394 |
0.36 |
|
| 2009 |
Martens L, Apweiler R. Algorithms and databases. Methods in Molecular Biology (Clifton, N.J.). 564: 245-59. PMID 19544027 DOI: 10.1007/978-1-60761-157-8_14 |
0.423 |
|
| 2009 |
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, et al. Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clinical Chemistry and Laboratory Medicine : Cclm / Fescc. 47: 724-44. PMID 19527139 DOI: 10.1515/Cclm.2009.167 |
0.353 |
|
| 2009 |
Ilsley GR, Luscombe NM, Apweiler R. Know your limits: assumptions, constraints and interpretation in systems biology. Biochimica Et Biophysica Acta. 1794: 1280-7. PMID 19439202 DOI: 10.1016/J.Bbapap.2009.05.002 |
0.352 |
|
| 2009 |
Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, ... ... Apweiler R, et al. Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. Journal of Proteome Research. 8: 3689-92. PMID 19344107 DOI: 10.1021/Pr900023Z |
0.405 |
|
| 2009 |
Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands. Proteomics. 9: 218-22. PMID 19105180 DOI: 10.1002/Pmic.200800732 |
0.407 |
|
| 2009 |
Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, ... ... Apweiler R, et al. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics. 93: 213-20. PMID 19059335 DOI: 10.1016/J.Ygeno.2008.11.003 |
0.397 |
|
| 2009 |
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Research. 37: D396-403. PMID 18957448 DOI: 10.1093/Nar/Gkn803 |
0.442 |
|
| 2009 |
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, et al. InterPro: the integrative protein signature database. Nucleic Acids Research. 37: D211-5. PMID 18940856 DOI: 10.1093/Nar/Gkn785 |
0.496 |
|
| 2009 |
Huntley R, Dimmer E, Barrell D, Binns D, Apweiler R. The Gene Ontology Annotation (GOA) Database Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3154.1 |
0.354 |
|
| 2008 |
Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, et al. MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biology. 9: S5. PMID 18834496 DOI: 10.1186/Gb-2008-9-S2-S5 |
0.477 |
|
| 2008 |
Eisenacher M, Hardt T, Martens L, Häkkinen J, Apweiler R, Hamacher M, Meyer HE, Stephan C. Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain. Proteomics. 8: 4163-7. PMID 18814333 DOI: 10.1002/Pmic.200800515 |
0.439 |
|
| 2008 |
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R. Building a biological space based on protein sequence similarities and biological ontologies. Combinatorial Chemistry & High Throughput Screening. 11: 653-60. PMID 18795884 DOI: 10.2174/138620708785739925 |
0.475 |
|
| 2008 |
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. 26: 889-96. PMID 18688244 DOI: 10.1038/Nbt.1411 |
0.313 |
|
| 2008 |
Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H. The speciation of the proteome. Chemistry Central Journal. 2: 16. PMID 18638390 DOI: 10.1186/1752-153X-2-16 |
0.395 |
|
| 2008 |
Lovering RC, Dimmer E, Khodiyar VK, Barrell DG, Scambler P, Hubank M, Apweiler R, Talmud PJ. Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics. 8: 1950-3. PMID 18491309 DOI: 10.1002/Pmic.200800078 |
0.341 |
|
| 2008 |
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Research. 36: W372-6. PMID 18467421 DOI: 10.1093/Nar/Gkn252 |
0.386 |
|
| 2008 |
Mulder NJ, Apweiler R. The InterPro database and tools for protein domain analysis. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 2.7. PMID 18428686 DOI: 10.1002/0471250953.Bi0207S21 |
0.443 |
|
| 2008 |
Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R. UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics (Oxford, England). 24: 1321-2. PMID 18390879 DOI: 10.1093/Bioinformatics/Btn122 |
0.47 |
|
| 2008 |
Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P. Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics. 8: 1564-75. PMID 18348319 DOI: 10.1002/Pmic.200700851 |
0.335 |
|
| 2008 |
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea. Proteomics. 8: 1326-30. PMID 18318011 DOI: 10.1002/Pmic.200701098 |
0.423 |
|
| 2008 |
Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L. Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics. 8: 1138-48. PMID 18283668 DOI: 10.1002/Pmic.200700761 |
0.382 |
|
| 2008 |
Mulder NJ, Kersey P, Pruess M, Apweiler R. In silico characterization of proteins: UniProt, InterPro and Integr8. Molecular Biotechnology. 38: 165-77. PMID 18219596 DOI: 10.1007/S12033-007-9003-X |
0.529 |
|
| 2008 |
Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, ... ... Apweiler R, et al. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research. 36: D1028-33. PMID 18089549 DOI: 10.1093/Nar/Gkm978 |
0.45 |
|
| 2008 |
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H. Analyzing large-scale proteomics projects with latent semantic indexing. Journal of Proteome Research. 7: 182-91. PMID 18047271 DOI: 10.1021/Pr070461K |
0.437 |
|
| 2008 |
Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, ... ... Apweiler R, et al. Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Research. 36: D5-12. PMID 18039715 DOI: 10.1093/Nar/Gkm1018 |
0.443 |
|
| 2008 |
Harris MA, Deegan JI, Ireland A, Lomax J, Ashburner M, Tweedie S, Carbon S, Lewis S, Mungall C, Day-Richter J, Eilbeck K, Blake JA, Bult C, Diehl AD, Dolan M, ... ... Apweiler R, et al. The Gene Ontology project in 2008 Nucleic Acids Research. 36. PMID 17984083 DOI: 10.1093/Nar/Gkm883 |
0.402 |
|
| 2008 |
Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC. The Gene Ontology ! Providing a Functional Role in Proteomic Studies Proteomics. 8. DOI: 10.1002/Pmic.200800002 |
0.43 |
|
| 2007 |
Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, et al. Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics. Clinical Applications. 1: 148-56. PMID 21136664 DOI: 10.1002/Prca.200600771 |
0.337 |
|
| 2007 |
Sterk P, Kulikova T, Kersey P, Apweiler R. The EMBL Nucleotide Sequence and Genome Reviews Databases. Methods in Molecular Biology (Clifton, N.J.). 406: 1-21. PMID 18287686 DOI: 10.1007/978-1-59745-535-0_1 |
0.437 |
|
| 2007 |
Mulder N, Apweiler R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods in Molecular Biology (Clifton, N.J.). 396: 59-70. PMID 18025686 DOI: 10.1007/978-1-59745-515-2_5 |
0.511 |
|
| 2007 |
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. Bmc Bioinformatics. 8: 401. PMID 17945017 DOI: 10.1186/1471-2105-8-401 |
0.456 |
|
| 2007 |
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, ... ... Apweiler R, et al. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. Bmc Biology. 5: 44. PMID 17925023 DOI: 10.1186/1741-7007-5-44 |
0.393 |
|
| 2007 |
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/Nbt1347 |
0.458 |
|
| 2007 |
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, ... ... Apweiler R, et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotechnology. 25: 894-8. PMID 17687370 DOI: 10.1038/Nbt1324 |
0.362 |
|
| 2007 |
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/Nbt1329 |
0.447 |
|
| 2007 |
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France. Proteomics. 7: 3034-7. PMID 17683037 DOI: 10.1002/Pmic.200700554 |
0.401 |
|
| 2007 |
Hamacher M, Stephan C, Eisenacher M, Lewczuk P, Wiltfang J, Martens L, Vizcaíno JA, Kwon KH, Yoo JS, Park YM, Beckers J, Horsch M, de Angelis MH, Cho ZH, Apweiler R, et al. High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK. Proteomics. 7: 2490-6. PMID 17610211 DOI: 10.1002/Pmic.200700449 |
0.347 |
|
| 2007 |
Mueller M, Martens L, Apweiler R. Annotating the human proteome: beyond establishing a parts list. Biochimica Et Biophysica Acta. 1774: 175-91. PMID 17223395 DOI: 10.1016/J.Bbapap.2006.11.011 |
0.516 |
|
| 2007 |
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, et al. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research. 17: 175-83. PMID 17210932 DOI: 10.1101/Gr.5509507 |
0.436 |
|
| 2007 |
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, et al. New developments in the InterPro database. Nucleic Acids Research. 35: D224-8. PMID 17202162 DOI: 10.1093/Nar/Gkl841 |
0.494 |
|
| 2007 |
Orchard S, Jones P, Taylor C, Zhu W, Julian RK, Hermjakob H, Apweiler R. Proteomic data exchange and storage: the need for common standards and public repositories. Methods in Molecular Biology (Clifton, N.J.). 367: 261-70. PMID 17185781 DOI: 10.1385/1-59745-275-0:261 |
0.468 |
|
| 2007 |
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, ... ... Apweiler R, et al. EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Research. 35: D16-20. PMID 17148479 DOI: 10.1093/Nar/Gkl913 |
0.492 |
|
| 2007 |
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, ... ... Apweiler R, et al. IntAct--open source resource for molecular interaction data. Nucleic Acids Research. 35: D561-5. PMID 17145710 DOI: 10.1093/Nar/Gkl958 |
0.441 |
|
| 2006 |
Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R, Kirsch H, Rebholz-Schuhmann D. GOAnnotator: linking protein GO annotations to evidence text. Journal of Biomedical Discovery and Collaboration. 1: 19. PMID 17181854 DOI: 10.1186/1747-5333-1-19 |
0.465 |
|
| 2006 |
Kersey P, Apweiler R. Linking publication, gene and protein data. Nature Cell Biology. 8: 1183-9. PMID 17060904 DOI: 10.1038/Ncb1495 |
0.422 |
|
| 2006 |
Pruess M, Kersey P, Kulikova T, Apweiler R. Databases and resources for in silico proteome analysis. Methods of Biochemical Analysis. 49: 397-414. PMID 16929689 DOI: 10.1002/0471973165.Ch21 |
0.427 |
|
| 2006 |
Hamacher M, Apweiler R, Arnold G, Becker A, Blüggel M, Carrette O, Colvis C, Dunn MJ, Fröhlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Ji J, Kretzschmar H, et al. HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics. 6: 4890-8. PMID 16927433 DOI: 10.1002/Pmic.200600295 |
0.387 |
|
| 2006 |
Stephan C, Reidegeld KA, Hamacher M, van Hall A, Marcus K, Taylor C, Jones P, Müller M, Apweiler R, Martens L, Körting G, Chamrad DC, Thiele H, Blüggel M, Parkinson D, et al. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics. 6: 5015-29. PMID 16927432 DOI: 10.1002/Pmic.200600294 |
0.457 |
|
| 2006 |
Reidegeld KA, Müller M, Stephan C, Blüggel M, Hamacher M, Martens L, Körting G, Chamrad DC, Parkinson D, Apweiler R, Meyer HE, Marcus K. The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. Proteomics. 6: 4997-5014. PMID 16912976 DOI: 10.1002/Pmic.200600305 |
0.376 |
|
| 2006 |
Martens L, Müller M, Stephan C, Hamacher M, Reidegeld KA, Meyer HE, Blüggel M, Vandekerckhove J, Gevaert K, Apweiler R. A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies. Proteomics. 6: 5076-86. PMID 16912975 DOI: 10.1002/Pmic.200600291 |
0.377 |
|
| 2006 |
Mueller M, Martens L, Reidegeld KA, Hamacher M, Stephan C, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Meyer HE, Apweiler R. Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study. Proteomics. 6: 5059-75. PMID 16912974 DOI: 10.1002/Pmic.200600194 |
0.452 |
|
| 2006 |
Chamrad DC, Körting G, Schäfer H, Stephan C, Thiele H, Apweiler R, Meyer HE, Marcus K, Blüggel M. Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data. Proteomics. 6: 5048-58. PMID 16912973 DOI: 10.1002/Pmic.200600189 |
0.37 |
|
| 2006 |
Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R. The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). Omics : a Journal of Integrative Biology. 10: 145-51. PMID 16901219 DOI: 10.1089/Omi.2006.10.145 |
0.385 |
|
| 2006 |
Sterk P, Kersey PJ, Apweiler R. Genome Reviews: standardizing content and representation of information about complete genomes. Omics : a Journal of Integrative Biology. 10: 114-8. PMID 16901215 DOI: 10.1089/Omi.2006.10.114 |
0.375 |
|
| 2006 |
Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M. Evidence standards in experimental and inferential INSDC Third Party Annotation data. Omics : a Journal of Integrative Biology. 10: 105-13. PMID 16901214 DOI: 10.1089/Omi.2006.10.105 |
0.437 |
|
| 2006 |
Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, et al. Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA. Proteomics. 6: 4439-43. PMID 16897683 DOI: 10.1002/Pmic.200600452 |
0.408 |
|
| 2006 |
Whitfield EJ, Pruess M, Apweiler R. Bioinformatics database infrastructure for biotechnology research. Journal of Biotechnology. 124: 629-39. PMID 16757051 DOI: 10.1016/J.Jbiotec.2006.04.006 |
0.526 |
|
| 2006 |
Leinonen R, Nardone F, Zhu W, Apweiler R. UniSave: the UniProtKB sequence/annotation version database. Bioinformatics (Oxford, England). 22: 1284-5. PMID 16551660 DOI: 10.1093/Bioinformatics/Btl105 |
0.418 |
|
| 2006 |
Hamacher M, Stephan C, Blüggel M, Chamrad D, Körting G, Martens L, Müller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R. The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. Proteomics. 6: 1719-21. PMID 16525999 DOI: 10.1002/Pmic.200600069 |
0.347 |
|
| 2006 |
Côté RG, Jones P, Apweiler R, Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. Bmc Bioinformatics. 7: 97. PMID 16507094 DOI: 10.1186/1471-2105-7-97 |
0.415 |
|
| 2006 |
Hermjakob H, Apweiler R. The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Review of Proteomics. 3: 1-3. PMID 16445344 DOI: 10.1586/14789450.3.1.1 |
0.482 |
|
| 2006 |
Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R. Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics. 6: 738-41. PMID 16411267 DOI: 10.1002/Pmic.200500868 |
0.436 |
|
| 2006 |
Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R. PRIDE: a public repository of protein and peptide identifications for the proteomics community Nucleic Acids Research.. 34: D659-663. PMID 16381953 DOI: 10.1093/Nar/Gkj138 |
0.44 |
|
| 2006 |
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research. 34: D187-91. PMID 16381842 DOI: 10.1093/Nar/Gkj161 |
0.516 |
|
| 2006 |
Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, ... ... Apweiler R, et al. EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Research. 34: D10-5. PMID 16381823 DOI: 10.1093/Nar/Gkj130 |
0.506 |
|
| 2006 |
Mulder NJ, Fleischmann W, Kanapin A, Apweiler R. InterPro as a new tool for complete genome analysis: An example of comparative analysis Biophysics. 51: 587-591. DOI: 10.1134/S0006350906040117 |
0.492 |
|
| 2005 |
Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R. Human proteome organisation proteomics standards initiative pre-congress initiative Proteomics. 5: 4651-4652. PMID 16287159 DOI: 10.1002/Pmic.200500727 |
0.466 |
|
| 2005 |
Stephan C, Hamacher M, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schäfer H, Martens L, Jones P, Müller M, Auyeung K, Taylor C, ... ... Apweiler R, et al. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK - Setting the analysis frame Proteomics. 5: 3560-3562. PMID 16167371 DOI: 10.1002/Pmic.200500580 |
0.356 |
|
| 2005 |
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK, Apweiler R. Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005). Proteomics. 5: 3552-5. PMID 16167370 DOI: 10.1002/Pmic.200500626 |
0.435 |
|
| 2005 |
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, ... ... Apweiler R, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/Science.1112014 |
0.336 |
|
| 2005 |
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5: 3226-45. PMID 16104056 DOI: 10.1002/Pmic.200500358 |
0.405 |
|
| 2005 |
Martens L, Hermjakob H, Jones P, Adamsk M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R. PRIDE: The proteomics identifications database Proteomics. 5: 3537-3545. PMID 16041671 DOI: 10.1002/Pmic.200401303 |
0.515 |
|
| 2005 |
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK, Apweiler R. Second proteomics standards initiative spring workshop. Expert Review of Proteomics. 2: 287-9. PMID 16000075 DOI: 10.1586/14789450.2.3.287 |
0.323 |
|
| 2005 |
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. InterProScan: Protein domains identifier Nucleic Acids Research. 33: W116-W120. PMID 15980438 DOI: 10.1093/Nar/Gki442 |
0.362 |
|
| 2005 |
Lee V, Camon E, Dimmer E, Barrell D, Apweiler R. Who tangos with GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools In Silico Biology. 5: 5-8. PMID 15972001 |
0.303 |
|
| 2005 |
Petryszak R, Kretschmann E, Wieser D, Apweiler R. The predictive power of the CluSTr database. Bioinformatics (Oxford, England). 21: 3604-9. PMID 15961444 DOI: 10.1093/Bioinformatics/Bti542 |
0.426 |
|
| 2005 |
Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA Bmc Bioinformatics. 6. PMID 15960829 DOI: 10.1186/1471-2105-6-S1-S17 |
0.469 |
|
| 2005 |
Jones P, Vinod N, Down T, Hackmann A, Kahari A, Kretschmann E, Quinn A, Wieser D, Hermjakob H, Apweiler R. Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics (Oxford, England). 21: 3198-9. PMID 15905273 DOI: 10.1093/Bioinformatics/Bti506 |
0.388 |
|
| 2005 |
Schneider M, Bairoch A, Wu CH, Apweiler R. Plant protein annotation in the UniProt Knowledgebase. Plant Physiology. 138: 59-66. PMID 15888679 DOI: 10.1104/Pp.104.058933 |
0.431 |
|
| 2005 |
Orchard S, Hermjakob H, Binz PA, Hoogland C, Taylor CF, Zhu W, Julian RK, Apweiler R. Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics. 5: 337-9. PMID 15700244 DOI: 10.1002/Pmic.200401158 |
0.435 |
|
| 2005 |
Orchard S, Hermjakob H, Apweiler R. Annotating the Human Proteome Molecular & Cellular Proteomics. 4: 435-440. PMID 15691850 DOI: 10.1074/Mcp.R500003-Mcp200 |
0.484 |
|
| 2005 |
Apweiler R, Cornish-Bowden A, Hofmeyr JH, Kettner C, Leyh TS, Schomburg D, Tipton K. The importance of uniformity in reporting protein-function data. Trends in Biochemical Sciences. 30: 11-2. PMID 15653320 DOI: 10.1016/J.Tibs.2004.11.002 |
0.477 |
|
| 2005 |
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, ... ... Apweiler R, et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Research. 33: D297-302. PMID 15608201 DOI: 10.1093/Nar/Gki039 |
0.442 |
|
| 2005 |
Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, Bates K, Browne P, van den Broek A, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Gamble J, Diez FG, ... ... Apweiler R, et al. The EMBL Nucleotide Sequence Database. Nucleic Acids Research. 33: D29-33. PMID 15608199 DOI: 10.1093/nar/gki098 |
0.346 |
|
| 2005 |
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, et al. InterPro, progress and status in 2005. Nucleic Acids Research. 33: D201-5. PMID 15608177 DOI: 10.1093/Nar/Gki106 |
0.446 |
|
| 2005 |
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. The Universal Protein Resource (UniProt). Nucleic Acids Research. 33: D154-9. PMID 15608167 DOI: 10.1093/Nar/Gki070 |
0.532 |
|
| 2004 |
Orchard S, Taylor C, Hermjakob H, Zhu W, Julian R, Apweiler R. Current status of proteomic standards development. Expert Review of Proteomics. 1: 179-83. PMID 15966812 DOI: 10.1586/14789450.1.2.179 |
0.454 |
|
| 2004 |
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, et al. A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnology. 22: 1459-66. PMID 15529173 DOI: 10.1038/Nbt1031 |
0.407 |
|
| 2004 |
Martin MJ, O'Donovan C, Apweiler R. Protein sequence database methods. Genetic Engineering. 26: 13-7. PMID 15387290 |
0.312 |
|
| 2004 |
Orchard S, Taylor CF, Hermjakob H, Weimin-Zhu, Julian RK, Apweiler R. Advances in the development of common interchange standards for proteomic data. Proteomics. 4: 2363-5. PMID 15274131 DOI: 10.1002/Pmic.200400884 |
0.426 |
|
| 2004 |
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R. The International Protein Index: an integrated database for proteomics experiments. Proteomics. 4: 1985-8. PMID 15221759 DOI: 10.1002/Pmic.200300721 |
0.521 |
|
| 2004 |
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, ... ... Apweiler R, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. Plos Biology. 2: e162. PMID 15103394 DOI: 10.1371/Journal.Pbio.0020162 |
0.378 |
|
| 2004 |
Leinonen R, Garcia Diez F, Binns D, Fleischmann W, Lopez R, Apweiler R. UniProt archive Bioinformatics. 20: 3236-3237. PMID 15044231 DOI: 10.1093/Bioinformatics/Bth191 |
0.487 |
|
| 2004 |
Apweiler R, Bairoch A, Wu CH. Protein sequence databases. Current Opinion in Chemical Biology. 8: 76-80. PMID 15036160 DOI: 10.1016/J.Cbpa.2003.12.004 |
0.503 |
|
| 2004 |
Orchard S, Hermjakob H, Julian RK, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R. Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics. 4: 490-1. PMID 14760721 DOI: 10.1002/Pmic.200300694 |
0.485 |
|
| 2004 |
Hermjakob H, Montecchi-Palazzi 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, ... ... Apweiler R, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 22: 177-83. PMID 14755292 DOI: 10.1038/Nbt926 |
0.449 |
|
| 2004 |
Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, ... Apweiler R, et al. IntAct: an open source molecular interaction database. Nucleic Acids Research. 32: D452-5. PMID 14681455 DOI: 10.1093/Nar/Gkh052 |
0.408 |
|
| 2004 |
Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R. The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Oncology Nucleic Acids Research. 32: D262-D266. PMID 14681408 DOI: 10.1093/Nar/Gkh021 |
0.517 |
|
| 2004 |
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. UniProt: the Universal Protein knowledgebase. Nucleic Acids Research. 32: D115-9. PMID 14681372 DOI: 10.1093/Nar/Gkh131 |
0.523 |
|
| 2004 |
Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, van den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, ... ... Apweiler R, et al. The EMBL Nucleotide Sequence Database. Nucleic Acids Research. 32: D27-30. PMID 14681351 DOI: 10.1093/nar/gkh120 |
0.394 |
|
| 2004 |
Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, Broek Avd, Cochrane G, Duggan K, Eberhardt RY, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, ... ... Apweiler R, et al. The EMBL Nucleotide Sequence Database Nucleic Acids Research. 25: 21-26. PMID 10592171 DOI: 10.1093/Nar/28.1.19 |
0.449 |
|
| 2004 |
Pruess M, Kersey PJ, Apweiler R. Integrating Genomic and Proteomic Data: The Integr8 Project Journal of Integrative Bioinformatics. 1: 108-115. DOI: 10.1515/Jib-2004-9 |
0.5 |
|
| 2004 |
Orchard S, Hermjakob H, Apweiler R. Proteomics and data standardisation Drug Discovery Today: Biosilico. 2: 91-93. DOI: 10.1016/S1741-8364(04)02405-9 |
0.429 |
|
| 2004 |
Martin MJ, O’Donovan C, Apweiler R. Protein Sequence Database Methods Genetic Engineering. 26: 13-17. DOI: 10.1007/978-0-306-48573-2_2 |
0.482 |
|
| 2004 |
Apweiler R. Protein Information Resource (PIR) Dictionary of Bioinformatics and Computational Biology. DOI: 10.1002/9780471650126.Dob0584.Pub2 |
0.378 |
|
| 2004 |
Apweiler R. Proteome Analysis Database Dictionary of Bioinformatics and Computational Biology. DOI: 10.1002/0471650129.Dob0591 |
0.437 |
|
| 2003 |
Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R. Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative. Comparative and Functional Genomics. 4: 203-6. PMID 18629121 DOI: 10.1002/Cfg.279 |
0.428 |
|
| 2003 |
Camon E, Barrell D, Brooksbank C, Magrane M, Apweiler R. The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro. Comparative and Functional Genomics. 4: 71-4. PMID 18629103 DOI: 10.1002/Cfg.235 |
0.517 |
|
| 2003 |
Orchard S, Kersey P, Hermjakob H, Apweiler R. The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data. Comparative and Functional Genomics. 4: 16-9. PMID 18629102 DOI: 10.1002/Cfg.232 |
0.419 |
|
| 2003 |
Orchard S, Zhu W, Julian RK, Hermjakob H, Apweiler R. Further advances in the development of a data interchange standard for proteomics data. Proteomics. 3: 2065-6. PMID 14625869 DOI: 10.1002/Pmic.200300588 |
0.38 |
|
| 2003 |
Orchard S, Hermjakob H, Apweiler R. The Proteomics Standards Initiative Proteomics. 3: 1374-1376. PMID 12872238 DOI: 10.1002/Pmic.200300496 |
0.474 |
|
| 2003 |
Apweiler R, Martin MJ, O'Donovan C, Pruess M. Managing core resources for genomics and proteomics Pharmacogenomics. 4: 343-350. PMID 12718724 DOI: 10.1517/Phgs.4.3.343.22689 |
0.493 |
|
| 2003 |
Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Research. 13: 662-72. PMID 12654719 DOI: 10.1101/Gr.461403 |
0.489 |
|
| 2003 |
Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Research. 31: 414-7. PMID 12520037 DOI: 10.1093/Nar/Gkg105 |
0.522 |
|
| 2003 |
Kriventseva EV, Servant F, Apweiler R. Improvements to CluSTr: The database of SWISS-PROT + TrEMBL protein clusters Nucleic Acids Research. 31: 388-389. PMID 12520029 DOI: 10.1093/Nar/Gkg035 |
0.448 |
|
| 2003 |
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research. 31: 365-70. PMID 12520024 DOI: 10.1093/Nar/Gkg095 |
0.479 |
|
| 2003 |
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, et al. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research. 31: 315-8. PMID 12520011 DOI: 10.1093/Nar/Gkg046 |
0.487 |
|
| 2003 |
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, et al. The European Bioinformatics Institute's data resources. Nucleic Acids Research. 31: 43-50. PMID 12519944 DOI: 10.1093/nar/gkg066 |
0.37 |
|
| 2003 |
Kersey PJ, Morris L, Hermjakob H, Apweiler R. Integr8: Enhanced Inter-Operability of European Molecular Biology Databases Methods of Information in Medicine. 42: 154-160. DOI: 10.1055/S-0038-1634327 |
0.432 |
|
| 2003 |
Mulder NJ, Apweiler R. UNIT 2.7 The InterPro Database and Tools for Protein Domain Analysis Current Protocols in Human Genetics. DOI: 10.1002/0471250953.Bi0207S02 |
0.442 |
|
| 2002 |
Hermjakob H, Apweiler R. TEMBLOR - Perspectives of EBI Database Services. Comparative and Functional Genomics. 3: 47-50. PMID 18628871 DOI: 10.1002/Cfg.133 |
0.528 |
|
| 2002 |
Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R. Applications of InterPro in protein annotation and genome analysis. Briefings in Bioinformatics. 3: 285-95. PMID 12230037 DOI: 10.1093/Bib/3.3.285 |
0.495 |
|
| 2002 |
O'Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Briefings in Bioinformatics. 3: 275-84. PMID 12230036 DOI: 10.1093/Bib/3.3.275 |
0.49 |
|
| 2002 |
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, et al. InterPro: an integrated documentation resource for protein families, domains and functional sites. Briefings in Bioinformatics. 3: 225-35. PMID 12230031 DOI: 10.1093/Bib/3.3.225 |
0.485 |
|
| 2002 |
Zdobnov EM, Lopez R, Apweiler R, Etzold T. The EBI SRS server-new features. Bioinformatics (Oxford, England). 18: 1149-50. PMID 12176845 DOI: 10.1093/Bioinformatics/18.8.1149 |
0.489 |
|
| 2002 |
Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E. Interactive InterPro-based comparisons of proteins in whole genomes. Bioinformatics (Oxford, England). 18: 374-5. PMID 11847096 DOI: 10.1093/Bioinformatics/18.2.374 |
0.49 |
|
| 2002 |
Zdobnov EM, Lopez R, Apweiler R, Etzold T. The EBI SRS server--recent developments. Bioinformatics (Oxford, England). 18: 368-73. PMID 11847095 DOI: 10.1093/Bioinformatics/18.2.368 |
0.458 |
|
| 2002 |
Mulder NJ, Apweiler R. Tools and resources for identifying protein families, domains and motifs Genome Biology. 3: 2001.1-2001.8. PMID 11806833 DOI: 10.1186/Gb-2001-3-1-Reviews2001 |
0.484 |
|
| 2002 |
Magrane M, Apweiler R. Organisation and standardisation of information in SWISS-PROT and TrEMBL Data Science Journal. 1: 13-18. DOI: 10.2481/Dsj.1.13 |
0.503 |
|
| 2001 |
Möller S, Schroeder M, Apweiler R. Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins Computers and Chemistry. 26: 41-49. PMID 11765850 DOI: 10.1016/S0097-8485(01)00098-5 |
0.368 |
|
| 2001 |
Kretschmann E, Fleischmann W, Apweiler R. Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT Bioinformatics. 17: 920-926. PMID 11673236 DOI: 10.1093/Bioinformatics/17.10.920 |
0.518 |
|
| 2001 |
Zdobnov EM, Apweiler R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (Oxford, England). 17: 847-8. PMID 11590104 DOI: 10.1093/Bioinformatics/17.9.847 |
0.454 |
|
| 2001 |
Apweiler R. Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences. Briefings in Bioinformatics. 2: 9-18. PMID 11465066 DOI: 10.1093/Bib/2.1.9 |
0.488 |
|
| 2001 |
Möller S, Croning MDR, Apweiler R. Evaluation of methods for the prediction of membrane spanning regions Bioinformatics. 17: 646-653. PMID 11448883 DOI: 10.1093/Bioinformatics/17.7.646 |
0.321 |
|
| 2001 |
Biswas M, Kanapin A, Apweiler R. Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL. Journal of Biosciences. 26: 277-284. PMID 11426064 DOI: 10.1007/Bf02703652 |
0.46 |
|
| 2001 |
Kriventseva EV, Biswas M, Apweiler R. Clustering and analysis of protein families. Current Opinion in Structural Biology. 11: 334-339. PMID 11406384 DOI: 10.1016/S0959-440X(00)00211-6 |
0.39 |
|
| 2001 |
O'Donovan C, Apweiler R, Bairoch A. The human proteomics initiative (HPI). Trends in Biotechnology. 19: 178-81. PMID 11301130 DOI: 10.1016/S0167-7799(01)01598-0 |
0.468 |
|
| 2001 |
Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. Nucleic Acids Research. 29: 44-8. PMID 11125045 DOI: 10.1093/Nar/29.1.44 |
0.5 |
|
| 2001 |
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research. 29: 37-40. PMID 11125043 DOI: 10.1093/Nar/29.1.37 |
0.465 |
|
| 2001 |
Kriventseva EV, Fleischmann W, Zdobnov EM, Apweiler R. CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Research. 29: 33-6. PMID 11125042 DOI: 10.1093/Nar/29.1.33 |
0.418 |
|
| 2001 |
Apweiler R, Kersey PJ, Junker V, Bairoch A. Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al. Bioinformatics. 17: 533-534. DOI: 10.1093/Bioinformatics/17.6.533 |
0.391 |
|
| 2000 |
Möller S, Kriventseva EV, Apweiler R. A collection of well characterised integral membrane proteins. Bioinformatics. 16: 1159-1160. PMID 11159338 DOI: 10.1093/Bioinformatics/16.12.1159 |
0.35 |
|
| 2000 |
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, et al. InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics (Oxford, England). 16: 1145-50. PMID 11159333 DOI: 10.1093/Bioinformatics/16.12.1145 |
0.391 |
|
| 2000 |
Kersey P, Hermjakob H, Apweiler R. VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. Bioinformatics (Oxford, England). 16: 1048-9. PMID 11159319 DOI: 10.1093/Bioinformatics/16.11.1048 |
0.405 |
|
| 2000 |
Apweiler R. Protein sequence databases Advances in Protein Chemistry. 54: 31-71. PMID 10829224 DOI: 10.1016/S0065-3233(00)54002-9 |
0.444 |
|
| 2000 |
Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O’Donovan C, Apweiler R. The role SWISS-PROT and TrEMBL play in the genome research environment. Journal of Biotechnology. 78: 221-234. PMID 10751683 DOI: 10.1016/S0168-1656(00)00198-X |
0.45 |
|
| 2000 |
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, et al. Comparative genomics of the eukaryotes. Science (New York, N.Y.). 287: 2204-15. PMID 10731134 DOI: 10.1126/Science.287.5461.2204 |
0.419 |
|
| 2000 |
Magrane M, Apweiler R. Mus musculus in the SWISS-PROT database: its relevance to developmental research. Genesis. 26: 1-4. PMID 10660667 DOI: 10.1002/(Sici)1526-968X(200001)26:1<1::Aid-Gene2>3.0.Co;2-F |
0.301 |
|
| 2000 |
Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research. 28: 45-8. PMID 10592178 DOI: 10.1093/Nar/28.1.45 |
0.499 |
|
| 1999 |
Junker VL, Apweiler R, Bairoch A. Representation of functional information in the SWISS-PROT data bank. Bioinformatics (Oxford, England). 15: 1066-7. PMID 10746001 DOI: 10.1093/Bioinformatics/15.12.1066 |
0.316 |
|
| 1999 |
Apweiler R, Hermjakob H, Sharon N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochimica Et Biophysica Acta. 1473: 4-8. PMID 10580125 DOI: 10.1016/S0304-4165(99)00165-8 |
0.372 |
|
| 1999 |
Hermjakob H, Fleischmann W, Apweiler R. Swissknife - 'lazy parsing' of SWISS-PROT entries. Bioinformatics. 15: 771-772. PMID 10498781 DOI: 10.1093/Bioinformatics/15.9.771 |
0.306 |
|
| 1997 |
Bairoch AM, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL Nucleic Acids Research. 25: 31-36. PMID 9016499 DOI: 10.1093/Nar/25.1.31 |
0.471 |
|
| 1996 |
Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL Nucleic Acids Research. 24: 21-25. PMID 8594581 DOI: 10.1093/Nar/24.1.21 |
0.47 |
|
| Show low-probability matches. |
