| Year |
Citation |
Score |
| 2024 |
Ross KE, Bastian FB, Buys M, Cook CE, D'Eustachio P, Harrison M, Hermjakob H, Li D, Lord P, Natale DA, Peters B, Sternberg PW, Su AI, Thakur M, Thomas PD, et al. Perspectives on tracking data reuse across biodata resources. Bioinformatics Advances. 4: vbae057. PMID 38721398 DOI: 10.1093/bioadv/vbae057 |
0.319 |
|
| 2023 |
Simona P, Panneerselvam K, Porras P, Duesbury M, Perfetto L, Licata L, Hermjakob H, Orchard S. The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study. Database : the Journal of Biological Databases and Curation. 2023. PMID 37819683 DOI: 10.1093/database/baad066 |
0.315 |
|
| 2023 |
Deutsch EW, Vizcaíno JA, Jones AR, Binz PA, Lam H, Klein J, Bittremieux W, Perez-Riverol Y, Tabb DL, Walzer M, Ricard-Blum S, Hermjakob H, Neumann S, Mak TD, Kawano S, et al. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of Proteome Research. PMID 36626722 DOI: 10.1021/acs.jproteome.2c00637 |
0.302 |
|
| 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 |
0.314 |
|
| 2021 |
Chen T, Ma J, Liu Y, Chen Z, Xiao N, Lu Y, Fu Y, Yang C, Li M, Wu S, Wang X, Li D, He F, Hermjakob H, Zhu Y. iProX in 2021: connecting proteomics data sharing with big data. Nucleic Acids Research. PMID 34871441 DOI: 10.1093/nar/gkab1081 |
0.381 |
|
| 2021 |
Del Toro N, Shrivastava A, Ragueneau E, Meldal B, Combe C, Barrera E, Perfetto L, How K, Ratan P, Shirodkar G, Lu O, Mészáros B, Watkins X, Pundir S, Licata L, ... ... Hermjakob H, et al. The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Research. PMID 34761267 DOI: 10.1093/nar/gkab1006 |
0.341 |
|
| 2021 |
Langenstein M, Hermjakob H, Llinares MB. A decoupled, modular and scriptable architecture for tools to curate data platforms. Bioinformatics (Oxford, England). PMID 33830216 DOI: 10.1093/bioinformatics/btab233 |
0.351 |
|
| 2020 |
Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, et al. Towards a unified open access dataset of molecular interactions. Nature Communications. 11: 6144. PMID 33262342 DOI: 10.1038/s41467-020-19942-z |
0.384 |
|
| 2020 |
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics : McP. PMID 32907876 DOI: 10.1074/Mcp.Tir120.002155 |
0.398 |
|
| 2020 |
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, ... ... Hermjakob H, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110. PMID 32845085 DOI: 10.15252/Msb.20199110 |
0.333 |
|
| 2020 |
Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, et al. The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics (Oxford, England). PMID 32637990 DOI: 10.1093/Bioinformatics/Btaa622 |
0.328 |
|
| 2020 |
Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, et al. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Journal of Integrative Bioinformatics. PMID 32598315 DOI: 10.1515/Jib-2020-0005 |
0.385 |
|
| 2020 |
Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 1-12. PMID 32486891 DOI: 10.1080/15548627.2020.1761659 |
0.381 |
|
| 2020 |
Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning BA, Hermjakob H, Perez-Riverol Y. The omics discovery REST interface. Nucleic Acids Research. PMID 32374843 DOI: 10.1093/Nar/Gkaa326 |
0.463 |
|
| 2020 |
Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, et al. Wikidata as a knowledge graph for the life sciences. Elife. 9. PMID 32180547 DOI: 10.7554/Elife.52614 |
0.351 |
|
| 2019 |
Viteri G, Matthews L, Varusai T, Gillespie M, Milacic M, Cook J, Weiser J, Shorser S, Sidiropoulos K, Fabregat A, Haw R, Wu G, Stein L, D'Eustachio P, Hermjakob H. Reactome and ORCID-fine-grained credit attribution for community curation. Database : the Journal of Biological Databases and Curation. 2019. PMID 31802127 DOI: 10.1093/Database/Baz123 |
0.409 |
|
| 2019 |
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, ... ... Hermjakob H, et al. BioModels-15 years of sharing computational models in life science. Nucleic Acids Research. PMID 31701150 DOI: 10.1093/Nar/Gkz1055 |
0.322 |
|
| 2019 |
Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, ... ... Hermjakob H, et al. The reactome pathway knowledgebase. Nucleic Acids Research. PMID 31691815 DOI: 10.1093/nar/gkz1031 |
0.3 |
|
| 2019 |
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, ... Hermjakob H, et al. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Research. PMID 31686107 DOI: 10.1093/Nar/Gkz984 |
0.473 |
|
| 2019 |
You K, Huang Q, Yu C, Shen B, Sevilla C, Shi M, Hermjakob H, Chen Y, Li T. PhaSepDB: a database of liquid-liquid phase separation related proteins. Nucleic Acids Research. PMID 31584089 DOI: 10.1093/Nar/Gkz847 |
0.341 |
|
| 2019 |
Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, et al. HENA, heterogeneous network-based data set for Alzheimer's disease. Scientific Data. 6: 151. PMID 31413325 DOI: 10.1038/S41597-019-0152-0 |
0.359 |
|
| 2019 |
Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H. Quantifying the impact of public omics data. Nature Communications. 10: 3512. PMID 31383865 DOI: 10.1038/S41467-019-11461-W |
0.451 |
|
| 2019 |
Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M. PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. Gigascience. 8. PMID 31363752 DOI: 10.1093/Gigascience/Giz088 |
0.342 |
|
| 2019 |
Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. A data citation roadmap for scholarly data repositories. Scientific Data. 6: 28. PMID 30971690 DOI: 10.1038/S41597-019-0031-8 |
0.433 |
|
| 2019 |
Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, et al. Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications. 10: 1098. PMID 30833551 DOI: 10.1038/S41467-019-08814-W |
0.303 |
|
| 2019 |
Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, et al. CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics (Oxford, England). PMID 30793173 DOI: 10.1093/Bioinformatics/Btz132 |
0.355 |
|
| 2019 |
Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, et al. Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications. 10: 10. PMID 30602777 DOI: 10.1038/S41467-018-07709-6 |
0.437 |
|
| 2018 |
Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, et al. A reference set of curated biomedical data and metadata from clinical case reports. Scientific Data. 5: 180258. PMID 30457569 DOI: 10.1038/Sdata.2018.258 |
0.345 |
|
| 2018 |
Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, ... ... Hermjakob H, et al. Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Research. PMID 30357405 DOI: 10.1093/Nar/Gky1001 |
0.384 |
|
| 2018 |
Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y. iProX: an integrated proteome resource. Nucleic Acids Research. PMID 30252093 DOI: 10.1093/Nar/Gky869 |
0.511 |
|
| 2018 |
Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Uniform resolution of compact identifiers for biomedical data. Scientific Data. 5: 180029. PMID 29737976 DOI: 10.1038/Sdata.2018.29 |
0.425 |
|
| 2018 |
Ping P, Hermjakob H, Polson JS, Benos PV, Wang W. Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. Circulation Research. 122: 1290-1301. PMID 29700073 DOI: 10.1161/Circresaha.117.310967 |
0.357 |
|
| 2018 |
Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, et al. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. Bmc Bioinformatics. 19: 134. PMID 29642841 DOI: 10.1186/S12859-018-2118-1 |
0.444 |
|
| 2018 |
Jupe S, Ray K, Duenas Roca C, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H. Interleukins and their signaling pathways in the Reactome biological pathway database. The Journal of Allergy and Clinical Immunology. PMID 29378288 DOI: 10.1016/J.Jaci.2017.12.992 |
0.353 |
|
| 2018 |
Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H. Reactome graph database: Efficient access to complex pathway data. Plos Computational Biology. 14: e1005968. PMID 29377902 DOI: 10.1371/Journal.Pcbi.1005968 |
0.419 |
|
| 2018 |
Lau E, Cao Q, Lam MPY, Wang J, Ng DCM, Bleakley BJ, Lee JM, Liem DA, Wang D, Hermjakob H, Ping P. Integrated omics dissection of proteome dynamics during cardiac remodeling. Nature Communications. 9: 120. PMID 29317621 DOI: 10.1038/S41467-017-02467-3 |
0.369 |
|
| 2018 |
Bai M, He M, Sun Q, Liao H, Shu K, Hermjakob H. A pipeline for identifying endogenous neuropeptides from spectral archives International Journal of Data Mining and Bioinformatics. 20: 12-35. DOI: 10.1504/Ijdmb.2018.10013377 |
0.313 |
|
| 2017 |
Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H. Reactome diagram viewer: Data structures and strategies to boost performance. Bioinformatics (Oxford, England). PMID 29186351 DOI: 10.1093/Bioinformatics/Btx752 |
0.401 |
|
| 2017 |
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, ... ... Hermjakob H, et al. The Reactome Pathway Knowledgebase. Nucleic Acids Research. PMID 29145629 DOI: 10.1093/nar/gkx1132 |
0.317 |
|
| 2017 |
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, ... ... Hermjakob H, et al. BioModels: expanding horizons to include more modelling approaches and formats. Nucleic Acids Research. PMID 29106614 DOI: 10.1093/Nar/Gkx1023 |
0.329 |
|
| 2017 |
Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, ... ... Hermjakob H, et al. Reactome enhanced pathway visualization. Bioinformatics (Oxford, England). 33: 3461-3467. PMID 29077811 DOI: 10.1093/Bioinformatics/Btx441 |
0.349 |
|
| 2017 |
Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J. ComplexViewer: visualization of curated macromolecular complexes. Bioinformatics. 33: 3673-3675. PMID 29036573 DOI: 10.1093/Bioinformatics/Btx497 |
0.359 |
|
| 2017 |
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, et al. The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. Journal of Proteome Research. PMID 28849660 DOI: 10.1021/Acs.Jproteome.7B00370 |
0.405 |
|
| 2017 |
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, ... Hermjakob H, et al. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. Plos Biology. 15: e2001414. PMID 28662064 DOI: 10.1371/Journal.Pbio.2001414 |
0.449 |
|
| 2017 |
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, ... ... Hermjakob H, et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nature Biotechnology. 35: 406-409. PMID 28486464 DOI: 10.1038/Nbt.3790 |
0.392 |
|
| 2017 |
Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach. Bmc Bioinformatics. 18: 142. PMID 28249561 DOI: 10.1186/S12859-017-1559-2 |
0.366 |
|
| 2016 |
Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P. Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome. Handbook of Experimental Pharmacology. PMID 27995389 DOI: 10.1007/164_2016_93 |
0.304 |
|
| 2016 |
Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D, Yu X. AAgAtlas 1.0: a human autoantigen database. Nucleic Acids Research. PMID 27924021 DOI: 10.1093/Nar/Gkw946 |
0.367 |
|
| 2016 |
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, ... Hermjakob H, et al. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Research. PMID 27924013 DOI: 10.1093/Nar/Gkw936 |
0.482 |
|
| 2016 |
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, ... ... Hermjakob H, et al. Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Research. PMID 27899665 DOI: 10.1093/Nar/Gkw1055 |
0.309 |
|
| 2016 |
Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics. PMID 27498275 DOI: 10.1016/J.Jprot.2016.08.002 |
0.386 |
|
| 2016 |
Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nature Methods. 13: 651-656. PMID 27493588 DOI: 10.1038/Nmeth.3902 |
0.315 |
|
| 2016 |
Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. Journal of Proteome Research. 15: 3961-3970. PMID 27490519 DOI: 10.1021/Acs.Jproteome.6B00392 |
0.483 |
|
| 2016 |
Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M. Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database : the Journal of Biological Databases and Curation. 2016. PMID 27270715 DOI: 10.1093/Database/Baw088 |
0.354 |
|
| 2016 |
Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y. Accurate estimation of Isoelectric Point of Protein and Peptide based on Amino Acid Sequences Bioinformatics. 32: 821-827. PMID 26568629 DOI: 10.1093/Bioinformatics/Btv674 |
0.392 |
|
| 2016 |
Perez-Riverol Y, Xu Q, Uszkoreit J, Griss J, Hermjakob H, Wang R, Vizcaíno JA. PRIDE Inspector Toolsuite: Moving towards a quality assessment tool for proteomics data standards and ProteomeXchange repositories F1000research. 5. DOI: 10.7490/F1000Research.1113064.1 |
0.374 |
|
| 2015 |
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C. The evolution of standards and data management practices in systems biology. Molecular Systems Biology. 11: 851. PMID 26700851 DOI: 10.15252/Msb.20156053 |
0.416 |
|
| 2015 |
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, ... ... Hermjakob H, et al. The Reactome pathway Knowledgebase. Nucleic Acids Research. PMID 26656494 DOI: 10.1093/Nar/Gkv1351 |
0.445 |
|
| 2015 |
Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Testing and validation of computational methods for mass spectrometry. Journal of Proteome Research. PMID 26549429 DOI: 10.1021/Acs.Jproteome.5B00852 |
0.375 |
|
| 2015 |
Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaino JA. PRIDE Inspector Toolsuite: moving towards a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets. Molecular & Cellular Proteomics : McP. PMID 26545397 DOI: 10.1074/Mcp.O115.050229 |
0.49 |
|
| 2015 |
Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and its related tools. Nucleic Acids Research. PMID 26527722 DOI: 10.1093/Nar/Gkv1145 |
0.539 |
|
| 2015 |
Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. Bioinformatics (Oxford, England). PMID 25910694 DOI: 10.1093/Bioinformatics/Btv250 |
0.492 |
|
| 2015 |
Reisinger F, Del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA. Introducing the PRIDE Archive RESTful web services. Nucleic Acids Research. 43: W599-604. PMID 25904633 DOI: 10.1093/Nar/Gkv382 |
0.444 |
|
| 2015 |
Vizcaíno JA, Barsnes H, Hermjakob H. Proteomics data visualisation. Proteomics. 15: 1339-40. PMID 25854789 DOI: 10.1002/Pmic.201570063 |
0.452 |
|
| 2015 |
Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR, Lindsey ML, Ping P. Harnessing the heart of big data. Circulation Research. 116: 1115-9. PMID 25814682 DOI: 10.1161/Circresaha.115.306013 |
0.427 |
|
| 2015 |
Orchard S, Hermjakob H. Shared resources, shared costs--leveraging biocuration resources. Database : the Journal of Biological Databases and Curation. 2015. PMID 25776020 DOI: 10.1093/Database/Bav009 |
0.431 |
|
| 2015 |
Jupe S, Fabregat A, Hermjakob H. Expression data analysis with reactome. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 49: 8.20.1-9. PMID 25754994 DOI: 10.1002/0471250953.Bi0820S49 |
0.35 |
|
| 2015 |
Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H. Development of data representation standards by the human proteome organization proteomics standards initiative. Journal of the American Medical Informatics Association : Jamia. 22: 495-506. PMID 25726569 DOI: 10.1093/Jamia/Ocv001 |
0.513 |
|
| 2015 |
Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H. Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database : the Journal of Biological Databases and Curation. 2015. PMID 25652942 DOI: 10.1093/Database/Bau131 |
0.387 |
|
| 2015 |
Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H. A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. Proteomics. 15: 1390-404. PMID 25648416 DOI: 10.1002/Pmic.201400390 |
0.444 |
|
| 2015 |
Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. SPARQL-enabled identifier conversion with Identifiers.org. Bioinformatics (Oxford, England). 31: 1875-7. PMID 25638809 DOI: 10.1093/Bioinformatics/Btv064 |
0.411 |
|
| 2015 |
Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA. A public repository for mass spectrometry imaging data. Analytical and Bioanalytical Chemistry. 407: 2027-33. PMID 25542566 DOI: 10.1007/S00216-014-8357-8 |
0.421 |
|
| 2015 |
Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA. Open source libraries and frameworks for biological data visualisation: a guide for developers. Proteomics. 15: 1356-74. PMID 25475079 DOI: 10.1002/Pmic.201400377 |
0.467 |
|
| 2015 |
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, ... ... Hermjakob H, et al. BioModels: ten-year anniversary. Nucleic Acids Research. 43: D542-8. PMID 25414348 DOI: 10.1093/Nar/Gku1181 |
0.374 |
|
| 2015 |
Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA. Identifying novel biomarkers through data mining-a realistic scenario? Proteomics. Clinical Applications. 9: 437-43. PMID 25347964 DOI: 10.1002/Prca.201400107 |
0.428 |
|
| 2015 |
Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, ... ... Hermjakob H, et al. The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Research. 43: D479-84. PMID 25313161 DOI: 10.1093/Nar/Gku975 |
0.389 |
|
| 2015 |
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics. 15: 930-49. PMID 25158685 DOI: 10.1002/Pmic.201400302 |
0.529 |
|
| 2015 |
Lovering RC, Rodriguez-Lopez M, Campbell NH, Huntley RP, Sawford T, O’Donovan C, Orchard S, Hermjakob H, Martin M, Mayr M, Humphries SE, Talmud PJ. The cardiovascular gene annotation initiative: Impact on data analysis Atherosclerosis. 241. DOI: 10.1016/J.Atherosclerosis.2015.04.135 |
0.343 |
|
| 2014 |
Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H. Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany. Proteomics. 14: 2363-8. PMID 25297050 DOI: 10.1002/Pmic.201470164 |
0.474 |
|
| 2014 |
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C. BioModels linked dataset. Bmc Systems Biology. 8: 91. PMID 25182954 DOI: 10.1186/S12918-014-0091-5 |
0.442 |
|
| 2014 |
Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, ... ... Hermjakob H, et al. BioJS: an open source standard for biological visualisation - its status in 2014. F1000research. 3: 55. PMID 25075290 DOI: 10.12688/F1000Research.3-55.V1 |
0.409 |
|
| 2014 |
Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA. How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics. 14: 2233-41. PMID 25047258 DOI: 10.1002/Pmic.201400120 |
0.399 |
|
| 2014 |
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, ... ... Hermjakob H, et al. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics : McP. 13: 2765-75. PMID 24980485 DOI: 10.1074/Mcp.O113.036681 |
0.458 |
|
| 2014 |
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, ... ... Hermjakob H, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics : McP. 13: 1905-13. PMID 24760958 DOI: 10.1074/Mcp.M113.035907 |
0.401 |
|
| 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, ... ... Hermjakob H, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology. 32: 223-6. PMID 24727771 DOI: 10.1038/Nbt.2839 |
0.433 |
|
| 2014 |
Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA. jmzTab: a java interface to the mzTab data standard. Proteomics. 14: 1328-32. PMID 24659499 DOI: 10.1002/Pmic.201300560 |
0.441 |
|
| 2014 |
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, ... ... Hermjakob H, et al. The Reactome pathway knowledgebase. Nucleic Acids Research. 42: D472-7. PMID 24243840 DOI: 10.1093/nar/gkt1102 |
0.338 |
|
| 2014 |
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, ... ... Hermjakob H, et al. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Research. 42: D358-63. PMID 24234451 DOI: 10.1093/Nar/Gkt1115 |
0.492 |
|
| 2014 |
Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochimica Et Biophysica Acta. 1844: 63-76. PMID 23467006 DOI: 10.1016/J.Bbapap.2013.02.032 |
0.453 |
|
| 2014 |
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, VizcaÃno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochimica Et Biophysica Acta. 1844: 98-107. PMID 23429179 DOI: 10.1016/J.Bbapap.2013.02.017 |
0.397 |
|
| 2014 |
Fabregat A, Weiser J, Jupe S, Garapati P, Forner O, Porras P, Haw R, D'Eustachio P, Stein L, Hermjakob H. Pathway Analysis Tool Suite F1000research. 5. DOI: 10.7490/F1000Research.1096786.1 |
0.316 |
|
| 2013 |
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, et al. Path2Models: large-scale generation of computational models from biochemical pathway maps. Bmc Systems Biology. 7: 116. PMID 24180668 DOI: 10.1186/1752-0509-7-116 |
0.376 |
|
| 2013 |
Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H. Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK. Proteomics. 13: 2931-7. PMID 24108681 DOI: 10.1002/Pmic.201370166 |
0.483 |
|
| 2013 |
Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ. Capturing cooperative interactions with the PSI-MI format. Database : the Journal of Biological Databases and Curation. 2013: bat066. PMID 24067240 DOI: 10.1093/Database/Bat066 |
0.404 |
|
| 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, ... ... Hermjakob H, 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 |
0.45 |
|
| 2013 |
Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR. Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Molecular & Cellular Proteomics : McP. 12: 3026-35. PMID 23813117 DOI: 10.1074/Mcp.O113.029777 |
0.45 |
|
| 2013 |
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, et al. iAnn: an event sharing platform for the life sciences. Bioinformatics (Oxford, England). 29: 1919-21. PMID 23742982 DOI: 10.1093/Bioinformatics/Btt306 |
0.35 |
|
| 2013 |
del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H. A new reference implementation of the PSICQUIC web service. Nucleic Acids Research. 41: W601-6. PMID 23671334 DOI: 10.1093/Nar/Gkt392 |
0.428 |
|
| 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 |
0.403 |
|
| 2013 |
Juty N, Le Novère N, Hermjakob H, Laibe C. Towards the collaborative curation of the registry underlying Identifiers.org. Database : the Journal of Biological Databases and Curation. 2013: bat017. PMID 23584831 DOI: 10.1093/Database/Bat017 |
0.422 |
|
| 2013 |
Csordas A, Wang R, RÃos D, Reisinger F, Foster JM, Slotta DJ, VizcaÃno JA, Hermjakob H. From Peptidome to PRIDE: public proteomics data migration at a large scale. Proteomics. 13: 1692-5. PMID 23533138 DOI: 10.1002/Pmic.201200514 |
0.5 |
|
| 2013 |
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, VizcaÃno JA, Hermjakob H, Stephan C, Meyer HE, et al. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database : the Journal of Biological Databases and Curation. 2013: bat009. PMID 23482073 DOI: 10.1093/Database/Bat009 |
0.461 |
|
| 2013 |
Gómez J, GarcÃa LJ, Salazar GA, Villaveces J, Gore S, GarcÃa A, MartÃn MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, et al. BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics (Oxford, England). 29: 1103-4. PMID 23435069 DOI: 10.1093/Bioinformatics/Btt100 |
0.392 |
|
| 2013 |
Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, et al. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. Journal of Proteomics. 87: 134-8. PMID 23376229 DOI: 10.1016/J.Jprot.2013.01.019 |
0.449 |
|
| 2013 |
Griss J, Foster JM, Hermjakob H, VizcaÃno JA. PRIDE Cluster: building a consensus of proteomics data. Nature Methods. 10: 95-6. PMID 23361086 DOI: 10.1038/Nmeth.2343 |
0.412 |
|
| 2013 |
VizcaÃno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, ... ... Hermjakob H, et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Research. 41: D1063-9. PMID 23203882 DOI: 10.1093/Nar/Gks1262 |
0.478 |
|
| 2013 |
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, ... ... Hermjakob H, et al. The EBI enzyme portal. Nucleic Acids Research. 41: D773-80. PMID 23175605 DOI: 10.1093/Nar/Gks1112 |
0.37 |
|
| 2012 |
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L. Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers. 4: 1180-211. PMID 24213504 DOI: 10.3390/Cancers4041180 |
0.32 |
|
| 2012 |
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J. Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. Bmc Bioinformatics. 13: 324. PMID 23216909 DOI: 10.1186/1471-2105-13-324 |
0.373 |
|
| 2012 |
Salazar GA, GarcÃa LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H. MyDas, an extensible Java DAS server. Plos One. 7: e44180. PMID 23028496 DOI: 10.1371/Journal.Pone.0044180 |
0.463 |
|
| 2012 |
Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H. Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics. 12: 2767-72. PMID 22969026 DOI: 10.1002/Pmic.201270126 |
0.485 |
|
| 2012 |
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, ... Hermjakob H, et al. The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Molecular & Cellular Proteomics : McP. 11: 1682-9. PMID 22949509 DOI: 10.1074/Mcp.O112.021543 |
0.418 |
|
| 2012 |
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR. A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. Omics : a Journal of Integrative Biology. 16: 431-42. PMID 22804616 DOI: 10.1089/Omi.2012.0022 |
0.446 |
|
| 2012 |
Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA. Improvements in the Protein Identifier Cross-Reference service. Nucleic Acids Research. 40: W276-80. PMID 22544604 DOI: 10.1093/Nar/Gks338 |
0.406 |
|
| 2012 |
Griss J, Reisinger F, Hermjakob H, Vizcaíno JA. jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics. 12: 795-8. PMID 22539430 DOI: 10.1002/Pmic.201100578 |
0.447 |
|
| 2012 |
Reisinger F, Krishna R, Ghali F, Ríos D, Hermjakob H, Vizcaíno JA, Jones AR. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics. 12: 790-4. PMID 22539429 DOI: 10.1002/Pmic.201100577 |
0.402 |
|
| 2012 |
Lam MP, Vivanco F, Scholten A, Hermjakob H, Van Eyk J, Ping P. HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease. Proteomics. 12: 749-51. PMID 22539426 DOI: 10.1002/Pmic.201270015 |
0.307 |
|
| 2012 |
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Brinkman F, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, ... ... Hermjakob H, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nature Methods. 9: 345-50. PMID 22453911 DOI: 10.1038/Nmeth.1931 |
0.461 |
|
| 2012 |
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H. PRIDE: quality control in a proteomics data repository. Database : the Journal of Biological Databases and Curation. 2012: bas004. PMID 22434838 DOI: 10.1093/Database/Bas004 |
0.456 |
|
| 2012 |
Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyzing protein-protein interaction networks. Journal of Proteome Research. 11: 2014-31. PMID 22385417 DOI: 10.1021/Pr201211W |
0.447 |
|
| 2012 |
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & Cellular Proteomics : McP. 11: M111.014381. PMID 22375074 DOI: 10.1074/Mcp.M111.014381 |
0.489 |
|
| 2012 |
Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nature Biotechnology. 30: 135-7. PMID 22318026 DOI: 10.1038/Nbt.2112 |
0.305 |
|
| 2012 |
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H. From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland. Proteomics. 12: 351-5. PMID 22290802 DOI: 10.1002/Pmic.201290016 |
0.485 |
|
| 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, ... Hermjakob H, et al. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics. 12: 340-5. PMID 22290800 DOI: 10.1002/Pmic.201290014 |
0.369 |
|
| 2012 |
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, ... ... Hermjakob H, et al. Toward interoperable bioscience data. Nature Genetics. 44: 121-6. PMID 22281772 DOI: 10.1038/Ng.1054 |
0.401 |
|
| 2012 |
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, ... ... Hermjakob H, et al. The IntAct molecular interaction database in 2012. Nucleic Acids Research. 40: D841-6. PMID 22121220 DOI: 10.1093/Nar/Gkr1088 |
0.481 |
|
| 2012 |
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. 12: 11-20. PMID 22069307 DOI: 10.1002/Pmic.201100562 |
0.456 |
|
| 2012 |
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Journal of Proteome Research. 11: 1412-9. PMID 22053864 DOI: 10.1021/Pr201071T |
0.457 |
|
| 2012 |
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman F, Cesareni G, Chatr-Aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, ... ... Hermjakob H, et al. Corrigendum: Protein interaction data curation: The International Molecular Exchange (IMEx) consortium (Nature Methods (2012) 9, (345-350)) Nature Methods. 9: 626. DOI: 10.1038/Nmeth0612-626A |
0.391 |
|
| 2011 |
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. Clinical Applications. 5: 580-9. PMID 22213554 DOI: 10.1002/prca.201100097 |
0.352 |
|
| 2011 |
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Molecular & Cellular Proteomics : McP. 10: O111.015446. PMID 22052993 DOI: 10.1074/Mcp.O111.015446 |
0.457 |
|
| 2011 |
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H. Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics. 11: 4284-90. PMID 22045680 DOI: 10.1002/Pmic.201190117 |
0.538 |
|
| 2011 |
Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D. Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database : the Journal of Biological Databases and Curation. 2011: bar047. PMID 22025670 DOI: 10.1093/Database/Bar047 |
0.415 |
|
| 2011 |
Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD. The Reactome BioMart. Database : the Journal of Biological Databases and Curation. 2011: bar031. PMID 22012987 DOI: 10.1093/Database/Bar031 |
0.462 |
|
| 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 |
0.456 |
|
| 2011 |
Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, ... ... Hermjakob H, et al. Minimum information about a bioactive entity (MIABE). Nature Reviews. Drug Discovery. 10: 661-9. PMID 21878981 DOI: 10.1038/Nrd3503 |
0.399 |
|
| 2011 |
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H. Dasty3, a WEB framework for DAS. Bioinformatics (Oxford, England). 27: 2616-7. PMID 21798964 DOI: 10.1093/Bioinformatics/Btr433 |
0.398 |
|
| 2011 |
Haw R, Hermjakob H, D'Eustachio P, Stein L. Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics. 11: 3598-613. PMID 21751369 DOI: 10.1002/Pmic.201100066 |
0.485 |
|
| 2011 |
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, ... ... Hermjakob H, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods. 8: 528-9. PMID 21716279 DOI: 10.1038/Nmeth.1637 |
0.373 |
|
| 2011 |
Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA. Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. Molecular & Cellular Proteomics : McP. 10: M111.008490. PMID 21700957 DOI: 10.1074/Mcp.M111.008490 |
0.435 |
|
| 2011 |
Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E. DAS writeback: a collaborative annotation system. Bmc Bioinformatics. 12: 143. PMID 21569281 DOI: 10.1186/1471-2105-12-143 |
0.393 |
|
| 2011 |
Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H. easyDAS: automatic creation of DAS servers. Bmc Bioinformatics. 12: 23. PMID 21244646 DOI: 10.1186/1471-2105-12-23 |
0.465 |
|
| 2011 |
Orchard S, Hermjakob H. Preparing molecular interaction data for publication. Methods in Molecular Biology (Clifton, N.J.). 694: 229-36. PMID 21082438 DOI: 10.1007/978-1-60761-977-2_15 |
0.427 |
|
| 2011 |
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, ... ... Hermjakob H, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research. 39: D691-7. PMID 21067998 DOI: 10.1093/Nar/Gkq1018 |
0.457 |
|
| 2011 |
Orchard S, Hermjakob H. Data standardization by the HUPO-PSI: how has the community benefitted? Methods in Molecular Biology (Clifton, N.J.). 696: 149-60. PMID 21063946 DOI: 10.1007/978-1-60761-987-1_9 |
0.476 |
|
| 2011 |
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, ... Hermjakob H, et al. mzML--a community standard for mass spectrometry data. Molecular & Cellular Proteomics : McP. 10: R110.000133. PMID 20716697 DOI: 10.1074/Mcp.R110.000133 |
0.441 |
|
| 2011 |
Binz PA, Hermjakob H, van der Vet P. The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'. Comparative and Functional Genomics. 5: 148-55. PMID 18629067 DOI: 10.1002/cfg.389 |
0.352 |
|
| 2010 |
Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, et al. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Standards in Genomic Sciences. 3: 259-66. PMID 21304730 DOI: 10.4056/Sigs.147362 |
0.376 |
|
| 2010 |
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS. Organelle proteomics experimental designs and analysis. Proteomics. 10: 3957-69. PMID 21080489 DOI: 10.1002/Pmic.201000244 |
0.392 |
|
| 2010 |
Orchard S, Jones A, Albar JP, Cho SY, Kwon KH, Lee C, Hermjakob H. Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics. 10: 3062-6. PMID 20806224 DOI: 10.1002/Pmic.201090075 |
0.456 |
|
| 2010 |
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics. 10: 3073-81. PMID 20677327 DOI: 10.1002/Pmic.201000120 |
0.458 |
|
| 2010 |
Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P. The systematic annotation of the three main GPCR families in Reactome. Database : the Journal of Biological Databases and Curation. 2010: baq018. PMID 20671204 DOI: 10.1093/Database/Baq018 |
0.379 |
|
| 2010 |
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H. implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics. 10: 1895-8. PMID 20623474 DOI: 10.1002/Pmic.201090034 |
0.432 |
|
| 2010 |
Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, ... ... Hermjakob H, et al. Minimum information about a protein affinity reagent (MIAPAR). Nature Biotechnology. 28: 650-3. PMID 20622827 DOI: 10.1038/Nbt0710-650 |
0.356 |
|
| 2010 |
Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Research. 38: W78-83. PMID 20519200 DOI: 10.1093/Nar/Gkq482 |
0.323 |
|
| 2010 |
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H. The Ontology Lookup Service: bigger and better. Nucleic Acids Research. 38: W155-60. PMID 20460452 DOI: 10.1093/Nar/Gkq331 |
0.422 |
|
| 2010 |
Orchard S, Aranda B, Hermjakob H. The publication and database deposition of molecular interaction data. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 25.3. PMID 20393973 DOI: 10.1002/0471140864.Ps2503S60 |
0.481 |
|
| 2010 |
Perreau VM, Orchard S, Adlard PA, Bellingham SA, Cappai R, Ciccotosto GD, Cowie TF, Crouch PJ, Duce JA, Evin G, Faux NG, Hill AF, Hung YH, James SA, Li QX, ... ... Hermjakob H, et al. A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease. Proteomics. 10: 2377-95. PMID 20391539 DOI: 10.1002/Pmic.200900773 |
0.33 |
|
| 2010 |
Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T. Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. The Plant Cell. 22: 997-1005. PMID 20371643 DOI: 10.1105/Tpc.109.072736 |
0.411 |
|
| 2010 |
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L. The Proteomics Identifications database: 2010 update. Nucleic Acids Research. 38: D736-42. PMID 19906717 DOI: 10.1093/Nar/Gkp964 |
0.49 |
|
| 2010 |
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, ... ... Hermjakob H, et al. The IntAct molecular interaction database in 2010. Nucleic Acids Research. 38: D525-31. PMID 19850723 DOI: 10.1093/Nar/Gkp878 |
0.466 |
|
| 2010 |
Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, ... ... Hermjakob H, et al. A community standard format for the representation of protein affinity reagents. Molecular & Cellular Proteomics : McP. 9: 1-10. PMID 19674966 DOI: 10.1074/Mcp.M900185-Mcp200 |
0.459 |
|
| 2009 |
Vizcaíno JA, Mueller M, Hermjakob H, Martens L. Charting online OMICS resources: A navigational chart for clinical researchers. Proteomics. Clinical Applications. 3: 18-29. PMID 21136933 DOI: 10.1002/Prca.200800082 |
0.462 |
|
| 2009 |
Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, ... ... Hermjakob H, et al. Recurated protein interaction datasets. Nature Methods. 6: 860-1. PMID 19935838 DOI: 10.1038/Nmeth1209-860 |
0.324 |
|
| 2009 |
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E. ENFIN--A European network for integrative systems biology. Comptes Rendus Biologies. 332: 1050-8. PMID 19909926 DOI: 10.1016/J.Crvi.2009.09.003 |
0.365 |
|
| 2009 |
Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: A framework to check MIAPE compliance of proteomics data Proteomics. 9: 5112-5119. PMID 19834897 DOI: 10.1002/Pmic.200900189 |
0.476 |
|
| 2009 |
Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H. Annual spring meeting of the proteomics standards initiative Proteomics. 9: 4429-4432. PMID 19670378 DOI: 10.1002/Pmic.200900407 |
0.478 |
|
| 2009 |
Orchard S, Binz PA, Hermjakob H. Second joint HUPO publication and proteomics standards initiative workshop Proteomics. 9: 4426-4428. PMID 19670377 DOI: 10.1002/Pmic.200900406 |
0.347 |
|
| 2009 |
Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L. A guide to the Proteomics Identifications Database proteomics data repository Proteomics. 9: 4276-4283. PMID 19662629 DOI: 10.1002/Pmic.200900402 |
0.495 |
|
| 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, ... ... Hermjakob H, 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 |
0.421 |
|
| 2009 |
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Research. 37: D619-22. PMID 18981052 DOI: 10.1093/Nar/Gkn863 |
0.46 |
|
| 2009 |
Vizcaino JA, Hermjakob H, Martens L. Present and future of proteomics data curation at the PRIDE database Nature Precedings. DOI: 10.1038/Npre.2009.3222.1 |
0.479 |
|
| 2008 |
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (Oxford, England). 24: 2767-72. PMID 18936051 DOI: 10.1093/Bioinformatics/Btn528 |
0.384 |
|
| 2008 |
O'Neill K, Garcia A, Schwegmann A, Jimenez RC, Jacobson D, Hermjakob H. OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. Bmc Bioinformatics. 9: 437. PMID 18925933 DOI: 10.1186/1471-2105-9-437 |
0.39 |
|
| 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, ... Hermjakob H, 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 |
0.485 |
|
| 2008 |
Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H. Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain Proteomics. 8: 4168-4172. PMID 18814335 DOI: 10.1002/Pmic.200800555 |
0.395 |
|
| 2008 |
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H. Dasty2, an Ajax protein DAS client. Bioinformatics (Oxford, England). 24: 2119-21. PMID 18694895 DOI: 10.1093/Bioinformatics/Btn387 |
0.396 |
|
| 2008 |
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, MacÃas JR, Reeves GA, Prlić A. Integrating biological data--the Distributed Annotation System. Bmc Bioinformatics. 9: S3. PMID 18673527 DOI: 10.1186/1471-2105-9-S8-S3 |
0.399 |
|
| 2008 |
Martens L, Palazzi LM, Hermjakob H. Data standards and controlled vocabularies for proteomics Methods in Molecular Biology. 484: 279-286. PMID 18592186 DOI: 10.1007/978-1-59745-398-1_18 |
0.476 |
|
| 2008 |
Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. InteroPORC: Automated inference of highly conserved protein interaction networks Bioinformatics. 24: 1625-1631. PMID 18508856 DOI: 10.1093/Bioinformatics/Btn249 |
0.405 |
|
| 2008 |
Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, et al. Calling on a million minds for community annotation in WikiProteins. Genome Biology. 9: R89. PMID 18507872 DOI: 10.1186/Gb-2008-9-5-R89 |
0.405 |
|
| 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 |
0.407 |
|
| 2008 |
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, ... ... Hermjakob H, et al. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology. 26: 541-7. PMID 18464787 DOI: 10.1038/Nbt1360 |
0.361 |
|
| 2008 |
Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, et al. ISPIDER Central: an integrated database web-server for proteomics Nucleic Acids Research. 36: W485-490. PMID 18440977 DOI: 10.1093/Nar/Gkn196 |
0.448 |
|
| 2008 |
Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H. 6th HUPO annual world congress - Proteomics standards initiative workshop: 6-10 October 2007, Seoul, Korea Proteomics. 8: 1331-1333. PMID 18318010 DOI: 10.1002/Pmic.200701086 |
0.389 |
|
| 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 |
0.366 |
|
| 2008 |
Orchard S, Hermjakob H. The HUPO proteomics standards initiative - Easing communication and minimizing data loss in a changing world Briefings in Bioinformatics. 9: 166-173. PMID 18065433 DOI: 10.1093/Bib/Bbm061 |
0.5 |
|
| 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 |
0.45 |
|
| 2008 |
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H. PRIDE: New developments and new datasets Nucleic Acids Research. 36: D878-D883. PMID 18033805 DOI: 10.1093/Nar/Gkm1021 |
0.476 |
|
| 2008 |
Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W. Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics (Oxford, England). 24: 1100-1. PMID 17989096 DOI: 10.1093/Bioinformatics/Btm518 |
0.381 |
|
| 2008 |
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H. Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics. 28-34. PMID 17893861 DOI: 10.1002/pmic.200700286 |
0.347 |
|
| 2008 |
Michaut M, Kerrien S, Montecchi-Palazzi L, Cassier-Chauvat C, Chauvat F, Aude J, Legrain P, Hermjakob H. InteroPORC: an automated tool to predict highly conserved protein interaction networks Bmc Bioinformatics. 9: 1-2. DOI: 10.1186/1471-2105-9-S10-P1 |
0.346 |
|
| 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 |
0.341 |
|
| 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 |
0.41 |
|
| 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, ... ... Hermjakob H, 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 |
0.441 |
|
| 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 |
0.443 |
|
| 2007 |
Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H. Five years of progress in the standardization of proteomics data 4 th annual spring workshop of the HUPO-proteomics standards initiative - April 23-25, 2007. Ecole Nationale Supérieure (ENS), Lyon, France Proteomics. 7: 3436-3440. PMID 17907277 DOI: 10.1002/Pmic.200700658 |
0.459 |
|
| 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, ... ... Hermjakob H, et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotechnology. 25: 894-8. PMID 17687370 DOI: 10.1038/Nbt1324 |
0.412 |
|
| 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, ... ... Hermjakob H, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/Nbt1329 |
0.474 |
|
| 2007 |
Martens L, Hermjakob H. Proteomics data validation: Why all must provide data Molecular Biosystems. 3: 518-522. PMID 17639125 DOI: 10.1039/B705178F |
0.419 |
|
| 2007 |
VizcaÃno JA, Martens L, Hermjakob H, Julian RK, Paton NW. The PSI formal document process and its implementation on the PSI website. Proteomics. 7: 2355-7. PMID 17570517 DOI: 10.1002/Pmic.200700064 |
0.358 |
|
| 2007 |
Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK, Hermjakob H. Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA. Proteomics. 7: 337-9. PMID 17274075 DOI: 10.1002/Pmic.200600915 |
0.361 |
|
| 2007 |
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Science. 5: 4. PMID 17270041 DOI: 10.1186/1477-5956-5-4 |
0.443 |
|
| 2007 |
Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, et al. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nature Methods. 4: 13-7. PMID 17195019 DOI: 10.1038/Nmeth0107-13 |
0.344 |
|
| 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 |
0.506 |
|
| 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, ... ... Hermjakob H, et al. IntAct--open source resource for molecular interaction data. Nucleic Acids Research. 35: D561-5. PMID 17145710 DOI: 10.1093/Nar/Gkl958 |
0.482 |
|
| 2007 |
Swainston N, Siepen JA, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. Pride Wizard: generation of standards compliant quantitative proteomics data Bmc Systems Biology. 1: 27. DOI: 10.1186/1752-0509-1-S1-P27 |
0.432 |
|
| 2007 |
Taussig MJ, Stoevesandt O, Borrebaeck CAK, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, et al. Erratum: Corrigendum: ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome Nature Methods. 4: 187-187. DOI: 10.1038/Nmeth0207-187A |
0.303 |
|
| 2007 |
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H. Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition Proteomics - Practical Proteomics. 2: 28-34. DOI: 10.1002/Pmic.200700286 |
0.452 |
|
| 2006 |
Hermjakob H. The HUPO proteomics standards initiative - Overcoming the fragmentation of proteomics data Proteomics. 1: 34-38. PMID 17031794 DOI: 10.1002/Pmic.200600537 |
0.523 |
|
| 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 |
0.38 |
|
| 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, ... ... Hermjakob H, 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 |
0.394 |
|
| 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 |
0.342 |
|
| 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 |
0.428 |
|
| 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 |
0.447 |
|
| 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 |
|
| 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 |
0.472 |
|
| 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 |
0.48 |
|
| 2005 |
Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics. 5: 3246-61. PMID 16104057 DOI: 10.1002/Pmic.200500186 |
0.445 |
|
| 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 |
0.383 |
|
| 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 |
0.507 |
|
| 2005 |
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics. 5: 3501-5. PMID 16041670 DOI: 10.1002/Pmic.200401302 |
0.478 |
|
| 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 |
0.328 |
|
| 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 |
0.338 |
|
| 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 |
0.471 |
|
| 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 |
0.395 |
|
| 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 |
0.5 |
|
| 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 |
0.455 |
|
| 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 |
0.467 |
|
| 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 |
0.529 |
|
| 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, 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 |
0.455 |
|
| 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, et al. IntAct: an open source molecular interaction database. Nucleic Acids Research. 32: D452-5. PMID 14681455 DOI: 10.1093/Nar/Gkh052 |
0.436 |
|
| 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 |
0.452 |
|
| 2004 |
Binz PA, Hermjakob H, van der Vet P. The ESF programme og Functional Genomics workshop on 'Data Integration in Functional Genomics: Application to biological pathways Comparative and Functional Genomics. 5: 148-155. DOI: 10.1002/Cfg.389 |
0.456 |
|
| 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 |
0.488 |
|
| 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 |
0.465 |
|
| 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 |
0.411 |
|
| 2003 |
Orchard S, Hermjakob H, Apweiler R. The Proteomics Standards Initiative Proteomics. 3: 1374-1376. PMID 12872238 DOI: 10.1002/Pmic.200300496 |
0.481 |
|
| 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 |
0.429 |
|
| 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 |
0.514 |
|
| 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, ... ... Hermjakob H, 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 |
0.376 |
|
| 2001 |
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Hermjakob H, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062 |
0.329 |
|
| 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 |
0.382 |
|
| 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 |
0.342 |
|
| 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 |
0.361 |
|
| 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 |
0.351 |
|
| 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 |
0.311 |
|
| 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 |
0.319 |
|
| Show low-probability matches. |