Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems

Silberberg M, Hermjakob H, Malik-Sheriff RS, Grecco HE.

2024

doi:10.1101/2024.01.10.574883.

The Reactome Pathway Knowledgebase 2024.

Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B, Petryszak R, Ragueneau E, Rothfels K, Sevilla C, Shamovsky V, Stephan R, Tiwari K, Varusai T, Weiser J, Wright A, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1025.

The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study.

Simona P, Panneerselvam K, Porras P, Duesbury M, Perfetto L, Licata L, Hermjakob H, Orchard S.

Database (Oxford), 2023

doi:10.1093/database/baad066.

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D.

Blood, 2023

doi:10.1182/blood.2023020118.

Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal.

Beavers D, Brunson T, Sanati N, Matthews L, Haw R, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G.

Curr Protoc, 2023

doi:10.1002/cpz1.845.

The landscape of microRNA interactions annotation: analysis of three rare disorders as case study

Simona P, Panneerselvam K, Porras P, Duesbury M, Perfetto L, Licata L, Hermjakob H, Orchard S.

2023

doi:10.1101/2023.06.20.545695.

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

Tiwari DD, Hoffmann N, Didi K, Deshpande S, Ghosh S, Nguyen TVN, Raman K, Hermjakob H, Sheriff R.

2023

doi:10.1101/2023.05.22.540599.

Human Autoantigen Atlas: Searching for the Hallmarks of Autoantigens.

Wang D, Yang D, Yang L, Diao L, Zhang Y, Li Y, Wang H, Ren J, Cheng L, Tan Q, Zhang R, Han X, Zhang X, Wang B, Li D, Chen M, Hermjakob H, Li Y, LaBaer J, Zhou Z, Yu X.

J Proteome Res, 2023

doi:10.1021/acs.jproteome.2c00799.

Using the Reactome Database.

Rothfels K, Milacic M, Matthews L, Haw R, Sevilla C, Gillespie M, Stephan R, Gong C, Ragueneau E, May B, Shamovsky V, Wright A, Weiser J, Beavers D, Conley P, Tiwari K, Jassal B, Griss J, Senff-Ribeiro A, Brunson T, Petryszak R, Hermjakob H, D'Eustachio P, Wu G, Stein L.

Curr Protoc, 2023

doi:10.1002/cpz1.722.

Network expansion of genetic associations defines a pleiotropy map of human cell biology.

Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, Del-Toro N, Gonzalez A, Zhang Q, Mountjoy E, Suveges D, Ochoa D, Ghoussaini M, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P.

Nat Genet, 2023

doi:10.1038/s41588-023-01327-9.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.

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, Mendoza L, Van Den Bossche T, Gabriels R, Bandeira N, Carver J, Pullman B, Sun Z, Hoffmann N, Shofstahl J, Zhu Y, Licata L, Quaglia F, Tosatto SCE, Orchard SE.

J Proteome Res, 2023

doi:10.1021/acs.jproteome.2c00637.

Systems Biology in ELIXIR: modelling in the spotlight

Martins dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Dominguez Del Angel V, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, Sheriff RSM, Suarez Diez M, Van Steen K, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM.

2022

doi:10.12688/f1000research.126734.1.

FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast

Ramachandran K, König M, Scharm M, Nguyen TVN, Hermjakob H, Waltemath D, Malik Sheriff RS.

2022

doi:10.20944/preprints202206.0137.v1.

KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study.

Füzi B, Malik-Sheriff RS, Manners EJ, Hermjakob H, Ecker GF.

J Cheminform, 2022

doi:10.1186/s13321-022-00615-6.

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S, Calzone L.

Brief Bioinform, 2022

doi:10.1093/bib/bbac212.

Understudied proteins: opportunities and challenges for functional proteomics.

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J.

Nat Methods, 2022

doi:10.1038/s41592-022-01454-x.

An open invitation to the Understudied Proteins Initiative.

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J.

Nat Biotechnol, 2022

doi:10.1038/s41587-022-01316-z.

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkac331.

iProX in 2021: connecting proteomics data sharing with big data.

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.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1081.

The European Bioinformatics Institute (EMBL-EBI) in 2021.

Cantelli G, Bateman A, Brooksbank C, Petrov AI, Malik-Sheriff RS, Ide-Smith M, Hermjakob H, Flicek P, Apweiler R, Birney E, McEntyre J.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1127.

The reactome pathway knowledgebase 2022.

Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1028.

The IntAct database: efficient access to fine-grained molecular interaction data.

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, Iannuccelli M, Pellegrini M, Martin MJ, Panni S, Duesbury M, Vallet SD, Rappsilber J, Ricard-Blum S, Cesareni G, Salwinski L, Orchard S, Porras P, Panneerselvam K, Hermjakob H.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1006.

Complex Portal 2022: new curation frontiers.

Meldal BHM, Perfetto L, Combe C, Lubiana T, Ferreira Cavalcante JV, Bye-A-Jee H, Waagmeester A, Del-Toro N, Shrivastava A, Barrera E, Wong E, Mlecnik B, Bindea G, Panneerselvam K, Willighagen E, Rappsilber J, Porras P, Hermjakob H, Orchard S.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab991.

COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community.

Mol Syst Biol, 2021

doi:10.15252/msb.202110851.

Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs.

Füzi B, Gurinova J, Hermjakob H, Ecker GF, Sheriff R.

Front Pharmacol, 2021

doi:10.3389/fphar.2021.708296.

Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community

König M, Grzegorzewski J, Golebiewski M, Hermjakob H, Hucka M, Olivier B, Keating S, Nickerson D, Schreiber F, Sheriff R, Waltemath D.

2021

doi:10.20944/preprints202108.0303.v2.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community.

Mol Syst Biol, 2021

doi:10.15252/msb.202110387.

Network expansion of genetic associations defines a pleiotropy map of human cell biology

Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, del-Toro N, Zhang Q, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P.

2021

doi:10.1101/2021.07.19.452924.

IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.

Ragueneau E, Shrivastava A, Morris JH, Del-Toro N, Hermjakob H, Porras P.

Bioinformatics, 2021

doi:10.1093/bioinformatics/btab319.

A decoupled, modular and scriptable architecture for tools to curate data platforms.

Langenstein M, Hermjakob H, Bernal Llinares M.

Bioinformatics, 2021

doi:10.1093/bioinformatics/btab233.

Exploring <i>Leishmania</i>-Host Interaction with Reactome, a Database of Biological Pathways and Processes

Murillo J, Jassal B, Gómez MA, Hermjakob H.

2021

doi:10.1101/2021.03.23.436718.

Analysing the yeast complexome-the Complex Portal rising to the challenge.

Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S, Porras P.

Nucleic Acids Res, 2021

doi:10.1093/nar/gkab077.

Reproducibility in systems biology modelling.

Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS.

Mol Syst Biol, 2021

doi:10.15252/msb.20209982.

Deep learning embedder method and tool for mass spectra similarity search.

Qin C, Luo X, Deng C, Shu K, Zhu W, Griss J, Hermjakob H, Bai M, Perez-Riverol Y.

J Proteomics, 2021

doi:10.1016/j.jprot.2020.104070.

Identifiers.org: Compact Identifier services in the cloud.

Bernal-Llinares M, Ferrer-Gómez J, Juty N, Goble C, Wimalaratne SM, Hermjakob H.

Bioinformatics, 2021

doi:10.1093/bioinformatics/btaa864.

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).

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, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M.

Bioinformatics, 2021

doi:10.1093/bioinformatics/btaa622.

Using Reactome to build an autophagy mechanism knowledgebase.

Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H.

Autophagy, 2021

doi:10.1080/15548627.2020.1761659.

Towards a unified open access dataset of molecular interactions.

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, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S.

Nat Commun, 2020

doi:10.1038/s41467-020-19942-z.

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions.

Perfetto L, Pastrello C, Del-Toro N, Duesbury M, Iannuccelli M, Kotlyar M, Licata L, Meldal B, Panneerselvam K, Panni S, Rahimzadeh N, Ricard-Blum S, Salwinski L, Shrivastava A, Cesareni G, Pellegrini M, Orchard S, Jurisica I, Hermjakob H, Porras P.

Database (Oxford), 2020

doi:10.1093/database/baaa096.

Analysing the Yeast Complexome - The Complex Portal rising to the challenge

Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S, Porras P.

2020

doi:10.1101/2020.11.03.367086.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Cristóbal Monraz Gómez L, Somers J, Hoch M, Gupta SK, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Leon MPd, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker J, Zucker J, Oxford K, Teuton J, Kocakaya E, Yağmur Summak G, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Ribeiro AS, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, Waard Ad, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Medina ME, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, Meulder BD, Dugourd A, Naldi A, Noë V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, the COVID-19 Disease Map Community.

2020

doi:10.1101/2020.10.26.356014.

A decoupled, modular and scriptable architecture for tools to curate data platforms

Langenstein M, Hermjakob H, Llinares MB.

2020

doi:10.1101/2020.09.28.282699.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

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, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, SBML Level 3 Community members.

Mol Syst Biol, 2020

doi:10.15252/msb.20199110.

Reproducibility in systems biology modelling

Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS.

2020

doi:10.1101/2020.08.07.239855.

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.

Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R.

Sci Data, 2020

doi:10.1038/s41597-020-00589-w.

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

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, Smith L, Stefan MI, Wittig U, Myers CJ.

J Integr Bioinform, 2020

doi:10.1515/jib-2020-0005.

BioModels Parameters: a treasure trove of parameter values from published systems biology models.

Glont M, Arankalle C, Tiwari K, Nguyen TVN, Hermjakob H, Malik-Sheriff RS.

Bioinformatics, 2020

doi:10.1093/bioinformatics/btaa560.

The omics discovery REST interface.

Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning BA, Hermjakob H, Perez-Riverol Y.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkaa326.

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.

Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R.

Sci Data, 2020

doi:10.1038/s41597-020-0477-8.

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Touré V, Vercruysse S, Acencio ML, Lovering R, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Licata L, Lægreid A, Mungall C, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Thieffry D, Thomas P, Türei D, Saez-Rodriguez J, Kuiper M.

2020

doi:10.20944/preprints202004.0480.v1.

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H.

2020

doi:10.1101/2020.04.16.044958.

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C.

Nat Biotechnol, 2020

doi:10.1038/s41587-020-0477-4.

Wikidata as a knowledge graph for the life sciences.

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, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI.

Elife, 2020

doi:10.7554/elife.52614.

MEMOTE for standardized genome-scale metabolic model testing.

Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C.

Nat Biotechnol, 2020

doi:10.1038/s41587-020-0446-y.

The Omics Discovery REST interface

Dass G, Vu M, Xu P, Audain E, Hitz M, Hermjakob H, Perez-Riverol Y.

2020

doi:10.1101/2020.02.10.939967.

BioModels-15 years of sharing computational models in life science.

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, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz1055.

The reactome pathway knowledgebase.

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, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz1031.

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

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, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz984.

PhaSepDB: a database of liquid-liquid phase separation related proteins.

You K, Huang Q, Yu C, Shen B, Sevilla C, Shi M, Hermjakob H, Chen Y, Li T.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz847.

Reactome and ORCID-fine-grained credit attribution for community curation.

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.

Database (Oxford), 2019

doi:10.1093/database/baz123.

Phoenix Enhancer: proteomics data mining using clustered spectra

Bai M, Qin C, Shu K, Griss J, Perez-Riverol Y, Zhu W, Hermjakob H.

2019

doi:10.1101/846303.

Wikidata as a FAIR knowledge graph for the life sciences

Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith O, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI.

2019

doi:10.1101/799684.

HENA, heterogeneous network-based data set for Alzheimer's disease.

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, Vilo J, Simonneau M, Peterson H.

Sci Data, 2019

doi:10.1038/s41597-019-0152-0.

Quantifying the impact of public omics data.

Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H.

Nat Commun, 2019

doi:10.1038/s41467-019-11461-w.

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.

Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M.

Gigascience, 2019

doi:10.1093/gigascience/giz088.

A data citation roadmap for scholarly data repositories.

Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T.

Sci Data, 2019

doi:10.1038/s41597-019-0031-8.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium contributing authors, 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, Porras P.

Nat Commun, 2019

doi:10.1038/s41467-019-08814-w.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

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, Touré V, Zobolas J, Licata L.

Bioinformatics, 2019

doi:10.1093/bioinformatics/btz132.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch 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, Hermjakob H, Orchard S, Porras P.

Nat Commun, 2019

doi:10.1038/s41467-018-07709-6.

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.

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, Porras P, Hermjakob H, Orchard S.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky1001.

iProX: an integrated proteome resource.

Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky869.

A reference set of curated biomedical data and metadata from clinical case reports.

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, Ping P.

Sci Data, 2018

doi:10.1038/sdata.2018.258.

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

Perfetto L, Acencio M, Bradley G, Cesareni G, Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Surdo PL, Lovering R, Orchard S, Porras P, Thomas P, Touré V, Zobolas J, Licata L.

2018

doi:10.1101/385773.

PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping

Hernández Sánchez LF, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M.

2018

doi:10.1101/375097.

Quantifying the impact of public omics data

Perez-Riverol Y, Zorin A, Dass G, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H.

2018

doi:10.1101/282517.

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist A, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kim HU, King Z, Koehorst JJ, Klamt S, Klipp E, Lakshmanan M, Le Novère N, Lee D, Lee SY, Lee S, Lewis NE, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Resendis-Antonio O, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Richelle A, Rocha I, Sanchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JA, Xavier JC, Yuan Q, Zakhartsev M, Zhang C.

2018

doi:10.1101/350991.

Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set

The IMEx Consortium Curators, del Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong L, Jurisica I, Hermjakob H, Orchard S, Porras P.

2018

doi:10.1101/346833.

Uniform resolution of compact identifiers for biomedical data.

Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T.

Sci Data, 2018

doi:10.1038/sdata.2018.29.

Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine.

Ping P, Hermjakob H, Polson JS, Benos PV, Wang W.

Circ Res, 2018

doi:10.1161/circresaha.117.310967.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

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, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S.

BMC Bioinformatics, 2018

doi:10.1186/s12859-018-2118-1.

Interleukins and their signaling pathways in the Reactome biological pathway database.

Jupe S, Ray K, Roca CD, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H.

J Allergy Clin Immunol, 2018

doi:10.1016/j.jaci.2017.12.992.

Reactome graph database: Efficient access to complex pathway data.

Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H.

PLoS Comput Biol, 2018

doi:10.1371/journal.pcbi.1005968.

Integrated omics dissection of proteome dynamics during cardiac remodeling.

Lau E, Cao Q, Lam MPY, Wang J, Ng DCM, Bleakley BJ, Lee JM, Liem DA, Wang D, Hermjakob H, Ping P.

Nat Commun, 2018

doi:10.1038/s41467-017-02467-3.

Reactome diagram viewer: data structures and strategies to boost performance.

Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H.

Bioinformatics, 2018

doi:10.1093/bioinformatics/btx752.

The Reactome Pathway Knowledgebase.

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, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res, 2018

doi:10.1093/nar/gkx1132.

BioModels: expanding horizons to include more modelling approaches and formats.

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, Le Novère N, Hermjakob H.

Nucleic Acids Res, 2018

doi:10.1093/nar/gkx1023.

Uniform resolution of compact identifiers for biomedical data

Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T.

2017

doi:10.1101/101279.

Reactome enhanced pathway visualization.

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, D'Eustachio P, Ping P, Hermjakob H, Fabregat A.

Bioinformatics, 2017

doi:10.1093/bioinformatics/btx441.

ComplexViewer: visualization of curated macromolecular complexes.

Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J.

Bioinformatics, 2017

doi:10.1093/bioinformatics/btx497.

Towards Coordinated International Support of Core Data Resources for the Life Sciences

Anderson W, Apweiler R, Bateman A, Bauer G, Berman H, Blake J, Blomberg N, Burley S, Cochrane G, Di Francesco V, Donohue T, Durinx C, Game A, Green E, Gojobori T, Goodhand P, Hamosh A, Hermjakob H, Kanehisa M, Kiley R, McEntyre J, McKibbin R, Miyano S, Pauly B, Perrimon N, Ragan M, Richards G, Teo Y, Westerfield M, Westhof E, Lasko P.

2017

doi:10.1101/110825.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

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, Walzer M, Jones AR.

J Proteome Res, 2017

doi:10.1021/acs.jproteome.7b00370.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

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, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol, 2017

doi:10.1371/journal.pbio.2001414.

Discovering and linking public omics data sets using the Omics Discovery Index.

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, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol, 2017

doi:10.1038/nbt.3790.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

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, Hermjakob H, Hériché J, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone S, Sariyar M, Snoep JL, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams AR, Wimalaratne S, Winfree L, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

2017

doi:10.1101/117812.

Data management: A global coalition to sustain core data.

Anderson WP, Global Life Science Data Resources Working Group.

Nature, 2017

doi:10.1038/543179a.

Reactome pathway analysis: a high-performance in-memory approach.

Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H.

BMC Bioinformatics, 2017

doi:10.1186/s12859-017-1559-2.

The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.

Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V.

CPT Pharmacometrics Syst Pharmacol, 2017

doi:10.1002/psp4.12155.

Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome.

Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P.

Handb Exp Pharmacol, 2017

doi:10.1007/164_2016_93.

AAgAtlas 1.0: a human autoantigen database.

Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D, Yu X.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkw946.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

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, Vizcaíno JA.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkw936.

Open Targets: a platform for therapeutic target identification and validation.

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, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkw1055.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

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.

J Proteomics, 2017

doi:10.1016/j.jprot.2016.08.002.

A Data Citation Roadmap for Scholarly Data Repositories

Fenner M, Crosas M, Grethe J, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T.

2016

doi:10.1101/097196.

Omics Discovery Index - Discovering and Linking Public Omics Datasets

Perez-Riverol Y, Bai M, Leprevost F, Squizzato S, Park YM, et al.

2016

doi:10.1101/049205.

2016 update of the PRIDE database and its related tools.

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.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkw880.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

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.

Nat Methods, 2016

doi:10.1038/nmeth.3902.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

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.

J Proteome Res, 2016

doi:10.1021/acs.jproteome.6b00392.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.

Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M.

Database (Oxford), 2016

doi:10.1093/database/baw088.

The Reactome pathway Knowledgebase.

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, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkv1351.

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.

Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y.

Bioinformatics, 2016

doi:10.1093/bioinformatics/btv674.

Testing and Validation of Computational Methods for Mass Spectrometry.

Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A.

J Proteome Res, 2016

doi:10.1021/acs.jproteome.5b00852.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

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, Vizcaíno JA.

Mol Cell Proteomics, 2016

doi:10.1074/mcp.o115.050229.

2016 update of the PRIDE database and its related tools.

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.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkv1145.

The cardiovascular gene annotation initiative: Impact on data analysis

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.

Atherosclerosis, 2015

doi:10.1016/j.atherosclerosis.2015.04.135.

The evolution of standards and data management practices in systems biology.

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.

Mol Syst Biol, 2015

doi:10.15252/msb.20156053.

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N.

CPT Pharmacometrics Syst Pharmacol, 2015

doi:10.1002/psp4.57.

BioModels: Content, Features, Functionality, and Use.

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.

CPT Pharmacometrics Syst Pharmacol, 2015

doi:10.1002/psp4.3.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics, 2015

doi:10.1093/bioinformatics/btv250.

Introducing the PRIDE Archive RESTful web services.

Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res, 2015

doi:10.1093/nar/gkv382.

Proteomics data visualisation.

Vizcaíno JA, Barsnes H, Hermjakob H.

Proteomics, 2015

doi:10.1002/pmic.201570063.

Harnessing the heart of big data.

Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR, Lindsey ML, Ping P.

Circ Res, 2015

doi:10.1161/circresaha.115.306013.

Shared resources, shared costs--leveraging biocuration resources.

Orchard S, Hermjakob H.

Database (Oxford), 2015

doi:10.1093/database/bav009.

Expression data analysis with Reactome.

Jupe S, Fabregat A, Hermjakob H.

Curr Protoc Bioinformatics, 2015

doi:10.1002/0471250953.bi0820s49.

Development of data representation standards by the human proteome organization proteomics standards initiative.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.

J Am Med Inform Assoc, 2015

doi:10.1093/jamia/ocv001.

A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.

Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H.

Proteomics, 2015

doi:10.1002/pmic.201400390.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

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.

Database (Oxford), 2015

doi:10.1093/database/bau131.

SPARQL-enabled identifier conversion with Identifiers.org.

Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.

Bioinformatics, 2015

doi:10.1093/bioinformatics/btv064.

A public repository for mass spectrometry imaging data.

Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA.

Anal Bioanal Chem, 2015

doi:10.1007/s00216-014-8357-8.

Open source libraries and frameworks for biological data visualisation: a guide for developers.

Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics, 2015

doi:10.1002/pmic.201400377.

BioModels: ten-year anniversary.

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, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku1181.

Identifying novel biomarkers through data mining-a realistic scenario?

Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics Clin Appl, 2015

doi:10.1002/prca.201400107.

The complex portal--an encyclopaedia of macromolecular complexes.

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, Wong ED, Hermjakob H, Orchard S.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku975.

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.

Proteomics, 2015

doi:10.1002/pmic.201400302.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics, 2014

doi:10.1002/pmic.201470164.

BioModels linked dataset.

Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C.

BMC Syst Biol, 2014

doi:10.1186/s12918-014-0091-5.

BioJS: an open source standard for biological visualisation - its status in 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, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H.

F1000Res, 2014

doi:10.12688/f1000research.3-55.v1.

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.

Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics, 2014

doi:10.1002/pmic.201400120.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

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, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics, 2014

doi:10.1074/mcp.o113.036681.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

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, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics, 2014

doi:10.1074/mcp.m113.035907.

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

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, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol, 2014

doi:10.1038/nbt.2839.

jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics, 2014

doi:10.1002/pmic.201300560.

The Reactome pathway knowledgebase.

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, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1102.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

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, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1115.

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.

Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR, Apweiler R, Ping P.

J Proteome Res, 2014

doi:10.1021/pr400539j.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.

Biochim Biophys Acta, 2014

doi:10.1016/j.bbapap.2013.02.032.

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.

Biochim Biophys Acta, 2014

doi:10.1016/j.bbapap.2013.02.017.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, 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, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol, 2013

doi:10.1186/1752-0509-7-116.

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics, 2013

doi:10.1002/pmic.201370166.

Capturing cooperative interactions with the PSI-MI format.

Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.

Database (Oxford), 2013

doi:10.1093/database/bat066.

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

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, Xu T, Weiss J, Duan H, Uhlen M, Yates JR, Apweiler R, Ge J, Hermjakob H, Ping P.

Circ Res, 2013

doi:10.1161/circresaha.113.301151.

Maximising proteomics data for the scientific community

Hermjakob H, Apweiler R.

European Pharmaceutical Review, 2013

doi:.

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.

Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR.

Mol Cell Proteomics, 2013

doi:10.1074/mcp.o113.029777.

iAnn: an event sharing platform for the life sciences.

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, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.

Bioinformatics, 2013

doi:10.1093/bioinformatics/btt306.

A new reference implementation of the PSICQUIC web service.

del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.

Nucleic Acids Res, 2013

doi:10.1093/nar/gkt392.

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA.

PLoS One, 2013

doi:10.1371/journal.pone.0061951.

Towards the collaborative curation of the registry underlying Identifiers.org.

Juty N, Le Novère N, Hermjakob H, Laibe C.

Database (Oxford), 2013

doi:10.1093/database/bat017.

From Peptidome to PRIDE: public proteomics data migration at a large scale.

Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H.

Proteomics, 2013

doi:10.1002/pmic.201200514.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M, HUPO-PSI Group.

Database (Oxford), 2013

doi:10.1093/database/bat009.

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.

Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V.

Anal Chem, 2013

doi:10.1021/ac303239g.

BioJS: an open source JavaScript framework for biological data visualization.

Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.

Bioinformatics, 2013

doi:10.1093/bioinformatics/btt100.

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

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, Guirola O, Bringas R, Cabrera G, Guillen G, Padron G, Gonzalez LJ, Besada V.

J Proteomics, 2013

doi:10.1016/j.jprot.2013.01.019.

PRIDE Cluster: building a consensus of proteomics data.

Griss J, Foster JM, Hermjakob H, Vizcaíno JA.

Nat Methods, 2013

doi:10.1038/nmeth.2343.

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.

Vizcaíno 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, Ríos D, Wang R, Hermjakob H.

Nucleic Acids Res, 2013

doi:10.1093/nar/gks1262.

The EBI enzyme portal.

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, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.

Nucleic Acids Res, 2013

doi:10.1093/nar/gks1112.

Shouldn't enantiomeric purity be included in the minimum information about a bioactive entity? Response from the MIABE group

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, Larminie C, Lynch N, Mann RK, Murray-Rust P, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.

Nat Rev Drug Discov, 2012

doi:10.1038/nrd3503-c2.

Annotating cancer variants and anti-cancer therapeutics in reactome.

Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.

Cancers (Basel), 2012

doi:10.3390/cancers4041180.

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.

Cancers (Basel), 2012

doi:10.3390/cancers4041180.

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.

Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.

BMC Bioinformatics, 2012

doi:10.1186/1471-2105-13-324.

MyDas, an extensible Java DAS server.

Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.

PLoS One, 2012

doi:10.1371/journal.pone.0044180.

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.

Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics, 2012

doi:10.1002/pmic.201270126.

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Côté 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, Vizcaíno JA.

Mol Cell Proteomics, 2012

doi:10.1074/mcp.o112.021543.

A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.

Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR.

OMICS, 2012

doi:10.1089/omi.2012.0022.

Improvements in the Protein Identifier Cross-Reference service.

Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res, 2012

doi:10.1093/nar/gks338.

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.

Proteomics, 2012

doi:10.1002/pmic.201100578.

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

Reisinger F, Krishna R, Ghali F, Ríos D, Hermjakob H, Vizcaíno JA, Jones AR.

Proteomics, 2012

doi:10.1002/pmic.201100577.

HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.

Lam MP, Vivanco F, Scholten A, Hermjakob H, Van Eyk J, Ping P.

Proteomics, 2012

doi:10.1002/pmic.201270015.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.

Nat Methods, 2012

doi:10.1038/nmeth.1931.

PRIDE: quality control in a proteomics data repository.

Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H.

Database (Oxford), 2012

doi:10.1093/database/bas004.

Analyzing protein-protein interaction networks.

Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE.

J Proteome Res, 2012

doi:10.1021/pr201211w.

The mzIdentML data standard for mass spectrometry-based proteomics results.

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, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.

Mol Cell Proteomics, 2012

doi:10.1074/mcp.m111.014381.

PRIDE Inspector: a tool to visualize and validate MS proteomics data.

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.

Nat Biotechnol, 2012

doi:10.1038/nbt.2112.

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H.

Proteomics, 2012

doi:10.1002/pmic.201290016.

The HUPO initiative on Model Organism Proteomes, iMOP.

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, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.

Proteomics, 2012

doi:10.1002/pmic.201290014.

Toward interoperable bioscience data.

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, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.

Nat Genet, 2012

doi:10.1038/ng.1054.

The IntAct molecular interaction database in 2012.

Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.

Nucleic Acids Res, 2012

doi:10.1093/nar/gkr1088.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

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, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Proteomics, 2012

doi:10.1002/pmic.201100562.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

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, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

J Proteome Res, 2012

doi:10.1021/pr201071t.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

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, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Proteomics Clin Appl, 2011

doi:10.1002/prca.201100097.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

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, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Mol Cell Proteomics, 2011

doi:10.1074/mcp.o111.015446.

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H.

Proteomics, 2011

doi:10.1002/pmic.201190117.

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.

Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.

Database (Oxford), 2011

doi:10.1093/database/bar047.

The Reactome BioMart.

Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.

Database (Oxford), 2011

doi:10.1093/database/bar031.

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.

Proteomics, 2011

doi:10.1002/pmic.201100363.

Minimum information about a bioactive entity (MIABE).

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, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.

Nat Rev Drug Discov, 2011

doi:10.1038/nrd3503.

Dasty3, a WEB framework for DAS.

Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H.

Bioinformatics, 2011

doi:10.1093/bioinformatics/btr433.

Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Haw R, Hermjakob H, D'Eustachio P, Stein L.

Proteomics, 2011

doi:10.1002/pmic.201100066.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

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, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods, 2011

doi:10.1038/nmeth.1637.

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.

Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics, 2011

doi:10.1074/mcp.m111.008490.

DAS writeback: a collaborative annotation system.

Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.

BMC Bioinformatics, 2011

doi:10.1186/1471-2105-12-143.

easyDAS: automatic creation of DAS servers.

Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H.

BMC Bioinformatics, 2011

doi:10.1186/1471-2105-12-23.

Preparing molecular interaction data for publication.

Orchard S, Hermjakob H.

Methods Mol Biol, 2011

doi:10.1007/978-1-60761-977-2_15.

Reactome: a database of reactions, pathways and biological processes.

Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.

Nucleic Acids Res, 2011

doi:10.1093/nar/gkq1018.

Data standardization by the HUPO-PSI: how has the community benefitted?

Orchard S, Hermjakob H.

Methods Mol Biol, 2011

doi:10.1007/978-1-60761-987-1_9.

mzML--a community standard for mass spectrometry data.

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, Binz PA, Deutsch EW.

Mol Cell Proteomics, 2011

doi:10.1074/mcp.r110.000133.

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

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, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.

Stand Genomic Sci, 2010

doi:10.4056/sigs.147362.

Organelle proteomics experimental designs and analysis.

Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS.

Proteomics, 2010

doi:10.1002/pmic.201000244.

Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea.

Orchard S, Jones A, Albar JP, Cho SY, Kwon KH, Lee C, Hermjakob H.

Proteomics, 2010

doi:10.1002/pmic.201090075.

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

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.

Proteomics, 2010

doi:10.1002/pmic.201000120.

The systematic annotation of the three main GPCR families in Reactome.

Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P.

Database (Oxford), 2010

doi:10.1093/database/baq018.

implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H.

Proteomics, 2010

doi:10.1002/pmic.201090034.

Minimum information about a protein affinity reagent (MIAPAR).

Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren PA, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H, Sherman D.

Nat Biotechnol, 2010

doi:10.1038/nbt0710-650.

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.

Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H.

Nucleic Acids Res, 2010

doi:10.1093/nar/gkq482.

The Ontology Lookup Service: bigger and better.

Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.

Nucleic Acids Res, 2010

doi:10.1093/nar/gkq331.

The publication and database deposition of molecular interaction data.

Orchard S, Aranda B, Hermjakob H.

Curr Protoc Protein Sci, 2010

doi:10.1002/0471140864.ps2503s60.

A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease.

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, Mok SS, Tew DJ, White AR, Bush AI, Hermjakob H, Masters CL.

Proteomics, 2010

doi:10.1002/pmic.200900773.

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.

Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T.

Plant Cell, 2010

doi:10.1105/tpc.109.072736.

The Proteomics Identifications database: 2010 update.

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.

Nucleic Acids Res, 2010

doi:10.1093/nar/gkp964.

The IntAct molecular interaction database in 2010.

Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.

Nucleic Acids Res, 2010

doi:10.1093/nar/gkp878.

A community standard format for the representation of protein affinity reagents.

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, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H.

Mol Cell Proteomics, 2010

doi:10.1074/mcp.m900185-mcp200.

New open drug activity data at EBI

Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J.

Chem Cent J, 2009

doi:10.1186/1752-153x-3-s1-o3.

Charting online OMICS resources: A navigational chart for clinical researchers.

Vizcaíno JA, Mueller M, Hermjakob H, Martens L.

Proteomics Clin Appl, 2009

doi:10.1002/prca.200800082.

Recurated protein interaction datasets.

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, Eisenberg D, Cesareni G, Hermjakob H.

Nat Methods, 2009

doi:10.1038/nmeth1209-860.

ENFIN--A European network for integrative systems biology.

Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E.

C R Biol, 2009

doi:10.1016/j.crvi.2009.09.003.

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.

Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H.

Proteomics, 2009

doi:10.1002/pmic.200900189.

Annual spring meeting of the Proteomics Standards Initiative.

Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H.

Proteomics, 2009

doi:10.1002/pmic.200900407.

Second Joint HUPO publication and Proteomics Standards Initiative workshop.

Orchard S, Binz PA, Hermjakob H.

Proteomics, 2009

doi:10.1002/pmic.200900406.

A guide to the Proteomics Identifications Database proteomics data repository.

Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.

Proteomics, 2009

doi:10.1002/pmic.200900402.

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.

Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R.

J Proteome Res, 2009

doi:10.1021/pr900023z.

Reactome knowledgebase of human biological pathways and processes.

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, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P.

Nucleic Acids Res, 2009

doi:10.1093/nar/gkn863.

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects

Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J.

2008

doi:.

EBI Proteomics Services

Hermjakob H.

Lect Notes Comput Sci, 2008

doi:10.1007/978-3-540-69828-9_21.

Infrastructure for distributed protein annotation

Reeves GA, Prlic A, Jimenez RC, Kulesha E, Hermjakob H.

2008

doi:10.1007/978-3-211-75123-7_18.

ENFIN - An Integrative Structure for Systems Biology

Reisinger F, Corpas M, Hancock J, Hermjakob H, Birney E, Kahlem P.

2008

doi:10.1007/978-3-540-69828-9_13.

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

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.

Bioinformatics, 2008

doi:10.1093/bioinformatics/btn528.

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.

O'Neill K, Garcia A, Schwegmann A, Jimenez RC, Jacobson D, Hermjakob H.

BMC Bioinformatics, 2008

doi:10.1186/1471-2105-9-437.

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.

Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.

Genome Biol, 2008

doi:10.1186/gb-2008-9-s2-s5.

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.

Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H.

Proteomics, 2008

doi:10.1002/pmic.200800555.

Dasty2, an Ajax protein DAS client.

Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H.

Bioinformatics, 2008

doi:10.1093/bioinformatics/btn387.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

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, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.

Nat Biotechnol, 2008

doi:10.1038/nbt.1411.

Integrating biological data--the Distributed Annotation System.

Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A.

BMC Bioinformatics, 2008

doi:10.1186/1471-2105-9-s8-s3.

Data standards and controlled vocabularies for proteomics.

Martens L, Palazzi LM, Hermjakob H.

Methods Mol Biol, 2008

doi:10.1007/978-1-59745-398-1_18.

InteroPORC: automated inference of highly conserved protein interaction networks.

Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H.

Bioinformatics, 2008

doi:10.1093/bioinformatics/btn249.

Calling on a million minds for community annotation in WikiProteins.

Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A.

Genome Biol, 2008

doi:10.1186/gb-2008-9-5-r89.

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.

Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.

Nucleic Acids Res, 2008

doi:10.1093/nar/gkn252.

The minimum information about a genome sequence (MIGS) specification.

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, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.

Nat Biotechnol, 2008

doi:10.1038/nbt1360.

ISPIDER Central: an integrated database web-server for proteomics.

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, Jones DT, Orengo CA, Hubbard SJ.

Nucleic Acids Res, 2008

doi:10.1093/nar/gkn196.

6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.

Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H.

Proteomics, 2008

doi:10.1002/pmic.200701086.

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.

Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L.

Proteomics, 2008

doi:10.1002/pmic.200700761.

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.

Orchard S, Hermjakob H.

Brief Bioinform, 2008

doi:10.1093/bib/bbm061.

Analyzing large-scale proteomics projects with latent semantic indexing.

Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H.

J Proteome Res, 2008

doi:10.1021/pr070461k.

PRIDE: new developments and new datasets.

Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.

Nucleic Acids Res, 2008

doi:10.1093/nar/gkm1021.

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.

Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W.

Bioinformatics, 2008

doi:10.1093/bioinformatics/btm518.

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

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 Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.

Nat Biotechnol. , 2007

doi:.

Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy.

Martens L, Orchard S, Apweiler R, Hermjakob H.

Mol Cell Proteomics , 2007

doi:.

Clinical proteomics: A need to define the field and to begin to set adequate standards.

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, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T.

Proteomics Clin Appl, 2007

doi:10.1002/prca.200600771.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.

BMC Bioinformatics, 2007

doi:10.1186/1471-2105-8-401.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

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, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.

BMC Biol, 2007

doi:10.1186/1741-7007-5-44.

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

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, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.

Nat Biotechnol, 2007

doi:10.1038/nbt1347.

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.

Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H.

Proteomics, 2007

doi:10.1002/pmic.200700658.

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.

Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.

Proteomics, 2007

doi:10.1002/pmic.200700286.

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.

Martens L, Orchard S, Apweiler R, Hermjakob H.

Mol Cell Proteomics, 2007

doi:10.1016/s1535-9476(20)31973-3.

The minimum information required for reporting a molecular interaction experiment (MIMIx).

Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.

Nat Biotechnol, 2007

doi:10.1038/nbt1324.

The minimum information about a proteomics experiment (MIAPE).

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, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H.

Nat Biotechnol, 2007

doi:10.1038/nbt1329.

Proteomics data validation: why all must provide data.

Martens L, Hermjakob H.

Mol Biosyst, 2007

doi:10.1039/b705178f.

The PSI formal document process and its implementation on the PSI website.

Vizcaíno JA, Martens L, Hermjakob H, Julian RK, Paton NW.

Proteomics, 2007

doi:10.1002/pmic.200700064.

The implications of alternative splicing in the ENCODE protein complement.

Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.

Proc Natl Acad Sci U S A, 2007

doi:10.1073/pnas.0700800104.

Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.

Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK, Hermjakob H.

Proteomics, 2007

doi:10.1002/pmic.200600915.

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.

Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ.

Proteome Sci, 2007

doi:10.1186/1477-5956-5-4.

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.

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, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M.

Nat Methods, 2007

doi:10.1038/nmeth0107-13.

Proteomic data exchange and storage: the need for common standards and public repositories.

Orchard S, Jones P, Taylor C, Zhu W, Julian RK, Hermjakob H, Apweiler R.

Methods Mol Biol, 2007

doi:10.1385/1-59745-275-0:261.

IntAct--open source resource for molecular interaction data.

Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H.

Nucleic Acids Res, 2007

doi:10.1093/nar/gkl958.

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia.

Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ.

Mol Psychiatry, 2007

doi:10.1038/sj.mp.4001880.

Guilt by association: using protein interactions and expression patterns to predict protein function

Orchard S, Hermjakob H.

2006

doi:.

Proteomic Data Standardization, Deposition and Exchange

Orchard S, Hermjakob H, Pruess M, Apweiler R.

2006

doi:10.1002/3527608230.ch2.

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

Hermjakob H.

Proteomics, 2006

doi:10.1002/pmic.200600537.

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).

Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R.

OMICS, 2006

doi:10.1089/omi.2006.10.145.

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, Wiemann S, Hermjakob H.

Proteomics, 2006

doi:10.1002/pmic.200600452.

A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report.

Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M.

Mol Cell Proteomics, 2006

doi:10.1074/mcp.t600020-mcp200.

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.

Hamacher M, Stephan C, Blüggel M, Chamrad D, Körting G, Martens L, Müller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R.

Proteomics, 2006

doi:10.1002/pmic.200600069.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

Côté RG, Jones P, Apweiler R, Hermjakob H.

BMC Bioinformatics, 2006

doi:10.1186/1471-2105-7-97.

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.

Hermjakob H, Apweiler R.

Expert Rev Proteomics, 2006

doi:10.1586/14789450.3.1.1.

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.

Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R.

Proteomics, 2006

doi:10.1002/pmic.200500868.

PRIDE: a public repository of protein and peptide identifications for the proteomics community.

Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R.

Nucleic Acids Res, 2006

doi:10.1093/nar/gkj138.

Protein interaction databases.

Hermjakob H, Apweiler R.

2005

doi:.

Data standardization and the HUPO proteomics standards initiative.

Taylor C, Hermjakob H, Apweiler R, Orchard S, Zhu W.

2005

doi:.

Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.

Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R.

Proteomics, 2005

doi:10.1002/pmic.200500727.

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).

Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK, Apweiler R.

Proteomics, 2005

doi:10.1002/pmic.200500626.

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.

Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ.

Proteomics, 2005

doi:10.1002/pmic.200500186.

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.

Omenn 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, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM.

Proteomics, 2005

doi:10.1002/pmic.200500358.

PRIDE: the proteomics identifications database.

Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R.

Proteomics, 2005

doi:10.1002/pmic.200401303.

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.

Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K.

Proteomics, 2005

doi:10.1002/pmic.200401302.

Second proteomics standards initiative spring workshop.

Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK, Apweiler R.

Expert Rev Proteomics, 2005

doi:10.1586/14789450.2.3.287.

Dasty and UniProt DAS: a perfect pair for protein feature visualization.

Jones P, Vinod N, Down T, Hackmann A, Kahari A, Kretschmann E, Quinn A, Wieser D, Hermjakob H, Apweiler R.

Bioinformatics, 2005

doi:10.1093/bioinformatics/bti506.

Annotating the human proteome.

Orchard S, Hermjakob H, Apweiler R.

Mol Cell Proteomics, 2005

doi:10.1074/mcp.r500003-mcp200.

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.

Orchard S, Montecchi-Palazzi L, Hermjakob H, Apweiler R.

Pac Symp Biocomput, 2005

doi:.

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.

Orchard S, Hermjakob H, Binz PA, Hoogland C, Taylor CF, Zhu W, Julian RK, Apweiler R.

Proteomics, 2005

doi:10.1002/pmic.200401158.

Proteomics and data standardisation

Orchard S, Hermjakob H, Apweiler R.

Drug Discov Today Biosilico, 2004

doi:10.1016/s1741-8364(04)02405-9.

The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'.

Binz PA, Hermjakob H, van der Vet P.

Comp Funct Genomics, 2004

doi:10.1002/cfg.389.

Current status of proteomic standards development.

Orchard S, Taylor C, Hermjakob H, Zhu W, Julian R, Apweiler R.

Expert Rev Proteomics, 2004

doi:10.1586/14789450.1.2.179.

A common open representation of mass spectrometry data and its application to proteomics research.

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, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.

Nat Biotechnol, 2004

doi:10.1038/nbt1031.

Advances in the development of common interchange standards for proteomic data.

Orchard S, Taylor CF, Hermjakob H, Weimin-Zhu, Julian RK, Apweiler R.

Proteomics, 2004

doi:10.1002/pmic.200400884.

IntAct: an open source molecular interaction database.

Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R.

Nucleic Acids Res, 2004

doi:10.1093/nar/gkh052.

Common interchange standards for proteomics data: Public availability of tools and schema.

Orchard S, Hermjakob H, Julian RK, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R.

Proteomics, 2004

doi:10.1002/pmic.200300694.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

Nat Biotechnol, 2004

doi:10.1038/nbt926.

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.

Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R.

Comp Funct Genomics, 2003

doi:10.1002/cfg.279.

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.

Orchard S, Kersey P, Hermjakob H, Apweiler R.

Comp Funct Genomics, 2003

doi:10.1002/cfg.232.

Integr8: enhanced inter-operability of European molecular biology databases.

Kersey PJ, Morris L, Hermjakob H, Apweiler R.

Methods Inf Med, 2003

doi:.

Further advances in the development of a data interchange standard for proteomics data.

Orchard S, Zhu W, Julian RK, Hermjakob H, Apweiler R.

Proteomics, 2003

doi:10.1002/pmic.200300588.

The proteomics standards initiative.

Orchard S, Hermjakob H, Apweiler R.

Proteomics, 2003

doi:10.1002/pmic.200300496.

TEMBLOR - Perspectives of EBI Database Services.

Hermjakob H, Apweiler R.

Comp Funct Genomics, 2002

doi:10.1002/cfg.133.

InterPro: an integrated documentation resource for protein families, domains and functional sites.

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, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium.

Brief Bioinform, 2002

doi:10.1093/bib/3.3.225.

InterProScan - an integration tool for the signature-recognition methods in InterPro.

Zdobnov EM, Hermjakob H, Apweiler R.

2001

doi:.

Initial sequencing and analysis of the human genome.

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, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium.

Nature, 2001

doi:10.1038/35057062.

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

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, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.

Nucleic Acids Res, 2001

doi:10.1093/nar/29.1.37.

InterPro--an integrated documentation resource for protein families, domains and functional sites.

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, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM, InterPro Consortium.

Bioinformatics, 2000

doi:10.1093/bioinformatics/16.12.1145.

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.

Kersey P, Hermjakob H, Apweiler R.

Bioinformatics, 2000

doi:10.1093/bioinformatics/16.11.1048.

A comparison of signal sequence prediction methods using a test set of signal peptides.

Menne KM, Hermjakob H, Apweiler R.

Bioinformatics, 2000

doi:10.1093/bioinformatics/16.8.741.

The role SWISS-PROT and TrEMBL play in the genome research environment.

Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O'Donovan C, Apweiler R.

J Biotechnol, 2000

doi:10.1016/s0168-1656(00)00198-x.

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.

Apweiler R, Hermjakob H, Sharon N.

Biochim Biophys Acta, 1999

doi:10.1016/s0304-4165(99)00165-8.

Swissknife - 'lazy parsing' of SWISS-PROT entries.

Hermjakob H, Fleischmann W, Apweiler R.

Bioinformatics, 1999

doi:10.1093/bioinformatics/15.9.771.

SWISS-PROT and its computer-annotated supplement TREMBL: How to produce high quality automatic annotation

Apweiler R, O'Donovan C, Martin MJ, Fleischmann W, Hermjakob H, Moeller S, Contrino S, Junker V.

1998

doi:.

SWISS-PROT and its computer-annotated supplement TREMBL: How to produce high quality automatic annotation

Apweiler R, O'Donovan C, Martin MJ, Fleischmann W, Hermjakob H, Moeller S, Contrino S, Junker V.

1998

doi:.

SPTR- A comprehensive, non-redundant and up-to-date protein sequence database.

Hermjakob H, Lang F, Apweiler R;.

The Bioinformer, 1998

doi:.

SPTR - A comprehensive, non-redundant and up-to-date view of the protein sequence world.

Hermjakob H, Lang F, Apweiler R;.

CCP11 Newsletter , 1998

doi:.

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.

Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel AE, Kel OV, Ignatieva EV, Ananko EA, Podkolodnaya OA, Kolpakov FA, Podkolodny NL, Kolchanov NA.

Nucleic Acids Res, 1998

doi:10.1093/nar/26.1.362.

RIFLE: rapid identification of microorganisms by fragment length evaluation.

Hermjakob H, Giegerich R, Arnold W.

Proc Int Conf Intell Syst Mol Biol, 1997

doi:.