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EMBL-EBI Proteomics & Metabolomics

Managing and reusing public proteomics & metabolomics data

Publications

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Publication year

Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.

Madrigal P, Thanki AS, Fexova S, Yu ID, Chatzigeorgiou A, Zucchi I, Marugan Calles JC, Vilmovsky L, Khen A, Zhao L, Erdos K, Kurri SR, Selvakumar S, Kumbham U, Prakash A, Wang S, Green A, Ribas CE, Sweeney B, Alegbe T, Suveges D, Hemrom A, Gomez Gutierrez DE, Insua S, Jeffryes M, Pearce M, Basutkar P, Kaforou M, Cunnington A, Levin M, Kumari S, Ware D, Goutte-Gattat D, Röper K, Brown NH, Hu Y, Perrimon N, Papatheodorou I, Brazma A, Hermjakob H, Harrison M, Ocaña D, Ochoa D, McDonagh EM, Bateman A, Keane T, Vizcaíno JA, Ernst C.

Nucleic acids research, 2025

doi:10.1093/nar/gkaf1238.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025.

Thakur M, Bosc N, Brooksbank C, Ernst C, Freeberg MA, Gurwitz KT, Hermjakob H, Hulcoop DG, Martin MJ, McDonagh EM, Mithani A, O'Boyle NM, Ochoa D, Payne T, Perez-Riverol Y, Sarkans U, Sokolov A, Staudt N, Stephenson JD, Tzampatzopoulou E, Vizcaíno JA, Zdrazil B, McEntyre J.

Nucleic acids research, 2025

doi:10.1093/nar/gkaf1078.

The ProteomeXchange consortium in 2026: making proteomics data FAIR.

Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Bandla C, Kamatchinathan S, Hewapathirana S, Sun Z, Kawano S, Okuda S, Connolly B, MacLean B, MacCoss MJ, Chen T, Zhu Y, Ishihama Y, Vizcaíno JA.

Nucleic acids research, 2025

doi:10.1093/nar/gkaf1146.

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.

Van Den Bossche T, Alexandrov T, Bilbao A, Bittremieux W, Brigante FI, Chambers MC, Charkow J, Deutsch E, Dowsey AW, El Abiead Y, Gabriels R, Hecht H, Heuckeroth S, Klein JA, Knierman M, Martens L, Moritz RL, McCall LI, Neumann S, Perez-Riverol Y, Röst HL, Price EJ, Shofstahl J, Tabb DL, Uszkoreit J, Vizcaíno JA, Wang M, Willems S, Winkelhardt D, Kohlbacher O, Wein SP.

Journal of proteome research, 2025

doi:10.1021/acs.jproteome.5c00435.

Translon: a single term for translated regions.

Świrski MI, Tierney JAS, Albà MM, Andreev DE, Aspden JL, Atkins JF, Bassani-Sternberg M, Berry MJ, Biffo S, Boris-Lawrie K, Borodovsky M, Brierley I, Brook M, Brunet MA, Bujnicki JM, Caliskan N, Calviello L, Carvunis AR, Cate JHD, Cenik C, Chang KY, Chen Y, Chothani S, Choudhary JS, Clark PL, Clauwaert J, Cooley L, Dassi E, Dean K, Diaz JJ, Dieterich C, Dikstein R, Dinman JD, Dmitriev SE, Dontsova OA, Dunham CM, Eswarappa SM, Farabaugh PJ, Faridi P, Fierro-Monti I, Firth AE, Gatfield D, Gebauer F, Gelfand MS, Gray NK, Green R, Hill CH, Hou YM, Hübner N, Ignatova Z, Ivanov P, Iwasaki S, Johnson R, Jomaa A, Jovanovic M, Jungreis I, Kellis M, Kieft JS, Kochetov AV, Koonin EV, Korostelev AA, Kufel J, Kulakovskiy IV, Kurian L, Lafontaine DLJ, Larsson O, Loughran G, Lukeš J, Mariotti M, Martens-Uzunova ES, Martinez TF, Matsumoto A, McManus J, Medenbach J, Melnikov SV, Menschaert G, Merchante C, Mikl M, Miller WA, Mühlemann O, Namy O, Nedialkova DD, Nosek J, Orchard S, Ozretić P, Pertea M, Pervouchine DD, Romão L, Ron D, Roucou X, Rubtsova MP, Ruiz-Orera J, Saghatelian A, Salzberg SL, Seale LA, Seoighe C, Sergiev PV, Shah P, Shirokikh N, Slavoff SA, Sonenberg N, Stasevich TJ, Szczesny RJ, Tamm T, Tchórzewski M, Topisirovic I, Tremblay ML, Tuller T, Ulitsky I, Valášek LS, Van Damme P, Viero G, Vizcaino JA, Vogel C, Wallace EWJ, Weissman JS, Westhof E, Whiffin N, Wilson DN, Xie Z, Yewdell JW, Yordanova MM, Yu CH, Yurchenko V, Zagrovic B, TRANSLACORE, Valen E, Baranov PV.

Nature methods, 2025

doi:10.1038/s41592-025-02810-3.

Author Correction: π-HuB: the proteomic navigator of the human body.

He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y, π-HuB Consortium.

Nature, 2025

doi:10.1038/s41586-024-08555-x.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE, R Leach A, Levchenko M, Marques D, McDonagh EM, Mithani A, Parkinson H, Perez-Riverol Y, Perova Z, Sarkans U, Tirunagari S, Tzampatzopoulou E, Venkatesan A, Vizcaino JA, Wingfield B, Zdrazil B, McEntyre J.

Nucleic acids research, 2025

doi:10.1093/nar/gkae1089.

REDIportal: toward an integrated view of the A-to-I editing.

D'Addabbo P, Cohen-Fultheim R, Twersky I, Fonzino A, Silvestris DA, Prakash A, Mazzacuva PL, Vizcaino JA, Green A, Sweeney B, Yates A, Lussi Y, Luo J, Martin MJ, Eisenberg E, Levanon EY, Pesole G, Picardi E.

Nucleic acids research, 2025

doi:10.1093/nar/gkae1083.

The PRIDE database at 20 years: 2025 update.

Perez-Riverol Y, Bandla C, Kundu DJ, Kamatchinathan S, Bai J, Hewapathirana S, John NS, Prakash A, Walzer M, Wang S, Vizcaíno JA.

Nucleic acids research, 2025

doi:10.1093/nar/gkae1011.

A standardized framework for circulating blood proteomics.

Cai X, Geyer PE, Perez-Riverol Y, Omenn GS, Dong L, Winkler R, Ahadi S, Lössl P, Yu X, Chang C, Ralser M, Jimenez CR, Zhao Y, Chen YJ, Poon TCW, Bache N, Shi L, Dai X, Wang Z, Zhu Y, Fang X, Schwenk JM, Van Eyk JE, Völker U, Guo T.

Nature genetics, 2025

doi:10.1038/s41588-025-02319-7.

Open-Source and FAIR Research Software for Proteomics.

Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE.

Journal of proteome research, 2025

doi:10.1021/acs.jproteome.4c01079.

Establishing the ELIXIR Microbiome Community.

Finn RD, Balech B, Burgin J, Chua P, Corre E, Cox CJ, Donati C, Dos Santos VM, Fosso B, Hancock J, Heil KF, Ishaque N, Kale V, Kunath BJ, Médigue C, Nogueira T, Pafilis E, Pesole G, Richardson L, Santamaria M, Strepis N, Van Den Bossche T, Vizcaíno JA, Zafeiropoulos H, Willassen NP, Pelletier E, Batut B.

F1000Research, 2024

doi:10.12688/f1000research.144515.2.

π-HuB: the proteomic navigator of the human body.

He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y, π-HuB Consortium.

Nature, 2024

doi:10.1038/s41586-024-08280-5.

The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data.

Kopczynski D, Ejsing CS, McDonald JG, Bamba T, Baker ES, Bertrand-Michel J, Brügger B, Coman C, Ellis SR, Garrett TJ, Griffiths WJ, Guan XL, Han X, Höring M, Holčapek M, Hoffmann N, Huynh K, Lehmann R, Jones JW, Kaddurah-Daouk R, Köfeler HC, Meikle PJ, Metz TO, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Torta F, Vizcaíno JA, Welti R, Wenk MR, Wolrab D, Xia Y, Ekroos K, Ahrends R, Liebisch G.

Journal of lipid research, 2024

doi:10.1016/j.jlr.2024.100621.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J.

Nucleic acids research, 2024

doi:10.1093/nar/gkad1088.

Expression Atlas update: insights from sequencing data at both bulk and single cell level.

George N, Fexova S, Fuentes AM, Madrigal P, Bi Y, Iqbal H, Kumbham U, Nolte NF, Zhao L, Thanki AS, Yu ID, Marugan Calles JC, Erdos K, Vilmovsky L, Kurri SR, Vathrakokoili-Pournara A, Osumi-Sutherland D, Prakash A, Wang S, Tello-Ruiz MK, Kumari S, Ware D, Goutte-Gattat D, Hu Y, Brown N, Perrimon N, Vizcaíno JA, Burdett T, Teichmann S, Brazma A, Papatheodorou I.

Nucleic acids research, 2024

doi:10.1093/nar/gkad1021.

OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.

Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni PD, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, Boudaud B, Bernt M, Patikas N, Pilz M, Startek MP, Kutuzova S, Heumos L, Charkow J, Sing JC, Feroz A, Siraj A, Weisser H, Dijkstra TMH, Perez-Riverol Y, Röst H, Kohlbacher O, Sachsenberg T.

Nature methods, 2024

doi:10.1038/s41592-024-02197-7.

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.

Bouyssié D, Altıner P, Capella-Gutierrez S, Fernández JM, Hagemeijer YP, Horvatovich P, Hubálek M, Levander F, Mauri P, Palmblad M, Raffelsberger W, Rodríguez-Navas L, Di Silvestre D, Kunkli BT, Uszkoreit J, Vandenbrouck Y, Vizcaíno JA, Winkelhardt D, Schwämmle V.

Journal of proteome research, 2023

doi:10.1021/acs.jproteome.3c00636.

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.

Journal of proteome research, 2023

doi:10.1021/acs.jproteome.2c00637.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, McEntyre J.

Nucleic acids research, 2023

doi:10.1093/nar/gkac1098.

The ProteomeXchange consortium at 10 years: 2023 update.

Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA.

Nucleic acids research, 2023

doi:10.1093/nar/gkac1040.

OpenMS 3 expands the frontiers of open-source computational mass spectrometry

Sachsenberg T, Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni P, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, Boudaud B, Bernt M, Patikas N, Pilz M, Startek MP, Kutuzova S, Heumos L, Charkow J, Sing J, Feroz A, Siraj A, Weisser H, Dijkstra T, Perez-Riverol Y, Röst H, Kohlbacher O.

Preprint, 2023

doi:10.21203/rs.3.rs-3286368/v1.

Expression Atlas update: gene and protein expression in multiple species.

Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1030.

The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information

Gill I, Griffiths E, Dooley D, Cameron R, Savić Kallesøe S, John NS, Sehar A, Gosal G, Alexander D, Chapel M, Croxen M, Delisle B, Di Tullio R, Gaston D, Duggan A, Guthrie J, Horsman M, Joshi E, Kearney L, Knox N, Lau L, LeBlanc J, Li V, Lyons P, MacKenzie K, McArthur A, Panousis E, Palmer J, Prystajecky N, Smith K, Tanner J, Townend C, Tyler A, Van Domselaar G, Hsiao W.

Preprint, 2022

doi:10.20944/preprints202206.0335.v1.

A proteomics sample metadata representation for multiomics integration, and big data analysis

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva E, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky L, Perez-Riverol Y.

Preprint, 2021

doi:10.1101/2021.05.21.445143.

A proteomics sample metadata representation for multiomics integration and big data analysis.

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y.

Nature communications, 2021

doi:10.1038/s41467-021-26111-3.

Universal Spectrum Identifier for mass spectra.

Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N.

Nature methods, 2021

doi:10.1038/s41592-021-01184-6.

Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson DW, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PE, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP.

PLoS genetics, 2021

doi:10.1371/journal.pgen.1009809.

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson DW, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PE, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP.

PLoS genetics, 2021

doi:10.1371/journal.pgen.1009679.

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.

Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I.

Nature methods, 2021

doi:10.1038/s41592-021-01102-w.

A high-stringency blueprint of the human proteome.

Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS.

Nature communications, 2020

doi:10.1038/s41467-020-19045-9.

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.

Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J.

Structure (London, England : 1993), 2020

doi:10.1016/j.str.2020.09.011.

Expression Atlas update: from tissues to single cells.

Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A.

Nucleic acids research, 2020

doi:10.1093/nar/gkz947.

Universal Spectrum Identifier for mass spectra

Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz P, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N.

Preprint, 2020

doi:10.1101/2020.12.07.415539.

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

Audain E, Wilsdon A, Breckpot J, Izarzugaza J, Fitzgerald T, Kahlert A, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett A, Belmont J, Benson D, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney P, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney B, Klaassen S, Kramer H, Marshall C, Milewicz D, Lemaire S, Coselli J, Mitchell M, Tomita-Mitchell A, Prakash S, Stamm K, Stewart A, Silversides C, Siebert R, Stiller B, Rosenfeld J, Vater I, Postma A, Caliebe A, Brook J, Andelfinger G, Hurles M, Thienpont B, Larsen L, Hitz M.

Preprint, 2020

doi:10.1101/2020.06.25.169573.

The functional landscape of the human phosphoproteome.

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P.

Nature biotechnology, 2019

doi:10.1038/s41587-019-0344-3.

A five-level classification system for proteoform identifications.

Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolić L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, Kelleher NL.

Nature methods, 2019

doi:10.1038/s41592-019-0573-x.

Proteomics Standards Initiative Extended FASTA Format.

Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

Journal of proteome research, 2019

doi:10.1021/acs.jproteome.9b00064.

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Katayama T, Kawashima S, Micklem G, Kawano S, Kim J, Kocbek S, Okamoto S, Wang Y, Wu H, Yamaguchi A, Yamamoto Y, Antezana E, Aoki-Kinoshita KF, Arakawa K, Banno M, Baran J, Bolleman JT, Bonnal RJP, Bono H, Fernández-Breis JT, Buels R, Campbell MP, Chiba H, Cock PJA, Cohen KB, Dumontier M, Fujisawa T, Fujiwara T, Garcia L, Gaudet P, Hattori E, Hoehndorf R, Itaya K, Ito M, Jamieson D, Jupp S, Juty N, Kalderimis A, Kato F, Kawaji H, Kawashima T, Kinjo AR, Komiyama Y, Kotera M, Kushida T, Malone J, Matsubara M, Mizuno S, Mizutani S, Mori H, Moriya Y, Murakami K, Nakazato T, Nishide H, Nishimura Y, Ogishima S, Ohta T, Okuda S, Ono H, Perez-Riverol Y, Shinmachi D, Splendiani A, Strozzi F, Suzuki S, Takehara J, Thompson M, Tokimatsu T, Uchiyama I, Verspoor K, Wilkinson MD, Wimalaratne S, Yamada I, Yamamoto N, Yarimizu M, Kawamoto S, Takagi T.

Preprint, 2019

doi:10.12688/f1000research.18238.1.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Binz P, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

Preprint, 2019

doi:10.1101/624494.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

Journal of proteome research, 2018

doi:10.1021/acs.jproteome.8b00485.

ProForma: A Standard Proteoform Notation.

LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO.

Journal of proteome research, 2018

doi:10.1021/acs.jproteome.7b00851.

The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic acids research, 2018

doi:10.1093/nar/gkx664.

Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.

Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG.

The Journal of experimental medicine, 2017

doi:10.1084/jem.20161382.

A community proposal to integrate proteomics activities in ELIXIR

Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJ, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.

Preprint, 2017

doi:10.12688/f1000research.11751.1.

A community proposal to integrate proteomics activities in ELIXIR.

Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.

F1000Research, 2017

doi:10.12688/f1000research.11751.1.

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.

Nature biotechnology, 2017

doi:10.1038/nbt.3790.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Caprez A, Batut B, Haudgaard M, Cokelaer T, Beauchamp KA, Pedersen BS, Hoogstrate Y, Bretaudeau A, Ryan D, Corguillé GL, Yusuf D, Luna-Valero S, Kirchner R, Brinda K, Wollmann T, Raden M, Heeringen SJv, Soranzo N, Pantano L, Charlop-Powers Z, Unneberg P, Smet MD, Martin M, Kuster GV, Antao T, Miladi M, Thornton K, Brueffer C, Beek Mvd, Maticzka D, Blank C, Will S, Gravouil K, Wolff J, Holtgrewe M, Fallmann J, Piro VC, Shlyakhter I, Yousif A, Mabon P, Zhang X, Shen W, Cabral J, Thomas C, Enns E, Brown J, Boekel J, Hollander Md, Kelleher J, Turaga N, Ruiter JRd, Bouvier D, Gladman S, Choudhary S, Harding N, Eggenhofer F, Kratz A, Fang Z, Kleinkauf R, Timm H, Cock PJA, Seiler E, Brislawn C, Nguyen H, Stovner EB, Ewels P, Chambers M, Johnson JE, Hägglund E, Ye S, Guimera RV, Pruesse E, Dunn WA, Parsons L, Patro R, Koppstein D, Grassi E, Wohlers I, Reynolds A, Cornwell M, Stoler N, Blankenberg D, He G, Bargull M, Junge A, Farouni R, Freeberg M, Singh S, Bogema DR, Cumbo F, Wang L, Larson DE, Workentine ML, Devisetty UK, Laurent S, Roger P, Garnier X, Agren R, Khan A, Eppley JM, Li W, Stöcker BK, Rausch T, Taylor J, Wright PR, Taranto AP, Chicco D, Sennblad B, Baaijens JA, Gopez M, Abdennur N, Milne I, Preussner J, Pinello L, Srivastava A, Chande AT, Kensche PR, Pirola Y, Knudsen M, Bruijn Id, Blin K, Gonnella G, Enache OM, Rai V, Waters NR, Hiltemann S, Bendall ML, Stahl C, Miles A, Boursin Y, Perez-Riverol Y, Schmeier S, Clarke E, Arvai K, Jung M, Domenico TD, Seiler J, Rasche E, Kornobis E, Beisser D, Rahmann S, Mikheyev AS, Tran C, Capellades J, Schröder C, Salatino AE, Dirmeier S, Webster TH, Moskalenko O, Stephen G, Köster J.

Preprint, 2017

doi:10.1101/207092.

Four simple recommendations to encourage best practices in research software.

Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.

F1000Research, 2017

doi:10.12688/f1000research.11407.1.

Erratum to: Making sense of big data in health research: towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome medicine, 2016

doi:10.1186/s13073-016-0376-y.

Ten Simple Rules for Taking Advantage of Git and GitHub.

Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.

PLoS computational biology, 2016

doi:10.1371/journal.pcbi.1004947.

Making sense of big data in health research: Towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome medicine, 2016

doi:10.1186/s13073-016-0323-y.

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS.

Journal of proteome research, 2015

doi:10.1021/pr5013009.

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.

Molecular & cellular proteomics : MCP, 2014

doi:10.1074/mcp.m113.035907.

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