2024

• Gretner A, Ragueneau A, Gong C, Prinz A, Gansberger S, Oyarzun I, Hermjakob H, Griss J, ReactomeGSA: new features to simplify public data reuse. Bioinformatics, Volume 40, Issue 6, June 2024; 10.1093/bioinformatics/btae338. Link
• Arora C, Matic M, DiChiaro P, Rosa NO, Carli F, Clubb L, Fard LAN, Kargas G, Diaferia G, Vukotic R, Licata L, Wu G, Natoli G, Gutkind JS, Raimondi F. The landscape of cancer rewired GPCR signaling axes. Cell Genomics, 2024. DOI: 10.1016/j.xgen.2024.100557. Link
• Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie M, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database, 2024. doi:10.1093/database/baae03. Link
• R. Stephan, Interleaved snowballing: Reducing the workload of literature curators. Arxiv, 2024 DOI: 10.48550/arXiv.2402.08339. Link.
• Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D'Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol. 2024 Feb 13;14:1282859. doi: 10.3389/fimmu.2023.1282859. Link
• 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. The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research, 2024. doi: 10.1093/nar/gkad1025. Link

2023

• Tiwari K, Matthews L, May B, Shamovsky V, Orlic-Milacic M, Rothfels K, Ragueneau E, Gong C, Stephan R, Li N, Wu G, Stein L, D'Eustachio P, Hermjakob H. ChatGPT usage in the Reactome curation process. bioRxiv [Preprint]. 2023 Nov 8:2023.11.08.566195. doi: 10.1101/2023.11.08.566195. Link
• 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. Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal. Curr Protoc. 2023 Jul;3(7):e845. doi: 10.1002/cpz1.845. PubMed
• Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G. Illuminating Dark Proteins using Reactome Pathways. bioRxiv [Preprint]. 2023 Jun 5:2023.06.05.543335. doi: 10.1101/2023.06.05.543335. PubMed
• 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. Using the Reactome Database. Curr Protoc. 2023 Apr;3(4):e722. doi: 10.1002/cpz1.722. PubMed

2022

• Wright AJ, Orlic-Milacic M, Rothfels K, Weiser J, Trinh QM, Jassal B, Haw RA, Stein LD. Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. Database (Oxford). 2022 Mar 28;2022:baac009. doi: 10.1093/database/baac009. PubMed
• 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. The reactome pathway knowledgebase 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692. doi: 10.1093/nar/gkab1028. PubMed

2021

• 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. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. Erratum in: Mol Syst Biol. 2021 Dec;17(12):e10851. PubMed

2020

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9:mcp.TIR120.002155. doi: 10.1074/mcp.TIR120.002155. PubMed.
• Varusai TM, Jupe S, Sevilla C, et al. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 2020;1‐12. doi:10.1080/15548627.2020.1761659. PubMed.
• 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. Wikidata as a knowledge graph for the life sciences. Elife. 2020 Mar 17;9. pii: e52614. doi: 10.7554/eLife.52614. PubMed.
• 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. The reactome pathway knowledgebase. Nucleic Acids Res. pii: gkz1031. doi:10.1093/nar/gkz1031. PubMed.
• Naithani S, Gupta P, Preece J, D'Eustachio P, Elser J, Kiff J, Dikeman D, Olson AJ, Wei S, Tello-Ruiz M, Cook J, Fabregat A, Cheng T, Bolton E, Muñoz-Pomer Fuentes A, Mohammed S, Papa-theodorou I, Stein L, Ware D, Jaiswal P. 2020. Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. gkz996, doi.org/10.1093/nar/gkz996. PubMed.
• Haw R, Loney F, Ong E, He Y, Wu G. Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods Mol Biol. 2020;2074:165–179. doi:10.1007/978-1-4939-9873-9_13. PubMed.

2019

• Blucher AS, McWeeney SK, Stein L, Wu G. Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz. F1000Res. 2019 Jun 20. PubMed.
• Viteri G, Matthews L, Varusai T, Gillespie M, Milacic M, Cook J, Weiser J, Shorser S, Sidiropoulos K, Fabregat A, Haw R, Wu G, Stein L, D'Eustachio P, Hermjakob H. Reactome and ORCID-fine-grained credit attribution for community curation. Database (Oxford). 2019 Jan 1. PubMed.

2018

• Jupe S, Ray K, Roca CD, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H. Interleukins and their signaling pathways in the Reactome biological pathway database. J Allergy Clin Immunol. Apr 14. PubMed.
• Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H. Reactome diagram viewer: data structures and strategies to boost performance. Bioinformatics. Apr 1. PubMed.
• Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H. Reactome graph database: Efficient access to complex pathway data. PLoS Comput Biol.Jan 29. PubMed.
• Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Duenas Roca C, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D’Eustachio P. The Reactome Pathway Knowledgebase.Nucleic Acids Research. Jan 4. PubMed.
• Loney F, Wu G. Automation of ReactomeFIViz via CyREST API. F1000Res. May 23. 2018. doi: 10.12688/f1000research.14776.2 PubMed.

2017

• Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D’Eustachio P, Ping P, Hermjakob H, Fabregat A. Reactome enhanced pathway visualization. Oxford Bioinformatics. July 6. PubMed.
• Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D’Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach.BMC Bioinformatics.Mar 2. PubMed.
• Wu G, Haw R. Functional Interaction Network Construction and Analysis for Disease Discovery.Methods Mol Biol. PubMed.

2016

• Hill DP, D’Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA. Modeling biochemical pathways in the gene ontology.Database (Oxford). 2016 Sep 1. PubMed.
• Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT. Reactome from a WikiPathways Perspective. PLoS Comput Biol. May. PubMed.
• 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. The Reactome pathway Knowledgebase.Nucleic Acids Res. Dec 9. PubMed.

2015

• McKay SJ, Weiser J. Installing a Local Copy of the Reactome Web Site and Knowledgebase. Curr ProtocBioinformatics. 50:9.10.1-9.10.10. PubMed.
• Jupe S, Fabregat A, and Hermjakob H.Expression data analysis with reactome.Curr Protoc Bioinformatics. Chapter 8 Unit8.20. PubMed.
• Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, and Hermjakob H.A visual review of the interactome of LRRK2: Using deep-curated molecular interactions data to represent biology.Proteomics. PubMed.

2014

• Wu G, Dawson E, Duong A, Haw R and Stein L.ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis.3:146F1000Research. PubMed.
• Jupe S, Jassal B, Williams M, and Wu G. A controlled vocabulary for pathway entities and events.Database (Oxford)Jun. PubMed.
• Backman S, Kollara A, Haw R, Stein L, Brown TJ. Glucocorticoid-Induced Reversal of Interleukin-1β-Stimulated Inflammatory Gene Expression in Human Oviductal Cells. PLoS ONE 9(5). PubMed.

2013

• Croft D, Fabregat Mundo A, 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 and D’Eustachio P.The Reactome pathway knowledgebase.Nucleic Acids Res. PubMed
• Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D’Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D. Gramene 2013: comparative plant genomics resources.Nucleic Acids Res.PubMed Croft, D. Building models using reactome pathways as templates.Methods Mol Biol. 1021:273-83. PubMed
• D’Eustachio, P. Pathway databases: making chemical and biological sense of the genomic data flood.Chem Biol. 20(5):629-35. PubMed

2012

• Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D’Eustachio P and Stein L. Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome.Cancers.4 (4), 1180-1211. PubMed.
• Wu G and Stein L. A network module-based method for identifying cancer prognostic signatures.Genome Biol. 13(12):R112. PubMed
• Haw R and Stein L. Using the reactome database.Curr Protoc Bioinformatics. Chapter 8:Unit 8.7. PubMed

2011

• Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U,Goodall AH,……….. Soranzo N. New gene functions in megakaryopoiesis and platelet formation.Nature. 480(7376):201-8. PubMed
• Ndegwa N, Côté RG, Ovelleiro D, D’Eustachio P, Hermjakob H, Vizcaíno JA, Croft D. Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.Database (Oxford). bar047. PubMed
• Haw RA, Croft D, Yung CK, Ndegwa N, D’Eustachio P, Hermjakob H, Stein LD. The Reactome BioMart.Database (Oxford). bar047. PubMed
• Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D’Eustachio P, Smith B, Blake JA, Wu C.The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics. 12:371. PubMed
• Haw R, Hermjakob H, D’Eustachio P, Stein L. Reactome pathway analysis to enrich biological discovery in proteomics data sets.Proteomics. 11(18):3598-613. PubMed
• Sawey ET, Chanrion M, Cai C, Wu G, Zhang J, Zender L, Zhao A, Busuttil RW, Yee H, Stein L, French DM, Finn RS, Lowe SW, and Powers S. Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by oncogenomic screening.Cancer Cell.19(3): 347-58. PubMed
• Jassal B. Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters.Human Genomics. 5(4):310-5. PubMed
• D’Eustachio P. Reactome knowledgebase of human biological pathways and processes.Methods Mol Biol.694:49-61. PubMed
• Gillespie M, Shamovsky V, D’Eustachio P. Human and chicken TLR pathways: manual curation and computer-based orthology analysis.Mammalian Genome.22(1-2):130-8. PubMed
• 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. Reactome: a database of reactions, pathways and biological processes.Nucleic Acids Res. (Database issue).D691-7. PubMed
• Dall’olio GM, Jassal B, Montanucci L, Gagneux P, Bertranpetit J, Laayouni H. The annotation of the Asparagine N-linked Glycosylation pathway in the Reactome Database.Glycobiology. 21(11):1395-400. PubMed

2010

• Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, ……. McCarthy MI. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.Nat Genet.42(7): 579-89. PubMed
• Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D’Eustachio P. The systematic annotation of the three main GPCR families in Reactome.Database (Oxford).baq018. PubMed
• Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.Nucleic Acids Res. (Web Server issue)38:W78-83. PubMed
• Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis.Genome Biol.11(5):R53. PubMed

2009

• Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D’Eustachio P. Reactome knowledgebase of human biological pathways and processes.Nucleic Acids Res.37:D619-22. PubMed

2007

• Vastrik I, D’Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.Reactome: a knowledge base of biologic pathways and processes.Genome Biol. 8:R39. PubMed
• Matthews L, D’Eustachio P, Gillespie M, Croft D, de Bono B, Gopinath G, Jassal B, Lewis S, Schmidt E, Vastrik I, Wu G, Birney E, Stein L. An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes.Bioinformatics Primer, NCI/Nature Pathway Interaction Database. doi:10.1038/pid.2007.3.

2005

• Joshi-Tope G, Gillespie M, Vastrik I, D’Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L. Reactome: a knowledgebase of biological pathways.Nucleic Acids Res.1:D428-32. PubMed

2004

• Stein LD. Using the Reactome database.Curr Protoc Bioinformatics.Chapter 8:Unit 8.7. PubMed

2003

• Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D’Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L. The Genome Knowledgebase: a resource for biologists and bioinformaticists.Cold Spring Harb Symp Quant Biol.68:237-43. PubMed