2026

• Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, Griss J, Hogue GFJ, Li NT, Matthews L, May B, Milacic M, Mohammadi H, Petryszak R, Rothfels K, Shamovsky V, Stephan R, Tiwari K, Weiser J, Wright A, Gillespie M, Wu G, Stein L, Hermjakob H, D'Eustachio P. The Reactome Knowledgebase 2026. Nucleic Acids Res. 2025 Nov 18. doi: 10.1093/nar/gkaf1223. PubMed.
• Mohammadi H, Almodaresi F, Hogue GFJ , Wright A, Orlic-Milacic M, Li NT, Mawani A, Stein L. React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase. bioRxiv 2025 Dec 12. Link
• Wu G, Matthews L, Boyer N, Milacic M, Beavers D, Li NT, May B, Rothfels K, Shamovsky V, Stephan R, Gillespie M, Hermjakob H, D'Eustachio P, Stein L. Application of Large Language Models for Annotating Genes into Reactome Pathways, bioRxiv 2025 Dec 20; Link

2025

• Matthews L, Cook J, Stephan R, Milacic M, Rothfels K, Shamovsky V, Jassal B, Haw R, Sevilla C, Gong C, Ragueneau E, May B, Wright A, Weiser J, Beavers D, Tiwari K, Senff-Ribeiro A, Varusai T, Hermjakob H, D'Eustachio P, Wu G, Stein L, Gillespie ME. Advancing curation of viral life cycles, host interactions, and therapeutics in Reactome. J Virol. 2025 May 20;99(5):e0202424. doi: 10.1128/jvi.02024-24. 2025 Apr 23. PubMed
• Smith NR, Giske NR, Sengupta SK, Conley P, Swain JR, Nair A, Fowler KL, Klocke C, Yoo YJ, Anderson AN, Sanati N, Torkenczy K, Adey AC, Fischer JM, Wu G, Wong MH. Dual states of murine Bmi1-expressing intestinal stem cells drive epithelial development utilizing non-canonical Wnt signaling. Dev Cell. 2025 Apr 16:S1534-5807(25)00177-7. doi: 10.1016/j.devcel.2025.03.014. PubMed

2024

• Grentner A, Ragueneau E, Gong C, Prinz A, Gansberger S, Oyarzun I, Hermjakob H, Griss J. ReactomeGSA: new features to simplify public data reuse. Bioinformatics. 2024 Jun 3;40(6):btae338. doi: 10.1093/bioinformatics/btae338. PubMed
• Arora C, Matic M, Bisceglia L, Di Chiaro P, De Oliveira Rosa N, Carli F, Clubb L, Nemati Fard LA, Kargas G, Diaferia GR, Vukotic R, Licata L, Wu G, Natoli G, Gutkind JS, Raimondi F. The landscape of cancer-rewired GPCR signaling axes. Cell Genom. 2024 May 8;4(5):100557. doi: 10.1016/j.xgen.2024.100557. PubMed
• Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, 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 (Oxford). 2024 May 7;2024:baae031. doi: 10.1093/database/baae031. PubMed
• R. Stephan, Interleaved snowballing: Reducing the workload of literature curators. Arxiv [Preprint]. 2024 Feb 13. 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. PubMed 
• 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 Res. 2024 Jan 5;52(D1):D672-D678. doi: 10.1093/nar/gkad1025. PubMed
• Li N, Orlic-Milacic M, Beavers D et al. Unlocking biological insights: Reactome's comprehensive pathway analysis and developmental lineage path project [version 1; not peer reviewed]. F1000Research 2024, 13:1013 (poster) (doi: 10.7490/f1000research.1119846.1)

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. doi: 10.15252/msb.202110851. 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 Dec;19(12):2115-2125. doi: 10.1074/mcp.TIR120.002155. Epub 2020 Sep 9. PubMed
• Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 2021 Jun;17(6):1543-1554. doi: 10.1080/15548627.2020.1761659. Epub 2020 Jun 2. 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: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. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed
• Naithani S, Gupta P, Preece J, D'Eustachio P, Elser JL, Garg P, Dikeman DA, Kiff J, Cook J, Olson A, Wei S, Tello-Ruiz MK, Mundo AF, Munoz-Pomer A, Mohammed S, Cheng T, Bolton E, Papatheodorou I, Stein L, Ware D, Jaiswal P. Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 2020 Jan 8;48(D1):D1093-D1103. doi: 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;8:908. doi: 10.12688/f1000research.19592.1. 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;2019:baz123. doi: 10.1093/database/baz123. 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. 2018 Apr;141(4):1411-1416. doi: 10.1016/j.jaci.2017.12.992. Epub 2018 Feb 21. 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. 2018 Apr 1;34(7):1208-1214. doi: 10.1093/bioinformatics/btx752. 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. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. PubMed
• 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. The Reactome Pathway Knowledgebase. Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655. doi: 10.1093/nar/gkx1132. PubMed
• Loney F, Wu G. Automation of ReactomeFIViz via CyREST API. F1000Res. 2018 May 2;7:531. 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. Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441. 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. 2017 Mar 2;18(1):142. doi: 10.1186/s12859-017-1559-2. PubMed
• Wu G, Haw R. Functional Interaction Network Construction and Analysis for Disease Discovery. Methods Mol Biol. 2017;1558:235-253. doi: 10.1007/978-1-4939-6783-4_11.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;2016:baw126. doi: 10.1093/database/baw126. 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. 2016 May 20;12(5):e1004941. doi: 10.1371/journal.pcbi.1004941. 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. 2016 Jan 4;44(D1):D481-7. doi: 10.1093/nar/gkv1351. Epub 2015 Dec 9. PubMed

2015

• McKay SJ, Weiser J. Installing a Local Copy of the Reactome Web Site and Knowledgebase. Curr Protoc Bioinformatics. 2015 Jun 19;50:9.10.1-9.10.10. doi: 10.1002/0471250953.bi0910s50. PubMed
• Jupe S, Fabregat A, Hermjakob H. Expression data analysis with Reactome. Curr Protoc Bioinformatics. 2015 Mar 9;49:8.20.1-8.20.9. doi: 10.1002/0471250953.bi0820s49. PubMed
• Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H. A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. Proteomics. 2015 Apr;15(8):1390-404. doi: 10.1002/pmic.201400390. Epub 2015 Mar 21. PubMed

2014

• Wu G, Dawson E, Duong A, Haw R, Stein L. ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis. F1000Res. 2014 Jul 1;3:146. doi: 10.12688/f1000research.4431.2. PubMed
• Jupe S, Jassal B, Williams M, Wu G. A controlled vocabulary for pathway entities and events. Database (Oxford). 2014 Jun 20;2014:bau060. doi: 10.1093/database/bau060. 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. 2014 May 21;9(5):e97997. doi: 10.1371/journal.pone.0097997.  PubMed

2013

• Croft D. Building models using Reactome pathways as templates. Methods Mol Biol. 2013;1021:273-83. doi: 10.1007/978-1-62703-450-0_14. 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. 2013 May 23;20(5):629-35. doi: 10.1016/j.chembiol.2013.03.018. PubMed

2012

• Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L. Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel). 2012 Nov 8;4(4):1180-211. doi: 10.3390/cancers4041180. PubMed.
• Wu G, Stein L. A network module-based method for identifying cancer prognostic signatures. Genome Biol. 2012 Dec 10;13(12):R112. doi: 10.1186/gb-2012-13-12-r112. PubMed
• Haw R, Stein L. Using the reactome database. Curr Protoc Bioinformatics. 2012 Jun;Chapter 8:8.7.1-8.7.23. doi: 10.1002/0471250953.bi0807s38.  PubMed

2011

• Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Mägi R, Meacham S, Okada Y, Pirastu N, Sorice R, Teumer A, Voss K, Zhang W, Ramirez-Solis R, Bis JC, Ellinghaus D, Gögele M, Hottenga JJ, Langenberg C, Kovacs P, O'Reilly PF, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, Ellen van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, D'Adamo P, Davies G, de Boer RA, de Geus EJ, Döring A, Elliott P, Erdmann J, Evans DM, Falchi M, Feng W, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kühnel B, Kyrtsonis MC, Lagou V, Lloyd-Jones H, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nakamura Y, Nauck M, Navis G, Nöthlings U, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Tang WH, Taylor K, Tenesa A, Lay Thein S, Tönjes A, Uda M, Ulivi S, van Veldhuisen DJ, Visscher PM, Völker U, Wichmann HE, Wiggins KL, Willemsen G, Yang TP, Hua Zhao J, Zitting P, Bradley JR, Dedoussis GV, Gasparini P, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, Joost van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Rendon A, Ferreira MA, Ouwehand WH, Soranzo N. New gene functions in megakaryopoiesis and platelet formation. Nature. 2011 Nov 30;480(7376):201-8. doi: 10.1038/nature10659. 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). 2011 Oct 23;2011:bar047. doi: 10.1093/database/bar047. PubMed
• Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD. The Reactome BioMart. Database (Oxford). 2011 Oct 19;2011:bar031. doi: 10.1093/database/bar031. 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. 2011 Sep 19;12:371. doi: 10.1186/1471-2105-12-371. PubMed
• Haw R, Hermjakob H, D'Eustachio P, Stein L. Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics. 2011 Sep;11(18):3598-613. doi: 10.1002/pmic.201100066. 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, Powers S. Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell. 2011 Mar 8;19(3):347-58. doi: 10.1016/j.ccr.2011.01.040. PubMed
• Jassal B. Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters. Hum Genomics. 2011 May;5(4):310-5. doi: 10.1186/1479-7364-5-4-310. PubMed
• D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Methods Mol Biol. 2011;694:49-61. doi: 10.1007/978-1-60761-977-2_4. PubMed
• Gillespie M, Shamovsky V, D'Eustachio P. Human and chicken TLR pathways: manual curation and computer-based orthology analysis. Mamm Genome. 2011 Feb;22(1-2):130-8. doi: 10.1007/s00335-010-9296-0. Epub 2010 Oct 30. 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. 2011 Jan;39(Database issue):D691-7. doi: 10.1093/nar/gkq1018. Epub 2010 Nov 9. 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. 2011 Nov;21(11):1395-400. doi: 10.1093/glycob/cwq215. Epub 2011 Jan 2. 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, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JR, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CN, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI; MAGIC investigators; GIANT Consortium. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet. 2010 Jul;42(7):579-89. doi: 10.1038/ng.609. Erratum in: Nat Genet. 2011 Apr;43(4):388. 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). 2010 Jul 29;2010:baq018. doi: 10.1093/database/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. 2010 Jul;38(Web Server issue):W78-83. doi: 10.1093/nar/gkq482. Epub 2010 Jun 2. PubMed
• Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010;11(5):R53. doi: 10.1186/gb-2010-11-5-r53. Epub 2010 May 19. 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. 2009 Jan;37(Database issue):D619-22. doi: 10.1093/nar/gkn863. Epub 2008 Nov 3. 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. 2007;8(3):R39. doi: 10.1186/gb-2007-8-3-r39. Erratum in: Genome Biol. 2009 Feb 4;10(2):402. Joshi-Tope, Geeta [removed]. 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. doi: 10.1093/nar/gki072. PubMed

2004

• Stein LD. Using the Reactome database.Curr Protoc Bioinformatics.Chapter 8:Unit 8.7. doi: 10.1002/0471250953.bi0807s7. 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. Doi: doi: 10.1101/sqb.2003.68.237. PubMed