2017

  • 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, Nov 14, Publisher.
  • 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 Protoc Bioinformatics. 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 Unit 8.20. 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. 3:146 F1000ResearchPubMed.
  • 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 ResPubMed 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.  Publisher
  • Wu G and Stein L. A network module-based method for identifying cancer prognostic signatures. Genome Biol. 13(12):R112. PubMed
  • Kim Y, Ignatchenko V, Yao CQ, Kalatskaya I, Nyalwidhe JO, Lance RS, Gramolini AO, Troyer DA, Stein LD, Boutros PC, Medin JA, Semmes OJ, Drake RR, Kislinger T. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics. 11(12):1870-84. PubMed
  • Haw R and Stein L. Using the reactome database. Curr Protoc Bioinformatics. Chapter 8:Unit 8.7. PubMed
  • Reveiller M, Ghatak S, Toia L, Kalatskaya I, Stein L, D’Souza M, Zhou Z, Bandla S, Gooding WE, Godfrey TE, Peters JH. Bile exposure inhibits expression of squamous differentiation genes in human esophageal epithelial cells. Ann Surg. 255(6):1113-20. PubMed
  • Sprowl JA, Reed K, Armstrong SR, Lanner C, Guo B, Kalatskaya I, Stein L, Hembruff SL, Tam A, Parissenti AM. Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells. Breast Cancer Res. 14(1):R2. 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
  • Ismail A, Bandla S, Reveiller M, Toia L, Zhou Z, Gooding WE, Kalatskaya I, Stein L, D’Souza M, Litle VR, Peters JH, Pennathur A, Luketich JD, Godfrey TE. Early G₁ cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma. Clin Cancer Res. 17(13):4513-22. 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. 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