Reactome Publications

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Reactome Publications

This is a listing of publications and references describing Reactome, contributed by the Reactome team.

Publications

Croft, D (2013) Building models using reactome pathways as templates. Methods Mol Biol. 1021:273-83. PubMed
D'Eustachio, P (2013) Pathway databases: making chemical and biological sense of the genomic data flood. Chem Biol. 20(5):629-35. PubMed
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P and Stein L (2012) Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome. Cancers 4 (4), 1180-1211. Direct from Publisher
Wu G and Stein L (2012) 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 (2013) 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 (2012) 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. (2012) Bile exposure inhibits expression of squamous differentiation genes in human esophageal epithelial cells. Ann Surg. 255(6):1113-20. PubMed
Jupe S, Akkerman JW, Soranzo N, Ouwehand WH. (2012) Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets. J Thromb Haemost. 2012 Nov;10(11):2399-402. doi: 10.1111/j.1538-7836.2012.04930.x. PubMed
Sprowl JA, Reed K, Armstrong SR, Lanner C, Guo B, Kalatskaya I, Stein L, Hembruff SL, Tam A, Parissenti AM. (2012) 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
Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, ...... Soranzo N. (2011) 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. (2011) 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. (2011) 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. (2011) The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics. 12:371. PubMed
Haw R, Hermjakob H, D'Eustachio P, Stein L. (2011) 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. (2011) 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. (2011) Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by oncogenomic screening. Cancer Cell 19(3): 347-58. PubMed
Jassal B. (2011) Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters. Human Genomics. 5(4):310-5.PubMed
D'Eustachio P. (2011) Reactome knowledgebase of human biological pathways and processes. Methods Mol Biol:694:49-61. PubMed
Gillespie M, Shamovsky V, D’Eustachio P. (2011) Human and chicken TLR pathways: manual curation and computer-based orthology analysis. Mammalian Genome:22(1-2):130-8. PubMedCentral
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. (2011) 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. (2011) The annotation of the Asparagine N-linked Glycosylation pathway in the Reactome Database. Glycobiology. 21(11):1395-400. PubMed
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. (2010) 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. (2010) The systematic annotation of the three main GPCR families in Reactome. Database:baq018. PubMed
Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. (2010) R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. 38(Web Server issue):W78-83. PubMed
Wu G, Feng X, Stein L. (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11(5):R53. PubMed
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. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37:D619-22. PubMed
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. (2007) 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 2007 doi:10.1038/pid.2007.3.
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. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 1:D428-32. PubMed
Stein LD. (2004) Using the Reactome database. Curr Protoc Bioinformatics. Chapter 8:Unit 8.7. PubMed
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. (2003) The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harb Symp Quant Biol. 68:237-43. PubMed

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