Reactome Publications

From ReactomeWiki

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

Publications

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.

Citing Reactome

The following are examples that can be used to cite Reactome.

To cite the Reactome project:
Please cite the two recent Reactome publications: Croft et al. 2011 and Matthews et al. 2009.

To cite a Reactome pathway:
Please use the appropriate DOI from the Table of Contents

To cite Reactome files obtained via the World Wide Web:
Reactome project. "Reactome" http://www.reactome.org/ (date of message or visit).

To cite Reactome files available for download:
Reactome project. "Reactome" http://www.reactome.org/download/ (date of access).

When citing information obtained in a search of Reactome it should be remembered that while Reactome strives to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available.

If you would like to review a list of papers that cite one or more of the Reactome publications, please follow this link.