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Items: 18

1.

Interactive or static reports to guide clinical interpretation of cancer genomics.

Gray SW, Gagan J, Cerami E, Cronin AM, Uno H, Oliver N, Lowenstein C, Lederman R, Revette A, Suarez A, Lee C, Bryan J, Sholl L, Van Allen EM.

J Am Med Inform Assoc. 2018 May 1;25(5):458-464. doi: 10.1093/jamia/ocx150.

2.

Institutional implementation of clinical tumor profiling on an unselected cancer population.

Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE.

JCI Insight. 2016 Nov 17;1(19):e87062. doi: 10.1172/jci.insight.87062.

3.

Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes.

Jones S, Stransky N, McCord CL, Cerami E, Lagowski J, Kelly D, Angiuoli SV, Sausen M, Kann L, Shukla M, Makar R, Wood LD, Diaz LA Jr, Lengauer C, Velculescu VE.

Nat Commun. 2014 Sep 19;5:5006. doi: 10.1038/ncomms6006.

4.

The landscape of kinase fusions in cancer.

Stransky N, Cerami E, Schalm S, Kim JL, Lengauer C.

Nat Commun. 2014 Sep 10;5:4846. doi: 10.1038/ncomms5846.

5.

PiHelper: an open source framework for drug-target and antibody-target data.

Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C.

Bioinformatics. 2013 Aug 15;29(16):2071-2. doi: 10.1093/bioinformatics/btt345. Epub 2013 Jun 12.

6.

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N.

Sci Signal. 2013 Apr 2;6(269):pl1. doi: 10.1126/scisignal.2004088.

7.

Using MEMo to discover mutual exclusivity modules in cancer.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N.

Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit 8.17. doi: 10.1002/0471250953.bi0817s41.

8.

BRCA1 immunohistochemistry in a molecularly characterized cohort of ovarian high-grade serous carcinomas.

Garg K, Levine DA, Olvera N, Dao F, Bisogna M, Secord AA, Berchuck A, Cerami E, Schultz N, Soslow RA.

Am J Surg Pathol. 2013 Jan;37(1):138-46. doi: 10.1097/PAS.0b013e31826cabbd.

9.

Comparative oncogenomics implicates the neurofibromin 1 gene (NF1) as a breast cancer driver.

Wallace MD, Pfefferle AD, Shen L, McNairn AJ, Cerami EG, Fallon BL, Rinaldi VD, Southard TL, Perou CM, Schimenti JC.

Genetics. 2012 Oct;192(2):385-96. doi: 10.1534/genetics.112.142802. Epub 2012 Jul 30.

10.

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N.

Cancer Discov. 2012 May;2(5):401-4. doi: 10.1158/2159-8290.CD-12-0095. Erratum in: Cancer Discov. 2012 Oct;2(10):960.

11.

Mutual exclusivity analysis identifies oncogenic network modules.

Ciriello G, Cerami E, Sander C, Schultz N.

Genome Res. 2012 Feb;22(2):398-406. doi: 10.1101/gr.125567.111. Epub 2011 Sep 9.

12.

Pathway Commons, a web resource for biological pathway data.

Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C.

Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. doi: 10.1093/nar/gkq1039. Epub 2010 Nov 10.

13.

Integrative genomic profiling of human prostate cancer.

Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL.

Cancer Cell. 2010 Jul 13;18(1):11-22. doi: 10.1016/j.ccr.2010.05.026. Epub 2010 Jun 24.

14.

Automated network analysis identifies core pathways in glioblastoma.

Cerami E, Demir E, Schultz N, Taylor BS, Sander C.

PLoS One. 2010 Feb 12;5(2):e8918. doi: 10.1371/journal.pone.0008918.

15.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

16.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.

BMC Biol. 2007 Oct 9;5:44.

17.

cPath: open source software for collecting, storing, and querying biological pathways.

Cerami EG, Bader GD, Gross BE, Sander C.

BMC Bioinformatics. 2006 Nov 13;7:497.

18.

Agile methods in biomedical software development: a multi-site experience report.

Kane DW, Hohman MM, Cerami EG, McCormick MW, Kuhlmman KF, Byrd JA.

BMC Bioinformatics. 2006 May 30;7:273.

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