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Genomics and Bioinformatics Group

2006 Publication

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Spotlight on molecular profiling: 'integromic' analysis of the NCI-60 cancer cell lines
Mol Cancer Ther. 2006;5:2601-2605
Weinstein JN

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set
Mol Cancer Ther. 2006;5:2606-2612
Ikediobi, O.N., Edkins, S., Stevens, C., O'Meara, S., Bignell, G., Teague, J., Butler, A., Buck, G., Gray, K., Halliday, K., Kosmidou, V., Lugg, R., Menzies, A., Perry, J., Petty, R., Raine, K., Shepherd, R., Small, A., Widaa, S., Varian, J., Reinhold, W., Weinstein, J.N., Stratton, M.R., Futreal, P.A., and Wooster, R.

Asparagine synthetase as a causal, predictive biomarker for L-asparaginase activity in ovarian cancer cells
Mol Cancer Ther. 2006;5:2613-2623
Lorenzi, P.L., Reinhold, W.C., Rudelius, M., Gunsior, M., Shankavaram, U., Bussey, K.J., Scherf, U., Eichler, G.S., Martin, S.E., Chin, K., Gray, J.W., Kohn, E.C., Horak, I.D., Von Hoff, D.D., Raffeld, M., Goldsmith, P.K., Caplen, N.J., and Weinstein, J.N.

Depicting combinatorial complexity with the molecular interaction map notation
Mol Syst Biol. 2006;2:51. Epub 2006 Oct 3.
Kohn KW, Aladjem MI, Kim S, Weinstein JN, and Pommier Y.

Activation of Aminoflavone (NSC 686288) by a Sulfotransferase Is Required for the Antiproliferative Effect of the Drug and for Induction of Histone γ-H2AX
Cancer Res. 2006 Oct 1;66(19):9656-64.
Ling-hua Meng, Uma Shankavaram, Chi Chen, Keli Agama, Hai-qing Fu, Frank J. Gonzalez, John Weinstein and Yves Pommier

Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma
Cancer Res. 2006 Jul 15;66(14):7216-24.
Riss J, Khanna C, Koo S, Chandramouli GV, Yang HH, Hu Y, Kleiner DE, Rosenwald A, Schaefer CF, Ben-Sasson SA, Yang L, Powell J, Kane DW, Star RA, Aprelikova O, Bauer K, Vasselli JR, Maranchie JK, Kohn KW, Buetow KH, Linehan WM, Weinstein JN, Lee MP, Klausner RD, Barrett JC.

Agile methods in biomedical software development: a multi-site experience report
BMC Bioinformatics. 2006 May 30;7(1):273
David W Kane, Moses M Hohman, Ethan G Cerami, Michael W McCormick, Karl F Kuhlmman and Jeff A Byrd

Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.
Genome Res. 2006 Jun;16(6):796-803.
Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA.

Chk2 Molecular Interaction Map and Rationale for Chk2 Inhibitors
Clin Cancer Res. 2006 May 1;12(9):2657-61.
Yves Pommier, John N. Weinstein, Mirit I. Aladjem and Kurt W. Kohn

Selective Toxicity of NSC73306 in MDR1-Positive Cells as a New Strategy to Circumvent Multidrug Resistance in Cancer
Cancer Res. 2006 May 1;66(9):4808-4815.
Joseph A. Ludwig, Gergely Szakács, Scott E. Martin, Benjamin F. Chu, Carol Cardarelli, Zuben E. Sauna, Natasha J. Caplen, Henry M. Fales, Suresh V. Ambudkar, John N. Weinstein and Michael M. Gottesman

Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
Mol Cancer Ther. 2006 Apr;5(4):853-67.
Kimberly J. Bussey, Koei Chin, Samir Lababidi, Mark Reimers, William C. Reinhold, Wen-Lin Kuo, Fuad Gwadry, Ajay, Hosein Kouros-Mehr, Jane Fridlyand, Ajay Jain, Colin Collins, Satoshi Nishizuka, Giovanni Tonon, Anna Roschke, Kristen Gehlhaus, Ilan Kirsch, Dominic A. Scudiero, Joe W. Gray and John N. Weinstein

AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
BMC Bioinformatics 2006, 7:192 doi:10.1186/1471-2105-7-192
Sylvia M Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland, Margot Sunshine, Uma Shankavaram, Frank Washburn, Daniel Asin, Hosein Kouros-Mehr, David Kane and John N Weinstein

Comparison of methods for sequential screening of large compound sets
Comb Chem High Throughput Screen. 2006 Feb;9(2):115-22.
Blower PE, Cross KP, Eichler GS, Myatt GJ, Weinstein JN, Yang C.


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