Publications

2005-2009

Topoisomerase I levels in the NCI-60 cancer cell line panel determined by validated ELISA and microarray analysis and correlation with indenoisoquinoline sensitivity.
Mol Cancer Ther. 2009 Jul;8(7):1878-84. Epub 2009 Jul 7
Pfister TD, Reinhold WC, Agama K, Gupta S, Khin SA, Kinders RJ, Parchment RE, Tomaszewski JE, Doroshow JH, Pommier Y.

Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database.
Mol Cancer Ther. 2009 Jul;8(7):2057-66. Epub 2009 Jul 7
Orina JN, Calcagno AM, Wu CP, Varma S, Shih J, Lin M, Eichler G, Weinstein JN, Pommier Y, Ambudkar SV, Gottesman MM, Gillet JP.

CellMiner: a relational database and query tool for the NCI-60 cancer cell lines.
BMC Bioinformatics. 2009 Jun 23;10:277
Shankavaram UT, Varma S, Kane D, Sunshine M, Chary KK, Reinhold WC, Pommier Y, Weinstein JN.

DNA fingerprinting of the NCI-60 cell line panel.
Mol Cancer Ther. 2009 Apr;8(4):713-24
Lorenzi PL, Reinhold WC, Varma S, Hutchinson AA, Pommier Y, Chanock SJ, Weinstein JN.

Asparagine synthetase is a predictive biomarker of L-asparaginase activity in ovarian cancer cell lines.
Mol Cancer Ther. 2008 Oct;7(10):3123-8
Lorenzi PL, Llamas J, Gunsior M, Ozbun L, Reinhold WC, Varma S, Ji H, Kim H, Hutchinson AA, Kohn EC, Goldsmith PK, Birrer MJ, Weinstein JN.

SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.
BMC Bioinformatics. 2008 Jul 18;9:313
Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN.

In vitro differential sensitivity of melanomas to phenothiazines is based on the presence of codon 600 BRAF mutation.
Mol Cancer Ther. 2008 Jun 4. [Epub ahead of print]
Ikediobi ON, Reimers M, Durinck S, Blower PE, Futreal AP, Stratton MR, Weinstein JN.

A Postgenomic Visual Icon.
Science. 2008 March 28;319(5871):1772
Weinstein JN.

The EDGE hypothesis: Epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer
Front Neuroendocrinol. 2008 Jan 8
Ruden DM, Jamison DC, Zeeberg BR, Garfinkel MD, Weinstein JN, Rasouli P, Lu X.

VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays.
BMC Bioinformatics. 2008 Jan 29;9(1):67
Kestler HA, Muller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN.

Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National CancerInstitute Anticancer Drug Screen.
Cancer Res. 2008 Jan 15;68(2):415-24.
Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, Trent JM, Bittner ML, Meltzer PS, Fornace AJ Jr.

Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers.
Mol Cancer Ther. 2008 Jan;7(1):10-8.
Stevens EV, Nishizuka S, Antony S, Reimers M, Varma S, Young L, Munson PJ, Weinstein JN, Kohn EC, Pommier Y.

MicroRNAs modulate the chemosensitivity of tumor cells.
Mol Cancer Ther. 2008 Jan;7(1):1-9.
Blower PE, Chung JH, Verducci JS, Lin S, Park JK, Dai Z, Liu CG, Schmittgen TD, Reinhold WC, Croce CM, Weinstein JN, Sadee W.

UPLC-ESI-TOFMS-Based Metabolomics and Gene Expression Dynamics Inspector Self-Organizing Metabolomic Maps as Tools for Understanding the Cellular Response to Ionizing Radiation.
Anal Chem. 2008 Jan 4
Patterson AD, Li H, Eichler GS, Krausz KW, Weinstein JN, Fornace AJ Jr, Gonzalez FJ, Idle JR.

Opportunities and challenges in ovarian cancer research, a perspective from the 11th Ovarian cancer action/HHMT Forum, Lake Como, March 2007
Gynecol Oncol. 2007 Dec 19
Ashworth A, Balkwill F, Bast RC Jr, Berek JS, Kaye A, Boyd JA, Mills G, Weinstein JN, Woolley K, Workman P.

The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data
Genome Biol. 2007 Sep 10;8(9):R187
Gabriel S Eichler, Mark Reimers, David Kane and John N Weinstein

A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
Proc Natl Acad Sci U S A. 2007 Jul 31
Lee JK, Havaleshko DM, Cho H, Weinstein JN, Kaldjian EP, Karpovich J, Grimshaw A, Theodorescu D.

AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
Bioinformatics. 2007 Jul 27
Liu H, Zeeberg BR, Gang Q, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC, Kane DW, Weinstein JN

Signal pathway profiling of epithelial and stromal compartments of colonic carcinoma reveals epithelial-mesenchymal transition
Oncogene. 2007 Jul 9
Sheehan KM, Gulmann C, Eichler GS, Weinstein JN, Barrett HL, Kay EW, Conroy RM, Liotta LA, Petricoin EF

MicroRNA expression profiles for the NCI-60 cancer cell panel
Mol Cancer Ther 2007;6(5):1483-91
Blower PE, Verducci JS, Lin S, Zhou J, Chung JH, Dai Z, Liu CG, Reinhold W, Lorenzi PL, Kaldjian EP, Croce CM, Weinstein JN, Sadee W.

Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study
Mol Cancer Ther 2007;6(3):820-32
Shankavaram UT, Reinhold WC, Nishizuka S, Major S, Morita D, Chary KK, Reimers MA, Scherf U, Kahn A, Dolginow D, Cossman J, Kaldjian EP, Scudiero DA, Petricoin E, Liotta L, Lee JK, Weinstein JN

Multiplexing siRNAs to compress RNAi-based screen size in human cells
Nucleic Acids Res. 2007 Mar 28
Martin SE, Jones TL, Thomas CL, Lorenzi PL, Nguyen DA, Runfola T, Gunsior M, Weinstein JN, Goldsmith PK, Lader E, Huppi K, Caplen NJ

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis
BMC Bioinformatics. 2007 Mar 5;8(1):75
Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN.

Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells
Mol Cancer Ther. 2007 Feb;6(2):391-403.
Reinhold WC, Reimers MA, Maunakea AK, Kim S, Lababidi S, Scherf U, Shankavaram UT, Ziegler MS, Stewart C, Kouros-Mehr H, Cui H, Dolginow D, Scudiero DA, Pommier YG, Munroe DJ, Feinberg AP, Weinstein JN

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.

Biomarkers in Cancer Staging, Prognosis and Treatment Selection
Nature Reviews Cancer 5, 845-856 (2005)
Joseph A. Ludwig and John N. Weinstein

The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress
Cancer Res. 2005 Nov 15;65(22):10255-10264.
Frank Staib, Ana I. Robles, Lyuba Varticovski, Xin W. Wang, Barry R. Zeeberg, Michail Sirotin, Victor B. Zhurkin, Lorne J. Hofseth, S. Perwez Hussain, John N. Weinstein, Peter R. Galle and Curtis C. Harris

Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
Mol Biol Cell. 2005 Nov 2; [Epub ahead of print]
Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.

Nova regulates brain-specific splicing to shape the ynapse
Nat Genet. 2005 Aug;37(8):844-52. Epub 2005 Jul 24
Jernej Ule, Alja Ule, Joanna Spencer, Alan Williams, Jing-Shan Hu, Melissa Cline, Hui Wang, Tyson Clark, Claire Fraser, Matteo Ruggiu, Barry R Zeeberg, David Kane, John N Weinstein, John Blume and Robert B Darnell

High-Throughput GoMiner, an 'industrial-strength' integrative Gene Ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
BMC Bioinformatics. 2005 Jul 5;6(1):168.
Barry R Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W Kane, Mark Reimers, Robert Stephens, David Bryant, Stanley K Burt, Eldad Elnekave, Danielle M Hari, Thomas A Wynn, Charlotte Cunningham-Rundles, Donn M Stewart, David Nelson and John N Weinstein

Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases
BMC Bioinformatics. 2005 Jul 1;6(1):166.
Mark Reimers and John N Weinstein

Three microarray platforms: an analysis of their concordance in profiling gene expression
BMC Genomics. 2005 May 5;6(1):63.
Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES.

Workshop on Cancer Biometrics: Identifying Biomarkers and Surrogates of Cancer in Patients: A Meeting Held at the Masur Auditorium, National Institutes of Health.
J Immunother. 2005 March/April;28(2):79-119.
Lotze MT, Wang E, Marincola FM, Hanna N, Bugelski PJ, Burns CA, Coukos G, Damle N, Godfrey TE, Howell WM, Panelli MC, Perricone MA, Petricoin EF, Sauter G, Scheibenbogen C, Shivers SC, Taylor DL, Weinstein JN, Whiteside TL.

Karyotypic "state" as a potential determinant for anticancer drug discovery
Proc Natl Acad Sci U S A. 2005 Feb 9; [Epub ahead of print]
Roschke AV, Lababidi S, Tonon G, Gehlhaus KS, Bussey K, Weinstein JN, Kirsch IR

Identification of non-cross-resistant platinum compounds with novel cytotoxicity profiles using the NCI anticancer drug screen and clustered image map visualizations
Crit Rev Oncol Hematol. 2005 Jan;53(1):25-34.
Fojo T, Farrell N, Ortuzar W, Tanimura H, Weinstein J, Myers TG