2000-2004

2004

Integromic Analysis of the NCI-60 Cancer Cell Lines
Breast Dis. 2004;19:11-22.
Weinstein JN

Analysis of ATP-Binding Cassette Transporter Expression in Drug-Selected Cell Lines by a Microarray Dedicated to Multidrug Resistance.
Mol Pharmacol. 2004 Dec;66(6):1397-405. Epub 2004 Sep 01.
Annereau JP, Szakacs G, Tucker CJ, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg BR, Reinhold W, Weinstein JN, Pommier Y, Paules RS, and Gottesman MM

Is the Gene Expression Pattern of Lung Cancer Detected by Screening With Spiral Computed Tomography Different from That of Symptom-Detected Lung Cancer?
Clinical Cancer Research Vol. 10, 5973-5974, September 15, 2004
James L. Mulshine and John N. Weinstein

Predicting Drug Sensitivity and Resistance: Profiling ABC Transporter Genes in Cancer Cells
2004 Cell PressPII: Section: Cancer Cell, Vol 6, 129-137, August 2004
Gergely Szakács, Jean-Philippe Annereau, Samir Lababidi, Uma Shankavaram, Angela Arciello, Kimberly J. Bussey, William Reinhold, Yanping Guo, Gary D. Kruh, Mark Reimers, John N. Weinstein, and Michael M. Gottesman

Membrane Transporters and Channels: Role of the Transportome in Cancer Chemosensitivity and Chemoresistance
Cancer Res. 2004 Jun 15;64(12):4294-301
Huang Y, Anderle P, Bussey KJ, Barbacioru C, Shankavaram U, Dai Z, Reinhold WC, Papp A, Weinstein JN, Sadée W.

Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics
BMC Bioinformatics 2004, 5:80 doi:10.1186/1471-2105-5-80
Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, Marston Linehan, J. Carl Barrett and John N Weinstein

Apoptosis Defects and Chemotherapy Resistance: Molecular Interaction Maps and Networks
Oncogene. 2004 Apr 12;23(16):2934-49
Yves Pommier, Olivier Sordet, Smitha Antony, Richard L Hayward and Kurt W Kohn

Properties of Switch-like Bioregulatory Networks Studied by Simulation of the Hypoxia Response Control System
Mol Biol Cell. 2004 Jul;15(7):3042-52
Kurt W. Kohn, Joseph Riss, Olga Aprelikova, John N. Weinstein, Yves Pommier, and J. Carl Barrett

Molecular Interaction Maps--A Diagrammatic Graphical Language for Bioregulatory Networks
Sci. STKE, Vol. 2004, Issue 222, pp. pe8
Mirit I. Aladjem, Stefania Pasa, Silvio Parodi, John N. Weinstein, Yves Pommier, and Kurt W. Kohn

Cancer Drug Discovery: Genomics, Proteomics, and Bioinformatics
Molecular Target Therapy of Cancer, Vol. 1, in press
Weinstein, J.N., Nishizuka, S., Reinhold, W.C., Bussey, K., Kim, S., Major, S., Lababidi, S., Feng, W., Wang, G., Raffeld, M., Sunshine, M., Narasimhan, S., Zeeberg, B., Wang, M., Lee, J.K., and Kane, D.

Linking Drugs and Genes: Pharmacogenomics, Pharmacoproteomics, Bioinformatics, and the NCI-60.
Oncogenomics: Molecular Approaches to Cancer. ISBN: 978-0-471-47664-1 Dec. 2004
Weinstein, J.N.

2003

Karyotypic complexity of the NCI-60 drug-screening panel
Cancer Res. 2003 Dec 15;63(24):8634-47
Roschke AV, Tonon G, Gehlhaus KS, McTyre N, Bussey KJ, Lababidi S, Scudiero DA, Weinstein JN, Kirsch IR

Comparing cDNA and Oligonucleotide Array Data: Concordance of Gene Expression Across Platforms for the NCI-60 Cancer Cells
Genome Biol. 2003;4(12):R82
Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau JP, Shankavaram U, Lababidi S, Smith LH, Gottesman MM, Weinstein JN.

Proteomic Profiling of the NCI-60 Cancer Cell Lines Using New High-density Reverse-phase Lysate Microarrays
Proceedings of the National Academy of Science USA 2003 November 25th; 100(24): 14229-14234
Satoshi Nishizuka, Lu Charboneau, Lynn Young, Sylvia Major, William C. Reinhold, Mark Waltham, Hosein Kouros-Mehr, Kimberly J. Bussey, Jae K. Lee, Virginia Espina, Peter J. Munson, Emanuel Petricoin III, Lance A. Liotta , and John N. Weinstein

Transcriptomic Analysis of the NCI-60 Cancer Cell Lines
C R Biol. 2003 Oct-Nov;326(10-11):909-20
Weinstein, J.N. and Pommier, Y.

Diagnostic Markers That Distinguish Colon and Ovarian Adenocarcinomas: Identification by Genomic, Proteomic, and Tissue Array Profiling
Cancer Res 2003 Sep 1;63(17):5243-50
Satoshi Nishizuka, Sing-Tsung Chen, Fuad G. Gwadry, Jes Alexander, Sylvia M. Major, Uwe Scherf, William C. Reinhold, Mark Waltham, Lu Charboneau, Lynn Young, Kimberly J. Bussey, Sohyoung Kim, Samir Lababidi, Jae K. Lee, Stefania Pittaluga, Dominic A. Scudiero, Edward A. Sausville, Peter J. Munson, Emmanuel F. Petricoin III, Lance A. Liotta, Stephen M. Hewitt, Mark Raffeld, and John N. Weinstein

Apoptosis induced by topoisomerase inhibitors
Curr Med Chem Anti-Canc Agents. 2003 Jul;3(4):271-90.
Sordet O, Khan QA, Kohn KW, Pommier Y.

Impact of p53-knockout and Topotecan Treatment on Gene Expression Profiles in Human Colon Carcinoma Cells: A Pharmacogenomics Study.
Cancer Res 2003 Jun 1;63(11):2782-93
Sayed S. Daoud, Peter J. Munson, William Reinhold, Lynn Young, Vinay V. Prabhu, Qiang Yu, Jihyun LaRose, Kurt W. Kohn, John N. Weinstein and Yves Pommier

Apoptotic Susceptibility of Cancer Cells Selected for Camptothecin Resistance: Gene Expression Profiling, Functional Analysis, and Molecular Interaction Mapping
Cancer Res 2003 Mar 1;63(5):1000-11
William C. Reinhold, Hosein Kouros-Mehr, Kurt W. Kohn, Alika K. Maunakea, Samir Lababidi, Anna Roschke, Kristen Stover, Jes Alexander, Panayotis Pantazis, Lance Miller, Edison Liu, Ilan R. Kirsch, Yoshimasa Urasaki, Yves Pommier, and John N. Weinstein

MatchMiner: A Tool for Batch Navigation among Gene and Gene Product Identifiers
Genome Biol, 4(4):R27
Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay, Weinstein JN

GoMiner: A Resource for Biological Interpretation of Genomic and Proteomic Data
Genome Biol, 4(4):R28
Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN

Cell cycle and checkpoints in oncology: new therapeutic targets
Med Sci (Paris). 2003 Feb;19(2):173-86
Pommier Y, Kohn KW

2002

Pharmacogenomic Analysis: Correlating Molecular Substructure Classes with Microarray Gene Expression Data
The Pharmacogenomics Journal (Nature) 2002; 2:259-271.
Blower, P., Jr., Yang, C., Fligner, M.A., Verducci, J.S., Yu, L., Richman, S. , and Weinstein, J.N.

Transcriptional Regulation of Mitotic Genes by Camptothecin-Induced DNA Damage: Microarray Analysis of Dose- and Time-Dependent Effects
Cancer Res 2002 Mar 15;62(6):1688-95
Zhou Y, Gwadry FG, Reinhold WC, Miller LD, Smith LH, Scherf U, Liu ET, Kohn KW, Pommier Y, Weinstein JN.

The Bioinformatics of Microarray Gene Expression Profiling
Cytometry 2002 Jan 1;47(1):46-9
Weinstein JN, Scherf U, Lee JK, Nishizuka S, Gwadry F, Bussey AK, Kim S, Smith LH, Tanabe L, Richman S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC.

'Omic' and Hypothesis-driven Research in the Molecular Pharmacology of Cancer
Curr Opin Pharmacol 2002 Aug;2(4):361-5
Weinstein JN.

2001

Chemosensitivity Prediction by Transcriptional Profiling.
Proc Natl Acad Sci U S A 2001 Sep 11;98(19):10787-92
by Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR.

The DNA-repair Gene MGMT and the Clinical Response of Gliomas to Alkylating Agents
New England J. Med. 344: 686 (2001)
by Weinstein, J.N.

Quantitative Structure-Antitumor Activity Relationships of Camptothecin Analogues: Cluster Analysis and Genetic Algorithm-Based Studies
J Med Chem 2001 Sep 27;44(20):3254-63
by Fan Y, Shi LM, Kohn KW, Pommier Y, Weinstein JN.

Comparison of a Neural Net-based QSAR Algorithm (PCANN) with Hologram- and Multiple Linear Regression-based QSAR Approaches: Application to 1,4-dihydropyridine-based Calcium Channel Antagonists
J Chem Inf Comput Sci 2001 May-Jun;41(3):505-11
by Viswanadhan VN, Mueller GA, Basak SC, Weinstein JN.

Searching for Pharmacogenomic Markers: the Synergy Between Omic and Hypothesis-Driven Research
Dis Markers 2001;17(2):77-88
by Weinstein JN.

Molecular Interaction Maps as Information Organizers and Simulation Guides
Chaos. 2001 Mar;11(1):84-97
by Kohn KW.

A Gene Expression Database for the Molecular Pharmacology of Cancer
Nature Genetics, volume 24, no 3 March 1st, 2000 pp:236-244
by Uwe Scherf , Douglas T. Ross , Mark Waltham , Lawrence H. Smith, Jae K. Lee, Lorraine Tanabe, Kurt W. Kohn, William C. Reinhold , Timothy G. Myers, Darren T.Andrews, Dominic A. Scudiero, Michael B. Eisen, Edward A. Sausville , Yves Pommier , David Botstein, Patrick O. Brown , and John N. Weinstein

Systematic Variation in Gene Expression Patterns in Human Cancer Cell Lines
Nature Genetics, 2000 March, 24(3):227-234
by Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Spellman, P., Iyer, V., Jeffrey, S.S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J.C.F., Lashkari, D., Shalon, D., Myers, T.G., Weinstein, J.N., Botstein, D., and Brown, P.O.

EDGAR: Extraction of Drugs, Genes and Relations from the Biomedical Literature
Pacific Symposium on Biocomputing 5:514-525 (2000)
by T.C. Rindflesch, Lorraine Tanabe, John N. Weinstein, and L. Hunter

Mining and Visualizing Large Anticancer Drug Discovery Databases
J Chem Inf Comput Sci. 2000; 40:367-379
by Leming M. Shi, Jae K. Lee, Yi Fan, Timothy G. Myers, Mark Waltham, Darren T. Andrews, Uwe Scherf, Kenneth D. Paull, and John N. Weinstein

Pharmacogenomics: Teaching Old Drugs New Tricks
New England J. Med. 343: 1408-1409 (2000)
by John N. Weinstein

Combination Gene Therapy: Synergistic Inhibition of Human Immunodeficiency Virus Tat and Rev Functions by a Single RNA Molecule
Lisziewicz J, Zeng G, Gratas C, Weinstein JN, Lori F.
Hum Gene Ther 2000 Apr 10;11(6):807-15

Molecular Targets in Cancer Drug Discovery: Cell-Based Profiling
Weinstein JN, Buolamwini JK.
Curr Pharm Des 2000 Mar;6(4):473-83