Genomics and Bioinformatics Group Genomics and Bioinformatics Group Genomics and Bioinformatics Group
Genomics and Bioinformatics Group

Selected Publications

Genomics and Bioinformatics Group
  Molec Maps
      Before 1999

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

An information-intensive approach to the molecular pharmacology of cancer.
Science 1997. 275:343-349.
Weinstein, J.N., Myers, T.G., O'Connor, P.M., Friend, S.H., Fornace, A.J., Kohn, K.W., Fojo, T., Bates, S.E., Rubinstein, L.V., Anderson, N.L., Buolamwini, J.K., van Osdol, W.W., Monks, A.P., Scudiero, D.A., Sausville, E.A., Zaharevitz, D.W., Bunow, B., Viswanadhan, V.N., Johnson, G.S., Wittes, R.E., and Paull, K.D.

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 synapse
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

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

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 Szak�cs, 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

Properties of Switch-like Bioregulatory Networks Studied by Simulation of the Hypoxia Response Control System
Mol Biol Cell. 2004 Apr 23 [Epub ahead of print]
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.
In: Brenner, C. and Duggan, D. (Eds.),Oncogenomics: Molecular Approaches to Cancer., Hoboken, N.J.,: John Wiley & sons. 2004: 117-137
Weinstein, J.N.

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

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

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

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.

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.

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

MedMiner: An internet tool for filtering and organizing biomedical information, with application to gene expression profiling.
BioTechniques. 1999; 27: 1210-1217
by Tanabe, L., Smith, L.H., Lee, J.K., Scherf, U., Hunter, L., and Weinstein, J.N.

The Complexity of Radiation Stress Responses: Analysis by Informatics and Functional Genomics Approaches
Gene Expr 1999;7(4-6):387-400
by Fornace AJ Jr, Amundson SA, Bittner M, Myers TG, Meltzer P, Weinsten JN, Trent J.

Gadd45, a p53-Responsive Stress Protein, Modifies DNA Accessibility on Damaged Chromatin
Mol Cell Biol 1999 Mar;19(3):1673-85
by Carrier F, Georgel PT, Pourquier P, Blake M, Kontny HU, Antinore MJ, Gariboldi M, Myers TG, Weinstein JN, Pommier Y, Fornace AJ Jr.

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