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CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines.

Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y.

iScience. 2018 Dec 21;10:247-264. doi: 10.1016/j.isci.2018.11.029. Epub 2018 Dec 12.


The NCI-60 Methylome and Its Integration into CellMiner.

Reinhold WC, Varma S, Sunshine M, Rajapakse V, Luna A, Kohn KW, Stevenson H, Wang Y, Heyn H, Nogales V, Moran S, Goldstein DJ, Doroshow JH, Meltzer PS, Esteller M, Pommier Y.

Cancer Res. 2017 Feb 1;77(3):601-612. doi: 10.1158/0008-5472.CAN-16-0655. Epub 2016 Dec 6.


Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response.

Luna A, McFadden GB, Aladjem MI, Kohn KW.

PLoS Comput Biol. 2015 May 28;11(5):e1004144. doi: 10.1371/journal.pcbi.1004144. eCollection 2015 May.


Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer.

Reinhold WC, Varma S, Rajapakse VN, Luna A, Sousa FG, Kohn KW, Pommier YG.

Hum Genet. 2015 Jan;134(1):3-11. doi: 10.1007/s00439-014-1482-9. Epub 2014 Sep 12. Review. Erratum in: Hum Genet. 2015 May;134(5):509.


NCI-60 whole exome sequencing and pharmacological CellMiner analyses.

Reinhold WC, Varma S, Sousa F, Sunshine M, Abaan OD, Davis SR, Reinhold SW, Kohn KW, Morris J, Meltzer PS, Doroshow JH, Pommier Y.

PLoS One. 2014 Jul 17;9(7):e101670. doi: 10.1371/journal.pone.0101670. eCollection 2014.


Gene expression correlations in human cancer cell lines define molecular interaction networks for epithelial phenotype.

Kohn KW, Zeeberg BM, Reinhold WC, Pommier Y.

PLoS One. 2014 Jun 18;9(6):e99269. doi: 10.1371/journal.pone.0099269. eCollection 2014.


SIRT1/PARP1 crosstalk: connecting DNA damage and metabolism.

Luna A, Aladjem MI, Kohn KW.

Genome Integr. 2013 Dec 20;4(1):6. doi: 10.1186/2041-9414-4-6.


Transcription poisoning by Topoisomerase I is controlled by gene length, splice sites, and miR-142-3p.

Solier S, Ryan MC, Martin SE, Varma S, Kohn KW, Liu H, Zeeberg BR, Pommier Y.

Cancer Res. 2013 Aug 1;73(15):4830-9. doi: 10.1158/0008-5472.CAN-12-3504. Epub 2013 Jun 20.


PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways.

Fried JY, van Iersel MP, Aladjem MI, Kohn KW, Luna A.

Bioinformatics. 2013 Jun 1;29(11):1465-6. doi: 10.1093/bioinformatics/btt146. Epub 2013 Apr 1.


Concordance of gene expression and functional correlation patterns across the NCI-60 cell lines and the Cancer Genome Atlas glioblastoma samples.

Zeeberg BR, Kohn KW, Kahn A, Larionov V, Weinstein JN, Reinhold W, Pommier Y.

PLoS One. 2012;7(7):e40062. doi: 10.1371/journal.pone.0040062. Epub 2012 Jul 26.


CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set.

Reinhold WC, Sunshine M, Liu H, Varma S, Kohn KW, Morris J, Doroshow J, Pommier Y.

Cancer Res. 2012 Jul 15;72(14):3499-511. doi: 10.1158/0008-5472.CAN-12-1370.


Heat shock protein 90α (HSP90α), a substrate and chaperone of DNA-PK necessary for the apoptotic response.

Solier S, Kohn KW, Scroggins B, Xu W, Trepel J, Neckers L, Pommier Y.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):12866-72. doi: 10.1073/pnas.1203617109. Epub 2012 Jul 2.


Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes.

Kohn KW, Zeeberg BR, Reinhold WC, Sunshine M, Luna A, Pommier Y.

PLoS One. 2012;7(5):e35716. doi: 10.1371/journal.pone.0035716. Epub 2012 May 3.


Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines.

Zeeberg BR, Reinhold W, Snajder R, Thallinger GG, Weinstein JN, Kohn KW, Pommier Y.

PLoS One. 2012;7(1):e30317. doi: 10.1371/journal.pone.0030317. Epub 2012 Jan 24.


PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.

Chandan K, van Iersel MP, Aladjem MI, Kohn KW, Luna A.

Bioinformatics. 2012 Mar 15;28(6):889-90. doi: 10.1093/bioinformatics/btr694. Epub 2011 Dec 22.


PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).

Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW.

Bioinformatics. 2011 Aug 1;27(15):2165-6. doi: 10.1093/bioinformatics/btr336. Epub 2011 Jun 2.


A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW.

BMC Bioinformatics. 2011 May 17;12:167. doi: 10.1186/1471-2105-12-167.


Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors.

Solier S, Barb J, Zeeberg BR, Varma S, Ryan MC, Kohn KW, Weinstein JN, Munson PJ, Pommier Y.

Cancer Res. 2010 Oct 15;70(20):8055-65. doi: 10.1158/0008-5472.CAN-10-2491. Epub 2010 Sep 3.


mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities.

Liu H, D'Andrade P, Fulmer-Smentek S, Lorenzi P, Kohn KW, Weinstein JN, Pommier Y, Reinhold WC.

Mol Cancer Ther. 2010 May;9(5):1080-91. doi: 10.1158/1535-7163.MCT-09-0965. Epub 2010 May 4.


Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage.

Kim S, Aladjem MI, McFadden GB, Kohn KW.

PLoS Comput Biol. 2010 Feb 5;6(2):e1000665. doi: 10.1371/journal.pcbi.1000665.


Ataxia telangiectasia mutated activation by transcription- and topoisomerase I-induced DNA double-strand breaks.

Sordet O, Redon CE, Guirouilh-Barbat J, Smith S, Solier S, Douarre C, Conti C, Nakamura AJ, Das BB, Nicolas E, Kohn KW, Bonner WM, Pommier Y.

EMBO Rep. 2009 Aug;10(8):887-93. doi: 10.1038/embor.2009.97. Epub 2009 Jun 26.


Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis.

Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.

Cell Cycle. 2009 Jul 15;8(14):2281-99. Epub 2009 Jul 26.


Death receptor-induced activation of the Chk2- and histone H2AX-associated DNA damage response pathways.

Solier S, Sordet O, Kohn KW, Pommier Y.

Mol Cell Biol. 2009 Jan;29(1):68-82. doi: 10.1128/MCB.00581-08. Epub 2008 Oct 27.


Chromatin challenges during DNA replication: a systems representation.

Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.

Mol Biol Cell. 2008 Jan;19(1):1-7. Epub 2007 Oct 24. Review.


HAUSP-regulated switch from auto- to p53 ubiquitination by Mdm2 (in silico discovery).

Brazhnik P, Kohn KW.

Math Biosci. 2007 Nov;210(1):60-77. Epub 2007 May 23.


Depicting combinatorial complexity with the molecular interaction map notation.

Kohn KW, Aladjem MI, Kim S, Weinstein JN, Pommier Y.

Mol Syst Biol. 2006;2:51. Epub 2006 Oct 3. Review.


Hereditary ataxia SCAN1 cells are defective for the repair of transcription-dependent topoisomerase I cleavage complexes.

Miao ZH, Agama K, Sordet O, Povirk L, Kohn KW, Pommier Y.

DNA Repair (Amst). 2006 Dec 9;5(12):1489-94. Epub 2006 Aug 28.


Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma.

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.

Cancer Res. 2006 Jul 15;66(14):7216-24.


4-nitroquinoline-1-oxide induces the formation of cellular topoisomerase I-DNA cleavage complexes.

Miao ZH, Rao VA, Agama K, Antony S, Kohn KW, Pommier Y.

Cancer Res. 2006 Jul 1;66(13):6540-5.


Circuit diagrams for biological networks.

Kohn KW, Aladjem MI.

Mol Syst Biol. 2006;2:2006.0002. Epub 2006 Jan 17. No abstract available.


Chk2 molecular interaction map and rationale for Chk2 inhibitors.

Pommier Y, Weinstein JN, Aladjem MI, Kohn KW.

Clin Cancer Res. 2006 May 1;12(9):2657-61.


A novel norindenoisoquinoline structure reveals a common interfacial inhibitor paradigm for ternary trapping of the topoisomerase I-DNA covalent complex.

Marchand C, Antony S, Kohn KW, Cushman M, Ioanoviciu A, Staker BL, Burgin AB, Stewart L, Pommier Y.

Mol Cancer Ther. 2006 Feb;5(2):287-95.


p21CDKN1A allows the repair of replication-mediated DNA double-strand breaks induced by topoisomerase I and is inactivated by the checkpoint kinase inhibitor 7-hydroxystaurosporine.

Furuta T, Hayward RL, Meng LH, Takemura H, Aune GJ, Bonner WM, Aladjem MI, Kohn KW, Pommier Y.

Oncogene. 2006 May 11;25(20):2839-49.


Molecular interaction maps of bioregulatory networks: a general rubric for systems biology.

Kohn KW, Aladjem MI, Weinstein JN, Pommier Y.

Mol Biol Cell. 2006 Jan;17(1):1-13. Epub 2005 Nov 2.


Targeting chk2 kinase: molecular interaction maps and therapeutic rationale.

Pommier Y, Sordet O, Rao VA, Zhang H, Kohn KW.

Curr Pharm Des. 2005;11(22):2855-72. Review.


Molecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage.

Kohn KW, Pommier Y.

Biochem Biophys Res Commun. 2005 Jun 10;331(3):816-27. Review.


Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system.

Kohn KW, Riss J, Aprelikova O, Weinstein JN, Pommier Y, Barrett JC.

Mol Biol Cell. 2004 Jul;15(7):3042-52. Epub 2004 Apr 23.


Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks.

Pommier Y, Sordet O, Antony S, Hayward RL, Kohn KW.

Oncogene. 2004 Apr 12;23(16):2934-49. Review.


Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks.

Aladjem MI, Pasa S, Parodi S, Weinstein JN, Pommier Y, Kohn KW.

Sci STKE. 2004 Feb 24;2004(222):pe8. Review.


Repair of and checkpoint response to topoisomerase I-mediated DNA damage.

Pommier Y, Redon C, Rao VA, Seiler JA, Sordet O, Takemura H, Antony S, Meng L, Liao Z, Kohlhagen G, Zhang H, Kohn KW.

Mutat Res. 2003 Nov 27;532(1-2):173-203. Review.


[Cell cycle and checkpoints in oncology: new therapeutic targets].

Pommier Y, Kohn KW.

Med Sci (Paris). 2003 Feb;19(2):173-86. Review. French.


Impact of p53 knockout and topotecan treatment on gene expression profiles in human colon carcinoma cells: a pharmacogenomic study.

Daoud SS, Munson PJ, Reinhold W, Young L, Prabhu VV, Yu Q, LaRose J, Kohn KW, Weinstein JN, Pommier Y.

Cancer Res. 2003 Jun 1;63(11):2782-93.


Apoptosis induced by topoisomerase inhibitors.

Sordet O, Khan QA, Kohn KW, Pommier Y.

Curr Med Chem Anticancer Agents. 2003 Jul;3(4):271-90. Review.


Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping.

Reinhold WC, Kouros-Mehr H, Kohn KW, Maunakea AK, Lababidi S, Roschke A, Stover K, Alexander J, Pantazis P, Miller L, Liu E, Kirsch IR, Urasaki Y, Pommier Y, Weinstein JN.

Cancer Res. 2003 Mar 1;63(5):1000-11.


Importance of the fourth alpha-helix within the CAP homology domain of type II topoisomerase for DNA cleavage site recognition and quinolone action.

Strumberg D, Nitiss JL, Dong J, Walker J, Nicklaus MC, Kohn KW, Heddle JG, Maxwell A, Seeber S, Pommier Y.

Antimicrob Agents Chemother. 2002 Sep;46(9):2735-46.


Transcriptional regulation of mitotic genes by camptothecin-induced DNA damage: microarray analysis of dose- and time-dependent effects.

Zhou Y, Gwadry FG, Reinhold WC, Miller LD, Smith LH, Scherf U, Liu ET, Kohn KW, Pommier Y, Weinstein JN.

Cancer Res. 2002 Mar 15;62(6):1688-95.

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