Publications

2010-2014

NCI-60 Whole Exome Sequencing and Pharmacological CellMiner Analyses.
PLoS One. 2014 Jul 17;9(7).e101670.
Reinhold WC, Varma S, Sousa F, Sunshine M, Abaan OD, Davis SR, Reinhold SW, Kohn KW, Morris J, Meltzer PS, Doroshow JH, Pommier Y.

Gene Expression Correlations in Human Cancer Cell Lines Define Molecular Interaction Networks for Epithelial Phenotype
PLoS One. 2014 Jun 18;9(6).e99269.
Kurt W. Kohn, Barry M. Zeeberg, William C. Reinhold, Yves Pommier.

High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner.
PLoS One. 2014 Mar 26;9(3):e92047.
Varma S, Pommier Y, Sunshine M, Weinstein JN, Reinhold WC.

Commentary on "MelanomaDB: a web tool for integrative analysis of melanoma genomic information to identify disease-associated molecular pathways".
Front Genet. 2013; 4: 156. Epub 2013 August 13.
Reinhold WC.

The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology.
Cancer Res. 2013 Jul 15;73(14):4372-82. Epub 2013 Jul 15.
Abaan OD, Polley EC, Davis SR, Zhu YJ, Bilke S, Walker RL, Pineda M, Gindin Y, Jiang Y, Reinhold WC, Holbeck SL, Simon RM, Doroshow JH, Pommier Y, Meltzer PS.

Tumor suppressor miR-375 regulates MYC expression via repression of CIP2A coding sequence through multiple miRNA-mRNA interactions.
Mol Biol Cell. 2013 Jun;24(11):1638-48, Epub 2013 Apr 3.
Jung HM, Patel RS, Phillips BL, Wang H, Cohen DM, Reinhold WC, Chang LJ, Yang LJ, Chan EK.

USP7 and Daxx regulate mitosis progression and taxane sensitivity by affecting stability of Aurora-A kinase
Cell Death Differ. 2013 May;20(5):721-31, Epub 2013 Jan 25.
Giovinazzi S, Morozov VM, Summers MK, Reinhold WC, Ishov AM.

Entry Tropism of BK and Merkel Cell Polyomaviruses in Cell Culture.
PLoS One. 2012;7(7):e42181. Epub 2012 Jul 31.
Schowalter RM, Reinhold WC, Buck CB.

CellMiner: A Web-Based Suite of Genomic and Pharmacologic Tools to Explore Transcript and Drug Patterns in the NCI-60 Cell Line Set.
Cancer Res. 2012 Jul 15;72(14):3499-511.
Reinhold WC, Sunshine M, Liu H, Varma S, Kohn KW, Morris J, Doroshow J, Pommier Y.

Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families.
Genes Chromosomes Cancer. 2012 Jun 26. doi: 10.1002/gcc.21977. [Epub ahead of print]
Kouprina N, Lee NC, Pavlicek A, Samoshkin A, Kim JH, Lee HS, Varma S, Reinhold WC, Otstot J, Solomon G, Davis S, Meltzer PS, Schleutker J, Larionov V.

Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes.
PLoS One. 2012;7(5):e35716. Epub 2012 May 3.
Kohn KW, Zeeberg BR, Reinhold WC, Sunshine M, Luna A, Pommier Y.

Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap Trios, and relation to fragile site location.
PLoS One. 2012;7(2):e31628. Epub 2012 Feb 9.
Ruan X, Kocher JP, Pommier Y, Liu H, Reinhold WC.

Functional Categories Associated with Clusters of Genes That Are Co-Expressed across the NCI-60 Cancer Cell Lines.
PLoS One 7(1): e30317. doi:10.1371/journal.pone.0030317.
Zeeberg BR, Reinhold W, Snajder R, Thallinger GG, Weinstein JN, Kohn KW, Pommier Y.

Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents
PNAS: July 27, 2012.
Gabriele Zoppoli, Marie Regairaz, Elisabetta Leo, William C. Reinhold, Sudhir Varma, Alberto Ballestrero, James H. Doroshow, and Yves Pommier.

PathVisio-Validator: A Rule-based Validation Plugin for Graphical Pathway Notations.
Bioinformatics. 2011 Dec 22. [Epub ahead of print].
Chandan K, van Iersel MP, Aladjem MI, Kohn KW, Luna A.

Identification of a Predominant Co-Regulation among Kinetochore Genes, Prospective Regulatory Elements, and Association with Genomic Instability.
PLoS One. 2011;6(10):e25991. Epub 2011 Oct 10.
Reinhold WC, Erliandri I, Liu H, Zoppoli G, Pommier Y, Larionov V.

Genome-wide depletion of replication initiation events in highly transcribed regions.
Genome Research. 2011 Sep 22. [Epub ahead of print].
Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI.

CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute.
Oncogene (2011) 30, 403-418; doi:10.1038/onc.2011.283; Epub 18 July 2011.
Zoppoli G, Solier S, Reinhold WC, Liu H, Connelly JW Jr, Monks A, Shoemaker RH, Abaan OD, Davis SR, Meltzer PS, Doroshow JH, Pommier Y.

G4 motifs correlate with promoter-proximal transcriptional pausing of human genes.
Nucleic Acids Research, 2011 Jul;39(12):4975-83. Epub 2011 Mar 3.
Eddy J, Vallur AC, Varma S, Liu H, Reinhold W, Pommier Y and Maizels N.

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).
Bioinformatics. 2011 Aug 1;27(15):2165-6. Epub 2011 Jun 2.
Luna A, Sunshine M, van Iersel MP, Aladjem MI, Kohn KW.

A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method.
BMC Bioinformatics. 2011 May 17;12:167.
Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW.

Coordinated regulation of mitochondrial topoisomerase IB with mitochondrial nuclear encoded genes and MYC.
Nucleic Acids Research, 2011, doi: 10.1093/nar/gkr208
Zoppoli G, Douarre C, Dalla Rosa I, Liu H, Reinhold W, Pommier Y.

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis.
BMC Bioinformatics 2011, 2011 Feb 10;12:52
Barry R Zeeberg, Hongfang Liu, Ari B Kahn, Martin Ehler, Vinodh N Rajapakse, Robert F Bonner, Jacob D Brown, Brian P Brooks, Vladimir L Larionov, William Reinhold, John N Weinstein and Yves G Pommier.

Novel regulation of nuclear factor-YB by miR-485-3p affects the expression of DNA topoisomerase II╬▒ and drug responsiveness
Mol Pharmacol. 2011 Jan 20. [Epub ahead of print]
Chen CF, He X, Arslan AD, Mo YY, Reinhold WC, Pommier Y, Beck WT.

Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors.
Cancer Res 2010, 70(20):8055-8065.
Solier S, Barb J, Zeeberg BR, Varma S, Ryan MC, Kohn KW, Weinstein JN, Munson PJ, Pommier Y.

Genome-wide mRNA and microRNA profiling of the NCI 60 cell-line screen and comparison of FdUMP[10] with fluorouracil, floxuridine, and topoisomerase 1 poisons.
Mol Cancer Ther. 2010 Dec;9(12):3105-14.
Gmeiner WH, Reinhold W, Pommier Y.

Ontogenomic study of the relationship between number of gene splice variants and GO categorization.
Bioinformatics. 2010 Aug 15;26(16):1945-9. Epub 2010 Jul 8.
Kahn AB, Zeeberg BR, Ryan MC, Jamison DC, Rockoff DM, Pommier Y, Weinstein JN.

mRNA and microRNA Expression Profiles of the NCI-60 Integrated with Drug Activities.
Mol Cancer Ther May 2010 9; 1080 [Epub ahead of print]
Liu H, D'Andrade P, Fulmer-Smentek S, Lorenzi P, Kohn K, Weinstein J, Pommier Y and Reinhold W.

Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron.
Cancer Res. 2010 Mar 15;70(6):2191-203. Epub 2010 Mar 9.
Reinhold WC, Mergny JL, Liu H, Ryan M, Pfister TD, Kinders R, Parchment R, Doroshow J, Weinstein JN, Pommier Y.

Regulation of Human Skin Pigmentation in situ by Repetitive UV Exposure: Molecular Characterization of Responses to UVA and/or UVB.
J Invest Dermatol. 2010 Feb 11. [Epub ahead of print]
Choi W, Miyamura Y, Wolber R, Smuda C, Reinhold W, Liu H, Kolbe L, Hearing VJ.

Multifactorial regulation of E-cadherin expression: an integrative study.
Mol Cancer Ther. 2010 Jan;9(1):1-16. Epub 2010 Jan 6.
Reinhold WC, Reimers MA, Lorenzi P, Ho J, Shankavaram UT, Ziegler MS, Bussey KJ, Nishizuka S, Ikediobi O, Pommier YG, Weinstein JN.