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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 NF-YB by miR-485-3p affects expression of DNA topoisomerase II{alpha} 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.
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