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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.


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.


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.


Nonlinear gene cluster analysis with labeling for microarray gene expression data in organ development.

Ehler M, Rajapakse VN, Zeeberg BR, Brooks BP, Brown J, Czaja W, Bonner RF.

BMC Proc. 2011 May 28;5 Suppl 2:S3. doi: 10.1186/1753-6561-5-S2-S3.


RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis.

Zeeberg BR, Liu H, Kahn AB, Ehler M, Rajapakse VN, Bonner RF, Brown JD, Brooks BP, Larionov VL, Reinhold W, Weinstein JN, Pommier YG.

BMC Bioinformatics. 2011 Feb 10;12:52. doi: 10.1186/1471-2105-12-52.


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.


Ontogenomic study of the relationship between number of gene splice variants and GO categorization.

Kahn AB, Zeeberg BR, Ryan MC, Jamison DC, Rockoff DM, Pommier Y, Weinstein JN.

Bioinformatics. 2010 Aug 15;26(16):1945-9. doi: 10.1093/bioinformatics/btq335. Epub 2010 Jul 8.


SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.

Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN.

BMC Bioinformatics. 2008 Jul 18;9:313. doi: 10.1186/1471-2105-9-313.


The EDGE hypothesis: epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer.

Ruden DM, Jamison DC, Zeeberg BR, Garfinkel MD, Weinstein JN, Rasouli P, Lu X.

Front Neuroendocrinol. 2008 Jun;29(3):428-44. doi: 10.1016/j.yfrne.2007.12.004. Epub 2008 Jan 8. Review.


VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays.

Kestler HA, Müller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN.

BMC Bioinformatics. 2008 Jan 29;9:67. doi: 10.1186/1471-2105-9-67.


AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.

Liu H, Zeeberg BR, Qu G, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC, Kane DW, Weinstein JN.

Bioinformatics. 2007 Sep 15;23(18):2385-90. Epub 2007 Jul 27.


SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN.

BMC Bioinformatics. 2007 Mar 5;8:75.


Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.

Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Chow W, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA.

Genome Res. 2006 Jun;16(6):796-803. Epub 2006 May 3. Erratum in: Genome Res. 2006 Jul;16(7):947. Chow, William [added].


The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress.

Staib F, Robles AI, Varticovski L, Wang XW, Zeeberg BR, Sirotin M, Zhurkin VB, Hofseth LJ, Hussain SP, Weinstein JN, Galle PR, Harris CC.

Cancer Res. 2005 Nov 15;65(22):10255-64.


Nova regulates brain-specific splicing to shape the synapse.

Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB.

Nat Genet. 2005 Aug;37(8):844-52. Epub 2005 Jul 24.


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).

Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN.

BMC Bioinformatics. 2005 Jul 5;6:168.


Analysis of ATP-binding cassette transporter expression in drug-selected cell lines by a microarray dedicated to multidrug resistance.

Annereau JP, Szakács G, Tucker CJ, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg BR, Reinhold W, Weinstein JN, Pommier Y, Paules RS, Gottesman MM.

Mol Pharmacol. 2004 Dec;66(6):1397-405. Epub 2004 Sep 1.


Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics.

Zeeberg BR, Riss J, Kane DW, Bussey KJ, Uchio E, Linehan WM, Barrett JC, Weinstein JN.

BMC Bioinformatics. 2004 Jun 23;5:80.


Development of gene ontology tool for biological interpretation of genomic and proteomic data.

Feng W, Wang G, Zeeberg BR, Guo K, Fojo AT, Kane DW, Reinhold WC, Lababidi S, Weinstein JN, Wang MD.

AMIA Annu Symp Proc. 2003:839.

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