John N. Weinstein

Yunxin Chen, Hui Yao, Erika J. Thompson, Nizar M. Tannir, John N. Weinstein, Xiaoping Su: VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics 29(2): 266-267 (2013)

Ken Chen, John W. Wallis, Cyriac Kandoth, Joelle M. Kalicki-Veizer, Karen L. Mungall, Andrew J. Mungall, Steven J. M. Jones, Marco A. Marra, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, John N. Weinstein, Li Ding: BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics 28(14): 1923-1924 (2012)

Xiaoping Su, Li Zhang, Jianping Zhang, Funda Meric-Bernstam, John N. Weinstein: PurityEst: estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics 28(17): 2265-2266 (2012)

Michael C. Ryan, James A. Cleland, RyangGuk Kim, Wing Chung Wong, John N. Weinstein: SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts. Bioinformatics 28(18): 2385-2387 (2012)

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

Blaise Hanczar, Jianping Hua, Chao Sima, John N. Weinstein, Michael L. Bittner, Edward R. Dougherty: Small-sample precision of ROC-related estimates. Bioinformatics 26(6): 822-830 (2010)

Ari B. Kahn, Barry Zeeberg, Michael C. Ryan, D. Curtis Jamison, David M. Rockoff, Yves Pommier, John N. Weinstein: Ontogenomic study of the relationship between number of gene splice variants and GO categorization. Bioinformatics 26(16): 1945-1949 (2010)

Helena F. Deus, Diogo F. Veiga, Pablo R. Freire, John N. Weinstein, Gordon B. Mills, Jonas S. Almeida: Exposing the cancer genome atlas as a SPARQL endpoint. Journal of Biomedical Informatics 43(6): 998-1008 (2010)

Hans A. Kestler, André Müller, Johann M. Kraus, Malte Buchholz, Thomas M. Gress, Hongfang Liu, David W. Kane, Barry Zeeberg, John N. Weinstein: VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9 (2008)

Michael C. Ryan, Barry Zeeberg, Natasha J. Caplen, James A. Cleland, Ari B. Kahn, Hongfang Liu, John N. Weinstein: SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 9 (2008)

Uma T. Shankavaram, Sudhir Varma, David W. Kane, Margot Sunshine, Krishna Chary, William C. Reinhold, John N. Weinstein: CellMiner: A Database Tool for the NCI-60 Cancer Cell Lines. BIOCOMP 2008: 315-323

Hongfang Liu, Barry Zeeberg, Gang Qu, Akif Günes Koru, Alessandro Ferrucci, Ari B. Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein: AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics 23(18): 2385-2390 (2007)

Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry Zeeberg, D. Curtis Jamison, John N. Weinstein: SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. BMC Bioinformatics 8 (2007)

Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Børresen-Dale, Zohar Yakhini: Framework for Identifying Common Aberrations in DNA Copy Number Data. RECOMB 2007: 122-136

Sylvia M. Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland, Margot Sunshine, Uma T. Shankavaram, Frank Washburn, Daniel Asin, Hosein Kouros-Mehr, David W. Kane, John N. Weinstein: AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. BMC Bioinformatics 7: 192 (2006)

Mark Reimers, John N. Weinstein: Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics 6: 166 (2005)

Barry Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W. Kane, Mark Reimers, Robert M. Stephens, David Bryant, Stanley K. Burt, Eldad Elnekave, Danielle M. Hari, Thomas A. Wynn, Charlotte Cunningham-Rundles, Donn M. Stewart, David Nelson, John N. Weinstein: 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 6: 168 (2005)

Barry Zeeberg, Joseph Riss, David W. Kane, Kimberly J. Bussey, Edward Uchio, W. Marston Linehan, J. Carl Barrett, John N. Weinstein: Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics 5: 80 (2004)

Sohyoung Kim, John N. Weinstein, John J. Grefenstette: Inference of large-scale topology of gene regulation networks by neural nets. SMC 2003: 3969-3975

Vellarkad N. Viswanadhan, Geoffrey A. Mueller, Subhash C. Basak, John N. Weinstein: 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. Journal of Chemical Information and Computer Sciences 41(3): 505-511 (2001)

Leming M. Shi, Yi Fan, Jae K. Lee, Mark Waltham, Darren T. Andrews, Uwe Scherf, Kenneth D. Paull, John N. Weinstein: Mining and Visualizing Large Anticancer Drug Discovery Databases. Journal of Chemical Information and Computer Sciences 40(2): 367-379 (2000)

Leming M. Shi, Yi Fan, Timothy G. Myers, Patrick M. O'Connor, Kenneth D. Paull, Stephen H. Friend, John N. Weinstein: Mining the NCI Anticancer Drug Discovery Databases: Genetic Function Approximation for the QSAR Study of Anticancer Ellipticine Analogues. Journal of Chemical Information and Computer Sciences 38(2): 189-199 (1998)