John N. Weinstein

Publication Activity (10 Years)

Years Active: 1997-2022
Publications (10 Years): 7

Top Topics

Top Venues

Nucleic Acids Res.

Publications

Huma Shehwana, Shwetha V. Kumar, James M. Melott, Mary A. Rohrdanz, Chris Wakefield, Zhenlin Ju, Doris R. Siwak, Yiling Lu, Bradley M. Broom, John N. Weinstein, Gordon B. Mills, Rehan Akbani
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data. Bioinform. 38 (22) (2022)
Michael C. Ryan, Mark Stucky, Chris Wakefield, James M. Melott, Rehan Akbani, John N. Weinstein, Bradley M. Broom
Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. F1000Research 8 (2019)
Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su, Philip L. Lorenzi
ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments. BMC Bioinform. 20 (1) (2019)
Di Du, Chia-Hua Chang, Yumeng Wang, Pan Tong, Wai Kin Chan, Yulun Chiu, Bo Peng, Lin Tan, John N. Weinstein, Philip L. Lorenzi
Response envelope analysis for quantitative evaluation of drug combinations. Bioinform. 35 (19) (2019)
Bo Peng, Gao Wang, Jun Ma, Man Chong Leong, Chris Wakefield, James M. Melott, Yulun Chiu, Di Du, John N. Weinstein
SoS Notebook: an interactive multi-language data analysis environment. Bioinform. 34 (21) (2018)
James M. Melott, John N. Weinstein, Bradley M. Broom
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. Bioinform. 32 (2) (2016)
Michael C. Ryan, Wing Chung Wong, Robert Brown, Rehan Akbani, Xiaoping Su, Bradley M. Broom, James M. Melott, John N. Weinstein
TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. Nucleic Acids Res. 44 (Database-Issue) (2016)
Zhenlin Ju, Wenbin Liu, Paul L. Roebuck, Doris R. Siwak, Nianxiang Zhang, Yiling Lu, Michael A. Davies, Rehan Akbani, John N. Weinstein, Gordon B. Mills, Kevin R. Coombes
Development of a robust classifier for quality control of reverse-phase protein arrays. Bioinform. 31 (6) (2015)
Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G. W. Verhaak
PRADA: pipeline for RNA sequencing data analysis. Bioinform. 30 (15) (2014)
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. Bioinform. 29 (2) (2013)
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. Bioinform. 28 (18) (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. Bioinform. 28 (17) (2012)
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. Bioinform. 28 (14) (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 Bioinform. 12 (2011)
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. Bioinform. 26 (16) (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. J. Biomed. Informatics 43 (6) (2010)
Blaise Hanczar, Jianping Hua, Chao Sima, John N. Weinstein, Michael L. Bittner, Edward R. Dougherty
Small-sample precision of ROC-related estimates. Bioinform. 26 (6) (2010)
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)
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 Bioinform. 9 (2008)
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 Bioinform. 9 (2008)
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 Bioinform. 8 (2007)
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. Bioinform. 23 (18) (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)
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 Bioinform. 7 (2006)
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 Bioinform. 6 (2005)
Mark Reimers, John N. Weinstein
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases. BMC Bioinform. 6 (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 Bioinform. 5 (2004)
Weimin Feng, Geoffrey Wang, Barry Zeeberg, Kejiao Guo, Anthony T. Fojo, David W. Kane, William C. Reinhold, Samir Lababidi, John N. Weinstein, May D. Wang
Development of Gene Ontology Tool for Biological Interpretation of Genomic and Proteomic Data. AMIA (2003)
Sohyoung Kim, John N. Weinstein, John J. Grefenstette
Inference of large-scale topology of gene regulation networks by neural nets. SMC (2003)
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. J. Chem. Inf. Comput. Sci. 41 (3) (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. J. Chem. Inf. Comput. Sci. 40 (2) (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. J. Chem. Inf. Comput. Sci. 38 (2) (1998)
Leming M. Shi, Yi Fan, Timothy G. Myers, John N. Weinstein
Genetic function approximation in the molecular pharmacology of cancer. ICNN (1997)