Genetic function approximation in the molecular pharmacology of cancer. - Leming M. Shi; Yi Fan; Timothy G. Myers 001; John N. Weinstein (ICNN, 1997)

Mining the NCI Anticancer Drug Discovery Databases: Genetic Function Approximation for the QSAR Study of Anticancer Ellipticine Analogues. - Leming M. Shi; Yi Fan; Timothy G. Myers 001; Patrick M. O'Connor; Kenneth D. Paull; Stephen H. Friend; John N. Weinstein (J. Chem. Inf. Comput. Sci., 1998)

Mining and Visualizing Large Anticancer Drug Discovery Databases. - Leming M. Shi; Yi Fan; Jae K. Lee; Mark Waltham; Darren T. Andrews; Uwe Scherf; Kenneth D. Paull; John N. Weinstein (J. Chem. Inf. Comput. Sci., 2000)

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. - Vellarkad N. Viswanadhan; Geoffrey A. Mueller; Subhash C. Basak; John N. Weinstein (J. Chem. Inf. Comput. Sci., 2001)

Development of Gene Ontology Tool for Biological Interpretation of Genomic and Proteomic Data. - 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 (AMIA, 2003)

Inference of large-scale topology of gene regulation networks by neural nets. - Sohyoung Kim; John N. Weinstein; John J. Grefenstette (SMC, 2003)

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

Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases. - Mark Reimers; John N. Weinstein (BMC Bioinform., 2005)

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). - 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; et al. (BMC Bioinform., 2005)

AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. - 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 (BMC Bioinform., 2006)

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

AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. - Hongfang Liu; Barry Zeeberg; Gang Qu 001; 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 (Bioinform., 2007)

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

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

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

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

Small-sample precision of ROC-related estimates. - Blaise Hanczar; Jianping Hua; Chao Sima; John N. Weinstein; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2010)

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

Exposing the cancer genome atlas as a SPARQL endpoint. - Helena F. Deus; Diogo F. Veiga; Pablo R. Freire; John N. Weinstein; Gordon B. Mills; Jonas S. Almeida (J. Biomed. Informatics, 2010)

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. - 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 (BMC Bioinform., 2011)

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. - Ken Chen 001; 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; et al. (Bioinform., 2012)

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

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

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

PRADA: pipeline for RNA sequencing data analysis. - 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 (Bioinform., 2014)

Development of a robust classifier for quality control of reverse-phase protein arrays. - 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 (Bioinform., 2015)

PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. - James M. Melott; John N. Weinstein; Bradley M. Broom (Bioinform., 2016)

TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. - Michael C. Ryan; Wing Chung Wong; Robert Brown; Rehan Akbani; Xiaoping Su; Bradley M. Broom; James M. Melott; John N. Weinstein (Nucleic Acids Res., 2016)

SoS Notebook: an interactive multi-language data analysis environment. - Bo Peng 001; Gao Wang; Jun Ma; Man Chong Leong; Chris Wakefield; James M. Melott; Yulun Chiu; Di Du; John N. Weinstein (Bioinform., 2018)

Response envelope analysis for quantitative evaluation of drug combinations. - Di Du; Chia-Hua Chang; Yumeng Wang; Pan Tong; Wai Kin Chan; Yulun Chiu; Bo Peng 001; Lin Tan 002; John N. Weinstein; Philip L. Lorenzi (Bioinform., 2019)

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments. - Di Du; Lin Tan 002; Yumeng Wang; Bo Peng 001; John N. Weinstein; Fredric E. Wondisford; Xiaoyang Su; Philip L. Lorenzi (BMC Bioinform., 2019)

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. - Michael C. Ryan; Mark Stucky; Chris Wakefield; James M. Melott; Rehan Akbani; John N. Weinstein; Bradley M. Broom (F1000Research, 2019)

RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data. - 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 (Bioinform., 2022)

TCGA Kidney Cancers. - John N. Weinstein; Eric A. Collisson; Gordon B. Mills; Kenna R. Mills Shaw; Brad A. Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M. Stuart (UCI Machine Learning Repository, 2023)