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ORCIDJohn N. Weinstein
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2020 – today
- 2023
[d1]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:
TCGA Kidney Cancers. UCI Machine Learning Repository, 2023
- 2022
- [j27]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): 5131-5133 (2022)
2010 – 2019
- 2019
- [j26]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): 3761-3770 (2019) - [j25]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): 89:1-89:9 (2019) - [i1]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: 1750 (2019) - 2018
- [j24]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): 3768-3770 (2018) - 2016
- [j23]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): 312-314 (2016) - [j22]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): 1018-1022 (2016) - 2015
- [j21]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): 912-918 (2015) - 2014
- [j20]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): 2224-2226 (2014) - 2013
- [j19]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): 266-267 (2013) - 2012
- [j18]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): 1923-1924 (2012) - [j17]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): 2265-2266 (2012) - [j16]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): 2385-2387 (2012) - 2011
- [j15]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: 52 (2011) - 2010
- [j14]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): 822-830 (2010) - [j13]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): 1945-1949 (2010) - [j12]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): 998-1008 (2010)
2000 – 2009
- 2008
- [j11]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) - [j10]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) - [c5]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 - 2007
- [j9]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): 2385-2390 (2007) - [j8]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) - [c4]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 - 2006
- [j7]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: 192 (2006) - 2005
- [j6]Mark Reimers, John N. Weinstein:
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases. BMC Bioinform. 6: 166 (2005) - [j5]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: 168 (2005) - 2004
- [j4]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: 80 (2004) - 2003
- [c3]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 - [c2]Sohyoung Kim, John N. Weinstein, John J. Grefenstette:
Inference of large-scale topology of gene regulation networks by neural nets. SMC 2003: 3969-3975 - 2001
- [j3]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): 505-511 (2001) - 2000
- [j2]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): 367-379 (2000)
1990 – 1999
- 1998
- [j1]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): 189-199 (1998) - 1997
- [c1]Leming M. Shi, Yi Fan, Timothy G. Myers, John N. Weinstein:
Genetic function approximation in the molecular pharmacology of cancer. ICNN 1997: 2490-2493
Coauthor Index
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