John N Weinstein

John N Weinstein

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John N Weinstein

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Response envelope analysis for quantitative evaluation of drug combinations.

Bioinformatics 2019 Oct;35(19):3761-3770

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz091DOI Listing
October 2019

Integrated transcriptomic-genomic tool Texomer profiles cancer tissues.

Nat Methods 2019 05 15;16(5):401-404. Epub 2019 Apr 15.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41592-019-0388-9DOI Listing
May 2019

ZC3H12A Expression in Different Stages of Colorectal Cancer.

Oncoscience 2019 Mar 2;6(3-4):301-311. Epub 2019 Apr 2.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.18632/oncoscience.480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508193PMC
March 2019

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments.

BMC Bioinformatics 2019 Feb 19;20(1):89. Epub 2019 Feb 19.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12859-019-2669-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381631PMC
February 2019

Assessment of l-Asparaginase Pharmacodynamics in Mouse Models of Cancer.

Metabolites 2019 Jan 9;9(1). Epub 2019 Jan 9.

Department of Bioinformatics and Computational Biology and The Proteomics and Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/metabo9010010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359345PMC
January 2019

Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers.

Commun Biol 2018 21;1:234. Epub 2018 Dec 21.

1Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA.

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http://www.nature.com/articles/s42003-018-0239-8
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http://dx.doi.org/10.1038/s42003-018-0239-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303286PMC
December 2018

SoS Notebook: an interactive multi-language data analysis environment.

Bioinformatics 2018 11;34(21):3768-3770

Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198852PMC
November 2018

Clinical significance of FBXO17 gene expression in high-grade glioma.

BMC Cancer 2018 Jul 31;18(1):773. Epub 2018 Jul 31.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12885-018-4680-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069786PMC
July 2018

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.

Cell Rep 2018 04;23(1):255-269.e4

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183043
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http://dx.doi.org/10.1016/j.celrep.2018.03.077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5916795PMC
April 2018

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Cell 2018 04;173(2):386-399.e12

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.03.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890960PMC
April 2018

Predicting high-risk endometrioid carcinomas using proteins.

Oncotarget 2018 Apr 13;9(28):19704-19715. Epub 2018 Apr 13.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.18632/oncotarget.24803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5929419PMC
April 2018

Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas.

Cancer Res 2017 11;77(21):e51-e54

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679242PMC
November 2017

A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations.

Cancer Cell 2017 06 18;31(6):820-832.e3. Epub 2017 May 18.

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502825PMC
June 2017

Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype.

Sci Rep 2017 02 6;7:41960. Epub 2017 Feb 6.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1038/srep41960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292751PMC
February 2017

Altered Expression and Splicing of ESRP1 in Malignant Melanoma Correlates with Epithelial-Mesenchymal Status and Tumor-Associated Immune Cytolytic Activity.

Cancer Immunol Res 2016 06 4;4(6):552-61. Epub 2016 Apr 4.

Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Regeneron Pharmaceuticals Inc., Tarrytown, New York.

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http://dx.doi.org/10.1158/2326-6066.CIR-15-0255DOI Listing
June 2016

PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.

Bioinformatics 2016 Jan 23;32(2):312-4. Epub 2015 Sep 23.

Department of Bioinformatics and Computational Biology and.

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http://dx.doi.org/10.1093/bioinformatics/btv554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907393PMC
January 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner.

PLoS One 2014 26;9(3):e92047. Epub 2014 Mar 26.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092047PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966786PMC
December 2015

TransVar: a multilevel variant annotator for precision genomics.

Nat Methods 2015 Nov;12(11):1002-3

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1038/nmeth.3622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772859PMC
November 2015

Invasive Bladder Cancer: Genomic Insights and Therapeutic Promise.

Clin Cancer Res 2015 Oct;21(20):4514-24

The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts. Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-14-1215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610178PMC
October 2015

TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer.

Cancer Res 2015 Sep 24;75(18):3728-37. Epub 2015 Jul 24.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. The University of Texas Graduate School of Biomedical Sciences, Houston, Texas. Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas.

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http://cancerres.aacrjournals.org/content/75/18/3728.full.pd
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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
Publisher Site
http://dx.doi.org/10.1158/0008-5472.CAN-15-0273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573884PMC
September 2015

Catalytic Role of the Substrate Defines Specificity of Therapeutic l-Asparaginase.

J Mol Biol 2015 Aug 2;427(17):2867-85. Epub 2015 Jul 2.

Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM 87185-1315, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.06.017DOI Listing
August 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Development of a robust classifier for quality control of reverse-phase protein arrays.

Bioinformatics 2015 Mar 6;31(6):912-8. Epub 2014 Nov 6.

Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375399PMC
March 2015

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution.

Genome Res 2015 Mar 3;25(3):316-27. Epub 2015 Feb 3.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;

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http://dx.doi.org/10.1101/gr.180612.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352879PMC
March 2015

Tissue-specific isoform switch and DNA hypomethylation of the pyruvate kinase PKM gene in human cancers.

Oncotarget 2014 Sep;5(18):8202-10

Department of Neuro-Oncology, The University of Texas M. D. Anderson Cancer Center, The University of Texas - Houston Health Science Center, Houston, USA.

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http://www.oncotarget.com/fulltext/1159
Publisher Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226677PMC
http://dx.doi.org/10.18632/oncotarget.1159DOI Listing
September 2014

PRADA: pipeline for RNA sequencing data analysis.

Bioinformatics 2014 Aug 1;30(15):2224-6. Epub 2014 Apr 1.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103589PMC
August 2014

A curated census of autophagy-modulating proteins and small molecules: candidate targets for cancer therapy.

Autophagy 2014 Jul 12;10(7):1316-26. Epub 2014 May 12.

Department of Bioinformatics and Computational Biology; The University of Texas MD Anderson Cancer Center; Houston, TX USA; Department of Systems Biology; The University of Texas MD Anderson Cancer Center; Houston, TX USA.

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http://dx.doi.org/10.4161/auto.28773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203555PMC
July 2014

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

Nat Biotechnol 2014 Jul 22;32(7):644-52. Epub 2014 Jun 22.

1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USA. [2] Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA. [3].

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http://www.nature.com/articles/nbt.2940
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http://dx.doi.org/10.1038/nbt.2940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102885PMC
July 2014

An artifact in LC-MS/MS measurement of glutamine and glutamic acid: in-source cyclization to pyroglutamic acid.

Anal Chem 2014 Jun 5;86(12):5633-7. Epub 2014 Jun 5.

Department of Bioinformatics and Computational Biology and ‡Proteomics and Metabolomics Facility, Department of Pathology, MD Anderson Cancer Center, University of Texas , Houston, Texas 77054, United States.

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http://dx.doi.org/10.1021/ac501451vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063328PMC
June 2014

Tumor subtype-specific cancer-testis antigens as potential biomarkers and immunotherapeutic targets for cancers.

Cancer Immunol Res 2014 Apr 25;2(4):371-9. Epub 2013 Nov 25.

Authors' Affiliations: Departments of Ludwig Collaborative Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.

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http://dx.doi.org/10.1158/2326-6066.CIR-13-0088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4007352PMC
April 2014

Targeted metabolomic analysis of amino acid response to L-asparaginase in adherent cells.

Metabolomics 2014 7;10(5):909-919. Epub 2014 Feb 7.

Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, University of Texas, Houston, TX 77054 USA ; Department of Systems Biology, MD Anderson Cancer Center, University of Texas, Houston, TX 77054 USA.

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http://dx.doi.org/10.1007/s11306-014-0634-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145215PMC
February 2014

Cancer: Discrepancies in drug sensitivity.

Nature 2013 Dec 27;504(7480):381-3. Epub 2013 Nov 27.

Department of Bioinformatics and Computational Biology and the Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.

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http://www.nature.com/articles/nature12839
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http://dx.doi.org/10.1038/nature12839DOI Listing
December 2013

TCPA: a resource for cancer functional proteomics data.

Nat Methods 2013 Nov 15;10(11):1046-7. Epub 2013 Sep 15.

1] Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA. [2].

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http://dx.doi.org/10.1038/nmeth.2650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076789PMC
November 2013

Measurement of DNA concentration as a normalization strategy for metabolomic data from adherent cell lines.

Anal Chem 2013 Oct 2;85(20):9536-42. Epub 2013 Oct 2.

Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX, 77030, United States.

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http://dx.doi.org/10.1021/ac401559vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868625PMC
October 2013

The Cancer Genome Atlas Pan-Cancer analysis project.

Nat Genet 2013 Oct;45(10):1113-20

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/ng.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919969PMC
October 2013

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.

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http://dx.doi.org/10.1056/NEJMoa1301689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767041PMC
May 2013

Concordance of gene expression and functional correlation patterns across the NCI-60 cell lines and the Cancer Genome Atlas glioblastoma samples.

PLoS One 2012 26;7(7):e40062. Epub 2012 Jul 26.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040062PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406063PMC
April 2013

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.

Bioinformatics 2013 Jan 17;29(2):266-7. Epub 2012 Nov 17.

Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bts665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546792PMC
January 2013

PurityEst: estimating purity of human tumor samples using next-generation sequencing data.

Bioinformatics 2012 Sep 28;28(17):2265-6. Epub 2012 Jun 28.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426843PMC
September 2012

Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines.

PLoS One 2012 24;7(1):e30317. Epub 2012 Jan 24.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030317PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265467PMC
June 2012

Drug discovery: Cell lines battle cancer.

Authors:
John N Weinstein

Nature 2012 Mar 28;483(7391):544-5. Epub 2012 Mar 28.

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http://dx.doi.org/10.1038/483544aDOI Listing
March 2012

MicroRNAs in cancer pharmacology and therapeutics: exploiting a natural synergy between '-omic' and hypothesis-driven research.

Authors:
John N Weinstein

Mol Cancer Ther 2011 Nov;10(11):2021

The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Department of Systems Biology, Houston, TX 77030-4009, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-11-0766DOI Listing
November 2011

Metabolomics reveals attenuation of the SLC6A20 kidney transporter in nonhuman primate and mouse models of type 2 diabetes mellitus.

J Biol Chem 2011 Jun 12;286(22):19511-22. Epub 2011 Apr 12.

Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1074/jbc.M111.221739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103330PMC
June 2011

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

BMC Bioinformatics 2011 Feb 10;12:52. Epub 2011 Feb 10.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Room 5068, Building 37, 37 Convent Drive, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1186/1471-2105-12-52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3223614PMC
February 2011

MODULATION OF AUTOPHAGY AND ITS POTENTIAL FOR CANCER THERAPY.

Drugs Future 2011 ;36(12)

Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239665PMC
http://dx.doi.org/10.1358/dof.2011.036.12.1711892DOI Listing
January 2011

Exposing the cancer genome atlas as a SPARQL endpoint.

J Biomed Inform 2010 Dec;43(6):998-1008

Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Unit 1410, Houston, TX 77230-1402, USA.

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http://dx.doi.org/10.1016/j.jbi.2010.09.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071752PMC
December 2010

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

Bioinformatics 2010 Aug 8;26(16):1945-9. Epub 2010 Jul 8.

Department of Bioinformatics, George Mason University, Fairfax, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916722PMC
August 2010

Dihydroartemisinin accelerates c-MYC oncoprotein degradation and induces apoptosis in c-MYC-overexpressing tumor cells.

Biochem Pharmacol 2010 Jul 3;80(1):22-30. Epub 2010 Mar 3.

Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Rd., Shanghai 201203, PR China.

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http://dx.doi.org/10.1016/j.bcp.2010.02.016DOI Listing
July 2010

mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities.

Mol Cancer Ther 2010 May 4;9(5):1080-91. Epub 2010 May 4.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-09-0965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879615PMC
May 2010

Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron.

Cancer Res 2010 Mar 9;70(6):2191-203. Epub 2010 Mar 9.

Laboratory of Molecular Pharmacology and Developmental Therapeutics Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-09-3528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922994PMC
March 2010

Integrative analysis of proteomic signatures, mutations, and drug responsiveness in the NCI 60 cancer cell line set.

Mol Cancer Ther 2010 Feb 2;9(2):257-67. Epub 2010 Feb 2.

Department of Melanoma Medical Oncology and Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 0904, Houston, TX 77030, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-09-0743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085051PMC
February 2010

Multifactorial regulation of E-cadherin expression: an integrative study.

Mol Cancer Ther 2010 Jan 6;9(1):1-16. Epub 2010 Jan 6.

Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-09-0321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821037PMC
January 2010