Jianjiong Gao

Jianjiong Gao

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Jianjiong Gao

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Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal.

Mol Cell Proteomics 2019 Sep 15;18(9):1893-1898. Epub 2019 Jul 15.

‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065

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http://dx.doi.org/10.1074/mcp.TIR119.001673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731080PMC
September 2019

G2S: a web-service for annotating genomic variants on 3D protein structures.

Bioinformatics 2018 06;34(11):1949-1950

Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972642PMC
June 2018

Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer.

Cancer Cell 2018 01;33(1):125-136.e3

Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765991PMC
January 2018

Multicenter phase II study of temozolomide and myeloablative chemotherapy with autologous stem cell transplant for newly diagnosed anaplastic oligodendroglioma.

Neuro Oncol 2017 Oct;19(10):1380-1390

Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1093/neuonc/nox086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596171PMC
October 2017

Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.

Authors:
Ahmet Zehir Ryma Benayed Ronak H Shah Aijazuddin Syed Sumit Middha Hyunjae R Kim Preethi Srinivasan Jianjiong Gao Debyani Chakravarty Sean M Devlin Matthew D Hellmann David A Barron Alison M Schram Meera Hameed Snjezana Dogan Dara S Ross Jaclyn F Hechtman Deborah F DeLair JinJuan Yao Diana L Mandelker Donavan T Cheng Raghu Chandramohan Abhinita S Mohanty Ryan N Ptashkin Gowtham Jayakumaran Meera Prasad Mustafa H Syed Anoop Balakrishnan Rema Zhen Y Liu Khedoudja Nafa Laetitia Borsu Justyna Sadowska Jacklyn Casanova Ruben Bacares Iwona J Kiecka Anna Razumova Julie B Son Lisa Stewart Tessara Baldi Kerry A Mullaney Hikmat Al-Ahmadie Efsevia Vakiani Adam A Abeshouse Alexander V Penson Philip Jonsson Niedzica Camacho Matthew T Chang Helen H Won Benjamin E Gross Ritika Kundra Zachary J Heins Hsiao-Wei Chen Sarah Phillips Hongxin Zhang Jiaojiao Wang Angelica Ochoa Jonathan Wills Michael Eubank Stacy B Thomas Stuart M Gardos Dalicia N Reales Jesse Galle Robert Durany Roy Cambria Wassim Abida Andrea Cercek Darren R Feldman Mrinal M Gounder A Ari Hakimi James J Harding Gopa Iyer Yelena Y Janjigian Emmet J Jordan Ciara M Kelly Maeve A Lowery Luc G T Morris Antonio M Omuro Nitya Raj Pedram Razavi Alexander N Shoushtari Neerav Shukla Tara E Soumerai Anna M Varghese Rona Yaeger Jonathan Coleman Bernard Bochner Gregory J Riely Leonard B Saltz Howard I Scher Paul J Sabbatini Mark E Robson David S Klimstra Barry S Taylor Jose Baselga Nikolaus Schultz David M Hyman Maria E Arcila David B Solit Marc Ladanyi Michael F Berger

Nat Med 2017 08;23(8):1004

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http://dx.doi.org/10.1038/nm0817-1004cDOI Listing
August 2017

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.

Bioinformatics 2017 Jul;33(14):2238-2240

Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859976PMC
July 2017

OncoKB: A Precision Oncology Knowledge Base.

JCO Precis Oncol 2017 Jul 16;2017. Epub 2017 May 16.

, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Gynecologic Medical Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Breast Medicine Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Breast Medicine Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center , New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Head and Neck Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , , Department of Hematology and Oncology, Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92675, USA; , Department of R&D and Bioinformatics, Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92675, USA; , Head and Neck Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Gynecologic Medical Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Sarcoma Medical Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; Genitourinary Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Developmental Therapeutics, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Sarcoma Medical Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Department of Oncology and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Genitourinary Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA , Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Developmental Therapeutics, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; , Breast Medicine Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Developmental Therapeutics, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Genitourinary Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Weill Cornell Medical College, New York, NY USA; , Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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https://www.researchgate.net/profile/Debyani_Chakravarty/pub
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http://ascopubs.org/doi/10.1200/PO.17.00011
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5586540PMC
http://dx.doi.org/10.1200/PO.17.00011DOI Listing
July 2017

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.

Authors:
Ahmet Zehir Ryma Benayed Ronak H Shah Aijazuddin Syed Sumit Middha Hyunjae R Kim Preethi Srinivasan Jianjiong Gao Debyani Chakravarty Sean M Devlin Matthew D Hellmann David A Barron Alison M Schram Meera Hameed Snjezana Dogan Dara S Ross Jaclyn F Hechtman Deborah F DeLair JinJuan Yao Diana L Mandelker Donavan T Cheng Raghu Chandramohan Abhinita S Mohanty Ryan N Ptashkin Gowtham Jayakumaran Meera Prasad Mustafa H Syed Anoop Balakrishnan Rema Zhen Y Liu Khedoudja Nafa Laetitia Borsu Justyna Sadowska Jacklyn Casanova Ruben Bacares Iwona J Kiecka Anna Razumova Julie B Son Lisa Stewart Tessara Baldi Kerry A Mullaney Hikmat Al-Ahmadie Efsevia Vakiani Adam A Abeshouse Alexander V Penson Philip Jonsson Niedzica Camacho Matthew T Chang Helen H Won Benjamin E Gross Ritika Kundra Zachary J Heins Hsiao-Wei Chen Sarah Phillips Hongxin Zhang Jiaojiao Wang Angelica Ochoa Jonathan Wills Michael Eubank Stacy B Thomas Stuart M Gardos Dalicia N Reales Jesse Galle Robert Durany Roy Cambria Wassim Abida Andrea Cercek Darren R Feldman Mrinal M Gounder A Ari Hakimi James J Harding Gopa Iyer Yelena Y Janjigian Emmet J Jordan Ciara M Kelly Maeve A Lowery Luc G T Morris Antonio M Omuro Nitya Raj Pedram Razavi Alexander N Shoushtari Neerav Shukla Tara E Soumerai Anna M Varghese Rona Yaeger Jonathan Coleman Bernard Bochner Gregory J Riely Leonard B Saltz Howard I Scher Paul J Sabbatini Mark E Robson David S Klimstra Barry S Taylor Jose Baselga Nikolaus Schultz David M Hyman Maria E Arcila David B Solit Marc Ladanyi Michael F Berger

Nat Med 2017 Jun 8;23(6):703-713. Epub 2017 May 8.

Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

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http://www.nature.com/doifinder/10.1038/nm.4333
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http://dx.doi.org/10.1038/nm.4333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461196PMC
June 2017

Overcome tumor heterogeneity-imposed therapeutic barriers through convergent genomic biomarker discovery: A braided cancer river model of kidney cancer.

Semin Cell Dev Biol 2017 04 8;64:98-106. Epub 2016 Sep 8.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States.

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http://dx.doi.org/10.1016/j.semcdb.2016.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522717PMC
April 2017

An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types.

Bioinformatics 2016 06 3;32(11):1643-51. Epub 2015 Dec 3.

Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892411PMC
June 2016

Integrated Genomics for Pinpointing Survival Loci within Arm-Level Somatic Copy Number Alterations.

Cancer Cell 2016 05;29(5):737-750

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cellular and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864611PMC
May 2016

rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R.

Bioinformatics 2016 04 3;32(8):1272-4. Epub 2015 Dec 3.

Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907377PMC
April 2016

Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

Clin Lab Med 2016 Mar;36(1):153-81

Memorial Sloan Kettering Cancer Center, 417 East 68th Street, New York, NY 10065, USA.

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http://dx.doi.org/10.1016/j.cll.2015.09.013DOI Listing
March 2016

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer.

Nucleic Acids Res 2016 Jan 20;44(D1):D986-91. Epub 2015 Nov 20.

Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK

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http://dx.doi.org/10.1093/nar/gkv1132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702822PMC
January 2016

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains.

Cell Syst 2015 Sep 23;1(3):197-209. Epub 2015 Sep 23.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2015.08.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982675PMC
September 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

Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

Surg Pathol Clin 2015 Jun 31;8(2):269-88. Epub 2015 Mar 31.

Memorial Sloan Kettering Cancer Center, 417 East 68th Street, New York, NY 10065, USA.

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http://dx.doi.org/10.1016/j.path.2015.02.015DOI Listing
June 2015

Integrative clinical genomics of advanced prostate cancer.

Cell 2015 May;161(5):1215-1228

Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484602PMC
May 2015

Disrupting KATP channels diminishes the estrogen-mediated protection in female mutant mice during ischemia-reperfusion.

Clin Proteomics 2014 6;11(1):19. Epub 2014 May 6.

Department of Medicine, University of Wisconsin, Room 8418, WIMR II, 1111 Highland Ave., Madison, WI 53705, USA.

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http://dx.doi.org/10.1186/1559-0275-11-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047774PMC
June 2014

Recurrent SMARCA4 mutations in small cell carcinoma of the ovary.

Nat Genet 2014 May 23;46(5):424-6. Epub 2014 Mar 23.

1] Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [2].

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http://dx.doi.org/10.1038/ng.2922DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699446PMC
May 2014

Collection, integration and analysis of cancer genomic profiles: from data to insight.

Curr Opin Genet Dev 2014 Feb 27;24:92-8. Epub 2014 Feb 27.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, Box 460, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2013.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084973PMC
February 2014

P³DB 3.0: From plant phosphorylation sites to protein networks.

Nucleic Acids Res 2014 Jan 15;42(Database issue):D1206-13. Epub 2013 Nov 15.

Department of Computer Science, University of Missouri, Columbia, MO 65211, USA, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA, School of Communication and Information Engineering, Shanghai University, Shanghai 200444, People's Republic of China, Department of Biology, Brandeis University, MA 02453, USA, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA and Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1093/nar/gkt1135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965113PMC
January 2014

Correlation between posttranslational modification and intrinsic disorder in protein.

Pac Symp Biocomput 2012 :94-103

Department of Computer Science, CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA.

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http://psb.stanford.edu/psb-online/proceedings/psb12/gao.pdf
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120255PMC
December 2013

PiHelper: an open source framework for drug-target and antibody-target data.

Bioinformatics 2013 Aug 12;29(16):2071-2. Epub 2013 Jun 12.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722529PMC
August 2013

P(3)DB: An Integrated Database for Plant Protein Phosphorylation.

Front Plant Sci 2012 7;3:206. Epub 2012 Sep 7.

Department of Computer Science, University of Missouri Columbia, MO, USA.

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http://journal.frontiersin.org/article/10.3389/fpls.2012.002
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http://dx.doi.org/10.3389/fpls.2012.00206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435559PMC
September 2012

Predicting and analyzing protein phosphorylation sites in plants using musite.

Front Plant Sci 2012 21;3:186. Epub 2012 Aug 21.

Department of Computer Science, University of Missouri Columbia, MO, USA.

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http://dx.doi.org/10.3389/fpls.2012.00186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3423629PMC
August 2012

Phosphoproteomic analysis of seed maturation in Arabidopsis, rapeseed, and soybean.

Plant Physiol 2012 May 22;159(1):517-28. Epub 2012 Mar 22.

Department of Biochemistry, Christopher S. Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1104/pp.111.191700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375983PMC
May 2012

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.

Mol Cell Proteomics 2010 Dec 11;9(12):2586-600. Epub 2010 Aug 11.

Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1074/mcp.M110.001388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101956PMC
December 2010

Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif.

BMC Genomics 2010 Dec 1;11 Suppl 3:S1. Epub 2010 Dec 1.

Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu 210029, China.

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http://dx.doi.org/10.1186/1471-2164-11-S3-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999339PMC
December 2010

The Musite open-source framework for phosphorylation-site prediction.

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S9. Epub 2010 Dec 21.

Department of Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-11-S12-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040535PMC
December 2010

P3DB: a plant protein phosphorylation database.

Nucleic Acids Res 2009 Jan 17;37(Database issue):D960-2. Epub 2008 Oct 17.

Department of Computer Science, Department of Biochemistry and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1093/nar/gkn733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686431PMC
January 2009