Publications by authors named "Yasin Senbabaoglu"

23Publications

Non-conventional Inhibitory CD4Foxp3PD-1 T Cells as a Biomarker of Immune Checkpoint Blockade Activity.

Cancer Cell 2018 06;33(6):1017-1032.e7

Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medicine, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.05.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648657PMC
June 2018

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

Cell Rep 2016 Mar 3;14(10):2476-89. Epub 2016 Mar 3.

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing 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. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794376PMC
March 2016

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

PLoS Comput Biol 2016 Feb 29;12(2):e1004765. Epub 2016 Feb 29.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771175PMC
February 2016

Mitochondrial DNA copy number variation across human cancers.

Elife 2016 Feb 22;5. Epub 2016 Feb 22.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.

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http://dx.doi.org/10.7554/eLife.10769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775221PMC
February 2016

Graph Curvature for Differentiating Cancer Networks.

Sci Rep 2015 Jul 14;5:12323. Epub 2015 Jul 14.

Departments of Computer Science and Applied Mathematics/Statistics, Stony Brook University, Stony Brook, NY 11794.

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http://dx.doi.org/10.1038/srep12323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500997PMC
July 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

Notch reporter activity in breast cancer cell lines identifies a subset of cells with stem cell activity.

Mol Cancer Ther 2015 Mar 11;14(3):779-787. Epub 2015 Feb 11.

Georgia Regents University Cancer Center, Department of Biochemistry and Molecular Biology 1410 Laney Walker Blvd. CN2136 Augusta, GA 30912.

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http://dx.doi.org/10.1158/1535-7163.MCT-14-0228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456218PMC
March 2015

Critical limitations of consensus clustering in class discovery.

Sci Rep 2014 Aug 27;4:6207. Epub 2014 Aug 27.

Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/srep06207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145288PMC
August 2014

Emerging landscape of oncogenic signatures across human cancers.

Nat Genet 2013 Oct;45(10):1127-33

Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.2762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320046PMC
October 2013

OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks.

Bioinformatics 2013 Jun 10;29(11):1416-23. Epub 2013 Apr 10.

IBISC EA 4526, Université d'Évry-Val d'Essonne, Évry, France.

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http://dx.doi.org/10.1093/bioinformatics/btt167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661057PMC
June 2013

Genomic estimates of aneuploid content in glioblastoma multiforme and improved classification.

Clin Cancer Res 2012 Oct 21;18(20):5595-605. Epub 2012 Aug 21.

Bioinformatics Program, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-1427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477792PMC
October 2012