2020

Molecular Oncology

7 July 2020

Role of ultraviolet mutational signature versus tumor mutation burden in predicting response to immunotherapy

Timothy V. Pham, Amélie Boichard, Aaron Goodman, Paul Riviere, Huwate Yeerna, Pablo Tamayo, and Razelle Kurzrock

Nucleic Acids Research

11 June 2020

Tissue- and development-stage–specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples

Anshuman Panda, Anupama Yadav, Huwate Yeerna, Amartya Singh, Michael Biehl, Markus Lux, Alexander Schulz, Tyler Klecha, Sebastian Doniach, Hossein Khiabanian, Shridar Ganesan, Pablo Tamayo, Gyan Bhanot

Molecular Cancer Therapeutics

Volume 19, Issue 3, 23 January 2020

Macrophage Syk-PI3Kγ inhibits anti-tumor immunity: SRX3207, a novel dual Syk-PI3K inhibitory chemotype relieves tumor immunosuppression

Shweta Joshi, Kevin X Liu, Muamera Zulcic, Alok R. Singh, Dylan Skola, Christopher K. Glass, P. Dominick Sanders, Andrew B Sharabi, Timothy V. Pham, Pablo Tamayo, Daniel Shiang, Huy Q. Dinh, Catherine C. Hedrick, Guillermo A. Morales, Joseph R. Garlich and Donald L. Durden

Clincal Cancer Research

Volume 26, Issue 11, 13 January 2020

Cannabinoids promote progression of HPV positive head and neck squamous cell carcinoma via p38 MAPK activation

Chao Liu, Sayed H Sadat, Koji Ebisumoto, Akihiro Sakai, Bharat A Panuganti, Shuling Ren, Yusuke Goto, Sunny Haft, Takahito Fukusumi, Mizuo Ando, Yuki Saito, Theresa Guo, Pablo Tamayo, Huwate Yeerna, William Kim, Jacqueline Hubbard, Andrew B Sharabi, J. Silvio Gutkind and Joseph A. Califano

eLife

Article 53003, 8 January 2020

STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation of human cells

Jong Wook Kim, Christian Berrios, Miju Kim, Amy E Schade, Guillaume Adelmant, Huwate Yeerna, Emily Damato, Amanda Balboni Iniguez, Laurence Florens, Michael P Washburn, Kim Stegmaier, Nathanael S Gray, Pablo Tamayo, Ole Gjoerup, Jarrod A Marto, James DeCaprio, William C Hahn

2019

Oncotarget

Volume 10, Number 59, 29 October 2019

The multikinase inhibitor RXDX-105 is effective against neuroblastoma in vitro and in vivo

Sean M. Flynn, Jacqueline Lesperance, Andrew Macias, Nikki Phanhthilath, Megan Rose Paul, Jong Wook Kim, Pablo Tamayo and Peter E. Zage

iScience

Volume 19, 27 September 2019

Cyclin E Overexpression in Human Mammary Epithelial Cells Promotes Epithelial Cancer-Specific Copy Number Alterations

Servando Giraldez, Pablo Tamayo, Nathan Wineinger, William Kim, and Steven I. Reed

Cancer Research

Volume 79, Issue 17, 1 September 2019

Metformin inhibits progression of Head and Neck Squamous Cell Carcinoma by acting Directly on Carcinoma Initiating Cells

Xingyu Wu, Huwate Yeerna, Yusuke Goto, Toshinori Ando, Victoria H Wu, Xuefeng Zhang, Zhiyong Wang, Panomwat Amornphimoltham, Anne N. Murphy, Pablo Tamayo, Qianming Chen, Scott M. Lippman and J. Silvio Gutkind

Journal of Biological Chemistry

Volume 294, Number 29, 5 June 2019

Illuminating the Onco-GPCRome: Novel G protein-coupled receptor-driven oncocrine networks and targets for cancer immunotherapy

Victoria Wu, Huwate Yeerna, Nijiro Nohata, Joshua Chiou, Olivier Harismendy, Francesco Raimondi, Asuka Inoue, Robert B. Russell, Pablo Tamayo and J. Silvio Gutkind

Nature Communications

Volume 10, Article number: 2188, 16 May 2019

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

Mizuo Ando, Yuki Saito, Guorong Xu, Nam Q. Bui, Kate Medetgul-Ernar, Minya Pu, Kathleen Fisch, Shuling Ren, Akihiro Sakai, Takahito Fukusumi, Chao Liu, Sunny Haft, John Pang, Adam Mark, Daria A. Gaykalova, Theresa Guo, Alexander V. Favorov, Srinivasan Yegnasubramanian, Elana J. Fertig, Patrick Ha, Pablo Tamayo, Tatsuya Yamasoba, Trey Ideker, Karen Messer & Joseph A. Califano

Journal of Theoretical Biology

Volume 474, 7 August 2019

Modelling bistable tumour population dynamics to design effective treatment strategies

Andrei R. Akhmetzhanov, Jong Wook Kim, Ryan Sullivan, Robert A. Beckman, Pablo Tamayo, Chen-Hsiang Yeang

Cancer Cell

Volume 35, Issue 3, 18 March 2019

A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK

Xiaodong Feng, Nadia Arang, Damiano Cosimo Rigiracciolo, Joo Sang Lee, Huwate Yeerna, Zhiyong Wang, Simone Lubrano, Ayush Kishore, Jonathan A. Pachter, Gabriele M. König, Marcello Maggiolini, Evi Kostenis, David D. Schlaepfer, Pablo Tamayo, Qianming Chen, Eytan Ruppin, J. Silvio Gutkind

Molecular & Cellular Proteomics

Volume 3, 1 March 2019

A Curated Resource for Phosphosite-specific Signature Analysis

Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, Matthew Szucs, Filip Mundt, Dominique Forestier, Judit Jane-Valbuena, Hasmik Keshishian, Michael A. Gillette, Pablo Tamayo, Jill P. Mesirov, Jacob D. Jaffe, Steven A. Carr and D. R. Mani

2018

Cell Systems

Volume 7, Issue 6, 26 December 2018

Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding

Yan Wu, Pablo Tamayo, and Kun Zhang

OncoImmunology

Volume 8, Issue 3, Article: 1550341, 24 December 2018

APOBEC-related mutagenesis and neo-peptide hydrophobicity: implications for response to immunotherapy

Amélie Boichard, Timothy V. Pham, Huwate Yeerna, Aaron Goodman, Pablo Tamayo, Scott Lippman, Garrett M. Framton, Igor F. Tsigelny & Razelle Kurzrock

Cancers

Volume 11, Issue 1, 21 December 2018

Comprehensive Genomic Profiling Reveals Diverse but Actionable Molecular Portfolios across Hematologic Malignancies: Implications for Next Generation Clinical Trials

Natalie Galanina, Rafael Bejar, Michael Choi, Aaron Goodman, Matthew Wieduwilt, Carolyn Mulroney, Lisa Kim, Huwate Yeerna, Pablo Tamayo, Jo-Anne Vergilio, Tariq I. Mughal, Vincent Miller, Catriona Jamieson, and Razelle Kurzrock

Blood

Volume 132, Issue Suppl 1, 29 November 2018

DNA Methylation Identifies Genetically and Prognostically Distinct Subtypes of MDS

Brian M Reilly, Tiffany N Tanaka, Dinh Diep, Huwate Yeerna, Pablo Tamayo, Kun Zhang and Rafael Bejar

Cancer Cell

Volume 34, Issue 3, 10 September 2018

Overcoming Resistance to Dual Innate Immune and MEK Inhibition Downstream of KRAS

Shunsuke Kitajima, Hajime Asahina, Ting Chen, Sujuan Guo, Laura Gutierrez Quiceno, Jillian D.Cavanaugh, Ashley A. Merlino, Shoichiro Tange, Hideki Terai, Jong Wook Kim, Xiaoen Wang, Shan Zhou, Man Xu, Stephen Wang, Zehua Zhu, Tran C.Thai, Chiaki Takahashi, Yujin Wang, Richard Neve, Susanna Stinson, Pablo Tamayo, Hideo Watanabe, Paul T.Kirschmeier, Kwok-KinWong, David A. Barbie

Cancer Cell

Volume 34, Issue 3, 10 September 2018

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups

Tenley C.Archer, Tobias Ehrenberger, Filip Mundt, Maxwell P.Gold, Karsten Krug, Clarence K. Mah, Elizabeth L. Mahoney, Colin J.Daniel, Alexander LeNail, Divya Ramamoorthy, Philipp Mertins, D. R. Mani, Hailei Zhang, Michael A.Gillette, Karl Clauser, Michael Noble, Lauren C.Tang, Jessica Pierre-François, Jacob Silterra, James Jensen, Pablo Tamayo, Andrey Korshunov, Stefan M. Pfister, Marcel Kool, Paul A. Northcott, Rosalie C. Sears, Jonathan O. Lipton, Steven A. Carr, Jill P. Mesirov, Scott L. Pomeroy, Ernest Fraenkel

Nature Medicine

Volume 24, 23 July 2018

Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses

Israel Cañadas, Rohit Thummalapalli, Jong Wook Kim, Shunsuke Kitajima, Russell William Jenkins, Camilla Laulund Christensen, Marco Campisi, Yanan Kuang, Yanxi Zhang, Evisa Gjini, Gao Zhang, Tian Tian, Debattama Rai. Sen, Diana Miao, Yu Imamura, Tran Thai, Brandon Piel, Hideki Terai, Amir Reza Aref, Timothy Hagan, Shohei Koyama, Masayuki Watanabe, Hideo Baba, Anika Elise Adeni, Christine Anne Lydon, Pablo Tamayo, Zhi Wei, Meenhard Herlyn, Thanh Uyen Barbie, Ravindra Uppaluri, Lynnette Marie Sholl, Ewa Sicinska, Jacob Sands, Scott Rodig, Kwok Kin Wong, Cloud Peter Paweletz, Hideo Watanabe & David Allen Barbie

Nature Communications

Volume 9, Article number: 2372, 9 July 2018

Assembly and activation of the Hippo signalome by FAT1 tumor suppressor

Daniel Martin, Maria S. Degese, Lynn Vitale-Cross, Ramiro Iglesias-Bartolome, Juan Luis Callejas Valera, Zhiyong Wang, Xiaodong Feng, Huwate Yeerna, Vachan Vadmal, Toshiro Moroishi, Rick F. Thorne, Moraima Zaida, Bradford Siegele, Sok C. Cheong, Alfredo A. Molinolo, Yardena Samuels, Pablo Tamayo, Kun Liang Guan, Scott M. Lippman, J. Guy Lyons & J. Silvio Gutkind

Nature Genetics

Volume 50, 28 June 2018

Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer

Srinivas R. Viswanathan, Marina F. Nogueira, Colin G. Buss, John M. Krill-Burger, Mathias J. Wawer, Edyta Malolepsza, Ashton C. Berger, Peter S. Choi, Juliann Shih, Alison M. Taylor, Benjamin Tanenbaum, Chandra Sekhar Pedamallu, Andrew D. Cherniack, Pablo Tamayo, Craig A. Strathdee, Kasper Lage, Steven A. Carr, Monica Schenone, Sangeeta N. Bhatia, Francisca Vazquez, Aviad Tsherniak, William C. Hahn & Matthew Meyerson

JCO Precision Oncology

Original Report, 1 June 2018

Genomic and Proteomic Alterations in Desmoplastic Small Round Blue-Cell Tumors

Ajaz Bulbul, John Paul Shen, Pablo Tamayo, and Hatim Husain, and Joanne Xiu

Cancer Cell

Volume 6, Issue 4, 25 April 2018

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

Justin K. Huang, Daniel E.Carlin, Michael Ku Yu, Wei Zhang, Jason F.Kreisberg, Pablo Tamayo, Trey Ideker

2017

Cancer Discovery

Volume 7, Issue 9, 31 August 2017

Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations

Franklin W. Huang, Juan Miguel Mosquera, Andrea Garofalo, Coyin Oh, Maria Baco, Ali Amin-Mansour, Bokang Rabasha, Samira Bahl, Stephanie A. Mullane, Brian D. Robinson, Saud Aldubayan, Francesca Khani, Beerinder Karir, Eejung Kim, Jeremy Chimene-Weiss, Matan Hofree, Alessandro Romanel, Joseph R. Osborne, Jong Wook Kim, Gissou Azabdaftari, Anna Woloszynska-Read, Karen Sfanos, Angelo M. De Marzo, Francesca Demichelis, Stacey Gabriel, Eliezer M. Van Allen, Jill Mesirov, Pablo Tamayo, Mark A. Rubin, Isaac J. Powell and Levi A. Garraway

Cell Systems

Volume 5, Issue 2, 23 August 2017

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States

Jong Wook Kim, Omar O. Abudayyeh, Huwate Yeerna, Chen-Hsiang Yeang, Michelle Stewart, Russell W. Jenkins, Shunsuke Kitajima, David J. Konieczkowski, Kate Medetgul-Ernar, Taylor Cavazos, Clarence Mah, Stephanie Ting, Eliezer M. Van Allen, Ofir Cohen, John Mcdermott, Emily Damato, Andrew J. Aguirre, Jonathan Liang, Arthur Liberzon, Gabriella Alexe, John Doench, Mahmoud Ghandi, Francisca Vazquez, Barbara A. Weir, Aviad Tsherniak, Aravind Subramanian, Karina Meneses-Cime, Jason Park, Paul Clemons, Levi A. Garraway, David Thomas, Jesse S. Boehm, David A. Barbie, William C. Hahn, Jill P. Mesirov, Pablo Tamayo

Cell Systems

Volume 5, Issue 2, 23 August 2017

The GenePattern Notebook Environment

Michael Reich, Thorin Tabor, Ted Liefeld, Helga Thorvaldsdóttir, Barbara Hill, Pablo Tamayo, Jill P. Mesirov

Nature

Volume 547, 27 July 2017

Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway

Vasanthi S. Viswanathan, Matthew J. Ryan, Harshil D. Dhruv, Shubhroz Gill, Ossia M. Eichhoff, Brinton Seashore-Ludlow, Samuel D. Kaffenberger, John K. Eaton, Kenichi Shimada, Andrew J. Aguirre, Srinivas R. Viswanathan, Shrikanta Chattopadhyay, Pablo Tamayo, Wan Seok Yang, Matthew G. Rees, Sixun Chen, Zarko V. Boskovic, Sarah Javaid, Cherrie Huang, Xiaoyun Wu, Yuen-Yi Tseng, Elisabeth M. Roider, Dong Gao, James M. Cleary, Brian M. Wolpin, Jill P. Mesirov, Daniel A. Haber, Jeffrey A. Engelman, Jesse S. Boehm, Joanne D. Kotz, Cindy S. Hon, Yu Chen, William C. Hahn, Mitchell P. Levesque, John G. Doench, Michael E. Berens, Alykhan F. Shamji, Paul A. Clemons, Brent R. Stockwell & Stuart L. Schreiber

Genome Biology

Volume 18, 27 July 2017

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin and Ekta Khurana

Cancer Cell

Volume 6, Issue 4, 25 April 2018

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

Vasanthi S. Viswanathan, Matthew J. Ryan, Harshil D. Dhruv, Shubhroz Gill, Ossia M. Eichhoff, Brinton Seashore-Ludlow, Samuel D. Kaffenberger, John K. Eaton, Kenichi Shimada, Andrew J. Aguirre, Srinivas R. Viswanathan, Shrikanta Chattopadhyay, Pablo Tamayo, Wan Seok Yang, Matthew G. Rees, Sixun Chen, Zarko V. Boskovic, Sarah Javaid, Cherrie Huang, Xiaoyun Wu, Yuen-Yi Tseng, Elisabeth M. Roider, Dong Gao, James M. Cleary, Brian M. Wolpin, Jill P. Mesirov, Daniel A. Haber, Jeffrey A. Engelman, Jesse S. Boehm, Joanne D. Kotz, Cindy S. Hon, Yu Chen, William C. Hahn, Mitchell P. Levesque, John G. Doench, Michael E. Berens, Alykhan F. Shamji, Paul A. Clemons, Brent R. Stockwell & Stuart L. Schreiber

Cancer Discovery

Volume 7, Issue 3, 5 March 2017

OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma

Gaylor Boulay, Mary E. Awad, Nicolo Riggi, Tenley C. Archer, Sowmya Iyer, Wannaporn E. Boonseng, Nikki E. Rossetti, Beverly Naigles, Shruthi Rengarajan, Angela Volorio, James C. Kim, Jill P. Mesirov, Pablo Tamayo, Scott L. Pomeroy, Martin J. Aryee and Miguel N. Rivera

2016

Cell Systems

Volume 3, Issue 3, 28 September 2016

Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers

Joseph Rosenbluh, Johnathan Mercer, Yashaswi Shrestha, Rachel Oliver, Pablo Tamayo, John G. Doench, Itay Tirosh, Federica Piccioni, Ella Hartenian, Heiko Horn, Lola Fagbami, David E. Root, Jacob Jaffe, Kasper Lage, Jesse S. Boehm, William C. Hahn

Cancer Cell

Volume 30, Issue 2, 8 August 2016

High-throughput Phenotyping of Lung Cancer Somatic Mutations

Alice H. Berger, Angela N. Brooks, Xiaoyun Wu, Yashaswi Shrestha, Candace Chouinard, Federica Piccioni, Mukta Bagul, Atanas Kamburov, Marcin Imielinski, Larson Hogstrom, Cong Zhu, Xiaoping Yang, Sasha Pantel, Ryo Sakai, Jacqueline Watson, Nathan Kaplan, Joshua D. Campbell, Shantanu Singh, David E. Root, Rajiv Narayan, Ted Natoli, David L. Lahr, Itay Tirosh, Pablo Tamayo, Gad Getz, Bang Wong, John Doench, Aravind Subramanian, Todd R. Golub, Matthew Meyerson, and Jesse S. Boehm

Clinical Cancer Research

Volume 22, Issue 15, 1 August 2016

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets

Allison R. Hanaford, Tenley C. Archer, Antoinette Price, Ulf D. Kahlert, Jarek Maciaczyk, Guido Nikkhah, Jong Wook Kim, Tobias Ehrenberger, Paul A. Clemons, Vlado Dančík, Brinton Seashore-Ludlow, Vasanthi Viswanathan, Michelle L. Stewart, Matthew G. Rees, Alykhan Shamji, Stuart Schreiber, Ernest Fraenkel, Scott L. Pomeroy, Jill P. Mesirov, Pablo Tamayo, Charles G. Eberhart and Eric H. Raabe

Cancer Discovery

Volume 6, Issue 7, 1 July 2016

Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles

Eejung Kim, Nina Ilic, Yashaswi Shrestha, Lihua Zou, Atanas Kamburov, Cong Zhu, Xiaoping Yang, Rakela Lubonja, Nancy Tran, Cindy Nguyen, Michael S. Lawrence, Federica Piccioni, Mukta Bagul, John G. Doench, Candace R. Chouinard, Xiaoyun Wu, Larson Hogstrom, Ted Natoli, Pablo Tamayo, Heiko Horn, Steven M. Corsello, Kasper Lage, David E. Root, Aravind Subramanian, Todd R. Golub, Gad Getz, Jesse S. Boehm and William C. Hahn

Cell Press

Volume 16, Issue 3, 19 July 2016

Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels

Matteo D’Antonio, Pablo Tamayo, Jill P. Mesirov, Kelly A. Frazer

Nature Biotechnology

Volume 34, Issue 5, 18 April 2016

Characterizing genomic alterations in cancer by complementary functional associations

Jong Wook Kim, Olga B Botvinnik, Omar Abudayyeh, Chet Birger, Joseph Rosenbluh, Yashaswi Shrestha, Mohamed E Abazeed, Peter S Hammerman, Daniel DiCara, David J Konieczkowski, Cory M Johannessen, Arthur Liberzon, Amir Reza Alizad-Rahvar, Gabriela Alexe, Andrew Aguirre, Mahmoud Ghandi, Heidi Greulich, Francisca Vazquez, Barbara A Weir, Eliezer M Van Allen, Aviad Tsherniak, Diane D Shao, Travis I Zack, Michael Noble, Gad Getz, Rameen Beroukhim, Levi A Garraway, Masoud Ardakani, Chiara Romualdi, Gabriele Sales, David A Barbie, Jesse S Boehm, William C Hahn, Jill P Mesirov & Pablo Tamayo

Nature Communications

Volume 7, Article Number: 11428, 25 April 2016

A genetic basis for the variation in the vulnerability of cancer to DNA damage

Brian D. Yard, Drew J. Adams, Eui Kyu Chie, Pablo Tamayo, Jessica S. Battaglia, Priyanka Gopal, Kevin Rogacki, Bradley E. Pearson, James Phillips, Daniel P. Raymond, Nathan A. Pennell, Francisco Almeida, Jaime H. Cheah, Paul A. Clemons, Alykhan Shamji, Craig D. Peacock, Stuart L. Schreiber, Peter S. Hammerman & Mohamed E. Abazeed

Nature Biotechnology

Volume 34, Issue 4, 29 February 2016

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

Channing Yu, Aristotle M Mannan, Griselda Metta Yvone, Kenneth N Ross, Yan-Ling Zhang, Melissa A Marton, Bradley R Taylor, Andrew Crenshaw, Joshua Z Gould, Pablo Tamayo, Barbara A Weir, Aviad Tsherniak, Bang Wong, Levi A Garraway, Alykhan F Shamji, Michelle A Palmer, Michael A Foley, Wendy Winckler, Stuart L Schreiber, Andrew L Kung & Todd R Golub

Statistical Methods in Medical Research

Volume 25, Issue 1, 1 February 2016

The limitations of simple gene set enrichment analysis assuming gene independence

Pablo Tamayo,1 George Steinhardt,2 Arthur Liberzon,1 and Jill P. Mesirov

Cell Press Immunity

Volume 44, Issue 1, 19 January 2016

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

Jernej Godec, Yan Tan, Arthur Liberzon, Pablo Tamayo, Sanchita Bhattacharya, Atul J. Butte, Jill P. Mesirov, W. Nicholas Haining

Cell Press Neuron

Volume 89, Issue 1, 6 January 2016

Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation

Xiaodong Zhu, David Girardo, Eve-Ellen Govek, Keisha John, Marian Mellén, Pablo Tamayo, Jill P. Mesirov, and Mary E Hatten