Publications
2022
Clinical Genitourinary Cancer
Volume 20, Issue 6, December 2022
The Prognostic Significance of Homologous Recombination Repair Pathway Alterations in Metastatic Hormone Sensitive Prostate Cancer
Aaron M.Lee, Ava Saidian, Justin Shaya, Taylor Nonato, Angelo Cabal, J. Michael Randall, Frederick Millard, Tyler Stewart, Brent Rose, Pablo Tamayo, Rana R. McKay
Journal of Translational Medicine
Article 527, 12 November 2022
Differential regulation of TNFα and IL-6 expression contributes to immune evasion in prostate cancer
Ida Deichaite, Timothy J. Sears, Leisa Sutton, Daniel Rebibo, Kylie Morgan, Tyler Nelson, Brent Rose, Pablo Tamayo, Napoleone Ferrara, Fotis Asimakopoulos & Hannah Carter
bioRxiv
2 August 2022
Differential Analysis of Stromal-Epithelial Interactions between In Situ and Invasive Breast Cancer using Gene Expression Profiling
Adam Officer, Andre M. Dempsey, Lyndsay M. Murrow, Zev Gartner, Pablo Tamayo, Christina Yau, Olivier Harismendy
bioRxiv
11 July 2022
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS
Jeanette Johnson, Ashley Tsang, Jacob T. Mitchell, Emily Davis-Marcisak, Thomas Sherman, Ted Liefeld, Melanie Loth, Loyal A Goff, Jacquelyn Zimmerman, Ben Kinny-Köster, Elizabeth Jaffee, Pablo Tamayo, Jill P. Mesirov, Michael Reich, Elana J. Fertig, Genevieve L. Stein-O’Brien
Nature Communications
Volume 13, Article 1899, 7 April 2022
CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity
Davide Bernareggi, Qi Xie, Briana C. Prager, Jiyoung Yun, Luisjesus S. Cruz, Timothy V. Pham, William Kim, Xiqing Lee, Michael Coffey, Cristina Zalfa, Pardis Azmoon, Huang Zhu, Pablo Tamayo, Jeremy N. Rich & Dan S. Kaufman
Cancer Medicine
Volume 11, Issue 3, February 2022
Analysis of CDK12 alterations in a pan-cancer database
Elizabeth Pan, Angelo Cabal, Juan Javier-DesLoges, Devin Patel, Justine Panian, Suzanna Lee, Justin Shaya, Taylor Nonato, Xiaojun Xu, Tyler Stewart, Brent Rose, Ahmed Shabaik, Ezra Cohen, Razelle Kurzrock, Pablo Tamayo, Rana R. McKay
2021
Cancer Medicine
12 December 2021
Analysis of CDK12 alterations in a pan-cancer database
Elizabeth Pan, Angelo Cabal, Juan Javier-DesLoges, Devin Patel, Justine Panian, Suzanna Lee, Justin Shaya, Taylor Nonato, Xiaojun Xu, Tyler Stewart, Brent Rose, Ahmed Shabaik, Ezra Cohen, Razelle Kurzrock, Pablo Tamayo, Rana R. McKay
Molecular Cancer Therapeutics
Volume 20, Issue 10, 1 October 2021
KIT low Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor
Sudeep Banerjee, Hyunho Yoon, Stephanie Ting, Chih-Min Tang, Mayra Yebra, Alexander T. Wenzel, Huwate Yeerna, Jill P. Mesirov, Robert J. Wechsler-Reya, Pablo Tamayo and Jason K. Sicklick
Cancer Medicine
Volume 39, Issue 12, 30 August 2021
Human induced pluripotent stem cell-derived macrophages ameliorate liver fibrosis
Somayeh Pouyanfard, Nairika Meshgin, Luisjesus S Cruz, Karin Diggle, Hamidreza Hashemi, Timothy V Pham, Manuel Fierro, Pablo Tamayo, Andrea Fanjul, Tatiana Kisseleva, Dan S Kaufman
Cancer Letters
Volume 504, 28 April 2021
TORC1/2 kinase inhibition depletes glutathione and synergizes with carboplatin to suppress the growth of MYC-driven medulloblastoma
Rachael E.Maynard, Brad Poore, Allison R.Hanaford, Khoa Pham, Madison James, Jesse Alt, Youngran Park, Barbara S.Slusher, Pablo Tamayo, Jill Mesirov, Tenley C.Archer, Scott L.Pomeroy, Charles G.Eberhart, Eric H.Raabe
Cell
Volume 184, Issue 5, 4 March 2021
An expanded universe of cancer targets
William C. Hahn, Joel S. Bader, Theodore P. Braun, Andrea Califano, Paul A. Clemons, Brian J. Druker, Andrew J.Ewald, Haian Fu, Subhashini Jagu, Christopher J. Kemp, William Kim, Calvin J. Kuo, Michael McManus, Gordon B. Mills, Xiulei Mo, Nidhi Sahni, Stuart L.Schreiber, Jessica A.Talamas, Pablo Tamayo, Jeffrey W.Tyner, Bridget K. Wagner, William A.Weiss, Daniela S. Gerhard
Cancers
Volume 13, Issue 4, 16 February 2021
BTK Inhibition Reverses MDSC-Mediated Immunosuppression and Enhances Response to Anti-PDL1 Therapy in Neuroblastoma
Mehreen Ishfaq, Timothy Pham, Cooper Beaman, Pablo Tamayo, Alice L Yu, Shweta Joshi
Nature Communications
Volume 12, Article Number: 784, 4 February 2021
SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation
Jingting Li, Xiaojun Xu, Manisha Tiwari, Yifang Chen, Mackenzie Fuller, Varun Bansal, Pablo Tamayo, Soumita Das, Pradipta Ghosh, George L. Sen
https://github.githubassets.com/images/search-key-slash.svg2020
Cancer Research
Volume 80, Issue 23, December 2020
Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma
Jessica M. Rusert, Edwin F. Juarez, Sebastian Brabetz, James Jensen, Alexandra Garancher, Lianne Q. Chau, Silvia K. Tacheva-Grigorova, Sameerah Wahab, Yoko T. Udaka, Darren Finlay, Huriye Seker-Cin, Brendan Reardon, Susanne Gröbner, Jonathan Serrano, Jonas Ecker, Lin Qi, Mari Kogiso, Yuchen Du, Patricia A. Baxter, Jacob J. Henderson, Michael E. Berens, Kristiina Vuori, Till Milde, Yoon-Jae Cho, Xiao-Nan Li, James M. Olson, Iris Reyes, Matija Snuderl, Terence C. Wong, David P. Dimmock, Shareef A. Nahas, Denise Malicki, John R. Crawford, Michael L. Levy, Eliezer M. Van Allen, Stefan M. Pfister, Pablo Tamayo, Marcel Kool, Jill P. Mesirov and Robert J. Wechsler-Reya
Anticancer Research
Volume 40, Issue 11, November 2020
WNT Signaling Driven by R-spondin 1 and LGR6 in High-grade Serous Ovarian Cancer
Sanghoon Lee, John Jun, William J Kim, Pablo Tamayo, Stephen B Howell
Journal of Investigative Dermatology
Volume 140, Issue 10, 1 October 2020
TEAD1 and TEAD3 Play Redundant Roles in the Regulation of Human Epidermal Proliferation
Jingting Li, Manisha Tiwari, Xiaojun Xu, Yifang Chen, Pablo Tamayo, George L Sen
Oncogene
Volume 39, 26 August 2020
HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers
Shuling Ren, Daria A. Gaykalova, Theresa Guo, Alexander V. Favorov, Elana J. Fertig, Pablo Tamayo, Juan Luis Callejas-Valera, Mike Allevato, Mara Gilardi, Jessica Santos, Takahito Fukusumi, Akihiro Sakai, Mizuo Ando, Sayed Sadat, Chao Liu, Guorong Xu, Kathleen M. Fisch, Zhiyong Wang, Alfredo A. Molinolo, J. Silvio Gutkind, Trey Ideker, Wayne M. Koch, Joseph A. Califano
Molecular Oncology
Volume 14, Issue 8, August 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
Molecular Cancer Research
Volume 18, Issue 7, July 2020
Mesenchymal and MAPK Expression Signatures Associate with Telomerase Promoter Mutations in Multiple Cancers
Josh Lewis Stern, Grace Hibshman, Kevin Hu, Sarah E. Ferrara, James C. Costello, William Kim, Pablo Tamayo, Thomas R. Cech and Franklin W. Huang
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