Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning

por Gönen, Mehmet, Margolin, Adam A.
Publicado 2014

Simulation Studies as Designed Experiments: The Comparison of Penalized Regression Models in the “Large p, Small n” Setting

por Chaibub Neto, Elias, Bare, J. Christopher, Margolin, Adam A.
Publicado 2014

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding

por Margolin, Adam A, Palomero, Teresa, Ferrando, Adolfo A, Califano, Andrea, Stolovitzky, Gustavo
Publicado 2007

Toward better benchmarking: challenge-based methods assessment in cancer genomics

por Boutros, Paul C, Margolin, Adam A, Stuart, Joshua M, Califano, Andrea, Stolovitzky, Gustavo
Publicado 2014

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

por Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo Dalla, Califano, Andrea
Publicado 2006

Empirical Bayes Analysis of Quantitative Proteomics Experiments

por Margolin, Adam A., Ong, Shao-En, Schenone, Monica, Gould, Robert, Schreiber, Stuart L., Carr, Steven A., Golub, Todd R.
Publicado 2009

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas

por Omberg, Larsson, Ellrott, Kyle, Yuan, Yuan, Kandoth, Cyriac, Wong, Chris, Kellen, Michael R, Friend, Stephen H, Stuart, Josh, Liang, Han, Margolin, Adam A
Publicado 2013

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

por Gurun, Burcu, Horton, Wesley, Murugan, Dhaarini, Zhu, Biqing, Leyshock, Patrick, Kumar, Sushil, Byrne, Katelyn T., Vonderheide, Robert H., Margolin, Adam A., Mori, Motomi, Spellman, Paul T., Coussens, Lisa M., Speed, Terence P.
Publicado 2023

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

por Gurun, Burcu, Horton, Wesley, Murugan, Dhaarini, Zhu, Biqing, Leyshock, Patrick, Kumar, Sushil, Byrne, Katelyn T., Vonderheide, Robert H., Margolin, Adam A., Mori, Motomi, Spellman, Paul T., Coussens, Lisa M., Speed, Terence P.
Publicado 2023

Genome-wide Identification of Post-translational Modulators of Transcription Factor Activity in Human B-Cells

por Wang, Kai, Saito, Masumichi, Bisikirska, Brygida C., Alvarez, Mariano J., Lim, Wei Keat, Rajbhandari, Presha, Shen, Qiong, Nemenman, Ilya, Basso, Katia, Margolin, Adam A., Klein, Ulf, Dalla-Favera, Riccardo, Califano, Andrea
Publicado 2009

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

por Sendorek, Dorota H., Caloian, Cristian, Ellrott, Kyle, Bare, J. Christopher, Yamaguchi, Takafumi N., Ewing, Adam D., Houlahan, Kathleen E., Norman, Thea C., Margolin, Adam A., Stuart, Joshua M., Boutros, Paul C.
Publicado 2018

Valection: design optimization for validation and verification studies

por Cooper, Christopher I, Yao, Delia, Sendorek, Dorota H, Yamaguchi, Takafumi N, P’ng, Christine, Houlahan, Kathleen E, Caloian, Cristian, Fraser, Michael, Ellrott, Kyle, Margolin, Adam A, Bristow, Robert G, Stuart, Joshua M, Boutros, Paul C
Publicado 2018

ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens

por Shao, Diane D., Tsherniak, Aviad, Gopal, Shuba, Weir, Barbara A., Tamayo, Pablo, Stransky, Nicolas, Schumacher, Steven E., Zack, Travis I., Beroukhim, Rameen, Garraway, Levi A., Margolin, Adam A., Root, David E., Hahn, William C., Mesirov, Jill P.
Publicado 2013

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

por Ewing, Adam D, Houlahan, Kathleen E, Hu, Yin, Ellrott, Kyle, Caloian, Cristian, Yamaguchi, Takafumi N, Bare, J Christopher, P’ng, Christine, Waggott, Daryl, Sabelnykova, Veronica Y, Kellen, Michael R, Norman, Thea C, Haussler, David, Friend, Stephen H, Stolovitzky, Gustavo, Margolin, Adam A, Stuart, Joshua M, Boutros, Paul C
Publicado 2015

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

por Yuan, Yuan, Van Allen, Eliezer M., Omberg, Larsson, Wagle, Nikhil, Amin-Mansour, Ali, Sokolov, Artem, Byers, Lauren A., Xu, Yanxun, Hess, Kenneth R., Diao, Lixia, Han, Leng, Huang, Xuelin, Lawrence, Michael S., Weinstein, John N., Stuart, Josh M., Mills, Gordon B., Garraway, Levi A., Margolin, Adam A., Getz, Gad, Liang, Han
Publicado 2014

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

por Lee, Anna Y., Ewing, Adam D., Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen E., Bare, J. Christopher, Espiritu, Shadrielle Melijah G., Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi N., Kellen, Michael R., Chen, Ken, Norman, Thea C., Friend, Stephen H., Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam A., Stuart, Joshua M., Boutros, Paul C.
Publicado 2018

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

por Bilal, Erhan, Dutkowski, Janusz, Guinney, Justin, Jang, In Sock, Logsdon, Benjamin A., Pandey, Gaurav, Sauerwine, Benjamin A., Shimoni, Yishai, Moen Vollan, Hans Kristian, Mecham, Brigham H., Rueda, Oscar M., Tost, Jorg, Curtis, Christina, Alvarez, Mariano J., Kristensen, Vessela N., Aparicio, Samuel, Børresen-Dale, Anne-Lise, Caldas, Carlos, Califano, Andrea, Friend, Stephen H., Ideker, Trey, Schadt, Eric E., Stolovitzky, Gustavo A., Margolin, Adam A.
Publicado 2013

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

por Wagner, Alex H., Walsh, Brian, Mayfield, Georgia, Tamborero, David, Sonkin, Dmitriy, Krysiak, Kilannin, Deu-Pons, Jordi, Duren, Ryan P., Gao, Jianjiong, McMurry, Julie, Patterson, Sara, del Vecchio Fitz, Catherine, Pitel, Beth A., Sezerman, Ozman U., Ellrott, Kyle, Warner, Jeremy L., Rieke, Damian T., Aittokallio, Tero, Cerami, Ethan, Ritter, Deborah I., Schriml, Lynn M., Freimuth, Robert R., Haendel, Melissa, Raca, Gordana, Madhavan, Subha, Baudis, Michael, Beckmann, Jacques S., Dienstmann, Rodrigo, Chakravarty, Debyani, Li, Xuan Shirley, Mockus, Susan, Elemento, Olivier, Schultz, Nikolaus, Lopez-Bigas, Nuria, Lawler, Mark, Goecks, Jeremy, Griffith, Malachi, Griffith, Obi L., Margolin, Adam A.
Publicado 2020

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

por Griffith, Malachi, Spies, Nicholas C, Krysiak, Kilannin, McMichael, Joshua F, Coffman, Adam C, Danos, Arpad M, Ainscough, Benjamin J, Ramirez, Cody A, Rieke, Damian T, Kujan, Lynzey, Barnell, Erica K, Wagner, Alex H, Skidmore, Zachary L, Wollam, Amber, Liu, Connor J, Jones, Martin R, Bilski, Rachel L, Lesurf, Robert, Feng, Yan-Yang, Shah, Nakul M, Bonakdar, Melika, Trani, Lee, Matlock, Matthew, Ramu, Avinash, Campbell, Katie M, Spies, Gregory C, Graubert, Aaron P, Gangavarapu, Karthik, Eldred, James M, Larson, David E, Walker, Jason R, Good, Benjamin M, Wu, Chunlei, Su, Andrew I, Dienstmann, Rodrigo, Margolin, Adam A, Tamborero, David, Lopez-Bigas, Nuria, Jones, Steven J M, Bose, Ron, Spencer, David H, Wartman, Lukas D, Wilson, Richard K, Mardis, Elaine R, Griffith, Obi L
Publicado 2017

The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity

por Barretina, Jordi, Caponigro, Giordano, Stransky, Nicolas, Venkatesan, Kavitha, Margolin, Adam A., Kim, Sungjoon, Wilson, Christopher J., Lehár, Joseph, Kryukov, Gregory V., Sonkin, Dmitriy, Reddy, Anupama, Liu, Manway, Murray, Lauren, Berger, Michael F., Monahan, John E., Morais, Paula, Meltzer, Jodi, Korejwa, Adam, Jané-Valbuena, Judit, Mapa, Felipa A., Thibault, Joseph, Bric-Furlong, Eva, Raman, Pichai, Shipway, Aaron, Engels, Ingo H., Cheng, Jill, Yu, Guoying K., Yu, Jianjun, Aspesi, Peter, de Silva, Melanie, Jagtap, Kalpana, Jones, Michael D., Wang, Li, Hatton, Charles, Palescandolo, Emanuele, Gupta, Supriya, Mahan, Scott, Sougnez, Carrie, Onofrio, Robert C., Liefeld, Ted, MacConaill, Laura, Winckler, Wendy, Reich, Michael, Li, Nanxin, Mesirov, Jill P., Gabriel, Stacey B., Getz, Gad, Ardlie, Kristin, Chan, Vivien, Myer, Vic E., Weber, Barbara L., Porter, Jeff, Warmuth, Markus, Finan, Peter, Harris, Jennifer L., Meyerson, Matthew, Golub, Todd R., Morrissey, Michael P., Sellers, William R., Schlegel, Robert, Garraway, Levi A.
Publicado 2012