Modeling clinical and molecular covariates of mutational process activity in cancer

Por Robinson, Welles, Sharan, Roded, Leiserson, Mark D M
Publicado no Bioinformatics (2019)

A weighted exact test for mutually exclusive mutations in cancer

Por Leiserson, Mark D.M., Reyna, Matthew A., Raphael, Benjamin J.
Publicado no Bioinformatics (2016)

Hierarchical HotNet: identifying hierarchies of altered subnetworks

Por Reyna, Matthew A, Leiserson, Mark D M, Raphael, Benjamin J
Publicado no Bioinformatics (2018)

Simultaneous Identification of Multiple Driver Pathways in Cancer

Por Leiserson, Mark D. M., Blokh, Dima, Sharan, Roded, Raphael, Benjamin J.
Publicado em 2013

Precision Oncology: The Road Ahead

Por Senft, Daniela, Leiserson, Mark D M, Ruppin, Eytan, Ronai, Zéev A
Publicado no Trends Mol Med (2017)

DNA REPAIR FOOTPRINT UNCOVERS CONTRIBUTION OF DNA REPAIR MECHANISM TO MUTATIONAL SIGNATURES

Por Wojtowicz, Damian, Leiserson, Mark D.M., Sharan, Roded, Przytycka, Teresa M.
Publicado no Pac Symp Biocomput (2020)

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

Por Leiserson, Mark D.M., Tatar, Diana, Cowen, Lenore J., Hescott, Benjamin J.
Publicado em 2011

Erratum to: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer

Por Leiserson, Mark D. M., Wu, Hsin-Ta, Vandin, Fabio, Raphael, Benjamin J.
Publicado no Genome Biol (2016)

Criticality in tumor evolution and clinical outcome

Por Persi, Erez, Wolf, Yuri I., Leiserson, Mark D. M., Koonin, Eugene V., Ruppin, Eytan
Publicado no Proc Natl Acad Sci U S A (2018)

A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer

Por Sason, Itay, Wojtowicz, Damian, Robinson, Welles, Leiserson, Mark D.M., Przytycka, Teresa M., Sharan, Roded
Publicado no iScience (2020)

Functional protein representations from biological networks enable diverse cross-species inference

Por Fan, Jason, Cannistra, Anthony, Fried, Inbar, Lim, Tim, Schaffner, Thomas, Crovella, Mark, Hescott, Benjamin, Leiserson, Mark D M
Publicado no Nucleic Acids Res (2019)

Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer

Por Wojtowicz, Damian, Sason, Itay, Huang, Xiaoqing, Kim, Yoo-Ah, Leiserson, Mark D. M., Przytycka, Teresa M., Sharan, Roded
Publicado no Genome Med (2019)

Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer

Por Kim, Yoo-Ah, Wojtowicz, Damian, Sarto Basso, Rebecca, Sason, Itay, Robinson, Welles, Hochbaum, Dorit S., Leiserson, Mark D. M., Sharan, Roded, Vadin, Fabio, Przytycka, Teresa M.
Publicado no Genome Med (2020)

A multifactorial model of T cell expansion and durable clinical benefit in response to a PD-L1 inhibitor

Por Leiserson, Mark D. M., Syrgkanis, Vasilis, Gilson, Amy, Dudik, Miroslav, Gillett, Sharon, Chayes, Jennifer, Borgs, Christian, Bajorin, Dean F., Rosenberg, Jonathan E., Funt, Samuel, Snyder, Alexandra, Mackey, Lester
Publicado no PLoS One (2018)

Pan-Cancer Network Analysis Identifies Combinations of Rare Somatic Mutations across Pathways and Protein Complexes

Por Leiserson, Mark D.M., Vandin, Fabio, Wu, Hsin-Ta, Dobson, Jason R., Eldridge, Jonathan V., Thomas, Jacob L., Papoutsaki, Alexandra, Kim, Younhun, Niu, Beifang, McLellan, Michael, Lawrence, Michael S., Gonzalez-Perez, Abel, Tamborero, David, Cheng, Yuwei, Ryslik, Gregory A., Lopez-Bigas, Nuria, Getz, Gad, Ding, Li, Raphael, Benjamin J.
Publicado no Nat Genet (2014)

Mutational landscape and significance across 12 major cancer types

Por Kandoth, Cyriac, McLellan, Michael D., Vandin, Fabio, Ye, Kai, Niu, Beifang, Lu, Charles, Xie, Mingchao, Zhang, Qunyuan, McMichael, Joshua F., Wyczalkowski, Matthew A., Leiserson, Mark D. M., Miller, Christopher A., Welch, John S., Walter, Matthew J., Wendl, Michael C., Ley, Timothy J., Wilson, Richard K., Raphael, Benjamin J., Ding, Li
Publicado em 2013

Integrated Analysis of Germline and Somatic Variants in Ovarian Cancer

Por Kanchi, Krishna L., Johnson, Kimberly J., Lu, Charles, McLellan, Michael D., Leiserson, Mark D.M., Wendl, Michael C., Zhang, Qunyuan, Koboldt, Daniel C., Xie, Mingchao, Kandoth, Cyriac, McMichael, Joshua F., Wyczalkowski, Matthew A., Larson, David E., Schmidt, Heather K., Miller, Christopher A., Fulton, Robert S., Spellman, Paul T., Mardis, Elaine R., Druley, Todd E., Graubert, Timothy A., Goodfellow, Paul J., Raphael, Benjamin J., Wilson, Richard K., Ding, Li
Publicado em 2014

Patterns and functional implications of rare germline variants across 12 cancer types

Por Lu, Charles, Xie, Mingchao, Wendl, Michael C., Wang, Jiayin, McLellan, Michael D., Leiserson, Mark D. M., Huang, Kuan-lin, Wyczalkowski, Matthew A., Jayasinghe, Reyka, Banerjee, Tapahsama, Ning, Jie, Tripathi, Piyush, Zhang, Qunyuan, Niu, Beifang, Ye, Kai, Schmidt, Heather K., Fulton, Robert S., McMichael, Joshua F., Batra, Prag, Kandoth, Cyriac, Bharadwaj, Maheetha, Koboldt, Daniel C., Miller, Christopher A., Kanchi, Krishna L., Eldred, James M., Larson, David E., Welch, John S., You, Ming, Ozenberger, Bradley A., Govindan, Ramaswamy, Walter, Matthew J., Ellis, Matthew J., Mardis, Elaine R., Graubert, Timothy A., Dipersio, John F., Ley, Timothy J., Wilson, Richard K., Goodfellow, Paul J., Raphael, Benjamin J., Chen, Feng, Johnson, Kimberly J., Parvin, Jeffrey D., Ding, Li
Publicado no Nat Commun (2015)

Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma

Por Linehan, W. Marston, Spellman, Paul T., Ricketts, Christopher J., Creighton, Chad J., Fei, Suzanne S., Davis, Caleb, Wheeler, David A., Murray, Bradley A., Schmidt, Laura, Vocke, Cathy D., Peto, Myron, Al Mamun, Abu Amar M., Shinbrot, Eve, Sethi, Anurag, Brooks, Samira, Rathmell, W. Kimryn, Brooks, Angela N., Hoadley, Katherine A., Robertson, A. Gordon, Brooks, Denise, Bowlby, Reanne, Sadeghi, Sara, Shen, Hui, Weisenberger, Daniel J., Bootwalla, Moiz, Baylin, Stephen B., Laird, Peter W., Cherniack, Andrew D., Saksena, Gordon, Haake, Scott, Li, Jun, Liang, Han, Lu, Yiling, Mills, Gordon B., Akbani, Rehan, Leiserson, Mark D.M., Raphael, Benjamin J., Anur, Pavana, Bottaro, Donald, Albiges, Laurence, Barnabas, Nandita, Choueiri, Toni K., Czerniak, Bogdan, Godwin, Andrew K., Hakimi, A. Ari, Ho, Thai, Hsieh, James, Ittmann, Michael, Kim, William Y., Krishnan, Bhavani, Merino, Maria J., Mills Shaw, Kenna R., Reuter, Victor E., Reznik, Ed, Shelley, Carl Simon, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Tickoo, Satish, Burnett, Kenneth, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph D., Penny, Robert J., Shelton, Candace, Shelton, W. Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Avedon, Melissa T., Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Santos, Tracie, Wise, Lisa, Zmuda, Erik, Demchok, John A., Felau, Ina, Hutter, Carolyn M., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Ally, Adrian, Balasundaram, Miruna, Balu, Saianand, Beroukhim, Rameen, Bodenheimer, Tom, Buhay, Christian, Butterfield, Yaron S.N., Carlsen, Rebecca, Carter, Scott L., Chao, Hsu, Chuah, Eric, Clarke, Amanda, Covington, Kyle R., Dahdouli, Mahmoud, Dewal, Ninad, Dhalla, Noreen, Doddapaneni, HarshaVardhan, Drummond, Jennifer, Gabriel, Stacey B., Gibbs, Richard A., Guin, Ranabir, Hale, Walker, Hawes, Alicia, Hayes, D. Neil, Holt, Robert A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Steven J.M., Jones, Corbin D., Kalra, Divya, Kovar, Christie, Lewis, Lora, Li, Jie, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Moore, Richard A., Morton, Donna, Mose, Lisle E., Mungall, Andrew J., Muzny, Donna, Parker, Joel S., Perou, Charles M., Roach, Jeffrey, Schein, Jacqueline E., Schumacher, Steven E., Shi, Yan, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Soloway, Matthew G., Sougnez, Carrie, Tam, Angela, Tan, Donghui, Thiessen, Nina, Veluvolu, Umadevi, Wang, Min, Wilkerson, Matthew D., Wong, Tina, Wu, Junyuan, Xi, Liu, Zhou, Jane, Bedford, Jason, Chen, Fengju, Fu, Yao, Gerstein, Mark, Haussler, David, Kasaian, Katayoon, Lai, Phillip, Ling, Shiyun, Radenbaugh, Amie, Van Den Berg, David, Weinstein, John N., Zhu, Jingchun, Albert, Monique, Alexopoulou, Iakovina, Andersen, Jeremiah J, Auman, J. Todd, Bartlett, John, Bastacky, Sheldon, Bergsten, Julie, Blute, Michael L., Boice, Lori, Bollag, Roni J., Boyd, Jeff, Castle, Erik, Chen, Ying-Bei, Cheville, John C., Curley, Erin, Davies, Benjamin, DeVolk, April, Dhir, Rajiv, Dike, Laura, Eckman, John, Engel, Jay, Harr, Jodi, Hrebinko, Ronald, Huang, Mei, Huelsenbeck-Dill, Lori, Iacocca, Mary, Jacobs, Bruce, Lobis, Michael, Maranchie, Jodi K., McMeekin, Scott, Myers, Jerome, Nelson, Joel, Parfitt, Jeremy, Parwani, Anil, Petrelli, Nicholas, Rabeno, Brenda, Roy, Somak, Salner, Andrew L., Slaton, Joel, Stanton, Melissa, Thompson, R. Houston, Thorne, Leigh, Tucker, Kelinda, Weinberger, Paul M., Winemiller, Cythnia, Zach, Leigh Anne, Zuna, Rosemary
Publicado no N Engl J Med (2015)