Modeling clinical and molecular covariates of mutational process activity in cancer

von Robinson, Welles, Sharan, Roded, Leiserson, Mark D M
Veröffentlicht in Bioinformatics (2019)

A weighted exact test for mutually exclusive mutations in cancer

von Leiserson, Mark D.M., Reyna, Matthew A., Raphael, Benjamin J.
Veröffentlicht in Bioinformatics (2016)

Hierarchical HotNet: identifying hierarchies of altered subnetworks

von Reyna, Matthew A, Leiserson, Mark D M, Raphael, Benjamin J
Veröffentlicht in Bioinformatics (2018)

Simultaneous Identification of Multiple Driver Pathways in Cancer

von Leiserson, Mark D. M., Blokh, Dima, Sharan, Roded, Raphael, Benjamin J.
Veröffentlicht 2013

Precision Oncology: The Road Ahead

von Senft, Daniela, Leiserson, Mark D M, Ruppin, Eytan, Ronai, Zéev A
Veröffentlicht in Trends Mol Med (2017)

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

von Wojtowicz, Damian, Leiserson, Mark D.M., Sharan, Roded, Przytycka, Teresa M.
Veröffentlicht in Pac Symp Biocomput (2020)

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

von Leiserson, Mark D.M., Tatar, Diana, Cowen, Lenore J., Hescott, Benjamin J.
Veröffentlicht 2011

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

von Leiserson, Mark D. M., Wu, Hsin-Ta, Vandin, Fabio, Raphael, Benjamin J.
Veröffentlicht in Genome Biol (2016)

Criticality in tumor evolution and clinical outcome

von Persi, Erez, Wolf, Yuri I., Leiserson, Mark D. M., Koonin, Eugene V., Ruppin, Eytan
Veröffentlicht in Proc Natl Acad Sci U S A (2018)

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

von Sason, Itay, Wojtowicz, Damian, Robinson, Welles, Leiserson, Mark D.M., Przytycka, Teresa M., Sharan, Roded
Veröffentlicht in iScience (2020)

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

von Fan, Jason, Cannistra, Anthony, Fried, Inbar, Lim, Tim, Schaffner, Thomas, Crovella, Mark, Hescott, Benjamin, Leiserson, Mark D M
Veröffentlicht in Nucleic Acids Res (2019)

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

von Wojtowicz, Damian, Sason, Itay, Huang, Xiaoqing, Kim, Yoo-Ah, Leiserson, Mark D. M., Przytycka, Teresa M., Sharan, Roded
Veröffentlicht in Genome Med (2019)

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

von 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.
Veröffentlicht in Genome Med (2020)

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

von 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
Veröffentlicht in PLoS One (2018)

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

von 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.
Veröffentlicht in Nat Genet (2014)

Mutational landscape and significance across 12 major cancer types

von 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
Veröffentlicht 2013

Integrated Analysis of Germline and Somatic Variants in Ovarian Cancer

von 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
Veröffentlicht 2014

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

von 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
Veröffentlicht in Nat Commun (2015)

Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma

von 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
Veröffentlicht in N Engl J Med (2015)