Self assembly of model polymers into biological random networks

by Bailey, Matthew H.J., Wilson, Mark
Published in Comput Struct Biotechnol J (2021)

Characteristics of The Cancer Genome Atlas cases relative to U.S. general population cancer cases

by Wang, Xiaoyan, Steensma, Joseph T., Bailey, Matthew H., Feng, Qianxi, Padda, Hannah, Johnson, Kimberly J.
Published in Br J Cancer (2018)

Mitochondrial Haplotypes Associated with Biomarkers for Alzheimer’s Disease

by Ridge, Perry G., Koop, Andre, Maxwell, Taylor J., Bailey, Matthew H., Swerdlow, Russell H., Kauwe, John S. K., Honea, Robyn A.
Published 2013

Population substructure in Cache County, Utah: the Cache County study

by Sharp, Aaron R, Ridge, Perry G, Bailey, Matthew H, Boehme, Kevin L, Norton, Maria C, Tschanz, JoAnn T, Munger, Ronald G, Corcoran, Christopher D, Kauwe, John SK
Published 2014

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

by Ellrott, Kyle, Bailey, Matthew H., Saksena, Gordon, Covington, Kyle R., Kandoth, Cyriac, Stewart, Chip, Hess, Julian, Ma, Singer, McLellan, Michael, Sofia, Heidi J., Hutter, Carolyn, Getz, Gad, Wheeler, David, Ding, Li
Published in Cell Syst (2018)

Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging

by Ridge, Perry G, Maxwell, Taylor J, Foutz, Spencer J, Bailey, Matthew H, Corcoran, Christopher D, Tschanz, JoAnn T, Norton, Maria C, Munger, Ronald G, O'Brien, Elizabeth, Kerber, Richard A, Cawthon, Richard M, Kauwe, John SK
Published 2014

Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types

by Cao, Yanan, Zhou, Weiwei, Li, Lin, Wang, Jiaqian, Gao, Zhibo, Jiang, Yiran, Jiang, Xiuli, Shan, Aijing, Bailey, Matthew H., Huang, Kuan-lin, Sun, Sam Q., McLellan, Michael D., Niu, Beifang, Wang, Weiqing, Ding, Li, Ning, Guang
Published in Cell Res (2018)

Discovery of driver non-coding splice-site-creating mutations in cancer

by Cao, Song, Zhou, Daniel Cui, Oh, Clara, Jayasinghe, Reyka G., Zhao, Yanyan, Yoon, Christopher J., Wyczalkowski, Matthew A., Bailey, Matthew H., Tsou, Terrence, Gao, Qingsong, Malone, Andrew, Reynolds, Sheila, Shmulevich, Ilya, Wendl, Michael C., Chen, Feng, Ding, Li
Published in Nat Commun (2020)

Interpreting pathways to discover cancer driver genes with Moonlight

by Colaprico, Antonio, Olsen, Catharina, Bailey, Matthew H., Odom, Gabriel J., Terkelsen, Thilde, Silva, Tiago C., Olsen, André V., Cantini, Laura, Zinovyev, Andrei, Barillot, Emmanuel, Noushmehr, Houtan, Bertoli, Gloria, Castiglioni, Isabella, Cava, Claudia, Bontempi, Gianluca, Chen, Xi Steven, Papaleo, Elena
Published in Nat Commun (2020)

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

by Bailey, Matthew H., Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Li, Shantao, Kelso, Sean, Saksena, Gordon, Ellrott, Kyle, Wendl, Michael C., Wheeler, David A., Getz, Gad, Simpson, Jared T., Gerstein, Mark B., Ding, Li
Published in Nat Commun (2020)

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

by Bailey, Matthew H., Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Li, Shantao, Li, Yize, Kelso, Sean, Saksena, Gordon, Ellrott, Kyle, Wendl, Michael C., Wheeler, David A., Getz, Gad, Simpson, Jared T., Gerstein, Mark B., Ding, Li
Published in Nat Commun (2020)

Protein structure guided discovery of functional mutations across 19 cancer types

by Niu, Beifang, Scott, Adam D., Sengupta, Sohini, Bailey, Matthew H., Batra, Prag, Ning, Jie, Wyczalkowski, Matthew A., Liang, Wen-Wei, Zhang, Qunyuan, McLellan, Michael D., Sun, Sam Q., Tripathi, Piyush, Lou, Carolyn, Ye, Kai, Mashl, R. Jay, Wallis, John, Wendl, Michael C., Chen, Feng, Ding, Li
Published in Nat Genet (2016)

Genome-Wide Association Study of CSF Levels of 59 Alzheimer's Disease Candidate Proteins: Significant Associations with Proteins Involved in Amyloid Processing and Inflammation

by Kauwe, John S. K., Bailey, Matthew H., Ridge, Perry G., Perry, Rachel, Wadsworth, Mark E., Hoyt, Kaitlyn L., Staley, Lyndsay A., Karch, Celeste M., Harari, Oscar, Cruchaga, Carlos, Ainscough, Benjamin J., Bales, Kelly, Pickering, Eve H., Bertelsen, Sarah, Fagan, Anne M., Holtzman, David M., Morris, John C., Goate, Alison M.
Published 2014

Integrative omics analyses broaden treatment targets in human cancer

by Sengupta, Sohini, Sun, Sam Q., Huang, Kuan-lin, Oh, Clara, Bailey, Matthew H., Varghese, Rajees, Wyczalkowski, Matthew A., Ning, Jie, Tripathi, Piyush, McMichael, Joshua F., Johnson, Kimberly J., Kandoth, Cyriac, Welch, John, Ma, Cynthia, Wendl, Michael C., Payne, Samuel H., Fenyö, David, Townsend, Reid R., Dipersio, John F., Chen, Feng, Ding, Li
Published in Genome Med (2018)

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

by Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan-lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Josh M., Mills, Gordon B, Wyczalkowski, Matthew A., Vincent, Benjamin, Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David, Getz, Gad
Published in Cell (2018)

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

by Knijnenburg, Theo A., Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N., Li, Lei, Ding, Li, Mills, Gordon B., Laird, Peter W., Wheeler, David A., Shmulevich, Ilya, Monnat, Raymond J, Xiao, Yonghong, Wang, Chen
Published in Cell Rep (2018)

Comprehensive Characterization of Cancer Driver Genes and Mutations

by Bailey, Matthew H., Tokheim, Collin, Porta-Pardo, Eduard, Sengupta, Sohini, Bertrand, Denis, Weerasinghe, Amila, Colaprico, Antonio, Wendl, Michael C., Kim, Jaegil, Reardon, Brendan, Ng, Kwok-Shing, Jeong, Kang Jin, Cao, Song, Wang, Zixing, Gao, JianJiong, Gao, Qingsong, Wang, Fang, Liu, Eric Minwei, Mularoni, Loris, Rubio-Perez, Carlota, Nagarajan, Niranjan, Cortés-Ciriano, Isidro, Zhou, Daniel Cui, Liang, Wen-Wei, Hess, Julian M., Yellapantula, Venkata D., Tamborero, David, Gonzalez-Perez, Abel, Suphavilai, Chayaporn, Ko, Jia Yu, Khurana, Ekta, Park, Peter J., Van Allen, Eliezer, Liang, Han, Lawrence, Michael, Godzik, Adam, Lopez-Bigas, Nuria, Stuart, Josh, Wheeler, David, Getz, Gad, Chen, Ken, Lazar, Alexander J., Mills, Gordon B, Karchin, Rachel, Ding, Li
Published in Cell (2018)

Comprehensive Characterization of Cancer Driver Genes and Mutations

by Bailey, Matthew H., Tokheim, Collin, Porta-Pardo, Eduard, Sengupta, Sohini, Bertrand, Denis, Weerasinghe, Amila, Colaprico, Antonio, Wendl, Michael C., Kim, Jaegil, Reardon, Brendan, Ng, Patrick Kwok-Shing, Jeong, Kang Jin, Cao, Song, Wang, Zixing, Gao, Jianjiong, Gao, Qingsong, Wang, Fang, Liu, Eric Minwei, Mularoni, Loris, Rubio-Perez, Carlota, Nagarajan, Niranjan, Cortés-Ciriano, Isidro, Zhou, Daniel Cui, Liang, Wen-Wei, Hess, Julian M., Yellapantula, Venkata D., Tamborero, David, Gonzalez-Perez, Abel, Suphavilai, Chayaporn, Ko, Jia Yu, Khurana, Ekta, Park, Peter J., Van Allen, Eliezer M., Liang, Han, Lawrence, Michael S., Godzik, Adam, Lopez-Bigas, Nuria, Stuart, Josh, Wheeler, David, Getz, Gad, Chen, Ken, Lazar, Alexander J., Mills, Gordon B., Karchin, Rachel, Ding, Li
Published in Cell (2018)

Oncogenic Signaling Pathways in The Cancer Genome Atlas

by Sanchez-Vega, Francisco, Mina, Marco, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, La, Konnor C., Dimitriadoy, Sofia, Liu, David L., Kantheti, Havish S., Saghafinia, Sadegh, Chakravarty, Debyani, Daian, Foysal, Gao, Qingsong, Bailey, Matthew H., Liang, Wen-Wei, Foltz, Steven M., Shmulevich, Ilya, Ding, Li, Heins, Zachary, Ochoa, Angelica, Gross, Benjamin, Gao, Jianjiong, Zhang, Hongxin, Kundra, Ritika, Kandoth, Cyriac, Bahceci, Istemi, Dervishi, Leonard, Dogrusoz, Ugur, Zhou, Wanding, Shen, Hui, Laird, Peter W., Way, Gregory P., Greene, Casey S., Liang, Han, Xiao, Yonghong, Wang, Chen, Iavarone, Antonio, Berger, Alice H., Bivona, Trever G., Lazar, Alexander J., Hammer, Gary D., Giordano, Thomas, Kwong, Lawrence N., McArthur, Grant, Huang, Chenfei, Tward, Aaron D., Frederick, Mitchell J., McCormick, Frank, Meyerson, Matthew, Van Allen, Eliezer M., Cherniack, Andrew D., Ciriello, Giovanni, Sander, Chris, Schultz, Nikolaus
Published in Cell (2018)

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

by Woo, Xing Yi, Giordano, Jessica, Srivastava, Anuj, Zhao, Zi-Ming, Lloyd, Michael W., de Bruijn, Roebi, Suh, Yun-Suhk, Patidar, Rajesh, Chen, Li, Scherer, Sandra, Bailey, Matthew H., Yang, Chieh-Hsiang, Cortes-Sanchez, Emilio, Xi, Yuanxin, Wang, Jing, Wickramasinghe, Jayamanna, Kossenkov, Andrew V., Rebecca, Vito W., Sun, Hua, Mashl, R. Jay, Davies, Sherri R., Jeon, Ryan, Frech, Christian, Randjelovic, Jelena, Rosains, Jacqueline, Galimi, Francesco, Bertotti, Andrea, Lafferty, Adam, O’Farrell, Alice C., Modave, Elodie, Lambrechts, Diether, ter Brugge, Petra, Serra, Violeta, Marangoni, Elisabetta, El Botty, Rania, Kim, Hyunsoo, Kim, Jong-Il, Yang, Han-Kwang, Lee, Charles, Dean, Dennis A., Davis-Dusenbery, Brandi, Evrard, Yvonne A., Doroshow, James H., Welm, Alana L., Welm, Bryan E., Lewis, Michael T., Fang, Bingliang, Roth, Jack A., Meric-Bernstam, Funda, Herlyn, Meenhard, Davies, Michael A., Ding, Li, Li, Shunqiang, Govindan, Ramaswamy, Isella, Claudio, Moscow, Jeffrey A., Trusolino, Livio, Byrne, Annette T., Jonkers, Jos, Bult, Carol J., Medico, Enzo, Chuang, Jeffrey H.
Published in Nat Genet (2021)