MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Niu, Beifang, Ye, Kai, Zhang, Qunyuan, Lu, Charles, Xie, Mingchao, McLellan, Michael D, Wendl, Michael C, Ding, Li
Published in Bioinformatics (01.04.2014)
Published in Bioinformatics (01.04.2014)
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Mutational landscape and significance across 12 major cancer types
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
Published in Nature (London) (17.10.2013)
Published in Nature (London) (17.10.2013)
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Expanding the computational toolbox for mining cancer genomes
Ding, Li, Wendl, Michael C., McMichael, Joshua F., Raphael, Benjamin J.
Published in Nature reviews. Genetics (01.08.2014)
Published in Nature reviews. Genetics (01.08.2014)
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Journal Article
MuSiC: identifying mutational significance in cancer genomes
Dees, Nathan D, Zhang, Qunyuan, Kandoth, Cyriac, Wendl, Michael C, Schierding, William, Koboldt, Daniel C, Mooney, Thomas B, Callaway, Matthew B, Dooling, David, Mardis, Elaine R, Wilson, Richard K, Ding, Li
Published in Genome research (01.08.2012)
Published in Genome research (01.08.2012)
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Journal Article
Protein-structure-guided discovery of functional mutations across 19 cancer types
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 Nature genetics (01.08.2016)
Published in Nature genetics (01.08.2016)
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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Chen, Ken, Wallis, John W, McLellan, Michael D, Larson, David E, Kalicki, Joelle M, Pohl, Craig S, McGrath, Sean D, Wendl, Michael C, Zhang, Qunyuan, Locke, Devin P, Shi, Xiaoqi, Fulton, Robert S, Ley, Timothy J, Wilson, Richard K, Ding, Li, Mardis, Elaine R
Published in Nature methods (01.09.2009)
Published in Nature methods (01.09.2009)
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Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells
Young, Margaret A., Larson, David E., Sun, Chiao-Wang, George, Daniel R., Ding, Li, Miller, Christopher A., Lin, Ling, Pawlik, Kevin M., Chen, Ken, Fan, Xian, Schmidt, Heather, Kalicki-Veizer, Joelle, Cook, Lisa L., Swift, Gary W., Demeter, Ryan T., Wendl, Michael C., Sands, Mark S., Mardis, Elaine R., Wilson, Richard K., Townes, Tim M., Ley, Timothy J.
Published in Cell stem cell (04.05.2012)
Published in Cell stem cell (04.05.2012)
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Advances for studying clonal evolution in cancer
Ding, Li, Raphael, Benjamin J, Chen, Feng, Wendl, Michael C
Published in Cancer letters (01.11.2013)
Published in Cancer letters (01.11.2013)
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Journal Article
Systematic discovery of complex insertions and deletions in human cancers
Ye, Kai, Wang, Jiayin, Jayasinghe, Reyka, Lameijer, Eric-Wubbo, McMichael, Joshua F, Ning, Jie, McLellan, Michael D, Xie, Mingchao, Cao, Song, Yellapantula, Venkata, Huang, Kuan-lin, Scott, Adam, Foltz, Steven, Niu, Beifang, Johnson, Kimberly J, Moed, Matthijs, Slagboom, P Eline, Chen, Feng, Wendl, Michael C, Ding, Li
Published in Nature medicine (01.01.2016)
Published in Nature medicine (01.01.2016)
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Journal Article
Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases
Hoadley, Katherine A, Siegel, Marni B, Kanchi, Krishna L, Miller, Christopher A, Ding, Li, Zhao, Wei, He, Xiaping, Parker, Joel S, Wendl, Michael C, Fulton, Robert S, Demeter, Ryan T, Wilson, Richard K, Carey, Lisa A, Perou, Charles M, Mardis, Elaine R
Published in PLoS medicine (06.12.2016)
Published in PLoS medicine (06.12.2016)
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Journal Article
Discovery of driver non-coding splice-site-creating mutations in cancer
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 Nature communications (04.11.2020)
Published in Nature communications (04.11.2020)
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Divergent viral presentation among human tumors and adjacent normal tissues
Cao, Song, Wendl, Michael C., Wyczalkowski, Matthew A., Wylie, Kristine, Ye, Kai, Jayasinghe, Reyka, Xie, Mingchao, Wu, Song, Niu, Beifang, Grubb, Robert, Johnson, Kimberly J., Gay, Hiram, Chen, Ken, Rader, Janet S., Dipersio, John F., Chen, Feng, Ding, Li
Published in Scientific reports (24.06.2016)
Published in Scientific reports (24.06.2016)
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Spatially interacting phosphorylation sites and mutations in cancer
Huang, Kuan-lin, Scott, Adam D., Zhou, Daniel Cui, Wang, Liang-Bo, Weerasinghe, Amila, Elmas, Abdulkadir, Liu, Ruiyang, Wu, Yige, Wendl, Michael C., Wyczalkowski, Matthew A., Baral, Jessika, Sengupta, Sohini, Lai, Chin-Wen, Ruggles, Kelly, Payne, Samuel H., Raphael, Benjamin, Fenyö, David, Chen, Ken, Mills, Gordon, Ding, Li
Published in Nature communications (19.04.2021)
Published in Nature communications (19.04.2021)
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Journal Article
Clonal architectures and driver mutations in metastatic melanomas
Ding, Li, Kim, Minjung, Kanchi, Krishna L, Dees, Nathan D, Lu, Charles, Griffith, Malachi, Fenstermacher, David, Sung, Hyeran, Miller, Christopher A, Goetz, Brian, Wendl, Michael C, Griffith, Obi, Cornelius, Lynn A, Linette, Gerald P, McMichael, Joshua F, Sondak, Vernon K, Fields, Ryan C, Ley, Timothy J, Mulé, James J, Wilson, Richard K, Weber, Jeffrey S
Published in PloS one (13.11.2014)
Published in PloS one (13.11.2014)
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Optimizing Cancer Genome Sequencing and Analysis
Griffith, Malachi, Miller, Christopher A., Griffith, Obi L., Krysiak, Kilannin, Skidmore, Zachary L., Ramu, Avinash, Walker, Jason R., Dang, Ha X., Trani, Lee, Larson, David E., Demeter, Ryan T., Wendl, Michael C., McMichael, Joshua F., Austin, Rachel E., Magrini, Vincent, McGrath, Sean D., Ly, Amy, Kulkarni, Shashikant, Cordes, Matthew G., Fronick, Catrina C., Fulton, Robert S., Maher, Christopher A., Ding, Li, Klco, Jeffery M., Mardis, Elaine R., Ley, Timothy J., Wilson, Richard K.
Published in Cell systems (23.09.2015)
Published in Cell systems (23.09.2015)
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GenomeVIP: a cloud platform for genomic variant discovery and interpretation
Mashl, R Jay, Scott, Adam D, Huang, Kuan-Lin, Wyczalkowski, Matthew A, Yoon, Christopher J, Niu, Beifang, DeNardo, Erin, Yellapantula, Venkata D, Handsaker, Robert E, Chen, Ken, Koboldt, Daniel C, Ye, Kai, Fenyö, David, Raphael, Benjamin J, Wendl, Michael C, Ding, Li
Published in Genome research (01.08.2017)
Published in Genome research (01.08.2017)
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Journal Article
BreakPoint Surveyor: a pipeline for structural variant visualization
Wyczalkowski, Matthew A, Wylie, Kristine M, Cao, Song, McLellan, Michael D, Flynn, Jennifer, Huang, Mo, Ye, Kai, Fan, Xian, Chen, Ken, Wendl, Michael C, Ding, Li
Published in Bioinformatics (Oxford, England) (01.10.2017)
Published in Bioinformatics (Oxford, England) (01.10.2017)
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Journal Article
Integrative omics analyses broaden treatment targets in human cancer
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 medicine (27.07.2018)
Published in Genome medicine (27.07.2018)
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Journal Article
Correction: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases
Hoadley, Katherine A, Siegel, Marni B, Kanchi, Krishna L, Miller, Christopher A, Ding, Li, Zhao, Wei, He, Xiaping, Parker, Joel S, Wendl, Michael C, Fulton, Robert S, Demeter, Ryan T, Wilson, Richard K, Carey, Lisa A, Perou, Charles M, Mardis, Elaine R
Published in PLoS medicine (01.01.2017)
Published in PLoS medicine (01.01.2017)
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