Understanding genome structural variations

gan Abyzov, Alexej, Li, Shantao, Gerstein, Mark B.
Cyhoeddwyd yn Oncotarget (2015)

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations

gan Li, Shantao, Shuch, Brian M., Gerstein, Mark B.
Cyhoeddwyd yn PLoS Genet (2017)

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood

gan Li, Shantao, Crawford, Forrest W., Gerstein, Mark B.
Cyhoeddwyd yn Nat Commun (2020)

Predicting the frequencies of drug side effects

gan Galeano, Diego, Li, Shantao, Gerstein, Mark, Paccanaro, Alberto
Cyhoeddwyd yn Nat Commun (2020)

Landscape and variation of novel retroduplications in 26 human populations

gan Zhang, Yan, Li, Shantao, Abyzov, Alexej, Gerstein, Mark B.
Cyhoeddwyd yn PLoS Comput Biol (2017)

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation

gan Clarke, Declan, Sethi, Anurag, Li, Shantao, Kumar, Sushant, Chang, Richard W.F., Chen, Jieming, Gerstein, Mark
Cyhoeddwyd yn Structure (2016)

Genomics and data science: an application within an umbrella

gan Navarro, Fábio C. P., Mohsen, Hussein, Yan, Chengfei, Li, Shantao, Gu, Mengting, Meyerson, William, Gerstein, Mark
Cyhoeddwyd yn Genome Biol (2019)

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries

gan Zhou, Jie, Li, Shantao, Leung, Kevin K., O’Donovan, Brian, Zou, James Y., DeRisi, Joseph L., Wells, James A.
Cyhoeddwyd yn Proc Natl Acad Sci U S A (2020)

The real cost of sequencing: scaling computation to keep pace with data generation

gan Muir, Paul, Li, Shantao, Lou, Shaoke, Wang, Daifeng, Spakowicz, Daniel J, Salichos, Leonidas, Zhang, Jing, Weinstock, George M., Isaacs, Farren, Rozowsky, Joel, Gerstein, Mark
Cyhoeddwyd yn Genome Biol (2016)

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

gan Muir, Paul, Li, Shantao, Lou, Shaoke, Wang, Daifeng, Spakowicz, Daniel J., Salichos, Leonidas, Zhang, Jing, Weinstock, George M., Isaacs, Farren, Rozowsky, Joel, Gerstein, Mark
Cyhoeddwyd yn Genome Biol (2016)

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

gan Abyzov, Alexej, Li, Shantao, Kim, Daniel Rhee, Mohiyuddin, Marghoob, Stütz, Adrian M., Parrish, Nicholas F., Mu, Xinmeng Jasmine, Clark, Wyatt, Chen, Ken, Hurles, Matthew, Korbel, Jan O., Lam, Hugo Y. K., Lee, Charles, Gerstein, Mark B.
Cyhoeddwyd yn Nat Commun (2015)

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

gan Li, Xiaotong, Kumar, Sushant, Harmanci, Arif, Li, Shantao, Kitchen, Robert R., Zhang, Yan, Wali, Vikram B., Reddy, Sangeetha M., Woodward, Wendy A., Reuben, James M., Rozowsky, Joel, Hatzis, Christos, Ueno, Naoto T., Krishnamurthy, Savitri, Pusztai, Lajos, Gerstein, Mark
Cyhoeddwyd yn Genome Med (2021)

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

gan 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
Cyhoeddwyd yn Nat Commun (2020)

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

gan 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
Cyhoeddwyd yn Nat Commun (2020)

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

gan Kumar, Sushant, Warrell, Jonathan, Li, Shantao, McGillivray, Patrick D., Meyerson, William, Salichos, Leonidas, Harmanci, Arif, Martinez-Fundichely, Alexander, Chan, Calvin W.Y., Nielsen, Morten Muhlig, Lochovsky, Lucas, Zhang, Yan, Li, Xiaotong, Lou, Shaoke, Pedersen, Jakob Skou, Herrmann, Carl, Getz, Gad, Khurana, Ekta, Gerstein, Mark B.
Cyhoeddwyd yn Cell (2020)

An integrative ENCODE resource for cancer genomics

gan Zhang, Jing, Lee, Donghoon, Dhiman, Vineet, Jiang, Peng, Xu, Jie, McGillivray, Patrick, Yang, Hongbo, Liu, Jason, Meyerson, William, Clarke, Declan, Gu, Mengting, Li, Shantao, Lou, Shaoke, Xu, Jinrui, Lochovsky, Lucas, Ung, Matthew, Ma, Lijia, Yu, Shan, Cao, Qin, Harmanci, Arif, Yan, Koon-Kiu, Sethi, Anurag, Gürsoy, Gamze, Schoenberg, Michael Rutenberg, Rozowsky, Joel, Warrell, Jonathan, Emani, Prashant, Yang, Yucheng T., Galeev, Timur, Kong, Xiangmeng, Liu, Shuang, Li, Xiaotong, Krishnan, Jayanth, Feng, Yanlin, Rivera-Mulia, Juan Carlos, Adrian, Jessica, Broach, James R, Bolt, Michael, Moran, Jennifer, Fitzgerald, Dominic, Dileep, Vishnu, Liu, Tingting, Mei, Shenglin, Sasaki, Takayo, Trevilla-Garcia, Claudia, Wang, Su, Wang, Yanli, Zang, Chongzhi, Wang, Daifeng, Klein, Robert J., Snyder, Michael, Gilbert, David M., Yip, Kevin, Cheng, Chao, Yue, Feng, Liu, X. Shirley, White, Kevin P., Gerstein, Mark
Cyhoeddwyd yn Nat Commun (2020)

Multi-platform discovery of haplotype-resolved structural variation in human genomes

gan Chaisson, Mark J. P., Sanders, Ashley D., Zhao, Xuefang, Malhotra, Ankit, Porubsky, David, Rausch, Tobias, Gardner, Eugene J., Rodriguez, Oscar L., Guo, Li, Collins, Ryan L., Fan, Xian, Wen, Jia, Handsaker, Robert E., Fairley, Susan, Kronenberg, Zev N., Kong, Xiangmeng, Hormozdiari, Fereydoun, Lee, Dillon, Wenger, Aaron M., Hastie, Alex R., Antaki, Danny, Anantharaman, Thomas, Audano, Peter A., Brand, Harrison, Cantsilieris, Stuart, Cao, Han, Cerveira, Eliza, Chen, Chong, Chen, Xintong, Chin, Chen-Shan, Chong, Zechen, Chuang, Nelson T., Lambert, Christine C., Church, Deanna M., Clarke, Laura, Farrell, Andrew, Flores, Joey, Galeev, Timur, Gorkin, David U., Gujral, Madhusudan, Guryev, Victor, Heaton, William Haynes, Korlach, Jonas, Kumar, Sushant, Kwon, Jee Young, Lam, Ernest T., Lee, Jong Eun, Lee, Joyce, Lee, Wan-Ping, Lee, Sau Peng, Li, Shantao, Marks, Patrick, Viaud-Martinez, Karine, Meiers, Sascha, Munson, Katherine M., Navarro, Fabio C. P., Nelson, Bradley J., Nodzak, Conor, Noor, Amina, Kyriazopoulou-Panagiotopoulou, Sofia, Pang, Andy W. C., Qiu, Yunjiang, Rosanio, Gabriel, Ryan, Mallory, Stütz, Adrian, Spierings, Diana C. J., Ward, Alistair, Welch, AnneMarie E., Xiao, Ming, Xu, Wei, Zhang, Chengsheng, Zhu, Qihui, Zheng-Bradley, Xiangqun, Lowy, Ernesto, Yakneen, Sergei, McCarroll, Steven, Jun, Goo, Ding, Li, Koh, Chong Lek, Ren, Bing, Flicek, Paul, Chen, Ken, Gerstein, Mark B., Kwok, Pui-Yan, Lansdorp, Peter M., Marth, Gabor T., Sebat, Jonathan, Shi, Xinghua, Bashir, Ali, Ye, Kai, Devine, Scott E., Talkowski, Michael E., Mills, Ryan E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Lee, Charles
Cyhoeddwyd yn Nat Commun (2019)