Zobrazeno 1 - 10
of 43
pro vyhledávání: '"Shantao Li"'
Autor:
Xiaotong Li, Sushant Kumar, Arif Harmanci, Shantao Li, Robert R. Kitchen, Yan Zhang, Vikram B. Wali, Sangeetha M. Reddy, Wendy A. Woodward, James M. Reuben, Joel Rozowsky, Christos Hatzis, Naoto T. Ueno, Savitri Krishnamurthy, Lajos Pusztai, Mark Gerstein
Publikováno v:
Genome Medicine, Vol 13, Iss 1, Pp 1-14 (2021)
Abstract Background Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases. Meth
Externí odkaz:
https://doaj.org/article/1add699a6a154a93abe43aacbd318851
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)
Currently, the frequencies of drug side effects are determined in randomised controlled clinical trials. Here the authors develop an interpretable machine learning approach to predict the frequencies of unknown side effects for drugs with a small num
Externí odkaz:
https://doaj.org/article/e13f5df0401d4c95ac1e4ea0421f663b
Autor:
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-27 (2020)
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Gen
Externí odkaz:
https://doaj.org/article/d9cb28829f31451aa7d92697e8efd186
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)
The next generation sequencing has provided the opportunity to look for signatures of carcinogenesis on a genome wide scale. Here, the authors develop the algorithm, sigLASSO, that provides confidence in assigning mutational signatures when the mutat
Externí odkaz:
https://doaj.org/article/d51810b840e24277acd8a315057999a1
Autor:
Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T. Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J. Klein, Michael Snyder, David M. Gilbert, Kevin Yip, Chao Cheng, Feng Yue, X. Shirley Liu, Kevin P. White, Mark Gerstein
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-11 (2020)
ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis.
Externí odkaz:
https://doaj.org/article/d3ef1766b33842a5aa6bd3194efeba4e
Autor:
Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson, Mark Gerstein
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-11 (2019)
Abstract Data science allows the extraction of practical insights from large-scale data. Here, we contextualize it as an umbrella term, encompassing several disparate subdomains. We focus on how genomics fits as a specific application subdomain, in t
Externí odkaz:
https://doaj.org/article/87af48c4265343c5950599e90d4d8cd4
Autor:
Mark J. P. Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J. Gardner, Oscar L. Rodriguez, Li Guo, Ryan L. Collins, Xian Fan, Jia Wen, Robert E. Handsaker, Susan Fairley, Zev N. Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M. Wenger, Alex R. Hastie, Danny Antaki, Thomas Anantharaman, Peter A. Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Christine C. Lambert, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U. Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T. Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio C. P. Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W. C. Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C. J. Spierings, Alistair Ward, AnneMarie E. Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor T. Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael E. Talkowski, Ryan E. Mills, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, Charles Lee
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-16 (2019)
Structural variants (SVs) in human genomes contribute diversity and diseases. Here, the authors use a multi-platform strategy to generate haplotype-resolved SVs for three human parent–child trios.
Externí odkaz:
https://doaj.org/article/1bf8e1b79b09479e9b177f1082c620e1
Autor:
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-1 (2020)
Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w
Externí odkaz:
https://doaj.org/article/3c5eda289b8b41d49db0060d9ed67612
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 6, p e1005567 (2017)
Retroduplications come from reverse transcription of mRNAs and their insertion back into the genome. Here, we performed comprehensive discovery and analysis of retroduplications in a large cohort of 2,535 individuals from 26 human populations, as par
Externí odkaz:
https://doaj.org/article/e432ae4b3ff0423a890d46fa8fc0fae3
Publikováno v:
PLoS Genetics, Vol 13, Iss 3, p e1006685 (2017)
To date, studies on papillary renal-cell carcinoma (pRCC) have largely focused on coding alterations in traditional drivers, particularly the tyrosine-kinase, Met. However, for a significant fraction of tumors, researchers have been unable to determi
Externí odkaz:
https://doaj.org/article/608a149a09a043eebe7830c8c4ed2e72