Zobrazeno 1 - 10
of 60
pro vyhledávání: '"Shaoke Lou"'
Autor:
Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T Yang, Mark Gerstein
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 7, p e1011222 (2023)
The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in millions of deaths worldwide. The disease presents with various manifestations that can vary in severity and long-term outcomes. Previous efforts have contributed to the development
Externí odkaz:
https://doaj.org/article/d695763806e0400b833124b01159cec7
Publikováno v:
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-13 (2020)
Abstract Background The pathogenesis of asthma is a complex process involving multiple genes and pathways. Identifying biomarkers from asthma datasets, especially those that include heterogeneous subpopulations, is challenging. Potentially, autoencod
Externí odkaz:
https://doaj.org/article/3d7359749a0a4a5fa7ca97dd267509b1
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
Publikováno v:
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020)
Abstract Background During transcription, numerous transcription factors (TFs) bind to targets in a highly coordinated manner to control the gene expression. Alterations in groups of TF-binding profiles (i.e. “co-binding changes”) can affect the
Externí odkaz:
https://doaj.org/article/e96a1fd0895d48698bb3580f3a653e9d
Autor:
Jing Zhang, Jason Liu, Donghoon Lee, Jo-Jo Feng, Lucas Lochovsky, Shaoke Lou, Michael Rutenberg-Schoenberg, Mark Gerstein
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-13 (2020)
Abstract RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation and disease. Their binding sites cover more of the genome than coding exons; nevertheless, most noncoding variant prioritization methods only focus on transcriptio
Externí odkaz:
https://doaj.org/article/d5da4ad7e27047c7a1b4265132dc397a
Autor:
Daniel Spakowicz, Shaoke Lou, Brian Barron, Jose L. Gomez, Tianxiao Li, Qing Liu, Nicole Grant, Xiting Yan, Rebecca Hoyd, George Weinstock, Geoffrey L. Chupp, Mark Gerstein
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-22 (2020)
Abstract Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells an
Externí odkaz:
https://doaj.org/article/2079b140836940ff8bfe600c13e3a387
Autor:
Jason Liu, Daniel J Spakowicz, Garrett I Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn Presley, Ann Greene, Matthew Stults-Kolehmainen, Laura M Nally, Julien S Baker, Lisa M Fucito, Stuart A Weinzimer, Andrew V Papachristos, Mark Gerstein
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 8, p e1009303 (2021)
The development of mobile-health technology has the potential to revolutionize personalized medicine. Biomedical sensors (e.g., wearables) can assist with determining treatment plans for individuals, provide quantitative information to healthcare pro
Externí odkaz:
https://doaj.org/article/3f635a2ba0d14b759832399e7ba01013
Autor:
Shaoke Lou, Kellie A Cotter, Tianxiao Li, Jin Liang, Hussein Mohsen, Jason Liu, Jing Zhang, Sandra Cohen, Jinrui Xu, Haiyuan Yu, Mark A Rubin, Mark Gerstein
Publikováno v:
PLoS Genetics, Vol 15, Iss 8, p e1007860 (2019)
There has been much effort to prioritize genomic variants with respect to their impact on "function". However, function is often not precisely defined: sometimes it is the disease association of a variant; on other occasions, it reflects a molecular
Externí odkaz:
https://doaj.org/article/8a70e7fda7f040dc9b03896a73fb6ea0
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 7, p e1005647 (2017)
Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains (TADs). From a visual examination of the chromosomal contact map, however, it
Externí odkaz:
https://doaj.org/article/084b3d649ca440c5aca5ba3f4bf22adc
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 5, p e1004269 (2015)
The regulatory architecture of breast cancer is extraordinarily complex and gene misregulation can occur at many levels, with transcriptional malfunction being a major cause. This dysfunctional process typically involves additional regulatory modulat
Externí odkaz:
https://doaj.org/article/251deddcef9d4f7a9bb2a3941a0947c4