MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

od Yan, Koon-Kiu, Lou, Shaoke, Gerstein, Mark
Wydane w PLoS Comput Biol (2017)

Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer

od Ung, Matthew H., Varn, Frederick S., Lou, Shaoke, Cheng, Chao
Wydane w PLoS Comput Biol (2015)

AOBase: a database for antisense oligonucleotides selection and design

od Bo, Xiaochen, Lou, Shaoke, Sun, Daochun, Yang, Jing, Wang, Shengqi
Wydane 2006

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures

od Bo, Xiaochen, Lou, Shaoke, Sun, Daochun, Shu, Wenjie, Yang, Jing, Wang, Shengqi
Wydane 2006

Integrative Genomic Analyses Yields Cell Cycle Regulatory Programs with Prognostic Value

od Cheng, Chao, Lou, Shaoke, Andrews, Erik H., Ung, Matthew H., Varn, Frederick S.
Wydane w Mol Cancer Res (2016)

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients

od Lou, Shaoke, Li, Tianxiao, Spakowicz, Daniel, Yan, Xiting, Chupp, Geoffrey Lowell, Gerstein, Mark
Wydane w BMC Bioinformatics (2020)

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring

od Zhang, Jing, Liu, Jason, Lee, Donghoon, Lou, Shaoke, Chen, Zhanlin, Gürsoy, Gamze, Gerstein, Mark
Wydane w BMC Bioinformatics (2020)

TopicNet: a framework for measuring transcriptional regulatory network change

od Lou, Shaoke, Li, Tianxiao, Kong, Xiangmeng, Zhang, Jing, Liu, Jason, Lee, Donghoon, Gerstein, Mark
Wydane w Bioinformatics (2020)

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer

od Fu, Yao, Liu, Zhu, Lou, Shaoke, Bedford, Jason, Mu, Xinmeng Jasmine, Yip, Kevin Y, Khurana, Ekta, Gerstein, Mark
Wydane 2014

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

od Zhang, Jing, Liu, Jason, Lee, Donghoon, Feng, Jo-Jo, Lochovsky, Lucas, Lou, Shaoke, Rutenberg-Schoenberg, Michael, Gerstein, Mark
Wydane w Genome Biol (2020)

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

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

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

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

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner

od Lou, Shaoke, Cotter, Kellie A., Li, Tianxiao, Liang, Jin, Mohsen, Hussein, Liu, Jason, Zhang, Jing, Cohen, Sandra, Xu, Jinrui, Yu, Haiyuan, Rubin, Mark A., Gerstein, Mark
Wydane w PLoS Genet (2019)

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

od Spakowicz, Daniel, Lou, Shaoke, Barron, Brian, Gomez, Jose L., Li, Tianxiao, Liu, Qing, Grant, Nicole, Yan, Xiting, Hoyd, Rebecca, Weinstock, George, Chupp, Geoffrey L., Gerstein, Mark
Wydane w Genome Biol (2020)

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation

od Lou, Shaoke, Lee, Heung-Man, Qin, Hao, Li, Jing-Woei, Gao, Zhibo, Liu, Xin, Chan, Landon L, KL Lam, Vincent, So, Wing-Yee, Wang, Ying, Lok, Si, Wang, Jun, Ma, Ronald CW, Tsui, Stephen Kwok-Wing, Chan, Juliana CN, Chan, Ting-Fung, Yip, Kevin Y
Wydane 2014

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

od 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.
Wydane w Cell (2020)

Comprehensive functional genomic resource and integrative model for the human brain

od Wang, Daifeng, Liu, Shuang, Warrell, Jonathan, Won, Hyejung, Shi, Xu, Navarro, Fabio C. P., Clarke, Declan, Gu, Mengting, Emani, Prashant, Yang, Yucheng T., Xu, Min, Gandal, Michael J., Lou, Shaoke, Zhang, Jing, Park, Jonathan J., Yan, Chengfei, Rhie, Suhn Kyong, Manakongtreecheep, Kasidet, Zhou, Holly, Nathan, Aparna, Peters, Mette, Mattei, Eugenio, Fitzgerald, Dominic, Brunetti, Tonya, Moore, Jill, Jiang, Yan, Girdhar, Kiran, Hoffman, Gabriel E., Kalayci, Selim, Gümüş, Zeynep H., Crawford, Gregory E., Roussos, Panos, Akbarian, Schahram, Jaffe, Andrew E., White, Kevin P., Weng, Zhiping, Sestan, Nenad, Geschwind, Daniel H., Knowles, James A., Gerstein, Mark B.
Wydane w Science (2018)

An integrative ENCODE resource for cancer genomics

od 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
Wydane w Nat Commun (2020)