Systematic control of protein interactions for systems biology

por Bhardwaj, Nitin, Clarke, Declan, Gerstein, Mark
Publicado 2011

Localized structural frustration for evaluating the impact of sequence variants

por Kumar, Sushant, Clarke, Declan, Gerstein, Mark
Publicado en Nucleic Acids Res (2016)

Novel Insights through the Integration of Structural and Functional Genomics Data with Protein Networks

por Clarke, Declan, Bhardwaj, Nitin, Gerstein, Mark B.
Publicado en J Struct Biol (2012)

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures

por Kumar, Sushant, Clarke, Declan, Gerstein, Mark B.
Publicado en Proc Natl Acad Sci U S A (2019)

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions

por Bhardwaj, Nitin, Abyzov, Alexej, Clarke, Declan, Shou, Chong, Gerstein, Mark B
Publicado 2011

The Incorporation of Marine Coral Microparticles into Collagen-Based Scaffolds Promotes Osteogenesis of Human Mesenchymal Stromal Cells via Calcium Ion Signalling

por Sheehy, Eamon J., Lemoine, Mark, Clarke, Declan, Gonzalez Vazquez, Arlyng, O’Brien, Fergal J.
Publicado en Mar Drugs (2020)

Reads Meet Rotamers: Structural Biology in the Age of Next Generation Sequencing

por Sethi, Anurag, Clarke, Declan, Chen, Jieming, Kumar, Sushant, Galeev, Timur R, Regan, Lynne, Gerstein, Mark
Publicado en Curr Opin Struct Biol (2015)

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

por Clarke, Declan, Sethi, Anurag, Li, Shantao, Kumar, Sushant, Chang, Richard W.F., Chen, Jieming, Gerstein, Mark
Publicado en Structure (2016)

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

por Habegger, Lukas, Balasubramanian, Suganthi, Chen, David Z., Khurana, Ekta, Sboner, Andrea, Harmanci, Arif, Rozowsky, Joel, Clarke, Declan, Snyder, Michael, Gerstein, Mark
Publicado 2012

Comprehensive functional genomic resource and integrative model for the human brain

por 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.
Publicado en Science (2018)

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

por Khurana, Ekta, Fu, Yao, Colonna, Vincenza, Mu, Xinmeng Jasmine, Kang, Hyun Min, Lappalainen, Tuuli, Sboner, Andrea, Lochovsky, Lucas, Chen, Jieming, Harmanci, Arif, Das, Jishnu, Abyzov, Alexej, Balasubramanian, Suganthi, Beal, Kathryn, Chakravarty, Dimple, Challis, Daniel, Chen, Yuan, Clarke, Declan, Clarke, Laura, Cunningham, Fiona, Evani, Uday S., Flicek, Paul, Fragoza, Robert, Garrison, Erik, Gibbs, Richard, Gümüş, Zeynep H., Herrero, Javier, Kitabayashi, Naoki, Kong, Yong, Lage, Kasper, Liluashvili, Vaja, Lipkin, Steven M., MacArthur, Daniel G., Marth, Gabor, Muzny, Donna, Pers, Tune H., Ritchie, Graham R. S., Rosenfeld, Jeffrey A., Sisu, Cristina, Wei, Xiaomu, Wilson, Michael, Xue, Yali, Yu, Fuli, Dermitzakis, Emmanouil T., Yu, Haiyuan, Rubin, Mark A., Tyler-Smith, Chris, Gerstein, Mark
Publicado 2013

Architecture of the human regulatory network derived from ENCODE data

por Gerstein, Mark B., Kundaje, Anshul, Hariharan, Manoj, Landt, Stephen G., Yan, Koon-Kiu, Cheng, Chao, Mu, Xinmeng Jasmine, Khurana, Ekta, Rozowsky, Joel, Alexander, Roger, Min, Renqiang, Alves, Pedro, Abyzov, Alexej, Addleman, Nick, Bhardwaj, Nitin, Boyle, Alan P., Cayting, Philip, Charos, Alexandra, Chen, David Z., Cheng, Yong, Clarke, Declan, Eastman, Catharine, Euskirchen, Ghia, Frietze, Seth, Fu, Yao, Gertz, Jason, Grubert, Fabian, Harmanci, Arif, Jain, Preti, Kasowski, Maya, Lacroute, Phil, Leng, Jing (Jane), Lian, Jin, Monahan, Hannah, O'Geen, Henriette, Ouyang, Zhengqing, Partridge, E. Christopher, Patacsil, Dorrelyn, Pauli, Florencia, Raha, Debasish, Ramirez, Lucia, Reddy, Timothy E., Reed, Brian, Shi, Minyi, Slifer, Teri, Wang, Jing, Wu, Linfeng, Yang, Xinqiong, Yip, Kevin Y., Zilberman-Schapira, Gili, Batzoglou, Serafim, Sidow, Arend, Farnham, Peggy J., Myers, Richard M., Weissman, Sherman M., Snyder, Michael
Publicado 2012

An integrative ENCODE resource for cancer genomics

por 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
Publicado en Nat Commun (2020)