Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library by Korbel, Jan O, Gerstein, Mark B, Lam, Hugo Y K, Mu, Xinmeng Jasmine, Stütz, Adrian M, Tanzer, Andrea, Cayting, Philip D, Snyder, Michael, Kim, Philip M

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Comparative analysis of regulatory information and circuits across distant species by Boyle, Alan P., Araya, Carlos L., Brdlik, Cathleen, Cayting, Philip, Cheng, Chao, Cheng, Yong, Gardner, Kathryn, Hillier, LaDeana W., Janette, Judith, Jiang, Lixia, Kasper, Dionna, Kawli, Trupti, Kheradpour, Pouya, Kundaje, Anshul, Li, Jingyi Jessica, Ma, Lijia, Niu, Wei, Rehm, E. Jay, Rozowsky, Joel, Slattery, Matthew, Spokony, Rebecca, Terrell, Robert, Vafeados, Dionne, Wang, Daifeng, Weisdepp, Peter, Wu, Yi-Chieh, Xie, Dan, Yan, Koon-Kiu, Feingold, Elise A., Good, Peter J., Pazin, Michael J., Huang, Haiyan, Bickel, Peter J., Brenner, Steven E., Reinke, Valerie, Waterston, Robert H., Gerstein, Mark, White, Kevin P., Kellis, Manolis, Snyder, Michael

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Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes by Balasubramanian, Suganthi, Zheng, Deyou, Liu, Yuen-Jong, Fang, Gang, Frankish, Adam, Carriero, Nicholas, Robilotto, Rebecca, Cayting, Philip, Gerstein, Mark

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Uncovering trends in gene naming by Seringhaus, Michael R, Cayting, Philip D, Gerstein, Mark B

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Principles of regulatory information conservation between mouse and human by Cheng, Yong, Ma, Zhihai, Kim, Bong-Hyun, Wu, Weisheng, Cayting, Philip, Boyle, Alan P., Sundaram, Vasavi, Xing, Xiaoyun, Dogan, Nergiz, Li, Jingjing, Euskirchen, Ghia, Lin, Shin, Lin, Yiing, Visel, Axel, Kawli, Trupti, Yang, Xinqiong, Patacsil, Dorrelyn, Keller, Cheryl A., Giardine, Belinda, The Mouse ENCODE Consortium, Kundaje, Anshul, Wang, Ting, Pennacchio, Len A., Weng, Zhiping, Hardison, Ross C., Snyder, Michael P.

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia by Landt, Stephen G, Marinov, Georgi K, Kundaje, Anshul, Kheradpour, Pouya, Pauli, Florencia, Batzoglou, Serafim, Bernstein, Bradley E, Bickel, Peter, Brown, James B, Cayting, Philip, Chen, Yiwen, DeSalvo, Gilberto, Epstein, Charles, Fisher-Aylor, Katherine I, Euskirchen, Ghia, Gerstein, Mark, Gertz, Jason, Hartemink, Alexander J, Hoffman, Michael M, Iyer, Vishwanath R, Jung, Youngsook L, Karmakar, Subhradip, Kellis, Manolis, Kharchenko, Peter V, Li, Qunhua, Liu, Tao, Liu, X Shirley, Ma, Lijia, Milosavljevic, Aleksandar, Myers, Richard M, Park, Peter J, Pazin, Michael J, Perry, Marc D, Raha, Debasish, Reddy, Timothy E, Rozowsky, Joel, Shoresh, Noam, Sidow, Arend, Slattery, Matthew, Stamatoyannopoulos, John A, Tolstorukov, Michael Y, White, Kevin P, Xi, Simon, Farnham, Peggy J, Lieb, Jason D, Wold, Barbara J, Snyder, Michael

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Architecture of the human regulatory network derived from ENCODE data by 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, 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

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PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data by Korbel, Jan O, Abyzov, Alexej, Mu, Xinmeng Jasmine, Carriero, Nicholas, Cayting, Philip, Zhang, Zhengdong, Snyder, Michael, Gerstein, Mark B

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Segmental duplications in the human genome reveal details of pseudogene formation by Khurana, Ekta, Lam, Hugo Y.K, Cheng, Chao, Carriero, Nicholas, Cayting, Philip, Gerstein, Mark B

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Analysis of Nuclear Receptor Pseudogenes in Vertebrates: How the Silent Tell Their Stories by Zhang, Zhengdong D., Cayting, Philip, Weinstock, George, Gerstein, Mark

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Pseudofam: the pseudogene families database by Lam, Hugo Y.K, Khurana, Ekta, Fang, Gang, Cayting, Philip, Carriero, Nicholas, Cheung, Kei-Hoi, Gerstein, Mark B

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Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation by Karro, John E, Yan, Yangpan, Zheng, Deyou, Zhang, Zhaolei, Carriero, Nicholas, Cayting, Philip, Harrrison, Paul, Gerstein, Mark

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