Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

Por Macagno, Eduardo R, Gaasterland, Terry, Edsall, Lee, Bafna, Vineet, Soares, Marcelo B, Scheetz, Todd, Casavant, Thomas, Da Silva, Corinne, Wincker, Patrick, Tasiemski, Aurélie, Salzet, Michel
Publicado em 2010

A map of the cis-regulatory sequences in the mouse genome

Por Shen, Yin, Yue, Feng, McCleary, David F., Ye, Zhen, Edsall, Lee, Kuan, Samantha, Wagner, Ulrich, Dixon, Jesse, Lee, Leonard, Lobanenkov, Victor V., Ren, Bing
Publicado em 2012

Exome Analysis Identified a Novel Mutation in the RBP4 Gene in a Consanguineous Pedigree with Retinal Dystrophy and Developmental Abnormalities

Por Cukras, Catherine, Gaasterland, Terry, Lee, Pauline, Gudiseva, Harini V., Chavali, Venkata R. M., Pullakhandam, Raghu, Maranhao, Bruno, Edsall, Lee, Soares, Sandra, Reddy, G. Bhanuprakash, Sieving, Paul A., Ayyagari, Radha
Publicado em 2012

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions

Por Chen, Yongheng, Chen, Chunxia, Zhang, Zhe, Liu, Chun-Chi, Johnson, Matthew E., Espinoza, Celso A., Edsall, Lee E., Ren, Bing, Zhou, Xianghong Jasmine, Grant, Struan F.A., Wells, Andrew D., Chen, Lin
Publicado no Nucleic Acids Res (2015)

5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation

Por Hon, Gary C., Song, Chun-Xiao, Du, Tingting, Jin, Fulai, Selvaraj, Siddarth, Lee, Ah Young, Yen, Chia-an, Ye, Zhen, Mao, Shi-Qing, Wang, Bang-An, Kuan, Samantha, Edsall, Lee E., Zhao, Boxuan Simen, Xu, Guo-Liang, He, Chuan, Ren, Bing
Publicado no Mol Cell (2014)

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

Por Zhao, Qi, Kirkness, Ewen F, Caballero, Otavia L, Galante, Pedro A, Parmigiani, Raphael B, Edsall, Lee, Kuan, Samantha, Ye, Zhen, Levy, Samuel, Vasconcelos, Ana Tereza R, Ren, Bing, de Souza, Sandro J, Camargo, Anamaria A, Simpson, Andrew JG, Strausberg, Robert L
Publicado em 2010

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

Por Hon, Gary C., Hawkins, R. David, Caballero, Otavia L., Lo, Christine, Lister, Ryan, Pelizzola, Mattia, Valsesia, Armand, Ye, Zhen, Kuan, Samantha, Edsall, Lee E., Camargo, Anamaria Aranha, Stevenson, Brian J., Ecker, Joseph R., Bafna, Vineet, Strausberg, Robert L., Simpson, Andrew J., Ren, Bing
Publicado em 2012

Human DNA methylomes at base resolution show widespread epigenomic differences

Por Lister, Ryan, Pelizzola, Mattia, Dowen, Robert H., Hawkins, R. David, Hon, Gary, Tonti-Filippini, Julian, Nery, Joseph R., Lee, Leonard, Ye, Zhen, Ngo, Que-Minh, Edsall, Lee, Antosiewicz-Bourget, Jessica, Stewart, Ron, Ruotti, Victor, Millar, A. Harvey, Thomson, James A., Ren, Bing, Ecker, Joseph R.
Publicado em 2009

Integrative analysis of haplotype-resolved epigenomes across human tissues

Por Leung, Danny, Jung, Inkyung, Rajagopal, Nisha, Schmitt, Anthony, Selvaraj, Siddarth, Lee, Ah Young, Yen, Chia-An, Lin, Shin, Lin, Yiing, Qiu, Yunjiang, Xie, Wei, Yue, Feng, Hariharan, Manoj, Ray, Pradipta, Kuan, Samantha, Edsall, Lee, Yang, Hongbo, Chi, Neil C., Zhang, Michael Q., Ecker, Joseph R., Ren, Bing
Publicado no Nature (2015)

Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

Por Hawkins, R David, Hon, Gary C, Yang, Chuhu, Antosiewicz-Bourget, Jessica E, Lee, Leonard K, Ngo, Que-Minh, Klugman, Sarit, Ching, Keith A, Edsall, Lee E, Ye, Zhen, Kuan, Samantha, Yu, Pengzhi, Liu, Hui, Zhang, Xinmin, Green, Roland D, Lobanenkov, Victor V, Stewart, Ron, Thomson, James A, Ren, Bing
Publicado em 2011

Distinct Epigenomic Landscapes of Pluripotent and Lineage-committed Human Cells

Por Hawkins, R. David, Hon, Gary C., Lee, Leonard K., Ngo, QueMinh, Lister, Ryan, Pelizzola, Mattia, Edsall, Lee E., Kuan, Samantha, Luu, Ying, Klugman, Sarit, Antosiewicz-Bourget, Jessica, Ye, Zhen, Espinoza, Celso, Agarwahl, Saurabh, Shen, Li, Ruotti, Victor, Wang, Wei, Stewart, Ron, Thomson, James A., Ecker, Joseph R., Ren, Bing
Publicado em 2010

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

Por Galante, Pedro A. F., Parmigiani, Raphael B., Zhao, Qi, Caballero, Otávia L., de Souza, Jorge E., Navarro, Fábio C. P., Gerber, Alexandra L., Nicolás, Marisa F., Salim, Anna Christina M., Silva, Ana Paula M., Edsall, Lee, Devalle, Sylvie, Almeida, Luiz G., Ye, Zhen, Kuan, Samantha, Pinheiro, Daniel G., Tojal, Israel, Pedigoni, Renato G., de Sousa, Rodrigo G. M. A., Oliveira, Thiago Y. K., de Paula, Marcelo G., Ohno-Machado, Lucila, Kirkness, Ewen F., Levy, Samuel, da Silva, Wilson A., Vasconcelos, Ana Tereza R., Ren, Bing, Zago, Marco Antonio, Strausberg, Robert L., Simpson, Andrew J. G., de Souza, Sandro J., Camargo, Anamaria A.
Publicado em 2011

Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells

Por Garcia, Benjamin, Xie, Wei, Schultz, Matt, Lister, Ryan, Hou, Zhonggang, Rajagopal, Nisha, Ray, Pradipta, Whitaker, John W., Tian, Shulan, Hawkins, R. David, Leung, Danny, Yang, Hongbo, Wang, Tao, Lee, Ah Young, Swanson, Scott A., Zhang, Jiuchun, Zhu, Yun, Kim, Audrey, Nery, Joseph, Urich, Mark A., Kuan, Samantha, Yen, Chia-an, Klugman, Sarit, Yu, Pengzhi, Suknuntha, Kran, Propson, Nicholas E., Chen, Huaming, Edsall, Lee E., Wagner, Ulrich, Li, Yan, Ye, Zhen, Kulkarni, Ashwinikumar, Xuan, Zhenyu, Chung, Wen-yu, Chi, Neil C., Antosiewicz-Bourget, Jessica, Slukvin, Igor, Stewart, Ron, Zhang, Michael Q., Wang, Wei, Thomson, James A., Ecker, Joseph R., Ren, Bing
Publicado em 2013

Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells

Por Xie, Wei, Schultz, Matthew D., Lister, Ryan, Hou, Zhonggang, Rajagopal, Nisha, Ray, Pradipta, Whitaker, John W., Tian, Shulan, Hawkins, R. David, Leung, Danny, Yang, Hongbo, Wang, Tao, Lee, Ah Young, Swanson, Scott A., Zhang, Jiuchun, Zhu, Yun, Kim, Audrey, Nery, Joseph R., Urich, Mark A., Kuan, Samantha, Yen, Chia-an, Klugman, Sarit, Yu, Pengzhi, Suknuntha, Kran, Propson, Nicholas E., Chen, Huaming, Edsall, Lee E., Wagner, Ulrich, Li, Yan, Ye, Zhen, Kulkarni, Ashwinikumar, Xuan, Zhenyu, Chung, Wen-Yu, Chi, Neil C., Antosiewicz-Bourget, Jessica E., Slukvin, Igor, Stewart, Ron, Zhang, Michael Q., Wang, Wei, Thomson, James A., Ecker, Joseph R., Ren, Bing
Publicado em 2013

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Por Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa, Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie1, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, Adams, Leslie B
Publicado em 2012

A comparative encyclopedia of DNA elements in the mouse genome

Por Yue, Feng, Cheng, Yong, Breschi, Alessandra, Vierstra, Jeff, Wu, Weisheng, Ryba, Tyrone, Sandstrom, Richard, Ma, Zhihai, Davis, Carrie, Pope, Benjamin D., Shen, Yin, Pervouchine, Dmitri D., Djebali, Sarah, Thurman, Robert E., Kaul, Rajinder, Rynes, Eric, Kirilusha, Anthony, Marinov, Georgi K., Williams, Brian A., Trout, Diane, Amrhein, Henry, Fisher-Aylor, Katherine, Antoshechkin, Igor, DeSalvo, Gilberto, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Zaleski, Chris, Dobin, Alex, Prieto, Pablo, Lagarde, Julien, Bussotti, Giovanni, Tanzer, Andrea, Denas, Olgert, Li, Kanwei, Bender, M. A., Zhang, Miaohua, Byron, Rachel, Groudine, Mark T., McCleary, David, Pham, Long, Ye, Zhen, Kuan, Samantha, Edsall, Lee, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Kellis, Manolis, Keller, Cheryl A., Morrissey, Christapher S., Mishra, Tejaswini, Jain, Deepti, Dogan, Nergiz, Harris, Robert S., Cayting, Philip, Kawli, Trupti, Boyle, Alan P., Euskirchen, Ghia, Kundaje, Anshul, Lin, Shin, Lin, Yiing, Jansen, Camden, Malladi, Venkat S., Cline, Melissa S., Erickson, Drew T., Kirkup, Vanessa M., Learned, Katrina, Sloan, Cricket A., Rosenbloom, Kate R., Lacerda de Sousa, Beatriz, Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, James Kent, W., Ramalho Santos, Miguel, Herrero, Javier, Notredame, Cedric, Johnson, Audra, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Canfield, Theresa, Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Giste, Erika, Shafer, Anthony, Kutyavin, Tanya, Haugen, Eric, Dunn, Douglas, Reynolds, Alex P., Neph, Shane, Humbert, Richard, Scott Hansen, R., De Bruijn, Marella, Selleri, Licia, Rudensky, Alexander, Josefowicz, Steven, Samstein, Robert, Eichler, Evan E., Orkin, Stuart H., Levasseur, Dana, Papayannopoulou, Thalia, Chang, Kai-Hsin, Skoultchi, Arthur, Gosh, Srikanta, Disteche, Christine, Treuting, Piper, Wang, Yanli, Weiss, Mitchell J., Blobel, Gerd A., Cao, Xiaoyi, Zhong, Sheng, Wang, Ting, Good, Peter J., Lowdon, Rebecca F., Adams, Leslie B., Zhou, Xiao-Qiao, Pazin, Michael J., Feingold, Elise A., Wold, Barbara, Taylor, James, Mortazavi, Ali, Weissman, Sherman M., Stamatoyannopoulos, John A., Snyder, Michael P., Guigo, Roderic, Gingeras, Thomas R., Gilbert, David M., Hardison, Ross C., Beer, Michael A., Ren, Bing
Publicado no Nature (2014)