RTFBSDB: an integrated framework for transcription factor binding site analysis

por Wang, Zhong, Martins, André L., Danko, Charles G.
Publicado en Bioinformatics (2016)

Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo

por Guertin, Michael J., Martins, André L., Siepel, Adam, Lis, John T.
Publicado 2012

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

por Martins, André L, Walavalkar, Ninad M, Anderson, Warren D, Zang, Chongzhi, Guertin, Michael J
Publicado en Nucleic Acids Res (2018)

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

por Core, Leighton J., Martins, André L., Danko, Charles G., Waters, Colin, Siepel, Adam, Lis, John T.
Publicado en Nat Genet (2014)

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

por Fuda, Nicholas J., Guertin, Michael J., Sharma, Sumeet, Danko, Charles G., Martins, André L., Siepel, Adam, Lis, John T.
Publicado en PLoS Genet (2015)

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

por Danko, Charles G., Hah, Nasun, Luo, Xin, Martins, André L., Core, Leighton, Lis, John T., Siepel, Adam, Kraus, W. Lee
Publicado 2013

Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)

por Ma, Xin, Kelley, Joanna L., Eilertson, Kirsten, Musharoff, Shaila, Degenhardt, Jeremiah D., Martins, André L., Vinar, Tomas, Kosiol, Carolin, Siepel, Adam, Gutenkunst, Ryan N., Bustamante, Carlos D.
Publicado 2013

Identification of active transcriptional regulatory elements with GRO-seq

por Danko, Charles G., Hyland, Stephanie L., Core, Leighton J., Martins, Andre L., Waters, Colin T, Lee, Hyung Won, Cheung, Vivian G., Kraus, W. Lee, Lis, John T., Siepel, Adam
Publicado en Nat Methods (2015)

Dynamic evolution of regulatory element ensembles in primate CD4+ T-cells

por Danko, Charles G., Choate, Lauren A., Marks, Brooke A., Rice, Edward J., Wang, Zhong, Chu, Tinyi, Martins, Andre L., Dukler, Noah, Coonrod, Scott A., Tait Wojno, Elia D., Lis, John T., Kraus, W. Lee, Siepel, Adam
Publicado en Nat Ecol Evol (2018)

A high-resolution map of human evolutionary constraint using 29 mammals

por Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B., Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R, Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., Kellis, Manolis
Publicado 2011

Comparative and demographic analysis of orang-utan genomes

por Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Valle, Giuliano Della, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., Wilson, Richard K.
Publicado 2011