Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs von Green, Richard E., Braun, Edward L., Armstrong, Joel, Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Vandewege, Michael W., St. John, John A., Capella-Gutiérrez, Salvador, Castoe, Todd A., Kern, Colin, Fujita, Matthew K., Opazo, Juan C., Jurka, Jerzy, Kojima, Kenji K., Caballero, Juan, Hubley, Robert M., Smit, Arian F., Platt, Roy N., Lavoie, Christine A., Ramakodi, Meganathan P., Finger, John W., Suh, Alexander, Isberg, Sally R., Miles, Lee, Chong, Amanda Y., Jaratlerdsiri, Weerachai, Gongora, Jaime, Moran, Christopher, Iriarte, Andrés, McCormack, John, Burgess, Shane C., Edwards, Scott V., Lyons, Eric, Williams, Christina, Breen, Matthew, Howard, Jason T., Gresham, Cathy R., Peterson, Daniel G., Schmitz, Jürgen, Pollock, David D., Haussler, David, Triplett, Eric W., Zhang, Guojie, Irie, Naoki, Jarvis, Erich D., Brochu, Christopher A., Schmidt, Carl J., McCarthy, Fiona M., Faircloth, Brant C., Hoffmann, Federico G., Glenn, Travis C., Gabaldón, Toni, Paten, Benedict, Ray, David A.

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Evolutionary algorithms for the selection of single nucleotide polymorphisms von Hubley, Robert M, Zitzler, Eckart, Roach, Jared C

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PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer von Pagan, Heidi J T, Smith, Jeremy D, Hubley, Robert M, Ray, David A

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Evolution of the ancestral mammalian karyotype and syntenic regions von Damas, Joana, Corbo, Marco, Kim, Jaebum, Turner-Maier, Jason, Farré, Marta, Larkin, Denis M., Ryder, Oliver A., Steiner, Cynthia, Houck, Marlys L., Hall, Shaune, Shiue, Lily, Thomas, Stephen, Swale, Thomas, Daly, Mark, Korlach, Jonas, Uliano-Silva, Marcela, Mazzoni, Camila J., Birren, Bruce W., Genereux, Diane P., Johnson, Jeremy, Lindblad-Toh, Kerstin, Karlsson, Elinor K., Nweeiar, Martin T., Johnsonu, Rebecca N., Consortium, Zoonomia, Lewina, Harris A.

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A genomic timescale for placental mammal evolution von Foley, Nicole M, Mason, Victor C, Harris, Andrew J, Bredemeyer, Kevin R, Damas, Joana, Lewin, Harris A, Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Springer, Mark S, Murphy, William J

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Insights into mammalian TE diversity through the curation of 248 genome assemblies von Osmanski, Austin B, Paulat, Nicole S, Korstian, Jenny, Grimshaw, Jenna R, Halsey, Michaela, Sullivan, Kevin A M, Moreno-Santillán, Diana D, Crookshanks, Claudia, Roberts, Jacquelyn, Garcia, Carlos, Johnson, Matthew G, Densmore, Llewellyn D, Stevens, Richard D, Rosen, Jeb, Storer, Jessica M, Hubley, Robert, Smit, Arian F A, Dávalos, Liliana M, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Ray, David A

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Mammalian evolution of human cis-regulatory elements and transcription factor binding sites von Andrews, Gregory, Fan, Kaili, Pratt, Henry E, Phalke, Nishigandha, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Gazal, Steven, Moore, Jill E, Weng, Zhiping

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Relating enhancer genetic variation across mammals to complex phenotypes using machine learning von Kaplow, Irene M, Lawler, Alyssa J, Schäffer, Daniel E, Srinivasan, Chaitanya, Sestili, Heather H, Wirthlin, Morgan E, Phan, BaDoi N, Prasad, Kavya, Brown, Ashley R, Zhang, Xiaomeng, Foley, Kathleen, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Meyer, Wynn K, Pfenning, Andreas R

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Three-dimensional genome rewiring in loci with human accelerated regions von Keough, Kathleen C, Whalen, Sean, Inoue, Fumitaka, Przytycki, Pawel F, Fair, Tyler, Deng, Chengyu, Steyert, Marilyn, Ryu, Hane, Lindblad-Toh, Kerstin, Karlsson, Elinor, Nowakowski, Tomasz, Ahituv, Nadav, Pollen, Alex, Pollard, Katherine S

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The functional and evolutionary impacts of human-specific deletions in conserved elements von Xue, James R, Mackay-Smith, Ava, Mouri, Kousuke, Garcia, Meilin Fernandez, Dong, Michael X, Akers, Jared F, Noble, Mark, Li, Xue, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Noonan, James P, Capellini, Terence D, Brennand, Kristen J, Tewhey, Ryan, Sabeti, Pardis C, Reilly, Steven K

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Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs von Moon, Katherine L, Huson, Heather J, Morrill, Kathleen, Wang, Ming-Shan, Li, Xue, Srikanth, Krishnamoorthy, Lindblad-Toh, Kerstin, Svenson, Gavin J, Karlsson, Elinor K, Shapiro, Beth

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Using evolutionary constraint to define novel candidate driver genes in medulloblastoma von Roy, Ananya, Sakthikumar, Sharadha, Kozyrev, Sergey V, Nordin, Jessika, Pensch, Raphaela, Mäkeläinen, Suvi, Pettersson, Mats, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Forsberg-Nilsson, Karin

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RepeatModeler2 for automated genomic discovery of transposable element families von Flynn, Jullien M., Hubley, Robert, Goubert, Clément, Rosenb, Jeb, Clark, Andrew G., Feschotte, Cédric, Smit, Arian F.

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A Pragmatic Randomized Clinical Trial of Behavioral Activation for Depressed Pregnant Women von Dimidjian, Sona, Goodman, Sherryl H., Sherwood, Nancy E., Simon, Gregory E., Ludman, Evette, Gallop, Robert, Welch, Stacy Shaw, Boggs, Jennifer M., Metcalf, Christina A., Hubley, Sam, Powers, J. David, Beck, Arne

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Cracks, Gaps, and Holes in Validation Practice as Evidenced From a Validation Synthesis of the English Version of the Rosenberg Self-Esteem Scale von Hubley, Anita M., Ruddell, Robert J., Ma Zhu, Sophie

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A common open representation of mass spectrometry data and its application to proteomics research von Pedrioli, Patrick G A, Eng, Jimmy K, Hubley, Robert, Vogelzang, Mathijs, Deutsch, Eric W, Raught, Brian, Pratt, Brian, Nilsson, Erik, Angeletti, Ruth H, Apweiler, Rolf, Cheung, Kei, Costello, Catherine E, Hermjakob, Henning, Huang, Sequin, Julian, Randall K, Kapp, Eugene, McComb, Mark E, Oliver, Stephen G, Omenn, Gilbert, Paton, Norman W, Simpson, Richard, Smith, Richard, Taylor, Chris F, Zhu, Weimin, Aebersold, Ruedi

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The UCSC Genome Browser database: 2015 update von Rosenbloom, Kate R, Armstrong, Joel, Barber, Galt P, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Dreszer, Timothy R, Fujita, Pauline A, Guruvadoo, Luvina, Haeussler, Maximilian, Harte, Rachel A, Heitner, Steve, Hickey, Glenn, Hinrichs, Angie S, Hubley, Robert, Karolchik, Donna, Learned, Katrina, Lee, Brian T, Li, Chin H, Miga, Karen H, Nguyen, Ngan, Paten, Benedict, Raney, Brian J, Smit, Arian F A, Speir, Matthew L, Zweig, Ann S, Haussler, David, Kuhn, Robert M, Kent, W James

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The common marmoset genome provides insight into primate biology and evolution von Worley, Kim C, Warren, Wesley C, Rogers, Jeffrey, Locke, Devin, Muzny, Donna M, Mardis, Elaine R, Weinstock, George M, Tardif, Suzette D, Aagaard, Kjersti M, Archidiacono, Nicoletta, Wang, Qing, Warner, Crystal M, Wildman, Derek E, Witherspoon, David J, Wright, Rita A, Wu, Yuanqing, Xiao, Weimin, Xing, Jinchuan, Zhu, Baoli, Rayan, Nirmala Arul, Gibbs, Richard A, Wilson, Richard K, Batzer, Mark A, Beal, Kathryn, Brejova, Brona, Capozzi, Oronzo, Capuano, Saverio B, Casola, Claudio, Chandrabose, Mimi M, Dao, Marvin Diep, de Jong, Pieter J, del Rosario, Ricardo Cruz-Herrera, Delehaunty, Kkim D, Dinh, Huyen H, Eichler, Evan E, Fitzgerald, Stephen, Flicek, Paul, Fowler, R Gerald, Fronick, Catrina, Fulton, Lucinda A, Fulton, Robert S, Gabisi, Ramatu Ayiesha, Gerlach, Daniel, Graves, Tina A, Gunaratne, Preethi H, Hahn, Matthew W, Haig, David, Han, Yi, Harris, R Alan, Herrero, Javier, Hillier, LaDdeana W, Hubley, Robert, Jhangiani, Shalini N, Jorde, Lynn B, Joshi, Vandita, Karakor, Emre, Konkel, Miriam K, Kovar, Christie L, Kriventseva, Evgenia V, Lee, Sandra L, Liu, Yih-shin, Lopez, John, Lopez-Otin, Carlos, Mansfield, Keith G, Marques-Bonet, Tomas, Minx, Patrick, Misceo, Doriana, Moncrieff, J Scott, Morgan, Margaret B, Nazareth, Lynne V, Newsham, Irene, Nguyen, Ngoc Bich, Okwuonu, Geoffrey O, Prabhakar, Shyam, Pu, Ling-Ling, Quesada, Victor, Ranck, Megan C, Raney, Brian J, Deiros, David Rio, Rocchi, Mariano, Rodriguez, David, Ross, Corinna, Ruffier, Magali, Ruiz, San Juana, Sajjadian, Saba, Santibanez, Jireh, Schrider, Daniel R, Searle, Steve, Skaletsky, Helen, Soibam, Benjamin, Smit, Arian F A, Tennakoon, Jayantha B, Tomaska, Lubomir, Ullmer, Brygg, Vejnar, Charles E, Ventura, Mario, Vilella, Albert J, Vinar, Tomas, Vogel, Jan-Hinnerk, Walker, Jerilyn A

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TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation von Elliott, Tyler A, Heitkam, Tony, Hubley, Robert, Quesneville, Hadi, Suh, Alexander, Wheeler, Travis J

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Comparative and demographic analysis of orang-utan genomes von 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., 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.

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