Progressive Cactus is a multiple-genome aligner for the thousand-genome era von Armstrong, Joel, Hickey, Glenn, Diekhans, Mark, Fiddes, Ian T., Novak, Adam M., Deran, Alden, Fang, Qi, Xie, Duo, Feng, Shaohong, Stiller, Josefin, Genereux, Diane, Johnson, Jeremy, Marinescu, Voichita Dana, Alföldi, Jessica, Harris, Robert S., Lindblad-Toh, Kerstin, Haussler, David, Karlsson, Elinor, Jarvis, Erich D., Zhang, Guojie, Paten, Benedict

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Comparative genomics as a tool to understand evolution and disease von Alfoeldi, J, Lindblad-Toh, K

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Genome-wide synteny through highly sensitive sequence alignment: Satsuma von Grabherr, Manfred G., Russell, Pamela, Meyer, Miriah, Mauceli, Evan, Alföldi, Jessica, Di Palma, Federica, Lindblad-Toh, Kerstin

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FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome von Wucher, Valentin, Legeai, Fabrice, Hédan, Benoît, Rizk, Guillaume, Lagoutte, Lætitia, Leeb, Tosso, Jagannathan, Vidhya, Cadieu, Edouard, David, Audrey, Lohi, Hannes, Cirera, Susanna, Fredholm, Merete, Botherel, Nadine, Leegwater, Peter A J, Le Béguec, Céline, Fieten, Hille, Johnson, Jeremy, Alföldi, Jessica, André, Catherine, Lindblad-Toh, Kerstin, Hitte, Christophe, Derrien, Thomas

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Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators von Bellott, Daniel W., Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Zaghlul, Sara, Graves, Tina, Rock, Susie, Kremitzki, Colin, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Morton, Donna, Khan, Ziad, Lewis, Lora, Buhay, Christian, Wang, Qiaoyan, Watt, Jennifer, Holder, Michael, Lee, Sandy, Nazareth, Lynne, Alföldi, Jessica, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., Page, David C.

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SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma von Sakthikumar, Sharadha, Elvers, Ingegerd, Kim, Jaegil, Arendt, Maja L, Thomas, Rachael, Turner-Maier, Jason, Swofford, Ross, Johnson, Jeremy, Schumacher, Steven E, Alföldi, Jessica, Axelsson, Erik, Couto, C Guillermo, Kisseberth, William C, Pettersson, Mats E, Getz, Gad, Meadows, Jennifer R S, Modiano, Jaime F, Breen, Matthew, Kierczak, Marcin, Forsberg-Nilsson, Karin, Marinescu, Voichita D, Lindblad-Toh, Kerstin

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Convergent evolution of the genomes of marine mammals von Foote, Andrew D, Liu, Yue, Thomas, Gregg W C, Vinař, Tomáš, Alföldi, Jessica, Deng, Jixin, Dugan, Shannon, van Elk, Cornelis E, Hunter, Margaret E, Joshi, Vandita, Khan, Ziad, Kovar, Christie, Lee, Sandra L, Lindblad-Toh, Kerstin, Mancia, Annalaura, Nielsen, Rasmus, Qin, Xiang, Qu, Jiaxin, Raney, Brian J, Vijay, Nagarjun, Wolf, Jochen B W, Hahn, Matthew W, Muzny, Donna M, Worley, Kim C, Gilbert, M Thomas P, Gibbs, Richard A

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Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background von Elvers, Ingegerd, Turner-Maier, Jason, Swofford, Ross, Koltookian, Michele, Johnson, Jeremy, Stewart, Chip, Zhang, Cheng-Zhong, Schumacher, Steven E, Beroukhim, Rameen, Rosenberg, Mara, Thomas, Rachael, Mauceli, Evan, Getz, Gad, Palma, Federica Di, Modiano, Jaime F, Breen, Matthew, Lindblad-Toh, Kerstin, Alföldi, Jessica

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Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes von Eckalbar, Walter L, Hutchins, Elizabeth D, Markov, Glenn J, Allen, April N, Corneveaux, Jason J, Lindblad-Toh, Kerstin, Di Palma, Federica, Alföldi, Jessica, Huentelman, Matthew J, Kusumi, Kenro

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An Improved microRNA Annotation of the Canine Genome von Penso-Dolfin, Luca, Swofford, Ross, Johnson, Jeremy, Alföldi, Jessica, Lindblad-Toh, Kerstin, Swarbreck, David, Moxon, Simon, Di Palma, Federica

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The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations von Keane, Michael, Craig, Thomas, Alföldi, Jessica, Berlin, Aaron M, Johnson, Jeremy, Seluanov, Andrei, Gorbunova, Vera, Di Palma, Federica, Lindblad-Toh, Kerstin, Church, George M, de Magalhães, João Pedro

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Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals von Casewell, Nicholas R., Petras, Daniel, Card, Daren C., Suranse, Vivek, Mychajliw, Alexis M., Richards, David, Koludarov, Ivan, Albulescu, Laura-Oana, Slagboom, Julien, Hempel, Benjamin-Florian, Ngum, Neville M., Kennerley, Rosalind J., Brocca, Jorge L., Whiteley, Gareth, Harrison, Robert A., Bolton, Fiona M. S., Debono, Jordan, Vonk, Freek J., Alföldi, Jessica, Johnson, Jeremy, Karlsson, Elinor K., Lindblad-Toh, Kerstin, Mellor, Ian R., Süssmuth, Roderich D., Fry, Bryan G., Kuruppu, Sanjaya, Hodgson, Wayne C., Kool, Jeroen, Castoe, Todd A., Barnes, Ian, Sunagar, Kartik, Undheim, Eivind A. B., Turveyb, Samuel T.

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Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes von Soh, Y Q Shirleen, Alföldi, Jessica, Pyntikova, Tatyana, Brown, Laura G, Graves, Tina, Minx, Patrick J, Fulton, Robert S, Kremitzki, Colin, Koutseva, Natalia, Mueller, Jacob L, Rozen, Steve, Hughes, Jennifer F, Owens, Elaine, Womack, James E, Murphy, William J, Cao, Qing, de Jong, Pieter, Warren, Wesley C, Wilson, Richard K, Skaletsky, Helen, Page, David C

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A structural variation reference for medical and population genetics von Collins, Ryan L., Brand, Harrison, Karczewski, Konrad J., Zhao, Xuefang, Alföldi, Jessica, Francioli, Laurent C., Khera, Amit V., Lowther, Chelsea, Gauthier, Laura D., Wang, Harold, Watts, Nicholas A., Solomonson, Matthew, O’Donnell-Luria, Anne, Baumann, Alexander, Munshi, Ruchi, Walker, Mark, Whelan, Christopher W., Huang, Yongqing, Brookings, Ted, Sharpe, Ted, Stone, Matthew R., Valkanas, Elise, Fu, Jack, Tiao, Grace, Laricchia, Kristen M., Ruano-Rubio, Valentin, Stevens, Christine, Gupta, Namrata, Cusick, Caroline, Margolin, Lauren, Taylor, Kent D., Lin, Henry J., Rich, Stephen S., Post, Wendy S., Chen, Yii-Der Ida, Rotter, Jerome I., Nusbaum, Chad, Philippakis, Anthony, Lander, Eric, Gabriel, Stacey, Neale, Benjamin M., Kathiresan, Sekar, Daly, Mark J., Banks, Eric, MacArthur, Daniel G., Talkowski, Michael E.

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Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci von Lessard, Samuel, Francioli, Laurent, Alfoldi, Jessica, Tardif, Jean-Claude, Ellinor, Patrick T., MacArthur, Daniel G., Lettre, Guillaume, Orkin, Stuart H., Canver, Matthew C.

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A comprehensive genomic history of extinct and living elephants von Palkopoulou, Eleftheria, Lipson, Mark, Mallick, Swapan, Nielsen, Svend, Rohland, Nadin, Baleka, Sina, Karpinski, Emil, Ivancevic, Atma M., To, Thu-Hien, Kortschak, R. Daniel, Raison, Joy M., Qu, Zhipeng, Chin, Tat-Jun, Alt, Kurt W., Claesson, Stefan, Dalén, Love, MacPhee, Ross D. E., Meller, Harald, Roca, Alfred L., Ryder, Oliver A., Heiman, David, Young, Sarah, Breen, Matthew, Williams, Christina, Aken, Bronwen L., Ruffier, Magali, Karlsson, Elinor, Johnson, Jeremy, Di Palma, Federica, Alfoldi, Jessica, Adelson, David L., Mailund, Thomas, Munch, Kasper, Lindblad-Toh, Kerstin, Hofreiter, Michael, Poinar, Hendrik, Reich, David

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Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma von Megquier, Kate, Turner-Maier, Jason, Swofford, Ross, Kim, Jong-Hyuk, Sarver, Aaron L, Wang, Chao, Sakthikumar, Sharadha, Johnson, Jeremy, Koltookian, Michele, Lewellen, Mitzi, Scott, Milcah C, Schulte, Ashley J, Borst, Luke, Tonomura, Noriko, Alfoldi, Jessica, Painter, Corrie, Thomas, Rachael, Karlsson, Elinor K, Breen, Matthew, Modiano, Jaime F, Elvers, Ingegerd, Lindblad-Toh, Kerstin

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Evaluating drug targets through human loss-of-function genetic variation von Minikel, Eric Vallabh, Karczewski, Konrad J., Martin, Hilary C., Cummings, Beryl B., Whiffin, Nicola, Rhodes, Daniel, Alföldi, Jessica, Trembath, Richard C., van Heel, David A., Daly, Mark J., Schreiber, Stuart L., MacArthur, Daniel G.

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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication von Carneiro, Miguel, Rubin, Carl-Johan, Di Palma, Federica, Albert, Frank W., Alföldi, Jessica, Barrio, Alvaro Martinez, Pielberg, Gerli, Rafati, Nima, Sayyab, Shumaila, Turner-Maier, Jason, Younis, Shady, Afonso, Sandra, Aken, Bronwen, Alves, Joel M., Barrell, Daniel, Bolet, Gerard, Boucher, Samuel, Burbano, Hernán A., Campos, Rita, Chang, Jean L., Duranthon, Veronique, Fontanesi, Luca, Garreau, Hervé, Heiman, David, Johnson, Jeremy, Mage, Rose G., Peng, Ze, Queney, Guillaume, Rogel-Gaillard, Claire, Ruffier, Magali, Searle, Steve, Villafuerte, Rafael, Xiong, Anqi, Young, Sarah, Forsberg-Nilsson, Karin, Good, Jeffrey M., Lander, Eric S., Ferrand, Nuno, Lindblad-Toh, Kerstin, Andersson, Leif

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Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes von Wang, Qingbo, Pierce-Hoffman, Emma, Cummings, Beryl B., Alföldi, Jessica, Francioli, Laurent C., Gauthier, Laura D., Hill, Andrew J., O’Donnell-Luria, Anne H., Karczewski, Konrad J., MacArthur, Daniel G.

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