Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis von Pallavicini, Alberto, Canapa, Adriana, Barucca, Marco, Alfőldi, Jessica, Biscotti, Maria Assunta, Buonocore, Francesco, De Moro, Gianluca, Di Palma, Federica, Fausto, Anna Maria, Forconi, Mariko, Gerdol, Marco, Makapedua, Daisy Monica, Turner-Meier, Jason, Olmo, Ettore, Scapigliati, Giuseppe

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

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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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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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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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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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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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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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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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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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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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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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Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes von Broeckx, Bart J.G., Hitte, Christophe, Coopman, Frank, Verhoeven, Geert E.C., De Keulenaer, Sarah, De Meester, Ellen, Derrien, Thomas, Alfoldi, Jessica, Lindblad-Toh, Kerstin, Bosmans, Tim, Gielen, Ingrid, Van Bree, Henri, Van Ryssen, Bernadette, Saunders, Jimmy H., Van Nieuwerburgh, Filip, Deforce, Dieter

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The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling von Noh, Hyun Ji, Turner-Maier, Jason, Schulberg, S. Anne, Fitzgerald, Michael L., Johnson, Jeremy, Allen, Kaitlin N., Hückstädt, Luis A., Batten, Annabelle J., Alfoldi, Jessica, Costa, Daniel P., Karlsson, Elinor K., Zapol, Warren M., Buys, Emmanuel S., Lindblad-Toh, Kerstin, Hindle, Allyson G.

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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer von Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S., Knijnenburg, Theo A., Robertson, A. Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C., Huang, Kuan-lin, Newberg, Justin Y., Mashl, R. Jay, Romanel, Alessandro, Sayaman, Rosalyn W., Demichelis, Francesca, Felau, Ina, Frampton, Garrett M., Han, Seunghun, Hoadley, Katherine A., Kemal, Anab, Laird, Peter W., Lazar, Alexander J., Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K., Zenklusen, Jean C., Ziv, Elad, Aguet, Francois, Ding, Li, Demchok, John A., Mensah, Michael K.A., Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J., MacArthur, Daniel G., Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M., Cherniack, Andrew D., Beroukhim, Rameen

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