Search Results - "Rosen, Jeb R"

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements by Wirthlin, Morgan E, Schmid, Tobias A, Elie, Julie E, Zhang, Xiaomeng, Kowalczyk, Amanda, Redlich, Ruby, Shvareva, Varvara A, Rakuljic, Ashley, Ji, Maria B, Bhat, Ninad S, Kaplow, Irene M, Schäffer, Daniel E, Lawler, Alyssa J, Wang, Andrew Z, Phan, BaDoi N, Annaldasula, Siddharth, Brown, Ashley R, Lu, Tianyu, Lim, Byung Kook, Azim, Eiman, Clark, Nathan L, Meyer, Wynn K, Pond, Sergei L Kosakovsky, Chikina, Maria, Yartsev, Michael M, Pfenning, Andreas R, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Karlsson, Elinor K, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Lindblad-Toh, Kerstin, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer R S, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina

“…Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal…”
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Evolutionary constraint and innovation across hundreds of placental mammals by Christmas, Matthew J, Kaplow, Irene M, Genereux, Diane P, Dong, Michael X, Hughes, Graham M, Li, Xue, Sullivan, Patrick F, Hindle, Allyson G, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Breit, Ana M, Diekhans, Mark, Fanter, Cornelia, Foley, Nicole M, Goodman, Daniel B, Goodman, Linda, Keough, Kathleen C, Kirilenko, Bogdan, Kowalczyk, Amanda, Lawless, Colleen, Lind, Abigail L, Meadows, Jennifer R S, Moreira, Lucas R, Redlich, Ruby W, Ryan, Louise, Swofford, Ross, Valenzuela, Alejandro, Wagner, Franziska, Wallerman, Ola, Brown, Ashley R, Damas, Joana, Fan, Kaili, Gatesy, John, Grimshaw, Jenna, Johnson, Jeremy, Kozyrev, Sergey V, Lawler, Alyssa J, Marinescu, Voichita D, Morrill, Kathleen M, Osmanski, Austin, Paulat, Nicole S, Phan, BaDoi N, Reilly, Steven K, Schäffer, Daniel E, Steiner, Cynthia, Supple, Megan A, Wilder, Aryn P, Wirthlin, Morgan E, Xue, James R, Birren, Bruce W, Gazal, Steven, Hubley, Robert M, Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Meyer, Wynn K, Nweeia, Martin, Sabeti, Pardis C, Shapiro, Beth, Smit, Arian F A, Springer, Mark S, Teeling, Emma C, Weng, Zhiping, Hiller, Michael, Levesque, Danielle L, Lewin, Harris A, Murphy, William J, Navarro, Arcadi, Paten, Benedict, Pollard, Katherine S, Ray, David A, Ruf, Irina, Ryder, Oliver A, Pfenning, Andreas R, Lindblad-Toh, Kerstin, Karlsson, Elinor K

“…Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated,…”
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Evolution of the ancestral mammalian karyotype and syntenic regions by 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, Nweeia, Martin T, Johnson, Rebecca N, Lewin, Harris A

“…Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease…”
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A genomic timescale for placental mammal evolution by 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

“…The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive…”
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Integrating gene annotation with orthology inference at scale by Kirilenko, Bogdan M, Munegowda, Chetan, Osipova, Ekaterina, Jebb, David, Sharma, Virag, Blumer, Moritz, Morales, Ariadna E, Ahmed, Alexis-Walid, Kontopoulos, Dimitrios-Georgios, Hilgers, Leon, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Hiller, Michael

“…Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached…”
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Mammalian evolution of human cis-regulatory elements and transcription factor binding sites by Andrews, Gregory, Fan, Kaili, Pratt, Henry E, Phalke, Nishigandha, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Gazal, Steven, Moore, Jill E, Weng, Zhiping

“…Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241…”
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The contribution of historical processes to contemporary extinction risk in placental mammals by Wilder, Aryn P, Supple, Megan A, Subramanian, Ayshwarya, Mudide, Anish, Swofford, Ross, Serres-Armero, Aitor, Steiner, Cynthia, Koepfli, Klaus-Peter, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Marques-Bonet, Tomas, Munoz Fuentes, Violeta, Foley, Kathleen, Meyer, Wynn K, Ryder, Oliver A, Shapiro, Beth

“…Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between…”
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Insights into mammalian TE diversity through the curation of 248 genome assemblies by 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

“…We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found…”
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Relating enhancer genetic variation across mammals to complex phenotypes using machine learning by 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

“…Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene…”
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Three-dimensional genome rewiring in loci with human accelerated regions by 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

“…Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We…”
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The functional and evolutionary impacts of human-specific deletions in conserved elements by 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

“…Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved…”
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Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia by Paulat, Nicole S, Storer, Jessica M, Moreno-Santillán, Diana D, Osmanski, Austin B, Sullivan, Kevin A M, Grimshaw, Jenna R, Korstian, Jennifer, Halsey, Michaela, Garcia, Carlos J, Crookshanks, Claudia, Roberts, Jaquelyn, Smit, Arian F A, Hubley, Robert, Rosen, Jeb, Teeling, Emma C, Vernes, Sonja C, Myers, Eugene, Pippel, Martin, Brown, Thomas, Hiller, Michael, Rojas, Danny, Dávalos, Liliana M, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Ray, David A

“…Abstract Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera)…”
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Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs by 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

“…We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary…”
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Using evolutionary constraint to define novel candidate driver genes in medulloblastoma by Roy, Ananya, Sakthikumar, Sharadha, Kozyrev, Sergey V, Nordin, Jessika, Pensch, Raphaela, Mäkeläinen, Suvi, Pettersson, Mats, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Forsberg-Nilsson, Karin

“…Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed…”
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