Search Results - "Smit, Arian F"

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

“…The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as…”
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The Dfam community resource of transposable element families, sequence models, and genome annotations by Storer, Jessica, Hubley, Robert, Rosen, Jeb, Wheeler, Travis J, Smit, Arian F

“…Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0-3.3 releases of Dfam ( https://dfam.org )…”
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Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing by Roach, Jared C, Glusman, Gustavo, Smit, Arian F.A, Huff, Chad D, Hubley, Robert, Shannon, Paul T, Rowen, Lee, Pant, Krishna P, Goodman, Nathan, Bamshad, Michael, Shendure, Jay, Drmanac, Radoje, Jorde, Lynn B, Hood, Leroy, Galas, David J

“…We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate…”
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Dfam: a database of repetitive DNA based on profile hidden Markov models by Wheeler, Travis J, Clements, Jody, Eddy, Sean R, Hubley, Robert, Jones, Thomas A, Jurka, Jerzy, Smit, Arian F A, Finn, Robert D

“…We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which…”
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The genome of a songbird by Warren, Wesley C, Clayton, David F, Ellegren, Hans, Arnold, Arthur P, Hillier, LaDeana W, Künstner, Axel, Searle, Steve, White, Simon, Vilella, Albert J, Fairley, Susan, Heger, Andreas, Kong, Lesheng, Ponting, Chris P, Jarvis, Erich D, Mello, Claudio V, Minx, Pat, Lovell, Peter, Velho, Tarciso A. F, Ferris, Margaret, Balakrishnan, Christopher N, Sinha, Saurabh, Blatti, Charles, London, Sarah E, Li, Yun, Lin, Ya-Chi, George, Julia, Sweedler, Jonathan, Southey, Bruce, Gunaratne, Preethi, Watson, Michael, Nam, Kiwoong, Backström, Niclas, Smeds, Linnea, Nabholz, Benoit, Itoh, Yuichiro, Whitney, Osceola, Pfenning, Andreas R, Howard, Jason, Völker, Martin, Skinner, Bejamin M, Griffin, Darren K, Ye, Liang, McLaren, William M, Flicek, Paul, Quesada, Victor, Velasco, Gloria, Lopez-Otin, Carlos, Puente, Xose S, Olender, Tsviya, Lancet, Doron, Smit, Arian F. A, Hubley, Robert, Konkel, Miriam K, Walker, Jerilyn A, Batzer, Mark A, Gu, Wanjun, Pollock, David D, Chen, Lin, Cheng, Ze, Eichler, Evan E, Stapley, Jessica, Slate, Jon, Ekblom, Robert, Birkhead, Tim, Burke, Terry, Burt, David, Scharff, Constance, Adam, Iris, Richard, Hugues, Sultan, Marc, Soldatov, Alexey, Lehrach, Hans, Edwards, Scott V, Yang, Shiaw-Pyng, Li, XiaoChing, Graves, Tina, Fulton, Lucinda, Nelson, Joanne, Chinwalla, Asif, Hou, Shunfeng, Mardis, Elaine R, Wilson, Richard K

“…The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch…”
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Chromosomal Haplotypes by Genetic Phasing of Human Families by Roach, Jared C., Glusman, Gustavo, Hubley, Robert, Montsaroff, Stephen Z., Holloway, Alisha K., Mauldin, Denise E., Srivastava, Deepak, Garg, Vidu, Pollard, Katherine S., Galas, David J., Hood, Leroy, Smit, Arian F.A.

“…Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more…”
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Functional noncoding sequences derived from SINEs in the mammalian genome by Nishihara, Hidenori, Smit, Arian F A, Okada, Norihiro

“…Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective…”
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Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome by Han, Kyudong, Konkel, Miriam K, Xing, Jinchuan, Wang, Hui, Lee, Jungnam, Meyer, Thomas J, Huang, Charles T, Sandifer, Erin, Hebert, Kristi, Barnes, Erin W, Hubley, Robert, Miller, Webb, Smit, Arian F.A, Ullmer, Brygg, Batzer, Mark A

“…The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this…”
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Discovery of a new repeat family in the Callithrix jacchus genome by Konkel, Miriam K, Ullmer, Brygg, Arceneaux, Erika L, Sanampudi, Sreeja, Brantley, Sarah A, Hubley, Robert, Smit, Arian F A, Batzer, Mark A

“…We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of…”
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The Dfam database of repetitive DNA families by Hubley, Robert, Finn, Robert D, Clements, Jody, Eddy, Sean R, Jones, Thomas A, Bao, Weidong, Smit, Arian F A, Wheeler, Travis J

“…Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of…”
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Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes by Chong, Amanda Y, Kojima, Kenji K, Jurka, Jerzy, Ray, David A, Smit, Arian F A, Isberg, Sally R, Gongora, Jaime

“…Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be…”
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The UCSC Genome Browser database: 2015 update by 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

“…Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow,…”
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A comparative genomics multitool for scientific discovery and conservation by Genereux, Diane P, Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D, Murén, Eva, Juan, David

“…The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of…”
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A third approach to gene prediction suggests thousands of additional human transcribed regions by Glusman, Gustavo, Qin, Shizhen, El-Gewely, M Raafat, Siegel, Andrew F, Roach, Jared C, Hood, Leroy, Smit, Arian F A

“…The identification and characterization of the complete ensemble of genes is a main goal of deciphering the digital information stored in the human genome…”
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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs by 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.

“…To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three…”
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Methodologies for the De novo Discovery of Transposable Element Families by Storer, Jessica M, Hubley, Robert, Rosen, Jeb, Smit, Arian F A

“…The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE…”
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The transposable element-rich genome of the cereal pest Sitophilus oryzae by Parisot, Nicolas, Vargas-Chávez, Carlos, Goubert, Clément, Baa-Puyoulet, Patrice, Balmand, Séverine, Beranger, Louis, Blanc, Caroline, Bonnamour, Aymeric, Boulesteix, Matthieu, Burlet, Nelly, Calevro, Federica, Callaerts, Patrick, Chancy, Théo, Charles, Hubert, Colella, Stefano, Da Silva Barbosa, André, Dell'Aglio, Elisa, Di Genova, Alex, Febvay, Gérard, Gabaldón, Toni, Galvão Ferrarini, Mariana, Gerber, Alexandra, Gillet, Benjamin, Hubley, Robert, Hughes, Sandrine, Jacquin-Joly, Emmanuelle, Maire, Justin, Marcet-Houben, Marina, Masson, Florent, Meslin, Camille, Montagné, Nicolas, Moya, Andrés, Ribeiro de Vasconcelos, Ana Tereza, Richard, Gautier, Rosen, Jeb, Sagot, Marie-France, Smit, Arian F A, Storer, Jessica M, Vincent-Monegat, Carole, Vallier, Agnès, Vigneron, Aurélien, Zaidman-Rémy, Anna, Zamoum, Waël, Vieira, Cristina, Rebollo, Rita, Latorre, Amparo, Heddi, Abdelaziz

“…The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae…”
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Realistic artificial DNA sequences as negative controls for computational genomics by Caballero, Juan, Smit, Arian F A, Hood, Leroy, Glusman, Gustavo

“…A common practice in computational genomic analysis is to use a set of 'background' sequences as negative controls for evaluating the false-positive rates of…”
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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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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements by Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick G S, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian F A, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H, O'Neill, Rachel J

“…Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive…”
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