Search Results - "Smit, Arian F.A"

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…”
Get full text

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…”
Get full text

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…”
Get full text

Multiscale representation of genomic signals by Knijnenburg, Theo A, Ramsey, Stephen A, Berman, Benjamin P, Kennedy, Kathleen A, Smit, Arian F A, Wessels, Lodewyk F A, Laird, Peter W, Aderem, Alan, Shmulevich, Ilya

“…This framework for multiscale signal representation allows global analysis of genomic data at different length scales from base pairs to entire chromosomes and…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel by Moore, Richard C, Lee, Inyoul Y, Silverman, Gregory L, Harrison, Paul M, Strome, Robert, Heinrich, Cornelia, Karunaratne, Amila, Pasternak, Stephen H, Chishti, M.Azhar, Liang, Yan, Mastrangelo, Peter, Wang, Kai, Smit, Arian F.A, Katamine, Shigeru, Carlson, George A, Cohen, Fred E, Prusiner, Stanley B, Melton, David W, Tremblay, Patrick, Hood, Leroy E, Westaway, David

“…The novel locus Prnd is 16 kb downstream of the mouse prion protein (PrP) gene Prnp and encodes a 179 residue PrP-like protein designated doppel (Dpl). Prnd…”
Get full text

Identification of a new, abundant superfamily of mammalian LTR-transposons by SMIT, A. F. A

“…A new superfamily of mammalian transposable genetic elements is described with an estimated 40,000 to 100,000 members in both primate and rodent genomes…”
Get full text

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,…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

Aligning multiple genomic sequences with the threaded blockset aligner by Blanchette, Mathieu, Kent, W James, Riemer, Cathy, Elnitski, Laura, Smit, Arian F A, Roskin, Krishna M, Baertsch, Robert, Rosenbloom, Kate, Clawson, Hiram, Green, Eric D, Haussler, David, Miller, Webb

“…We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for…”
Get full text

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)…”
Get full text

Curation Guidelines for de novo Generated Transposable Element Families by Storer, Jessica M, Hubley, Robert, Rosen, Jeb, Smit, Arian F A

“…Transposable elements (TEs) have the ability to alter individual genomic landscapes and shape the course of evolution for species in which they reside. Such…”
Get more information

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…”
Get full text

The origin of interspersed repeats in the human genome by Smit, Arian FA

“…Over a third of the human genome consists of interspersed repetitive sequences which are primarily degenerate copies of transposable elements. In the past…”
Get full text

Tiggers and Other DNA Transposon Fossils in the Human Genome by Arian F. A. Smit, Riggs, Arthur D.

“…We report several classes of human interspersed repeats that resemble fossils of DNA transposons, elements that move by excision and reintegration in the…”
Get full text