Selscan: An efficient multithreaded program to perform EHH-based scans for positive selection

Autor: Hernandez, Ryan, Szpiech, ZA, Hernandez, RD

Publikováno v: Hernandez, Ryan; Szpiech, ZA; & Hernandez, RD. (2014). Selscan: An efficient multithreaded program to perform EHH-based scans for positive selection. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/2fs858tw

© 2014 The Author 2014.Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated genomic data sets grow larger, spanning thousands of samples and millions of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::701a6c0d5ce1e8bbb58ea05363985332
http://www.escholarship.org/uc/item/2fs858tw

Complete sequencing of ape genomes.

Autor: Yoo D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Rhie A; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Hebbar P; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Antonacci F; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy., Logsdon GA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA., Solar SJ; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Antipov D; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Pickett BD; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Safonova Y; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA., Montinaro F; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy.; Institute of Genomics, University of Tartu, Tartu, Estonia., Luo Y; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA., Malukiewicz J; Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany., Storer JM; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA., Lin J; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Sequeira AN; Department of Biology, Penn State University, University Park, PA 16802, USA., Mangan RJ; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Genetics Training Program, Harvard Medical School, Boston, MA 02115, USA., Hickey G; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Anez GM; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Balachandran P; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Bankevich A; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA., Beck CR; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA., Biddanda A; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA., Borchers M; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Bouffard GG; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Brannan E; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Brooks SY; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Carbone L; Department of Medicine, KCVI, Oregon Health Sciences University, Portland, OR, USA.; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA., Carrel L; PSU Medical School, Penn State University School of Medicine, Hershey, PA, USA., Chan AP; The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA., Crawford J; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Diekhans M; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Engelbrecht E; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA., Feschotte C; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA., Formenti G; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10021, USA., Garcia GH; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., de Gennaro L; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy., Gilbert D; San Diego Biomedical Research Institute, San Diego, CA, USA., Green RE; University of California Santa Cruz, Santa Cruz, CA, USA., Guarracino A; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA., Gupta I; Department of Computer Science and Engineering, University of California San Diego, CA, USA., Haddad D; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Han J; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China., Harris RS; Department of Biology, Penn State University, University Park, PA 16802, USA., Hartley GA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA., Harvey WT; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Hiller M; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany., Hoekzema K; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Houck ML; San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA., Jeong H; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Kamali K; Department of Biology, Penn State University, University Park, PA 16802, USA., Kellis M; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Kille B; Department of Computer Science, Rice University, Houston, TX 77005, USA., Lee C; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA., Lee Y; Laboratory of bioinformatics and population genetics, Interdisciplinary program in bioinformatics, Seoul National University, Republic of Korea., Lees W; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA.; Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel., Lewis AP; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Li Q; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA., Loftus M; Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA., Loh YHE; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Loucks H; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Ma J; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA., Mao Y; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.; Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China.; Shanghai Jiao Tong University Chongqing Research Institute, Chongqing, China., Martinez JFI; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA., Masterson P; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., McCoy RC; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA., McGrath B; Department of Biology, Penn State University, University Park, PA 16802, USA., McKinney S; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Meyer BS; Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany., Miga KH; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Mohanty SK; Department of Biology, Penn State University, University Park, PA 16802, USA., Munson KM; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Pal K; Department of Biology, Penn State University, University Park, PA 16802, USA., Pennell M; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Pevzner PA; Department of Computer Science and Engineering, University of California San Diego, CA, USA., Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Potapova T; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Ringeling FR; Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany., Roha JL; Department of Integrative Biology, University of California, Berkeley, Berkeley, USA., Ryder OA; San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA., Sacco S; University of California Santa Cruz, Santa Cruz, CA, USA., Saha S; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA., Sasaki T; San Diego Biomedical Research Institute, San Diego, CA, USA., Schatz MC; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA., Schork NJ; The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA., Shanks C; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Smeds L; Department of Biology, Penn State University, University Park, PA 16802, USA., Son DR; Department of Ecology, Evolution and Marine Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Steiner C; San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA., Sweeten AP; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Tassia MG; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA., Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Torres-González E; Department of Biology, Penn State University, University Park, PA 16802, USA., Trivedi M; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Wei W; School of Life Sciences, Westlake University, Hangzhou 310024, China.; National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China., Wertz J; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Yang M; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA., Zhang P; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA., Zhang S; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China., Zhang Y; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA., Zhang Z; Department of Computer Science and Engineering, University of California San Diego, CA, USA., Zhao SA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Zhu Y; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Jarvis ED; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Gerton JL; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Rivas-González I; Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany., Paten B; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA., Szpiech ZA; Department of Biology, Penn State University, University Park, PA 16802, USA., Huber CD; Department of Biology, Penn State University, University Park, PA 16802, USA., Lenz TL; Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany., Konkel MK; Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA., Yi SV; Department of Ecology, Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Canzar S; Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany., Watson CT; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA., Sudmant PH; Department of Integrative Biology, University of California, Berkeley, Berkeley, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley, USA., Molloy E; Department of Computer Science, University of Maryland, College Park, MD 20742, USA., Garrison E; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA., Lowe CB; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA., Ventura M; Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy., O'Neill RJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.; Departments of Molecular and Cell Biology, UConn Storrs, CT, USA., Koren S; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Makova KD; Department of Biology, Penn State University, University Park, PA 16802, USA., Phillippy AM; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Eichler EE; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 05. Date of Electronic Publication: 2024 Oct 05.

Differentiating mechanism from outcome for ancestry-assortative mating in admixed human populations.

Autor: Massey DJ; Department of Evolutionary Anthropology, Duke University, USA 27708., Szpiech ZA; Department of Biology, Pennsylvania State University, USA 16801.; Institute for Computational and Data Sciences, Pennsylvania State University, USA 16801., Goldberg A; Department of Evolutionary Anthropology, Duke University, USA 27708.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 06. Date of Electronic Publication: 2024 Jun 06.

The complete sequence and comparative analysis of ape sex chromosomes.

Autor: Makova KD; Penn State University, University Park, PA, USA. kdm16@psu.edu., Pickett BD; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Harris RS; Penn State University, University Park, PA, USA., Hartley GA; University of Connecticut, Storrs, CT, USA., Cechova M; University of California Santa Cruz, Santa Cruz, CA, USA., Pal K; Penn State University, University Park, PA, USA., Nurk S; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Yoo D; University of Washington School of Medicine, Seattle, WA, USA., Li Q; Johns Hopkins University, Baltimore, MD, USA., Hebbar P; University of California Santa Cruz, Santa Cruz, CA, USA., McGrath BC; Penn State University, University Park, PA, USA., Antonacci F; Università degli Studi di Bari Aldo Moro, Bari, Italy., Aubel M; University of Münster, Münster, Germany., Biddanda A; Johns Hopkins University, Baltimore, MD, USA., Borchers M; Stowers Institute, Kansas City, MO, USA., Bornberg-Bauer E; University of Münster, Münster, Germany.; MPI for Developmental Biology, Tübingen, Germany., Bouffard GG; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Brooks SY; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Carbone L; Oregon Health and Science University, Portland, OR, USA.; Oregon National Primate Research Center, Hillsboro, OR, USA., Carrel L; Penn State University School of Medicine, Hershey, PA, USA., Carroll A; Google, Mountain View, CA, USA., Chang PC; Google, Mountain View, CA, USA., Chin CS; Foundation of Biological Data Sciences, Belmont, CA, USA., Cook DE; Google, Mountain View, CA, USA., Craig SJC; Penn State University, University Park, PA, USA., de Gennaro L; Università degli Studi di Bari Aldo Moro, Bari, Italy., Diekhans M; University of California Santa Cruz, Santa Cruz, CA, USA., Dutra A; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Garcia GH; University of Washington School of Medicine, Seattle, WA, USA., Grady PGS; University of Connecticut, Storrs, CT, USA., Green RE; University of California Santa Cruz, Santa Cruz, CA, USA., Haddad D; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., Hallast P; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Harvey WT; University of Washington School of Medicine, Seattle, WA, USA., Hickey G; University of California Santa Cruz, Santa Cruz, CA, USA., Hillis DA; University of California Santa Barbara, Santa Barbara, CA, USA., Hoyt SJ; University of Connecticut, Storrs, CT, USA., Jeong H; University of Washington School of Medicine, Seattle, WA, USA., Kamali K; Penn State University, University Park, PA, USA., Pond SLK; Temple University, Philadelphia, PA, USA., LaPolice TM; Penn State University, University Park, PA, USA., Lee C; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Lewis AP; University of Washington School of Medicine, Seattle, WA, USA., Loh YE; University of California Santa Barbara, Santa Barbara, CA, USA., Masterson P; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., McGarvey KM; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., McCoy RC; Johns Hopkins University, Baltimore, MD, USA., Medvedev P; Penn State University, University Park, PA, USA., Miga KH; University of California Santa Cruz, Santa Cruz, CA, USA., Munson KM; University of Washington School of Medicine, Seattle, WA, USA., Pak E; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Paten B; University of California Santa Cruz, Santa Cruz, CA, USA., Pinto BJ; Arizona State University, Tempe, AZ, USA., Potapova T; Stowers Institute, Kansas City, MO, USA., Rhie A; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Rocha JL; University of California Berkeley, Berkeley, CA, USA., Ryabov F; Masters Program in National Research, University Higher School of Economics, Moscow, Russia., Ryder OA; San Diego Zoological Society, San Diego, CA, USA., Sacco S; University of California Santa Cruz, Santa Cruz, CA, USA., Shafin K; Google, Mountain View, CA, USA., Shepelev VA; Institute of Molecular Genetics, Moscow, Russia., Slon V; Tel Aviv University, Tel Aviv, Israel., Solar SJ; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Storer JM; University of Connecticut, Storrs, CT, USA., Sudmant PH; University of California Berkeley, Berkeley, CA, USA., Sweetalana; Penn State University, University Park, PA, USA., Sweeten A; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.; Johns Hopkins University, Baltimore, MD, USA., Tassia MG; Johns Hopkins University, Baltimore, MD, USA., Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., Ventura M; Università degli Studi di Bari Aldo Moro, Bari, Italy., Wilson MA; Arizona State University, Tempe, AZ, USA., Young AC; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Zeng H; Penn State University, University Park, PA, USA., Zhang X; Penn State University, University Park, PA, USA., Szpiech ZA; Penn State University, University Park, PA, USA., Huber CD; Penn State University, University Park, PA, USA., Gerton JL; Stowers Institute, Kansas City, MO, USA., Yi SV; University of California Santa Barbara, Santa Barbara, CA, USA., Schatz MC; Johns Hopkins University, Baltimore, MD, USA., Alexandrov IA; Tel Aviv University, Tel Aviv, Israel., Koren S; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., O'Neill RJ; University of Connecticut, Storrs, CT, USA., Eichler EE; University of Washington School of Medicine, Seattle, WA, USA. eee@gs.washington.edu.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. eee@gs.washington.edu., Phillippy AM; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. adam.phillippy@nih.gov.

Publikováno v: Nature [Nature] 2024 Jun; Vol. 630 (8016), pp. 401-411. Date of Electronic Publication: 2024 May 29.

selscan 2.0: scanning for sweeps in unphased data.

Autor: Szpiech ZA; Department of Biology, Penn State University, University Park, PA 16802, United States.; Institute for Computational and Data Sciences, Penn State University, University Park, PA 16802, United States.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jan 02; Vol. 40 (1).