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    Wyświetlanie 1-8 z 8
    Tytuł:
    DEPP: Deep Learning Enables Extending Species Trees using Single Genes.
    Autorzy:
    Jiang Y; Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
    Balaban M; Bioinformatics and Systems Biology Graduate Program, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
    Zhu Q; Center for Fundamental and Applied Microbiomics, Arizona State University, 1151 S Forest Ave, Tempe, AZ 85281, USA.
    Mirarab S; Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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    Źródło:
    Systematic biology [Syst Biol] 2023 May 19; Vol. 72 (1), pp. 17-34.
    Typ publikacji:
    Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, N.I.H., Extramural
    MeSH Terms:
    Deep Learning*
    Microbiota*/genetics
    Phylogeny ; RNA, Ribosomal, 16S/genetics ; Algorithms
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.
    Autorzy:
    Balaban M; Bioinformatics and System Biology Program, University of California San Diego, San Diego, CA 92093, USA.
    Bristy NA; Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh.
    Faisal A; Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh.
    Bayzid MS; Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh.
    Mirarab S; Bioinformatics and System Biology Program, University of California San Diego, San Diego, CA 92093, USA.
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    Źródło:
    Bioinformatics advances [Bioinform Adv] 2022 Aug 12; Vol. 2 (1), pp. vbac055. Date of Electronic Publication: 2022 Aug 12 (Print Publication: 2022).
    Typ publikacji:
    Journal Article
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.
    Autorzy:
    Balaban M; Bioinformatics and Systems Biology Graduate Program, UC San Diego, CA 92093, USA.
    Sarmashghi S; Department of Electrical and Computer Engineering, UC San Diego, CA 92093, USA.
    Mirarab S; Department of Electrical and Computer Engineering, UC San Diego, CA 92093, USA.
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    Źródło:
    Systematic biology [Syst Biol] 2020 May 01; Vol. 69 (3), pp. 566-578.
    Typ publikacji:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Phylogeny*
    Software*
    Classification/*methods
    Algorithms ; Base Sequence
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores.
    Autorzy:
    Rabiee M; Department of Computer Science and Engineering, UC San Diego, La Jolla, CA 92093, USA.
    Mirarab S; Department of Electrical and Computer Engineering, UC, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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    Źródło:
    Systematic biology [Syst Biol] 2020 Mar 01; Vol. 69 (2), pp. 384-391.
    Typ publikacji:
    Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Phylogeny*
    Software*
    Classification/*methods
    Sequence Analysis, DNA/*methods
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.
    Autorzy:
    Moshiri N; Bioinformatics and Systems Biology Graduate Program, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
    Mirarab S; Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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    Źródło:
    Systematic biology [Syst Biol] 2018 May 01; Vol. 67 (3), pp. 475-489.
    Typ publikacji:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Evolution, Molecular*
    Models, Biological*
    Phylogeny*
    Alu Elements/*genetics
    Classification/*methods
    Genome, Human/*genetics
    Humans
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.
    Autorzy:
    Mirarab S; Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA; and.
    Bayzid MS; Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA; and.
    Warnow T; Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA; and Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .
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    Źródło:
    Systematic biology [Syst Biol] 2016 May; Vol. 65 (3), pp. 366-80. Date of Electronic Publication: 2014 Aug 26.
    Typ publikacji:
    Journal Article
    MeSH Terms:
    Phylogeny*
    Classification/*methods
    Computer Simulation ; Gene Duplication ; Probability
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknieSzczegóły
    Tytuł:
    Phylogenomic analyses data of the avian phylogenomics project.
    Autorzy:
    Jarvis ED; Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA.
    Mirarab S; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA.
    Aberer AJ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
    Li B; China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
    Houde P; Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA.
    Li C; China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
    Ho SY; School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia.
    Faircloth BC; Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA ; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA.
    Nabholz B; CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II, Montpellier, France.
    Howard JT; Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA.
    Suh A; Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
    Weber CC; Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
    da Fonseca RR; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
    Alfaro-Núñez A; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
    Narula N; Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA ; Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan.
    Liu L; Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA.
    Burt D; Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK.
    Ellegren H; Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
    Edwards SV; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA.
    Stamatakis A; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany ; Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany.
    Mindell DP; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA.
    Cracraft J; Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA.
    Braun EL; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA.
    Warnow T; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA.
    Jun W; China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark ; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ; Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China ; Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong.
    Gilbert MT; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark ; Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia.
    Zhang G; China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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    Corporate Authors:
    Avian Phylogenomics Consortium
    Źródło:
    GigaScience [Gigascience] 2015 Feb 12; Vol. 4, pp. 4. Date of Electronic Publication: 2015 Feb 12 (Print Publication: 2015).
    Typ publikacji:
    Dataset; Journal Article
    MeSH Terms:
    Phylogeny*
    Birds/*genetics
    Animals ; Birds/classification ; Classification/methods ; DNA/chemistry ; DNA Transposable Elements ; Genome ; Genomics ; Sequence Alignment
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknieSzczegóły
    Tytuł:
    Data access for the 1,000 Plants (1KP) project.
    Autorzy:
    Matasci N; iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
    Hung LH; Department of Microbiology, University of Washington, Seattle 98109, WA, USA.
    Yan Z; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
    Carpenter EJ; Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada.
    Wickett NJ; Chicago Botanic Garden, Glencoe 60022, IL, USA ; Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA.
    Mirarab S; Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
    Nguyen N; Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
    Warnow T; Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
    Ayyampalayam S; Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
    Barker M; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
    Burleigh JG; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
    Gitzendanner MA; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
    Wafula E; Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
    Der JP; Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
    dePamphilis CW; Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
    Roure B; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada.
    Philippe H; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada ; CNRS, USR 2936, Station d' Ecologie Expérimentale du CNRS, Moulis 09200, France.
    Ruhfel BR; Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA.
    Miles NW; Florida Museum of Natural History, Gainesville, FL, 32611, USA.
    Graham SW; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
    Mathews S; Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA.
    Surek B; Botanical Institute, Universität zu Köln, Köln D-50674, Germany.
    Melkonian M; Botanical Institute, Universität zu Köln, Köln D-50674, Germany.
    Soltis DE; Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Gainesville, FL, 32611, USA ; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
    Soltis PS; Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Gainesville, FL, 32611, USA ; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
    Rothfels C; Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
    Pokorny L; Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain.
    Shaw JA; Department of Biology, Duke University, Durham, NC 27708, USA.
    DeGironimo L; New York Botanical Garden, Bronx, NY, 10458, USA.
    Stevenson DW; New York Botanical Garden, Bronx, NY, 10458, USA.
    Villarreal JC; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
    Chen T; Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China.
    Kutchan TM; Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
    Rolf M; Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
    Baucom RS; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
    Deyholos MK; Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada.
    Samudrala R; Department of Microbiology, University of Washington, Seattle 98109, WA, USA.
    Tian Z; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
    Wu X; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
    Sun X; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
    Zhang Y; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
    Wang J; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
    Leebens-Mack J; Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
    Wong GK; BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China ; Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada ; Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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    Źródło:
    GigaScience [Gigascience] 2014 Oct 27; Vol. 3, pp. 17. Date of Electronic Publication: 2014 Oct 27 (Print Publication: 2014).
    Typ publikacji:
    Journal Article; Review
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknieSzczegóły
      Wyświetlanie 1-8 z 8

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