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Tytuł:
Median quartet tree search algorithms using optimal subtree prune and regraft.
Autorzy:
Arasti S; Computer Science and Engineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
Mirarab S; Electrical and Computer Engineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. .
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Źródło:
Algorithms for molecular biology : AMB [Algorithms Mol Biol] 2024 Mar 13; Vol. 19 (1), pp. 12. Date of Electronic Publication: 2024 Mar 13.
Typ publikacji:
Journal Article
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
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:
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.
Autorzy:
Sarmashghi S; Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, California, United States of America.
Balaban M; Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America.
Rachtman E; Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America.
Touri B; Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, California, United States of America.
Mirarab S; Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, California, United States of America.
Bafna V; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, United States of America.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2021 Nov 15; Vol. 17 (11), pp. e1009449. Date of Electronic Publication: 2021 Nov 15 (Print Publication: 2021).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Algorithms*
Genome*
Repetitive Sequences, Nucleic Acid*
Software*
Genomics/*statistics & numerical data
Animals ; Computational Biology ; Computer Simulation ; Databases, Genetic/statistics & numerical data ; Humans ; Invertebrates/classification ; Invertebrates/genetics ; Least-Squares Analysis ; Linear Models ; Mammals/classification ; Mammals/genetics ; Models, Genetic ; Phylogeny ; Plants/classification ; Plants/genetics ; Vertebrates/classification ; Vertebrates/genetics
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:
Forcing external constraints on tree inference using ASTRAL.
Autorzy:
Rabiee M; Department of Computer Science and Engineering, UC San Diego, 9500 Gilman Dr, La Jolla, 92093, USA.
Mirarab S; Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Dr, La Jolla, 92093, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2020 Apr 16; Vol. 21 (Suppl 2), pp. 218. Date of Electronic Publication: 2020 Apr 16.
Typ publikacji:
Journal Article
MeSH Terms:
Phylogeny*
Genomics/*methods
Algorithms ; Computer Simulation ; Databases, Genetic ; Evolution, Molecular ; Genetic Speciation ; Heuristics ; Multigene Family ; Research Design ; Software
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:
TreeCluster: Clustering biological sequences using phylogenetic trees.
Autorzy:
Balaban M; Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA 92093, United States of America.
Moshiri N; Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA 92093, United States of America.
Mai U; Computer Science and Engineering, UC San Diego, La Jolla, CA 92093, United States of America.
Jia X; Department of Mathematics, UC San Diego, La Jolla, CA 92093, United States of America.
Mirarab S; Department of Electrical and Computer Engineering, UC San Diego, La Jolla, CA 92093, United States of America.
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Źródło:
PloS one [PLoS One] 2019 Aug 22; Vol. 14 (8), pp. e0221068. Date of Electronic Publication: 2019 Aug 22 (Print Publication: 2019).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Algorithms*
Phylogeny*
Computational Biology/*statistics & numerical data
HIV/*genetics
Microbiota/*genetics
Sequence Alignment/*statistics & numerical data
Base Sequence ; Cluster Analysis ; Computational Biology/methods ; HIV/classification ; HIV Infections/epidemiology ; HIV Infections/transmission ; HIV Infections/virology ; Humans ; Software
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits.
Autorzy:
Chen L; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Qiu Q; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Jiang Y; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Wang K; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Lin Z; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Li Z; Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
Bibi F; Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, 10115 Berlin, Germany.
Yang Y; State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
Wang J; Kunming Cell Bank, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Nie W; Kunming Cell Bank, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Su W; Kunming Cell Bank, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Liu G; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Li Q; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
Fu W; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Pan X; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Liu C; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Yang J; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Zhang C; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Yin Y; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Wang Y; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Zhao Y; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Zhang C; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Wang Z; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Qin Y; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Liu W; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Wang B; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Ren Y; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Zhang R; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Zeng Y; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
da Fonseca RR; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Wei B; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Li R; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Wan W; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Zhao R; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Zhu W; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Wang Y; College of Life and Geographic Sciences, Kashgar University, Kashgar 844000, China.
Duan S; Nowbio Biotechnology Company, Kunming 650201, China.
Gao Y; Nowbio Biotechnology Company, Kunming 650201, China.
Zhang YE; Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
Chen C; Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.; University of Chinese Academy of Sciences, Beijing 100049, China.
Hvilsom C; Copenhagen Zoo, Frederiksberg, Denmark.
Epps CW; Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.
Chemnick LG; San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.
Dong Y; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China.; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.
Mirarab S; Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Siegismund HR; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Ryder OA; San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.; Evolution, Behavior, and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA.
Gilbert MTP; EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.; Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway.
Lewin HA; Department of Evolution and Ecology and the UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
Zhang G; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. .; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Heller R; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark. .
Wang W; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. .; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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Źródło:
Science (New York, N.Y.) [Science] 2019 Jun 21; Vol. 364 (6446).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Genome*
Ruminants/*classification
Ruminants/*genetics
Animals ; Evolution, Molecular ; Phylogeny ; Sequence Analysis, DNA
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.
Autorzy:
Zhang C; Bioinformatics and Systems Biology, University of California at San Diego, 9500 Gilman Drive, La Jolla, 92093-0021, CA, USA.
Rabiee M; Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, 92093-0021, CA, USA.
Sayyari E; Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, 92093-0021, CA, USA.
Mirarab S; Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, 92093-0021, CA, USA. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2018 May 08; Vol. 19 (Suppl 6), pp. 153. Date of Electronic Publication: 2018 May 08.
Typ publikacji:
Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Algorithms*
Phylogeny*
Animals ; Birds/classification ; Birds/genetics ; Computer Simulation ; Databases, Genetic ; Models, Genetic ; Species Specificity ; Time Factors
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.
Autorzy:
Mai U; Computer Science and Engineering, University of California at San Diego, San Diego, 92093, CA, USA.
Mirarab S; Electrical and Computer Engineering, University of California at San Diego, San Diego, 92093, CA, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2018 May 08; Vol. 19 (Suppl 5), pp. 272. Date of Electronic Publication: 2018 May 08.
Typ publikacji:
Journal Article
MeSH Terms:
Algorithms*
Phylogeny*
Software*
Computational Biology/*methods
Mammals/*classification
Mammals/*genetics
Animals ; Datasets as Topic ; Genes ; Humans ; Models, Genetic ; Plants/classification ; Plants/genetics ; Species Specificity
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:
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.
Autorzy:
Mai U; Dept of Computer Science and Engineering, University of California at San Diego, San Diego, CA, United States of America.
Sayyari E; Dept of Electrical and Computer Engineering, University of California at San Diego, San Diego, CA, United States of America.
Mirarab S; Dept of Electrical and Computer Engineering, University of California at San Diego, San Diego, CA, United States of America.
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Źródło:
PloS one [PLoS One] 2017 Aug 11; Vol. 12 (8), pp. e0182238. Date of Electronic Publication: 2017 Aug 11 (Print Publication: 2017).
Typ publikacji:
Journal Article
MeSH Terms:
Algorithms*
Phylogeny*
Computer Simulation ; Databases as Topic ; Genes ; Species Specificity
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
HIPPI: highly accurate protein family classification with ensembles of HMMs.
Autorzy:
Nguyen NP; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, CA, USA.
Nute M; Department of Statistics, University of Illinois at Urbana-Champaign, 725 South Wright Street, Urbana, 61820, IL, USA.
Mirarab S; Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, CA, USA.
Warnow T; Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Ave, IL, Urbana, 61801, IL, USA. .; Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 Digital Computer Laboratory, Urbana, 61801, IL, USA. .; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, 61801, IL, USA. .; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, 61801, IL, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2016 Nov 11; Vol. 17 (Suppl 10), pp. 765. Date of Electronic Publication: 2016 Nov 11.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Algorithms*
Proteins/*classification
Computational Biology ; Databases, Protein ; Internet ; Markov Chains ; Proteins/chemistry ; Proteins/metabolism ; Sequence Alignment ; User-Computer Interface
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.
Autorzy:
Sayyari E; Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Dr, La Jolla CA, 92093, USA.
Mirarab S; Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Dr, La Jolla CA, 92093, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2016 Nov 11; Vol. 17 (Suppl 10), pp. 783. Date of Electronic Publication: 2016 Nov 11.
Typ publikacji:
Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Algorithms*
Animals ; Birds/classification ; Birds/genetics ; Databases, Genetic ; Mammals/classification ; Mammals/genetics ; Models, Genetic ; Phylogeny
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
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:
Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".
Autorzy:
Mirarab S; Department of Computer Science, University of Texas at Austin, Austin, TX, USA. Department of Electrical and Computer Engineering, University of California at San Diego, San Diego, CA, USA.
Bayzid MS; Department of Computer Science, University of Texas at Austin, Austin, TX, USA.
Boussau B; Laboratoire de Biométrie Biologie Evolutive, Université de Lyon, France.
Warnow T; Department of Computer Science, University of Texas at Austin, Austin, TX, USA. Departments of Bioengineering and Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA. .
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Źródło:
Science (New York, N.Y.) [Science] 2015 Oct 09; Vol. 350 (6257), pp. 171.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Comment
MeSH Terms:
Genome*
Phylogeny*
Birds/*classification
Birds/*genetics
Animals
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".
Autorzy:
Cracraft J; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. .
Houde P; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.
Ho SY; School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
Mindell DP; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Fjeldså J; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
Lindow B; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Edwards SV; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
Rahbek C; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK.
Mirarab S; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA.
Warnow T; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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, Western Australia 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.
Braun EL; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. .
Jarvis ED; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. .
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Źródło:
Science (New York, N.Y.) [Science] 2015 Sep 25; Vol. 349 (6255), pp. 1460.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Comment
MeSH Terms:
Genome*
Phylogeny*
Birds/*genetics
Animals
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses.
Autorzy:
Bayzid MS; Department of Computer Science, University of Texas at Austin, Austin, Texas, USA.
Mirarab S; Department of Computer Science, University of Texas at Austin, Austin, Texas, USA.
Boussau B; Laboratoire de Biométrie et Biologie Évolutive, Université de Lyons, France.
Warnow T; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Źródło:
PloS one [PLoS One] 2015 Jun 18; Vol. 10 (6), pp. e0129183. Date of Electronic Publication: 2015 Jun 18 (Print Publication: 2015).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Models, Theoretical*
Phylogeny*
Statistics as Topic*
Genomics/*methods
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
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