Yatish Turakhia

Title(s)Assistant Professor, Electrical and Computer Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0001-5600-2900 Additional info
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. bioRxiv. 2024 Jun 01. Gupta A, Mirarab S, Turakhia Y. PMID: 38854139; PMCID: PMC11160643.
      View in: PubMed   Mentions:
    2. A framework for automated scalable designation of viral pathogen lineages from genomic data. Nat Microbiol. 2024 Feb; 9(2):550-560. McBroome J, de Bernardi Schneider A, Roemer C, Wolfinger MT, Hinrichs AS, O'Toole AN, Ruis C, Turakhia Y, Rambaut A, Corbett-Detig R. PMID: 38316930; PMCID: PMC10847047.
      View in: PubMed   Mentions: 5     Fields:    
    3. SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus Evol. 2024; 10(1):vead085. de Bernardi Schneider A, Su M, Hinrichs AS, Wang J, Amin H, Bell J, Wadford DA, O'Toole Á, Scher E, Perry MD, Turakhia Y, De Maio N, Hughes S, Corbett-Detig R. PMID: 38361813; PMCID: PMC10868549.
      View in: PubMed   Mentions: 2  
    4. The ongoing evolution of UShER during the SARS-CoV-2 pandemic. Nat Genet. 2024 Jan; 56(1):4-7. Hinrichs A, Ye C, Turakhia Y, Corbett-Detig R. PMID: 38155331.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    5. Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations. Syst Biol. 2023 11 01; 72(5):1039-1051. Kramer AM, Thornlow B, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R. PMID: 37232476; PMCID: PMC10627557.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    6. DecentTree: scalable Neighbour-Joining for the genomic era. Bioinformatics. 2023 09 02; 39(9). Wang W, Barbetti J, Wong T, Thornlow B, Corbett-Detig R, Turakhia Y, Lanfear R, Minh BQ. PMID: 37651445; PMCID: PMC10491953.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    7. Tracking and curating putative SARS-CoV-2 recombinants with RIVET. Bioinformatics. 2023 09 02; 39(9). Smith K, Ye C, Turakhia Y. PMID: 37651464; PMCID: PMC10493179.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    8. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Mol Biol Evol. 2023 09 01; 40(9). Chen HI, Turakhia Y, Bejerano G, Kingsley DM. PMID: 37739926; PMCID: PMC10516590.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    9. A lung-specific mutational signature enables inference of viral and bacterial respiratory niche. Microb Genom. 2023 05; 9(5). Ruis C, Peacock TP, Polo LM, Masone D, Alvarez MS, Hinrichs AS, Turakhia Y, Cheng Y, McBroome J, Corbett-Detig R, Parkhill J, Floto RA. PMID: 37185044; PMCID: PMC10272861.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    10. Maximum likelihood pandemic-scale phylogenetics. Nat Genet. 2023 05; 55(5):746-752. De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. PMID: 37038003; PMCID: PMC10181937.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCellsPHPublic Health
    11. Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages. bioRxiv. 2023 Jan 31. Chen HI, Turakhia Y, Bejerano G, Kingsley DM. PMID: 36778215; PMCID: PMC9915506.
      View in: PubMed   Mentions:
    12. Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape. Nature. 2022 09; 609(7929):994-997. Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R. PMID: 35952714; PMCID: PMC9519458.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansCellsPHPublic Health
    13. matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2. Bioinformatics. 2022 08 02; 38(15):3734-3740. Ye C, Thornlow B, Hinrichs A, Kramer A, Mirchandani C, Torvi D, Lanfear R, Corbett-Detig R, Turakhia Y. PMID: 35731204; PMCID: PMC9344837.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCellsPHPublic Health
    14. Maximum likelihood pandemic-scale phylogenetics. bioRxiv. 2022 Jul 18. De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. PMID: 35350209; PMCID: PMC8963701.
      View in: PubMed   Mentions:
    15. Identifying SARS-CoV-2 regional introductions and transmission clusters in real time. Virus Evol. 2022; 8(1):veac048. McBroome J, Martin J, de Bernardi Schneider A, Turakhia Y, Corbett-Detig R. PMID: 35769891; PMCID: PMC9214145.
      View in: PubMed   Mentions: 13  
    16. Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches. bioRxiv. 2022 May 18. Thornlow B, Kramer A, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R. PMID: 35611334; PMCID: PMC9128781.
      View in: PubMed   Mentions: 1  
    17. phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets. PLoS Comput Biol. 2022 04; 18(4):e1010056. De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. PMID: 35486906; PMCID: PMC9094560.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCellsPHPublic Health
    18. Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference. Genome Biol Evol. 2022 03 02; 14(3). Schull JK, Turakhia Y, Hemker JA, Dally WJ, Bejerano G. PMID: 35171243; PMCID: PMC8920512.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    19. A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees. Mol Biol Evol. 2021 12 09; 38(12):5819-5824. McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. PMID: 34469548; PMCID: PMC8662617.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    20. Pandemic-scale phylogenetics. bioRxiv. 2021 Dec 06. Ye C, Thornlow B, Kramer A, McBroome J, Hinrichs A, Corbett-Detig R, Turakhia Y. PMID: 34927180; PMCID: PMC8679213.
      View in: PubMed   Mentions:
    21. phastSim: efficient simulation of sequence evolution for pandemic-scale datasets. bioRxiv. 2021 Sep 23. De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. PMID: 33758852; PMCID: PMC7987011.
      View in: PubMed   Mentions:
    22. A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees. bioRxiv. 2021 Jul 13. McBroome J, Thornlow B, Hinrichs AS, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. PMID: 33821270; PMCID: PMC8020970.
      View in: PubMed   Mentions:
    23. Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic. Nat Genet. 2021 06; 53(6):809-816. Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R. PMID: 33972780; PMCID: PMC9248294.
      View in: PubMed   Mentions: 184     Fields:    Translation:HumansCells
    24. Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2. Genome Biol Evol. 2021 05 07; 13(5). De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. PMID: 33895815; PMCID: PMC8135539.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    25. A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. bioRxiv. 2021 Apr 06. Thornlow B, Hinrichs AS, Jain M, Dhillon N, La S, Kapp JD, Anigbogu I, Cassatt-Johnstone M, McBroome J, Haeussler M, Turakhia Y, Chang T, Olsen HE, Sanford J, Stone M, Vaske O, Bjork I, Akeson M, Shapiro B, Haussler D, Kilpatrick AM, Corbett-Detig R. PMID: 33851162; PMCID: PMC8043452.
      View in: PubMed   Mentions: 1  
    26. Mutation rates and selection on synonymous mutations in SARS-CoV-2. bioRxiv. 2021 Jan 14. De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. PMID: 33469589; PMCID: PMC7814826.
      View in: PubMed   Mentions:
    27. Stability of SARS-CoV-2 phylogenies. PLoS Genet. 2020 11; 16(11):e1009175. Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. PMID: 33206635; PMCID: PMC7721162.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    28. Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic. bioRxiv. 2020 Sep 28. Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R. PMID: 33024970; PMCID: PMC7536873.
      View in: PubMed   Mentions:
    29. A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. Nucleic Acids Res. 2020 09 18; 48(16):e91. Turakhia Y, Chen HI, Marcovitz A, Bejerano G. PMID: 32614390; PMCID: PMC7498332.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    30. A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales. Proc Natl Acad Sci U S A. 2019 10 15; 116(42):21094-21103. Marcovitz A, Turakhia Y, Chen HI, Gloudemans M, Braun BA, Wang H, Bejerano G. PMID: 31570615; PMCID: PMC6800341.
      View in: PubMed   Mentions: 27     Fields:    Translation:Animals
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