These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

191 related articles for article (PubMed ID: 38577785)

  • 1. Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.
    Baril T; Galbraith J; Hayward A
    Mol Biol Evol; 2024 Apr; 41(4):. PubMed ID: 38577785
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.
    Ou S; Su W; Liao Y; Chougule K; Agda JRA; Hellinga AJ; Lugo CSB; Elliott TA; Ware D; Peterson T; Jiang N; Hirsch CN; Hufford MB
    Genome Biol; 2019 Dec; 20(1):275. PubMed ID: 31843001
    [TBL] [Abstract][Full Text] [Related]  

  • 3. RepeatModeler2 for automated genomic discovery of transposable element families.
    Flynn JM; Hubley R; Goubert C; Rosen J; Clark AG; Feschotte C; Smit AF
    Proc Natl Acad Sci U S A; 2020 Apr; 117(17):9451-9457. PubMed ID: 32300014
    [TBL] [Abstract][Full Text] [Related]  

  • 4. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea.
    Berthelier J; Casse N; Daccord N; Jamilloux V; Saint-Jean B; Carrier G
    BMC Genomics; 2018 May; 19(1):378. PubMed ID: 29783941
    [TBL] [Abstract][Full Text] [Related]  

  • 5. McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.
    Nelson MG; Linheiro RS; Bergman CM
    G3 (Bethesda); 2017 Aug; 7(8):2763-2778. PubMed ID: 28637810
    [TBL] [Abstract][Full Text] [Related]  

  • 6. An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.
    Rodriguez F; Arkhipova IR
    Methods Mol Biol; 2023; 2607():1-23. PubMed ID: 36449155
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads.
    Staton SE; Burke JM
    Bioinformatics; 2015 Jun; 31(11):1827-9. PubMed ID: 25644271
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.
    Janicki M; Rooke R; Yang G
    Chromosome Res; 2011 Aug; 19(6):787-808. PubMed ID: 21850457
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Considering transposable element diversification in de novo annotation approaches.
    Flutre T; Duprat E; Feuillet C; Quesneville H
    PLoS One; 2011 Jan; 6(1):e16526. PubMed ID: 21304975
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Species-specific chromatin landscape determines how transposable elements shape genome evolution.
    Huang Y; Shukla H; Lee YCG
    Elife; 2022 Aug; 11():. PubMed ID: 35997258
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.
    Platt RN; Blanco-Berdugo L; Ray DA
    Genome Biol Evol; 2016 Jan; 8(2):403-10. PubMed ID: 26802115
    [TBL] [Abstract][Full Text] [Related]  

  • 12. TERAD: Extraction of transposable element composition from RADseq data.
    Chak STC; Rubenstein DR
    Mol Ecol Resour; 2019 Nov; 19(6):1681-1688. PubMed ID: 31479576
    [TBL] [Abstract][Full Text] [Related]  

  • 13. TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome.
    Su W; Gu X; Peterson T
    Mol Plant; 2019 Mar; 12(3):447-460. PubMed ID: 30802553
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies.
    Gozashti L; Hoekstra HE
    Genome Biol; 2024 Jan; 25(1):4. PubMed ID: 38166955
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome.
    Bergman CM; Quesneville H; Anxolabéhère D; Ashburner M
    Genome Biol; 2006; 7(11):R112. PubMed ID: 17134480
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A Tutorial of EDTA: Extensive De Novo TE Annotator.
    Su W; Ou S; Hufford MB; Peterson T
    Methods Mol Biol; 2021; 2250():55-67. PubMed ID: 33900591
    [TBL] [Abstract][Full Text] [Related]  

  • 17. RepBox: a toolbox for the identification of repetitive elements.
    Burkes-Patton S; Cooper EA; Schlueter J
    BMC Bioinformatics; 2023 Aug; 24(1):317. PubMed ID: 37608271
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements.
    Panda K; Slotkin RK
    Plant Cell; 2020 Sep; 32(9):2687-2698. PubMed ID: 32647069
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Preparation of Non-overlapping Transposable Elements (TEs) Annotation by Interval Tree.
    Kojima S
    Methods Mol Biol; 2022; 2509():353-360. PubMed ID: 35796974
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes.
    Ecovoiu AA; Bologa AM; Chifiriuc DIM; Ciuca AM; Constantin ND; Ghionoiu IC; Ghita IC; Ratiu AC
    Int J Mol Sci; 2022 Oct; 23(20):. PubMed ID: 36293549
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.