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 *

115 related articles for article (PubMed ID: 37398387)

  • 1. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA.
    Gabriel L; Brůna T; Hoff KJ; Ebel M; Lomsadze A; Borodovsky M; Stanke M
    bioRxiv; 2024 Feb; ():. PubMed ID: 37398387
    [TBL] [Abstract][Full Text] [Related]  

  • 2. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA.
    Gabriel L; Brůna T; Hoff KJ; Ebel M; Lomsadze A; Borodovsky M; Stanke M
    Genome Res; 2024 Jun; 34(5):769-777. PubMed ID: 38866550
    [TBL] [Abstract][Full Text] [Related]  

  • 3. TSEBRA: transcript selector for BRAKER.
    Gabriel L; Hoff KJ; Brůna T; Borodovsky M; Stanke M
    BMC Bioinformatics; 2021 Nov; 22(1):566. PubMed ID: 34823473
    [TBL] [Abstract][Full Text] [Related]  

  • 4. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.
    Brůna T; Hoff KJ; Lomsadze A; Stanke M; Borodovsky M
    NAR Genom Bioinform; 2021 Mar; 3(1):lqaa108. PubMed ID: 33575650
    [TBL] [Abstract][Full Text] [Related]  

  • 5. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
    Hoff KJ; Lange S; Lomsadze A; Borodovsky M; Stanke M
    Bioinformatics; 2016 Mar; 32(5):767-9. PubMed ID: 26559507
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
    Bruna T; Lomsadze A; Borodovsky M
    bioRxiv; 2024 Apr; ():. PubMed ID: 36711453
    [TBL] [Abstract][Full Text] [Related]  

  • 7. GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
    Brůna T; Lomsadze A; Borodovsky M
    Genome Res; 2024 Jun; 34(5):757-768. PubMed ID: 38866548
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Whole-Genome Annotation with BRAKER.
    Hoff KJ; Lomsadze A; Borodovsky M; Stanke M
    Methods Mol Biol; 2019; 1962():65-95. PubMed ID: 31020555
    [TBL] [Abstract][Full Text] [Related]  

  • 9. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.
    Banerjee S; Bhandary P; Woodhouse M; Sen TZ; Wise RP; Andorf CM
    BMC Bioinformatics; 2021 Apr; 22(1):205. PubMed ID: 33879057
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Galba: genome annotation with miniprot and AUGUSTUS.
    Brůna T; Li H; Guhlin J; Honsel D; Herbold S; Stanke M; Nenasheva N; Ebel M; Gabriel L; Hoff KJ
    BMC Bioinformatics; 2023 Aug; 24(1):327. PubMed ID: 37653395
    [TBL] [Abstract][Full Text] [Related]  

  • 11. GALBA: Genome Annotation with Miniprot and AUGUSTUS.
    Brůna T; Li H; Guhlin J; Honsel D; Herbold S; Stanke M; Nenasheva N; Ebel M; Gabriel L; Hoff KJ
    bioRxiv; 2023 Apr; ():. PubMed ID: 37090650
    [TBL] [Abstract][Full Text] [Related]  

  • 12. CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
    Testa AC; Hane JK; Ellwood SR; Oliver RP
    BMC Genomics; 2015 Mar; 16(1):170. PubMed ID: 25887563
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.
    Lomsadze A; Burns PD; Borodovsky M
    Nucleic Acids Res; 2014 Sep; 42(15):e119. PubMed ID: 24990371
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
    Bai Y; Kinne J; Donham B; Jiang F; Ding L; Hassler JR; Kaufman RJ
    BMC Genomics; 2016 Aug; 17 Suppl 7(Suppl 7):503. PubMed ID: 27556805
    [TBL] [Abstract][Full Text] [Related]  

  • 15. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins.
    Brůna T; Lomsadze A; Borodovsky M
    NAR Genom Bioinform; 2020 Jun; 2(2):lqaa026. PubMed ID: 32440658
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data.
    Chan KL; Rosli R; Tatarinova TV; Hogan M; Firdaus-Raih M; Low EL
    BMC Bioinformatics; 2017 Jan; 18(Suppl 1):1426. PubMed ID: 28466793
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Multi-Genome Annotation with AUGUSTUS.
    Nachtweide S; Stanke M
    Methods Mol Biol; 2019; 1962():139-160. PubMed ID: 31020558
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome.
    Venkatraman M; Fleischer RC; Tsuchiya MTN
    Genome Biol Evol; 2021 May; 13(5):. PubMed ID: 33760049
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Illuminating the dark side of the human transcriptome with long read transcript sequencing.
    Kuo RI; Cheng Y; Zhang R; Brown JWS; Smith J; Archibald AL; Burt DW
    BMC Genomics; 2020 Oct; 21(1):751. PubMed ID: 33126848
    [TBL] [Abstract][Full Text] [Related]  

  • 20. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.
    Holt C; Yandell M
    BMC Bioinformatics; 2011 Dec; 12():491. PubMed ID: 22192575
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 6.