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 *

390 related articles for article (PubMed ID: 24990371)

  • 1. 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]  

  • 2. 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]  

  • 3. UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.
    Burns PD; Li Y; Ma J; Borodovsky M
    Nucleic Acids Res; 2014 Feb; 42(4):e25. PubMed ID: 24259430
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 6. Identification of protein coding regions in RNA transcripts.
    Tang S; Lomsadze A; Borodovsky M
    Nucleic Acids Res; 2015 Jul; 43(12):e78. PubMed ID: 25870408
    [TBL] [Abstract][Full Text] [Related]  

  • 7. VARUS: sampling complementary RNA reads from the sequence read archive.
    Stanke M; Bruhn W; Becker F; Hoff KJ
    BMC Bioinformatics; 2019 Nov; 20(1):558. PubMed ID: 31703556
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES.
    Borodovsky M; Lomsadze A
    Curr Protoc Bioinformatics; 2011 Sep; Chapter 4():4.6.1-4.6.10. PubMed ID: 21901742
    [TBL] [Abstract][Full Text] [Related]  

  • 9. JAGuaR: junction alignments to genome for RNA-seq reads.
    Butterfield YS; Kreitzman M; Thiessen N; Corbett RD; Li Y; Pang J; Ma YP; Jones SJ; Birol İ
    PLoS One; 2014; 9(7):e102398. PubMed ID: 25062255
    [TBL] [Abstract][Full Text] [Related]  

  • 10. FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.
    Xiao CL; Mai ZB; Lian XL; Zhong JY; Jin JJ; He QY; Zhang G
    PLoS One; 2014; 9(4):e94250. PubMed ID: 24743329
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Optimizing RNA-Seq Mapping with STAR.
    Dobin A; Gingeras TR
    Methods Mol Biol; 2016; 1415():245-62. PubMed ID: 27115637
    [TBL] [Abstract][Full Text] [Related]  

  • 12. 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]  

  • 13. 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]  

  • 14. Evaluation of tools for long read RNA-seq splice-aware alignment.
    Križanovic K; Echchiki A; Roux J; Šikic M
    Bioinformatics; 2018 Mar; 34(5):748-754. PubMed ID: 29069314
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Trimming of sequence reads alters RNA-Seq gene expression estimates.
    Williams CR; Baccarella A; Parrish JZ; Kim CC
    BMC Bioinformatics; 2016 Feb; 17():103. PubMed ID: 26911985
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Performance evaluation of lossy quality compression algorithms for RNA-seq data.
    Yu R; Yang W; Wang S
    BMC Bioinformatics; 2020 Jul; 21(1):321. PubMed ID: 32689929
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Near-optimal probabilistic RNA-seq quantification.
    Bray NL; Pimentel H; Melsted P; Pachter L
    Nat Biotechnol; 2016 May; 34(5):525-7. PubMed ID: 27043002
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. 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]  

  • 20. DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression.
    George NI; Chang CW
    BMC Bioinformatics; 2014 Mar; 15():92. PubMed ID: 24685233
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 20.