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 *

302 related articles for article (PubMed ID: 25140992)

  • 1. Profile hidden Markov models for the detection of viruses within metagenomic sequence data.
    Skewes-Cox P; Sharpton TJ; Pollard KS; DeRisi JL
    PLoS One; 2014; 9(8):e105067. PubMed ID: 25140992
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Extension of the viral ecology in humans using viral profile hidden Markov models.
    Bzhalava Z; Hultin E; Dillner J
    PLoS One; 2018; 13(1):e0190938. PubMed ID: 29351302
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.
    Vázquez-Castellanos JF; García-López R; Pérez-Brocal V; Pignatelli M; Moya A
    BMC Genomics; 2014 Jan; 15():37. PubMed ID: 24438450
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review.
    Yu R; Huang Z; Lam TYC; Sun Y
    Brief Bioinform; 2024 May; 25(4):. PubMed ID: 39003531
    [TBL] [Abstract][Full Text] [Related]  

  • 5. ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.
    Maarala AI; Bzhalava Z; Dillner J; Heljanko K; Bzhalava D
    Bioinformatics; 2018 Mar; 34(6):928-935. PubMed ID: 29106455
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Cataloguing the taxonomic origins of sequences from a heterogeneous sample using phylogenomics: applications in adventitious agent detection.
    Charlebois RL; Ng SH; Gisonni-Lex L; Mallet L
    PDA J Pharm Sci Technol; 2014; 68(6):602-18. PubMed ID: 25475635
    [TBL] [Abstract][Full Text] [Related]  

  • 7. RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data.
    Charon J; Buchmann JP; Sadiq S; Holmes EC
    Virus Evol; 2022; 8(2):veac082. PubMed ID: 36533143
    [TBL] [Abstract][Full Text] [Related]  

  • 8.
    MacDonald ML; Polson SW; Lee KH
    mSphere; 2021 Apr; 6(2):. PubMed ID: 33883263
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Accelerated Profile HMM Searches.
    Eddy SR
    PLoS Comput Biol; 2011 Oct; 7(10):e1002195. PubMed ID: 22039361
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Bioinformatic Approaches for Comparative Analysis of Viruses.
    Amgarten D; Upton C
    Methods Mol Biol; 2018; 1704():401-417. PubMed ID: 29277875
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Machine Learning for detection of viral sequences in human metagenomic datasets.
    Bzhalava Z; Tampuu A; Bała P; Vicente R; Dillner J
    BMC Bioinformatics; 2018 Sep; 19(1):336. PubMed ID: 30249176
    [TBL] [Abstract][Full Text] [Related]  

  • 12. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.
    Ren J; Ahlgren NA; Lu YY; Fuhrman JA; Sun F
    Microbiome; 2017 Jul; 5(1):69. PubMed ID: 28683828
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Profile Hidden Markov Models Are Not Identifiable.
    Pattabiraman S; Warnow T
    IEEE/ACM Trans Comput Biol Bioinform; 2021; 18(1):162-172. PubMed ID: 31425043
    [TBL] [Abstract][Full Text] [Related]  

  • 14. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.
    Lin YY; Hsieh CH; Chen JH; Lu X; Kao JH; Chen PJ; Chen DS; Wang HY
    BMC Bioinformatics; 2017 Apr; 18(1):223. PubMed ID: 28446139
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Cont-ID: detection of sample cross-contamination in viral metagenomic data.
    Rollin J; Rong W; Massart S
    BMC Biol; 2023 Oct; 21(1):217. PubMed ID: 37833740
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Bioinformatic Approaches for Comparative Analysis of Viruses.
    Dorlass EG; Amgarten DE
    Methods Mol Biol; 2024; 2802():395-425. PubMed ID: 38819566
    [TBL] [Abstract][Full Text] [Related]  

  • 17. VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.
    Liu G; Chen X; Luan Y; Li D
    Bioinformatics; 2024 Mar; 40(4):. PubMed ID: 38597887
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery.
    Kinsella CM; Deijs M; van der Hoek L
    Virus Res; 2019 Apr; 263():21-26. PubMed ID: 30578804
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
    Gough J; Karplus K; Hughey R; Chothia C
    J Mol Biol; 2001 Nov; 313(4):903-19. PubMed ID: 11697912
    [TBL] [Abstract][Full Text] [Related]  

  • 20.
    ; ; . PubMed ID:
    [No Abstract]   [Full Text] [Related]  

    [Next]    [New Search]
    of 16.