BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

296 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. 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]  

  • 5. 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]  

  • 6. 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]  

  • 7.
    MacDonald ML; Polson SW; Lee KH
    mSphere; 2021 Apr; 6(2):. PubMed ID: 33883263
    [TBL] [Abstract][Full Text] [Related]  

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

  • 9. 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]  

  • 10. 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]  

  • 11. 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]  

  • 12. 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]  

  • 13. 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]  

  • 14. 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]  

  • 15. 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]  

  • 16. 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]  

  • 17. 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]  

  • 18. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.
    de Vries JJC; Brown JR; Fischer N; Sidorov IA; Morfopoulou S; Huang J; Munnink BBO; Sayiner A; Bulgurcu A; Rodriguez C; Gricourt G; Keyaerts E; Beller L; Bachofen C; Kubacki J; Samuel C; Florian L; Dennis S; Beer M; Hoeper D; Huber M; Kufner V; Zaheri M; Lebrand A; Papa A; van Boheemen S; Kroes ACM; Breuer J; Lopez-Labrador FX; Claas ECJ
    J Clin Virol; 2021 Aug; 141():104908. PubMed ID: 34273858
    [TBL] [Abstract][Full Text] [Related]  

  • 19. ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples.
    Tampuu A; Bzhalava Z; Dillner J; Vicente R
    PLoS One; 2019; 14(9):e0222271. PubMed ID: 31509583
    [TBL] [Abstract][Full Text] [Related]  

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

    [Next]    [New Search]
    of 15.