BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

118 related articles for article (PubMed ID: 29385401)

  • 1. Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.
    Luo Z; Fan X; Su Y; Huang YS
    Bioinformatics; 2018 Jun; 34(12):2004-2011. PubMed ID: 29385401
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Somatic point mutation calling in low cellularity tumors.
    Kassahn KS; Holmes O; Nones K; Patch AM; Miller DK; Christ AN; Harliwong I; Bruxner TJ; Xu Q; Anderson M; Wood S; Leonard C; Taylor D; Newell F; Song S; Idrisoglu S; Nourse C; Nourbakhsh E; Manning S; Wani S; Steptoe A; Pajic M; Cowley MJ; Pinese M; Chang DK; Gill AJ; Johns AL; Wu J; Wilson PJ; Fink L; Biankin AV; Waddell N; Grimmond SM; Pearson JV
    PLoS One; 2013; 8(11):e74380. PubMed ID: 24250782
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma.
    Roberts HE; Lopopolo M; Pagnamenta AT; Sharma E; Parkes D; Lonie L; Freeman C; Knight SJL; Lunter G; Dreau H; Lockstone H; Taylor JC; Schuh A; Bowden R; Buck D
    Sci Rep; 2021 Mar; 11(1):6408. PubMed ID: 33742045
    [TBL] [Abstract][Full Text] [Related]  

  • 4. All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data.
    Loh JW; Guccione C; Di Clemente F; Riedlinger G; Ganesan S; Khiabanian H
    Bioinformatics; 2020 Apr; 36(7):2173-2180. PubMed ID: 31750888
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms.
    Arora K; Shah M; Johnson M; Sanghvi R; Shelton J; Nagulapalli K; Oschwald DM; Zody MC; Germer S; Jobanputra V; Carter J; Robine N
    Sci Rep; 2019 Dec; 9(1):19123. PubMed ID: 31836783
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing.
    Prodanov T; Bansal V
    Nat Commun; 2022 Jun; 13(1):3221. PubMed ID: 35680869
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.
    Mayrhofer M; DiLorenzo S; Isaksson A
    Genome Biol; 2013 Mar; 14(3):R24. PubMed ID: 23531354
    [TBL] [Abstract][Full Text] [Related]  

  • 8. CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data.
    Abécassis J; Reyal F; Vert JP
    Nat Commun; 2021 Sep; 12(1):5352. PubMed ID: 34504064
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Identifying tumor clones in sparse single-cell mutation data.
    Myers MA; Zaccaria S; Raphael BJ
    Bioinformatics; 2020 Jul; 36(Suppl_1):i186-i193. PubMed ID: 32657385
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Absolute quantification of somatic DNA alterations in human cancer.
    Carter SL; Cibulskis K; Helman E; McKenna A; Shen H; Zack T; Laird PW; Onofrio RC; Winckler W; Weir BA; Beroukhim R; Pellman D; Levine DA; Lander ES; Meyerson M; Getz G
    Nat Biotechnol; 2012 May; 30(5):413-21. PubMed ID: 22544022
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.
    Xiao W; Ren L; Chen Z; Fang LT; Zhao Y; Lack J; Guan M; Zhu B; Jaeger E; Kerrigan L; Blomquist TM; Hung T; Sultan M; Idler K; Lu C; Scherer A; Kusko R; Moos M; Xiao C; Sherry ST; Abaan OD; Chen W; Chen X; Nordlund J; Liljedahl U; Maestro R; Polano M; Drabek J; Vojta P; Kõks S; Reimann E; Madala BS; Mercer T; Miller C; Jacob H; Truong T; Moshrefi A; Natarajan A; Granat A; Schroth GP; Kalamegham R; Peters E; Petitjean V; Walton A; Shen TW; Talsania K; Vera CJ; Langenbach K; de Mars M; Hipp JA; Willey JC; Wang J; Shetty J; Kriga Y; Raziuddin A; Tran B; Zheng Y; Yu Y; Cam M; Jailwala P; Nguyen C; Meerzaman D; Chen Q; Yan C; Ernest B; Mehra U; Jensen RV; Jones W; Li JL; Papas BN; Pirooznia M; Chen YC; Seifuddin F; Li Z; Liu X; Resch W; Wang J; Wu L; Yavas G; Miles C; Ning B; Tong W; Mason CE; Donaldson E; Lababidi S; Staudt LM; Tezak Z; Hong H; Wang C; Shi L
    Nat Biotechnol; 2021 Sep; 39(9):1141-1150. PubMed ID: 34504346
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
    Watkins TBK; Colliver EC; Huska MR; Kaufmann TL; Lim EL; Duncan CB; Haase K; Van Loo P; Swanton C; McGranahan N; Schwarz RF
    PLoS Comput Biol; 2023 Oct; 19(10):e1011379. PubMed ID: 37871126
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Ploidy inference from single-cell data: application to human and mouse cell atlases.
    Takeuchi F; Kato N
    Genetics; 2024 Jun; 227(2):. PubMed ID: 38651869
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Inferring single-cell copy number profiles through cross-cell segmentation of read counts.
    Liu F; Shi F; Yu Z
    BMC Genomics; 2024 Jan; 25(1):25. PubMed ID: 38166601
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches.
    Pedersen BS; Bhetariya PJ; Brown J; Kravitz SN; Marth G; Jensen RL; Bronner MP; Underhill HR; Quinlan AR
    Genome Med; 2020 Jul; 12(1):62. PubMed ID: 32664994
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.
    Zaccaria S; Raphael BJ
    Nat Commun; 2020 Sep; 11(1):4301. PubMed ID: 32879317
    [TBL] [Abstract][Full Text] [Related]  

  • 17. DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors.
    Walter V; Nobel AB; Wright FA
    Bioinformatics; 2011 Mar; 27(5):678-85. PubMed ID: 21183584
    [TBL] [Abstract][Full Text] [Related]  

  • 18. CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data.
    Liu F; Shi F; Du F; Cao X; Yu Z
    Brief Bioinform; 2024 Mar; 25(3):. PubMed ID: 38670159
    [TBL] [Abstract][Full Text] [Related]  

  • 19. A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data.
    Vavoulis DV; Cutts A; Taylor JC; Schuh A
    Bioinformatics; 2021 Apr; 37(2):147-154. PubMed ID: 32722772
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring.
    Chu Y; Teng M; Wang Y
    BMC Bioinformatics; 2018 Apr; 19(Suppl 5):112. PubMed ID: 29671389
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 6.