BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

142 related articles for article (PubMed ID: 25398608)

  • 1. SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP.
    van Rens KE; Mäkinen V; Tomescu AI
    Bioinformatics; 2015 Apr; 31(7):1133-5. PubMed ID: 25398608
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Inference of tumor phylogenies with improved somatic mutation discovery.
    Salari R; Saleh SS; Kashef-Haghighi D; Khavari D; Newburger DE; West RB; Sidow A; Batzoglou S
    J Comput Biol; 2013 Nov; 20(11):933-44. PubMed ID: 24195709
    [TBL] [Abstract][Full Text] [Related]  

  • 3. SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing.
    Rozhoňová H; Danciu D; Stark S; Rätsch G; Kahles A; Lehmann KV
    Bioinformatics; 2022 Sep; 38(18):4293-4300. PubMed ID: 35900151
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Comparing a few SNP calling algorithms using low-coverage sequencing data.
    Yu X; Sun S
    BMC Bioinformatics; 2013 Sep; 14():274. PubMed ID: 24044377
    [TBL] [Abstract][Full Text] [Related]  

  • 5. SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.
    Kockan C; Hach F; Sarrafi I; Bell RH; McConeghy B; Beja K; Haegert A; Wyatt AW; Volik SV; Chi KN; Collins CC; Sahinalp SC
    Bioinformatics; 2017 Jan; 33(1):26-34. PubMed ID: 27531099
    [TBL] [Abstract][Full Text] [Related]  

  • 6. GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data.
    De Summa S; Malerba G; Pinto R; Mori A; Mijatovic V; Tommasi S
    BMC Bioinformatics; 2017 Mar; 18(Suppl 5):119. PubMed ID: 28361668
    [TBL] [Abstract][Full Text] [Related]  

  • 7. QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles.
    Van der Borght K; Thys K; Wetzels Y; Clement L; Verbist B; Reumers J; van Vlijmen H; Aerssens J
    BMC Bioinformatics; 2015 Nov; 16():379. PubMed ID: 26554718
    [TBL] [Abstract][Full Text] [Related]  

  • 8. PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.
    Malikic S; Mehrabadi FR; Ciccolella S; Rahman MK; Ricketts C; Haghshenas E; Seidman D; Hach F; Hajirasouliha I; Sahinalp SC
    Genome Res; 2019 Nov; 29(11):1860-1877. PubMed ID: 31628256
    [TBL] [Abstract][Full Text] [Related]  

  • 9. MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP.
    Husić E; Li X; Hujdurović A; Mehine M; Rizzi R; Mäkinen V; Milanič M; Tomescu AI
    Bioinformatics; 2019 Mar; 35(5):769-777. PubMed ID: 30101335
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Meltos: multi-sample tumor phylogeny reconstruction for structural variants.
    Ricketts C; Seidman D; Popic V; Hormozdiari F; Batzoglou S; Hajirasouliha I
    Bioinformatics; 2020 Feb; 36(4):1082-1090. PubMed ID: 31584621
    [TBL] [Abstract][Full Text] [Related]  

  • 11. ReliableGenome: annotation of genomic regions with high/low variant calling concordance.
    Popitsch N; ; Schuh A; Taylor JC
    Bioinformatics; 2017 Jan; 33(2):155-160. PubMed ID: 27605105
    [TBL] [Abstract][Full Text] [Related]  

  • 12. ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
    Piechotta M; Dieterich C
    Bioinformatics; 2013 Jul; 29(14):1809-10. PubMed ID: 23681124
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing.
    Hollegaard MV; Grauholm J; Nielsen R; Grove J; Mandrup S; Hougaard DM
    Mol Genet Metab; 2013; 110(1-2):65-72. PubMed ID: 23830478
    [TBL] [Abstract][Full Text] [Related]  

  • 14. MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data.
    Murillo GH; You N; Su X; Cui W; Reilly MP; Li M; Ning K; Cui X
    Bioinformatics; 2016 May; 32(10):1486-92. PubMed ID: 26787661
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Inferring clonal evolution of tumors from single nucleotide somatic mutations.
    Jiao W; Vembu S; Deshwar AG; Stein L; Morris Q
    BMC Bioinformatics; 2014 Feb; 15():35. PubMed ID: 24484323
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Evaluating the Calling Performance of a Rare Disease NGS Panel for Single Nucleotide and Copy Number Variants.
    Cacheiro P; Ordóñez-Ugalde A; Quintáns B; Piñeiro-Hermida S; Amigo J; García-Murias M; Pascual-Pascual SI; Grandas F; Arpa J; Carracedo A; Sobrido MJ
    Mol Diagn Ther; 2017 Jun; 21(3):303-313. PubMed ID: 28290094
    [TBL] [Abstract][Full Text] [Related]  

  • 17. FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.
    Wang W; Wang P; Xu F; Luo R; Wong MP; Lam TW; Wang J
    Bioinformatics; 2014 Sep; 30(17):2498-500. PubMed ID: 24833803
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Hidden Markov Models in Bioinformatics: SNV Inference from Next Generation Sequence.
    Bian J; Zhou X
    Methods Mol Biol; 2017; 1552():123-133. PubMed ID: 28224495
    [TBL] [Abstract][Full Text] [Related]  

  • 19. PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies.
    Liao P; Satten GA; Hu YJ
    Genet Epidemiol; 2017 Jul; 41(5):375-387. PubMed ID: 28560825
    [TBL] [Abstract][Full Text] [Related]  

  • 20. NGSphy: phylogenomic simulation of next-generation sequencing data.
    Escalona M; Rocha S; Posada D
    Bioinformatics; 2018 Jul; 34(14):2506-2507. PubMed ID: 29534152
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.