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 *

973 related articles for article (PubMed ID: 29596782)

  • 1. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.
    Ellrott K; Bailey MH; Saksena G; Covington KR; Kandoth C; Stewart C; Hess J; Ma S; Chiotti KE; McLellan M; Sofia HJ; Hutter C; Getz G; Wheeler D; Ding L; ;
    Cell Syst; 2018 Mar; 6(3):271-281.e7. PubMed ID: 29596782
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Mosdepth: quick coverage calculation for genomes and exomes.
    Pedersen BS; Quinlan AR
    Bioinformatics; 2018 Mar; 34(5):867-868. PubMed ID: 29096012
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Comparing somatic mutation-callers: beyond Venn diagrams.
    Kim SY; Speed TP
    BMC Bioinformatics; 2013 Jun; 14():189. PubMed ID: 23758877
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.
    Samadian S; Bruce JP; Pugh TJ
    PLoS Comput Biol; 2018 Mar; 14(3):e1006080. PubMed ID: 29590101
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples.
    Ji S; Zhu T; Sethia A; Wang W
    Genome Res; 2024 May; 34(4):633-641. PubMed ID: 38589250
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Halvade somatic: Somatic variant calling with Apache Spark.
    Decap D; de Schaetzen van Brienen L; Larmuseau M; Costanza P; Herzeel C; Wuyts R; Marchal K; Fostier J
    Gigascience; 2022 Jan; 11(1):. PubMed ID: 35022699
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Substantial batch effects in TCGA exome sequences undermine pan-cancer analysis of germline variants.
    Rasnic R; Brandes N; Zuk O; Linial M
    BMC Cancer; 2019 Aug; 19(1):783. PubMed ID: 31391007
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. h5vc: scalable nucleotide tallies with HDF5.
    Pyl PT; Gehring J; Fischer B; Huber W
    Bioinformatics; 2014 May; 30(10):1464-6. PubMed ID: 24451629
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Bioinformatics Analysis of Whole Exome Sequencing Data.
    Ulintz PJ; Wu W; Gates CM
    Methods Mol Biol; 2019; 1881():277-318. PubMed ID: 30350213
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers.
    Callari M; Sammut SJ; De Mattos-Arruda L; Bruna A; Rueda OM; Chin SF; Caldas C
    Genome Med; 2017 Apr; 9(1):35. PubMed ID: 28420412
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data.
    Karimnezhad A; Palidwor GA; Thavorn K; Stewart DJ; Campbell PA; Lo B; Perkins TJ
    BMC Med Genomics; 2020 Oct; 13(1):156. PubMed ID: 33059707
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.
    Favero F; Joshi T; Marquard AM; Birkbak NJ; Krzystanek M; Li Q; Szallasi Z; Eklund AC
    Ann Oncol; 2015 Jan; 26(1):64-70. PubMed ID: 25319062
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Challenges in exome analysis by LifeScope and its alternative computational pipelines.
    Pranckevičiene E; Rančelis T; Pranculis A; Kučinskas V
    BMC Res Notes; 2015 Sep; 8():421. PubMed ID: 26346699
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.
    Trubetskoy V; Rodriguez A; Dave U; Campbell N; Crawford EL; Cook EH; Sutcliffe JS; Foster I; Madduri R; Cox NJ; Davis LK
    Bioinformatics; 2015 Jan; 31(2):187-93. PubMed ID: 25270638
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.
    Sergi A; Beltrame L; Marchini S; Masseroli M
    BMC Bioinformatics; 2024 May; 25(1):180. PubMed ID: 38720249
    [TBL] [Abstract][Full Text] [Related]  

  • 17. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
    Koboldt DC; Zhang Q; Larson DE; Shen D; McLellan MD; Lin L; Miller CA; Mardis ER; Ding L; Wilson RK
    Genome Res; 2012 Mar; 22(3):568-76. PubMed ID: 22300766
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.
    Xu H; DiCarlo J; Satya RV; Peng Q; Wang Y
    BMC Genomics; 2014 Mar; 15():244. PubMed ID: 24678773
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
    Lee AY; Ewing AD; Ellrott K; Hu Y; Houlahan KE; Bare JC; Espiritu SMG; Huang V; Dang K; Chong Z; Caloian C; Yamaguchi TN; ; Kellen MR; Chen K; Norman TC; Friend SH; Guinney J; Stolovitzky G; Haussler D; Margolin AA; Stuart JM; Boutros PC
    Genome Biol; 2018 Nov; 19(1):188. PubMed ID: 30400818
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Semi-automated cancer genome analysis using high-performance computing.
    Crispatzu G; Kulkarni P; Toliat MR; Nürnberg P; Herling M; Herling CD; Frommolt P
    Hum Mutat; 2017 Oct; 38(10):1325-1335. PubMed ID: 28598576
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 49.