BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

361 related articles for article (PubMed ID: 30858580)

  • 1. Best practices for benchmarking germline small-variant calls in human genomes.
    Krusche P; Trigg L; Boutros PC; Mason CE; De La Vega FM; Moore BL; Gonzalez-Porta M; Eberle MA; Tezak Z; Lababidi S; Truty R; Asimenos G; Funke B; Fleharty M; Chapman BA; Salit M; Zook JM;
    Nat Biotechnol; 2019 May; 37(5):555-560. PubMed ID: 30858580
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays.
    Krishnan V; Utiramerur S; Ng Z; Datta S; Snyder MP; Ashley EA
    BMC Bioinformatics; 2021 Feb; 22(1):85. PubMed ID: 33627090
    [TBL] [Abstract][Full Text] [Related]  

  • 3. vcfdist: accurately benchmarking phased small variant calls in human genomes.
    Dunn T; Narayanasamy S
    Nat Commun; 2023 Dec; 14(1):8149. PubMed ID: 38071244
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. SMaSH: a benchmarking toolkit for human genome variant calling.
    Talwalkar A; Liptrap J; Newcomb J; Hartl C; Terhorst J; Curtis K; Bresler M; Song YS; Jordan MI; Patterson D
    Bioinformatics; 2014 Oct; 30(19):2787-95. PubMed ID: 24894505
    [TBL] [Abstract][Full Text] [Related]  

  • 6. An open resource for accurately benchmarking small variant and reference calls.
    Zook JM; McDaniel J; Olson ND; Wagner J; Parikh H; Heaton H; Irvine SA; Trigg L; Truty R; McLean CY; De La Vega FM; Xiao C; Sherry S; Salit M
    Nat Biotechnol; 2019 May; 37(5):561-566. PubMed ID: 30936564
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery.
    Barbitoff YA; Abasov R; Tvorogova VE; Glotov AS; Predeus AV
    BMC Genomics; 2022 Feb; 23(1):155. PubMed ID: 35193511
    [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. Systematic comparison of variant calling pipelines using gold standard personal exome variants.
    Hwang S; Kim E; Lee I; Marcotte EM
    Sci Rep; 2015 Dec; 5():17875. PubMed ID: 26639839
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.
    Ren L; Duan X; Dong L; Zhang R; Yang J; Gao Y; Peng R; Hou W; Liu Y; Li J; Yu Y; Zhang N; Shang J; Liang F; Wang D; Chen H; Sun L; Hao L; ; Scherer A; Nordlund J; Xiao W; Xu J; Tong W; Hu X; Jia P; Ye K; Li J; Jin L; Hong H; Wang J; Fan S; Fang X; Zheng Y; Shi L
    Genome Biol; 2023 Nov; 24(1):270. PubMed ID: 38012772
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Variant calling and benchmarking in an era of complete human genome sequences.
    Olson ND; Wagner J; Dwarshuis N; Miga KH; Sedlazeck FJ; Salit M; Zook JM
    Nat Rev Genet; 2023 Jul; 24(7):464-483. PubMed ID: 37059810
    [TBL] [Abstract][Full Text] [Related]  

  • 13. BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.
    Cantarel BL; Weaver D; McNeill N; Zhang J; Mackey AJ; Reese J
    BMC Bioinformatics; 2014 Apr; 15():104. PubMed ID: 24725768
    [TBL] [Abstract][Full Text] [Related]  

  • 14. svclassify: a method to establish benchmark structural variant calls.
    Parikh H; Mohiyuddin M; Lam HY; Iyer H; Chen D; Pratt M; Bartha G; Spies N; Losert W; Zook JM; Salit M
    BMC Genomics; 2016 Jan; 17():64. PubMed ID: 26772178
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.
    Eberle MA; Fritzilas E; Krusche P; Källberg M; Moore BL; Bekritsky MA; Iqbal Z; Chuang HY; Humphray SJ; Halpern AL; Kruglyak S; Margulies EH; McVean G; Bentley DR
    Genome Res; 2017 Jan; 27(1):157-164. PubMed ID: 27903644
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Set-theory based benchmarking of three different variant callers for targeted sequencing.
    Molina-Mora JA; Solano-Vargas M
    BMC Bioinformatics; 2021 Jan; 22(1):20. PubMed ID: 33413082
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.
    Hofmann AL; Behr J; Singer J; Kuipers J; Beisel C; Schraml P; Moch H; Beerenwinkel N
    BMC Bioinformatics; 2017 Jan; 18(1):8. PubMed ID: 28049408
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Impact of post-alignment processing in variant discovery from whole exome data.
    Tian S; Yan H; Kalmbach M; Slager SL
    BMC Bioinformatics; 2016 Oct; 17(1):403. PubMed ID: 27716037
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data.
    Kumaran M; Subramanian U; Devarajan B
    BMC Bioinformatics; 2019 Jun; 20(1):342. PubMed ID: 31208315
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Comprehensive benchmarking of SNV callers for highly admixed tumor data.
    Bohnert R; Vivas S; Jansen G
    PLoS One; 2017; 12(10):e0186175. PubMed ID: 29020110
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 19.