BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

351 related articles for article (PubMed ID: 27766961)

  • 1. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
    Toby IT; Levin MK; Salinas EA; Christley S; Bhattacharya S; Breden F; Buntzman A; Corrie B; Fonner J; Gupta NT; Hershberg U; Marthandan N; Rosenfeld A; Rounds W; Rubelt F; Scarborough W; Scott JK; Uduman M; Vander Heiden JA; Scheuermann RH; Monson N; Kleinstein SH; Cowell LG
    BMC Bioinformatics; 2016 Oct; 17(Suppl 13):333. PubMed ID: 27766961
    [TBL] [Abstract][Full Text] [Related]  

  • 2. VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.
    Christley S; Scarborough W; Salinas E; Rounds WH; Toby IT; Fonner JM; Levin MK; Kim M; Mock SA; Jordan C; Ostmeyer J; Buntzman A; Rubelt F; Davila ML; Monson NL; Scheuermann RH; Cowell LG
    Front Immunol; 2018; 9():976. PubMed ID: 29867956
    [TBL] [Abstract][Full Text] [Related]  

  • 3. IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS.
    Alamyar E; Duroux P; Lefranc MP; Giudicelli V
    Methods Mol Biol; 2012; 882():569-604. PubMed ID: 22665256
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.
    Gadala-Maria D; Yaari G; Uduman M; Kleinstein SH
    Proc Natl Acad Sci U S A; 2015 Feb; 112(8):E862-70. PubMed ID: 25675496
    [TBL] [Abstract][Full Text] [Related]  

  • 5. ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data.
    Rosenfeld AM; Meng W; Luning Prak ET; Hershberg U
    Front Immunol; 2018; 9():2107. PubMed ID: 30298069
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Analysis of Transcriptional Profiling of Immune Cells at the Single-Cell Level.
    Ferguson A; Chen K
    Methods Mol Biol; 2020; 2111():47-57. PubMed ID: 31933197
    [TBL] [Abstract][Full Text] [Related]  

  • 7. VDJviz: a versatile browser for immunogenomics data.
    Bagaev DV; Zvyagin IV; Putintseva EV; Izraelson M; Britanova OV; Chudakov DM; Shugay M
    BMC Genomics; 2016 Jun; 17():453. PubMed ID: 27297497
    [TBL] [Abstract][Full Text] [Related]  

  • 8. ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data.
    Vetter J; Schaller S; Heinzel A; Aschauer C; Reindl-Schwaighofer R; Jelencsics K; Hu K; Oberbauer R; Winkler SM
    BMC Bioinformatics; 2022 Jan; 23(1):21. PubMed ID: 34991455
    [TBL] [Abstract][Full Text] [Related]  

  • 9. From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences.
    Lane J; Duroux P; Lefranc MP
    BMC Bioinformatics; 2010 Apr; 11():223. PubMed ID: 20433708
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data.
    IJspeert H; van Schouwenburg PA; van Zessen D; Pico-Knijnenburg I; Stubbs AP; van der Burg M
    J Immunol; 2017 May; 198(10):4156-4165. PubMed ID: 28416602
    [TBL] [Abstract][Full Text] [Related]  

  • 11. AIRR Community Standardized Representations for Annotated Immune Repertoires.
    Vander Heiden JA; Marquez S; Marthandan N; Bukhari SAC; Busse CE; Corrie B; Hershberg U; Kleinstein SH; Matsen Iv FA; Ralph DK; Rosenfeld AM; Schramm CA; ; Christley S; Laserson U
    Front Immunol; 2018; 9():2206. PubMed ID: 30323809
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools.
    Bleakley K; Lefranc MP; Biau G
    BMC Bioinformatics; 2008 Oct; 9():408. PubMed ID: 18831754
    [TBL] [Abstract][Full Text] [Related]  

  • 13. IRProfiler - a software toolbox for high throughput immune receptor profiling.
    Maramis C; Gkoufas A; Vardi A; Stalika E; Stamatopoulos K; Hatzidimitriou A; Maglaveras N; Chouvarda I
    BMC Bioinformatics; 2018 Apr; 19(1):144. PubMed ID: 29669518
    [TBL] [Abstract][Full Text] [Related]  

  • 14. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data.
    Elhanati Y; Marcou Q; Mora T; Walczak AM
    Bioinformatics; 2016 Jul; 32(13):1943-51. PubMed ID: 27153709
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.
    Smelter A; Astra M; Moseley HN
    BMC Bioinformatics; 2017 Mar; 18(1):175. PubMed ID: 28302053
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.
    Zhang Y; Yang X; Zhang Y; Zhang Y; Wang M; Ou JX; Zhu Y; Zeng H; Wu J; Lan C; Zhou HW; Yang W; Zhang Z
    Brief Bioinform; 2020 Sep; 21(5):1706-1716. PubMed ID: 31624828
    [TBL] [Abstract][Full Text] [Related]  

  • 17. VDJbase: an adaptive immune receptor genotype and haplotype database.
    Omer A; Shemesh O; Peres A; Polak P; Shepherd AJ; Watson CT; Boyd SD; Collins AM; Lees W; Yaari G
    Nucleic Acids Res; 2020 Jan; 48(D1):D1051-D1056. PubMed ID: 31602484
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community.
    Christley S; Stervbo U; Cowell LG;
    Methods Mol Biol; 2022; 2453():439-446. PubMed ID: 35622338
    [TBL] [Abstract][Full Text] [Related]  

  • 19. ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline.
    Avram O; Vaisman-Mentesh A; Yehezkel D; Ashkenazy H; Pupko T; Wine Y
    Front Immunol; 2018; 9():1686. PubMed ID: 30105017
    [TBL] [Abstract][Full Text] [Related]  

  • 20. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.
    Song L; Cohen D; Ouyang Z; Cao Y; Hu X; Liu XS
    Nat Methods; 2021 Jun; 18(6):627-630. PubMed ID: 33986545
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 18.