BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

219 related articles for article (PubMed ID: 32154832)

  • 1. immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking.
    Weber CR; Akbar R; Yermanos A; Pavlović M; Snapkov I; Sandve GK; Reddy ST; Greiff V
    Bioinformatics; 2020 Jun; 36(11):3594-3596. PubMed ID: 32154832
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes.
    Han J; Masserey S; Shlesinger D; Kuhn R; Papadopoulou C; Agrafiotis A; Kreiner V; Dizerens R; Hong KL; Weber C; Greiff V; Oxenius A; Reddy ST; Yermanos A
    Bioinform Adv; 2022; 2(1):vbac062. PubMed ID: 36699357
    [TBL] [Abstract][Full Text] [Related]  

  • 3. simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods.
    Kanduri C; Scheffer L; Pavlović M; Rand KD; Chernigovskaya M; Pirvandy O; Yaari G; Greiff V; Sandve GK
    Gigascience; 2022 Dec; 12():. PubMed ID: 37848619
    [TBL] [Abstract][Full Text] [Related]  

  • 4. CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching.
    Rognes T; Scheffer L; Greiff V; Sandve GK
    Bioinformatics; 2022 Sep; 38(17):4230-4232. PubMed ID: 35852318
    [TBL] [Abstract][Full Text] [Related]  

  • 5. tcR: an R package for T cell receptor repertoire advanced data analysis.
    Nazarov VI; Pogorelyy MV; Komech EA; Zvyagin IV; Bolotin DA; Shugay M; Chudakov DM; Lebedev YB; Mamedov IZ
    BMC Bioinformatics; 2015 May; 16(1):175. PubMed ID: 26017500
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires.
    Cinelli M; Sun Y; Best K; Heather JM; Reich-Zeliger S; Shifrut E; Friedman N; Shawe-Taylor J; Chain B
    Bioinformatics; 2017 Apr; 33(7):951-955. PubMed ID: 28073756
    [TBL] [Abstract][Full Text] [Related]  

  • 7. AIRRSHIP: simulating human B cell receptor repertoire sequences.
    Sutherland C; Cowan GJM
    Bioinformatics; 2023 Jun; 39(6):. PubMed ID: 37279738
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim).
    Yermanos A; Greiff V; Krautler NJ; Menzel U; Dounas A; Miho E; Oxenius A; Stadler T; Reddy ST
    Bioinformatics; 2017 Dec; 33(24):3938-3946. PubMed ID: 28968873
    [TBL] [Abstract][Full Text] [Related]  

  • 9. IgSimulator: a versatile immunosequencing simulator.
    Safonova Y; Lapidus A; Lill J
    Bioinformatics; 2015 Oct; 31(19):3213-5. PubMed ID: 26007226
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation?
    Peacock T; Heather JM; Ronel T; Chain B
    Bioinformatics; 2021 May; 37(6):876-878. PubMed ID: 32853330
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Simulating Illumina metagenomic data with InSilicoSeq.
    Gourlé H; Karlsson-Lindsjö O; Hayer J; Bongcam-Rudloff E
    Bioinformatics; 2019 Feb; 35(3):521-522. PubMed ID: 30016412
    [TBL] [Abstract][Full Text] [Related]  

  • 13. IMPre: An Accurate and Efficient Software for Prediction of T- and B-Cell Receptor Germline Genes and Alleles from Rearranged Repertoire Data.
    Zhang W; Wang IM; Wang C; Lin L; Chai X; Wu J; Bett AJ; Dhanasekaran G; Casimiro DR; Liu X
    Front Immunol; 2016; 7():457. PubMed ID: 27867380
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R.
    Angelin-Bonnet O; Biggs PJ; Baldwin S; Thomson S; Vignes M
    Bioinformatics; 2020 May; 36(9):2938-2940. PubMed ID: 31960894
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'.
    Davydov AN; Bolotin DA; Poslavsky SV; Chudakov DM
    Brief Bioinform; 2023 Sep; 24(6):. PubMed ID: 37824737
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.
    Smakaj E; Babrak L; Ohlin M; Shugay M; Briney B; Tosoni D; Galli C; Grobelsek V; D'Angelo I; Olson B; Reddy S; Greiff V; Trück J; Marquez S; Lees W; Miho E
    Bioinformatics; 2020 Mar; 36(6):1731-1739. PubMed ID: 31873728
    [TBL] [Abstract][Full Text] [Related]  

  • 18. GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.
    Dickson A; Asgari E; McHardy AC; Mofrad MRK
    Bioinformatics; 2023 Feb; 39(2):. PubMed ID: 36786404
    [TBL] [Abstract][Full Text] [Related]  

  • 19. 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]  

  • 20. Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis.
    Galigalidou C; Zaragoza-Infante L; Chatzidimitriou A; Stamatopoulos K; Psomopoulos F; Agathangelidis A
    Methods Mol Biol; 2022; 2453():585-603. PubMed ID: 35622343
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.