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Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.
Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B. Thomas N, et al. Among authors: chain b. Bioinformatics. 2014 Nov 15;30(22):3181-8. doi: 10.1093/bioinformatics/btu523. Epub 2014 Aug 5. Bioinformatics. 2014. PMID: 25095879 Free PMC article.
In this study, we measure the frequency of different T-cell receptors (TcR) in CD4 + T cell populations of mice immunized with a complex antigen, killed Mycobacterium tuberculosis, using high throughput parallel sequencing of the TcRbeta chain. Our initial hypothesis that …
In this study, we measure the frequency of different T-cell receptors (TcR) in CD4 + T cell populations of mice immunized with a complex ant …
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.
Best K, Oakes T, Heather JM, Shawe-Taylor J, Chain B. Best K, et al. Among authors: chain b. Sci Rep. 2015 Oct 13;5:14629. doi: 10.1038/srep14629. Sci Rep. 2015. PMID: 26459131 Free PMC article.
The polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughput Sequencing (HTS), PCR is widely used to quantify transcript abundance for RNA-seq, and in the context of analysis of T and B cell …
The polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughp …
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. Cinelli M, et al. Among authors: chain b. Bioinformatics. 2017 Apr 1;33(7):951-955. doi: 10.1093/bioinformatics/btw771. Bioinformatics. 2017. PMID: 28073756 Free PMC article.
In this study we use high throughput sequencing to compare the global changes in T cell receptor beta chain complementarity determining region 3 (CDR3beta) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone. ...T …
In this study we use high throughput sequencing to compare the global changes in T cell receptor beta chain complementarity determini …
Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile.
Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Oakes T, et al. Among authors: chain b. Front Immunol. 2017 Oct 12;8:1267. doi: 10.3389/fimmu.2017.01267. eCollection 2017. Front Immunol. 2017. PMID: 29075258 Free PMC article.
Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation.
Gkazi AS, Margetts BK, Attenborough T, Mhaldien L, Standing JF, Oakes T, Heather JM, Booth J, Pasquet M, Chiesa R, Veys P, Klein N, Chain B, Callard R, Adams SP. Gkazi AS, et al. Among authors: chain b. Front Immunol. 2018 Nov 5;9:2547. doi: 10.3389/fimmu.2018.02547. eCollection 2018. Front Immunol. 2018. PMID: 30455696 Free PMC article.
286 results