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Items: 1 to 20 of 188

1.

Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms.

Bolotin DA, Mamedov IZ, Britanova OV, Zvyagin IV, Shagin D, Ustyugova SV, Turchaninova MA, Lukyanov S, Lebedev YB, Chudakov DM.

Eur J Immunol. 2012 Nov;42(11):3073-83. doi: 10.1002/eji.201242517. Epub 2012 Sep 24.

2.

Wrestling with the repertoire: the promise and perils of next generation sequencing for antigen receptors.

Baum PD, Venturi V, Price DA.

Eur J Immunol. 2012 Nov;42(11):2834-9. doi: 10.1002/eji.201242999.

3.

TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization.

Yang X, Liu D, Lv N, Zhao F, Liu F, Zou J, Chen Y, Xiao X, Wu J, Liu P, Gao J, Hu Y, Shi Y, Liu J, Zhang R, Chen C, Ma J, Gao GF, Zhu B.

J Immunol. 2015 Jan 1;194(1):446-54. doi: 10.4049/jimmunol.1400711. Epub 2014 Nov 17.

4.

Probing the T-cell receptor repertoire with deep sequencing.

Miconnet I.

Curr Opin HIV AIDS. 2012 Jan;7(1):64-70. doi: 10.1097/COH.0b013e32834ddcae. Review.

PMID:
22156841
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 28;16:175. doi: 10.1186/s12859-015-0613-1.

6.

3D: diversity, dynamics, differential testing - a proposed pipeline for analysis of next-generation sequencing T cell repertoire data.

Zhang L, Cham J, Paciorek A, Trager J, Sheikh N, Fong L.

BMC Bioinformatics. 2017 Feb 27;18(1):129. doi: 10.1186/s12859-017-1544-9.

7.

HLA typing by next-generation sequencing - getting closer to reality.

Gabriel C, Fürst D, Faé I, Wenda S, Zollikofer C, Mytilineos J, Fischer GF.

Tissue Antigens. 2014 Feb;83(2):65-75. doi: 10.1111/tan.12298. Review.

PMID:
24447174
8.

Next-generation sequencing and potential applications in fungal genomics.

Sanmiguel P.

Methods Mol Biol. 2011;722:51-60. doi: 10.1007/978-1-61779-040-9_4.

PMID:
21590412
9.

High Throughput Sequencing of T Cell Antigen Receptors Reveals a Conserved TCR Repertoire.

Hou X, Lu C, Chen S, Xie Q, Cui G, Chen J, Chen Z, Wu Z, Ding Y, Ye P, Dai Y, Diao H.

Medicine (Baltimore). 2016 Mar;95(10):e2839. doi: 10.1097/MD.0000000000002839.

10.

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

Scholz MB, Lo CC, Chain PS.

Curr Opin Biotechnol. 2012 Feb;23(1):9-15. doi: 10.1016/j.copbio.2011.11.013. Epub 2011 Dec 9. Review.

PMID:
22154470
11.

Next-generation sequencing and its applications in molecular diagnostics.

Su Z, Ning B, Fang H, Hong H, Perkins R, Tong W, Shi L.

Expert Rev Mol Diagn. 2011 Apr;11(3):333-43. doi: 10.1586/erm.11.3. Review.

PMID:
21463242
12.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y.

BMC Genomics. 2012 Jul 24;13:341. doi: 10.1186/1471-2164-13-341.

13.

Pollux: platform independent error correction of single and mixed genomes.

Marinier E, Brown DG, McConkey BJ.

BMC Bioinformatics. 2015 Jan 16;16:10. doi: 10.1186/s12859-014-0435-6.

14.

Library preparation methods for next-generation sequencing: tone down the bias.

van Dijk EL, Jaszczyszyn Y, Thermes C.

Exp Cell Res. 2014 Mar 10;322(1):12-20. doi: 10.1016/j.yexcr.2014.01.008. Epub 2014 Jan 15. Review.

PMID:
24440557
15.

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing.

Benichou J, Ben-Hamo R, Louzoun Y, Efroni S.

Immunology. 2012 Mar;135(3):183-91. doi: 10.1111/j.1365-2567.2011.03527.x. Review.

16.

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire.

Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL.

BMC Genomics. 2011 Feb 11;12:106. doi: 10.1186/1471-2164-12-106.

17.

A microfluidic DNA library preparation platform for next-generation sequencing.

Kim H, Jebrail MJ, Sinha A, Bent ZW, Solberg OD, Williams KP, Langevin SA, Renzi RF, Van De Vreugde JL, Meagher RJ, Schoeniger JS, Lane TW, Branda SS, Bartsch MS, Patel KD.

PLoS One. 2013 Jul 22;8(7):e68988. doi: 10.1371/journal.pone.0068988. Print 2013.

18.

Next-generation sequencing technologies and fragment assembly algorithms.

Lee H, Tang H.

Methods Mol Biol. 2012;855:155-74. doi: 10.1007/978-1-61779-582-4_5. Review.

PMID:
22407708
19.

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis.

Zhang W, Du Y, Su Z, Wang C, Zeng X, Zhang R, Hong X, Nie C, Wu J, Cao H, Xu X, Liu X.

Genetics. 2015 Oct;201(2):459-72. doi: 10.1534/genetics.115.176735. Epub 2015 Aug 21.

20.

SuperSAGE: powerful serial analysis of gene expression.

Matsumura H, Urasaki N, Yoshida K, Krüger DH, Kahl G, Terauchi R.

Methods Mol Biol. 2012;883:1-17. doi: 10.1007/978-1-61779-839-9_1.

PMID:
22589121

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