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Items: 22

1.

sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation.

Olson BJ, Moghimi P, Schramm CA, Obraztsova A, Ralph D, Vander Heiden JA, Shugay M, Shepherd AJ, Lees W, Matsen FA 4th.

Front Immunol. 2019 Nov 1;10:2533. doi: 10.3389/fimmu.2019.02533. eCollection 2019.

2.

Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.

Hoehn KB, Vander Heiden JA, Zhou JQ, Lunter G, Pybus OG, Kleinstein SH.

Proc Natl Acad Sci U S A. 2019 Nov 5;116(45):22664-22672. doi: 10.1073/pnas.1906020116. Epub 2019 Oct 21.

3.

Early B cell tolerance defects in neuromyelitis optica favour anti-AQP4 autoantibody production.

Cotzomi E, Stathopoulos P, Lee CS, Ritchie AM, Soltys JN, Delmotte FR, Oe T, Sng J, Jiang R, Ma AK, Vander Heiden JA, Kleinstein SH, Levy M, Bennett JL, Meffre E, O'Connor KC.

Brain. 2019 Jun 1;142(6):1598-1615. doi: 10.1093/brain/awz106.

PMID:
31056665
4.

Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data.

Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, O'Connor KC, Yaari G, Kleinstein SH.

Front Immunol. 2019 Feb 13;10:129. doi: 10.3389/fimmu.2019.00129. eCollection 2019.

5.

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; AIRR Community, Christley S, Laserson U.

Front Immunol. 2018 Sep 28;9:2206. doi: 10.3389/fimmu.2018.02206. eCollection 2018.

6.

Mutant Cellular AP-1 Proteins Promote Expression of a Subset of Epstein-Barr Virus Late Genes in the Absence of Lytic Viral DNA Replication.

Lyons DE, Yu KP, Vander Heiden JA, Heston L, Dittmer DP, El-Guindy A, Miller G.

J Virol. 2018 Sep 12;92(19). pii: e01062-18. doi: 10.1128/JVI.01062-18. Print 2018 Oct 1.

7.

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.

Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB.

Front Immunol. 2017 Nov 1;8:1418. doi: 10.3389/fimmu.2017.01418. eCollection 2017.

8.

Interleukin-10 from CD4+ follicular regulatory T cells promotes the germinal center response.

Laidlaw BJ, Lu Y, Amezquita RA, Weinstein JS, Vander Heiden JA, Gupta NT, Kleinstein SH, Kaech SM, Craft J.

Sci Immunol. 2017 Oct 20;2(16). pii: eaan4767. doi: 10.1126/sciimmunol.aan4767.

9.

The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires.

Bolen CR, Rubelt F, Vander Heiden JA, Davis MM.

BMC Bioinformatics. 2017 Mar 7;18(1):155. doi: 10.1186/s12859-017-1556-5.

10.

Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing.

Vander Heiden JA, Stathopoulos P, Zhou JQ, Chen L, Gilbert TJ, Bolen CR, Barohn RJ, Dimachkie MM, Ciafaloni E, Broering TJ, Vigneault F, Nowak RJ, Kleinstein SH, O'Connor KC.

J Immunol. 2017 Feb 15;198(4):1460-1473. doi: 10.4049/jimmunol.1601415. Epub 2017 Jan 13.

11.

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 6;17(Suppl 13):333.

12.

A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data.

Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O'Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH.

J Immunol. 2016 Nov 1;197(9):3566-3574. Epub 2016 Oct 5.

13.

Compromised fidelity of B-cell tolerance checkpoints in AChR and MuSK myasthenia gravis.

Lee JY, Stathopoulos P, Gupta S, Bannock JM, Barohn RJ, Cotzomi E, Dimachkie MM, Jacobson L, Lee CS, Morbach H, Querol L, Shan JL, Vander Heiden JA, Waters P, Vincent A, Nowak RJ, O'Connor KC.

Ann Clin Transl Neurol. 2016 Apr 27;3(6):443-54. doi: 10.1002/acn3.311. eCollection 2016 Jun.

14.

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells.

Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM.

Nat Commun. 2016 Mar 23;7:11112. doi: 10.1038/ncomms11112.

15.

The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales.

Yaari G, Benichou JI, Vander Heiden JA, Kleinstein SH, Louzoun Y.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140242. doi: 10.1098/rstb.2014.0242.

16.

Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation.

Di Niro R, Lee SJ, Vander Heiden JA, Elsner RA, Trivedi N, Bannock JM, Gupta NT, Kleinstein SH, Vigneault F, Gilbert TJ, Meffre E, McSorley SJ, Shlomchik MJ.

Immunity. 2015 Jul 21;43(1):120-31. doi: 10.1016/j.immuni.2015.06.013. Epub 2015 Jul 14.

17.

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.

Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH.

Bioinformatics. 2015 Oct 15;31(20):3356-8. doi: 10.1093/bioinformatics/btv359. Epub 2015 Jun 10.

18.

Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis.

Wu YC, James LK, Vander Heiden JA, Uduman M, Durham SR, Kleinstein SH, Kipling D, Gould HJ.

J Allergy Clin Immunol. 2014 Sep;134(3):604-12. doi: 10.1016/j.jaci.2014.07.010.

19.

B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.

Stern JN, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, Huttner AJ, Laman JD, Nagra RM, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH, Hafler DA, O'Connor KC.

Sci Transl Med. 2014 Aug 6;6(248):248ra107. doi: 10.1126/scitranslmed.3008879.

20.

High-resolution antibody dynamics of vaccine-induced immune responses.

Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4928-33. doi: 10.1073/pnas.1323862111. Epub 2014 Mar 17.

21.

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.

Vander Heiden JA, Yaari G, Uduman M, Stern JN, O'Connor KC, Hafler DA, Vigneault F, Kleinstein SH.

Bioinformatics. 2014 Jul 1;30(13):1930-2. doi: 10.1093/bioinformatics/btu138. Epub 2014 Mar 10.

22.

Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.

Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O'Connor KC, Hafler DA, Laserson U, Vigneault F, Kleinstein SH.

Front Immunol. 2013 Nov 15;4:358. doi: 10.3389/fimmu.2013.00358. eCollection 2013.

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