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Items: 1 to 50 of 107

1.

Overexpression of T-bet in HIV infection is associated with accumulation of B cells outside germinal centers and poor affinity maturation.

Austin JW, Buckner CM, Kardava L, Wang W, Zhang X, Melson VA, Swanson RG, Martins AJ, Zhou JQ, Hoehn KB, Fisk JN, Dimopoulos Y, Chassiakos A, O'Dell S, Smelkinson MG, Seamon CA, Kwan RW, Sneller MC, Pittaluga S, Doria-Rose NA, McDermott A, Li Y, Chun TW, Kleinstein SH, Tsang JS, Petrovas C, Moir S.

Sci Transl Med. 2019 Nov 27;11(520). pii: eaax0904. doi: 10.1126/scitranslmed.aax0904.

PMID:
31776286
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.

Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships.

Zhou JQ, Kleinstein SH.

J Immunol. 2019 Oct 1;203(7):1687-1692. doi: 10.4049/jimmunol.1900666. Epub 2019 Sep 4.

PMID:
31484734
4.

Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD-CD27- Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients.

Fraussen J, Marquez S, Takata K, Beckers L, Montes Diaz G, Zografou C, Van Wijmeersch B, Villar LM, O'Connor KC, Kleinstein SH, Somers V.

J Immunol. 2019 Sep 15;203(6):1650-1664. doi: 10.4049/jimmunol.1801236. Epub 2019 Aug 7.

PMID:
31391234
5.

Reporting and connecting cell type names and gating definitions through ontologies.

Overton JA, Vita R, Dunn P, Burel JG, Bukhari SAC, Cheung KH, Kleinstein SH, Diehl AD, Peters B.

BMC Bioinformatics. 2019 Apr 25;20(Suppl 5):182. doi: 10.1186/s12859-019-2725-5.

6.

Migrant memory B cells secrete luminal antibody in the vagina.

Oh JE, Iijima N, Song E, Lu P, Klein J, Jiang R, Kleinstein SH, Iwasaki A.

Nature. 2019 Jul;571(7763):122-126. doi: 10.1038/s41586-019-1285-1. Epub 2019 Jun 12.

7.

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
8.

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).

Meng H, Yaari G, Bolen CR, Avey S, Kleinstein SH.

PLoS Comput Biol. 2019 Apr 2;15(4):e1006899. doi: 10.1371/journal.pcbi.1006899. eCollection 2019 Apr.

9.

Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.

Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen Iv FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM.

Front Immunol. 2019 Mar 18;10:435. doi: 10.3389/fimmu.2019.00435. eCollection 2019. Review.

10.

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.

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; AIRR Community, Christley S, Laserson U.

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

12.

Affinity Maturation Is Impaired by Natural Killer Cell Suppression of Germinal Centers.

Rydyznski CE, Cranert SA, Zhou JQ, Xu H, Kleinstein SH, Singh H, Waggoner SN.

Cell Rep. 2018 Sep 25;24(13):3367-3373.e4. doi: 10.1016/j.celrep.2018.08.075.

13.

Local Clonal Diversification and Dissemination of B Lymphocytes in the Human Bronchial Mucosa.

Ohm-Laursen L, Meng H, Chen J, Zhou JQ, Corrigan CJ, Gould HJ, Kleinstein SH.

Front Immunol. 2018 Sep 7;9:1976. doi: 10.3389/fimmu.2018.01976. eCollection 2018.

14.

Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue.

Zhao Y, Uduman M, Siu JHY, Tull TJ, Sanderson JD, Wu YB, Zhou JQ, Petrov N, Ellis R, Todd K, Chavele KM, Guesdon W, Vossenkamper A, Jassem W, D'Cruz DP, Fear DJ, John S, Scheel-Toellner D, Hopkins C, Moreno E, Woodman NL, Ciccarelli F, Heck S, Kleinstein SH, Bemark M, Spencer J.

Nat Commun. 2018 Sep 21;9(1):3857. doi: 10.1038/s41467-018-06089-1.

15.

The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories.

Bukhari SAC, O'Connor MJ, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA, Rubelt F, Cheung KH, Kleinstein SH.

Front Immunol. 2018 Aug 16;9:1877. doi: 10.3389/fimmu.2018.01877. eCollection 2018.

16.

Optimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data.

Nouri N, Kleinstein SH.

Front Immunol. 2018 Jul 26;9:1687. doi: 10.3389/fimmu.2018.01687. eCollection 2018.

17.

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.

Bukhari SAC, Martínez-Romero M, O' Connor MJ, Egyedi AL, Willrett D, Graybeal J, Musen MA, Cheung KH, Kleinstein SH.

BMC Bioinformatics. 2018 Jul 16;19(1):268. doi: 10.1186/s12859-018-2247-6.

18.

A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.

Nouri N, Kleinstein SH.

Bioinformatics. 2018 Jul 1;34(13):i341-i349. doi: 10.1093/bioinformatics/bty235.

19.

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.

20.

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.

Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F; AIRR Community, Luning Prak ET, Kleinstein SH.

Nat Immunol. 2017 Nov 16;18(12):1274-1278. doi: 10.1038/ni.3873. No abstract available.

21.

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.

22.

Multiple network-constrained regressions expand insights into influenza vaccination responses.

Avey S, Mohanty S, Wilson J, Zapata H, Joshi SR, Siconolfi B, Tsang S, Shaw AC, Kleinstein SH.

Bioinformatics. 2017 Jul 15;33(14):i208-i216. doi: 10.1093/bioinformatics/btx260.

23.

Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data".

Watson CT, Matsen FA 4th, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE.

J Immunol. 2017 May 1;198(9):3371-3373. doi: 10.4049/jimmunol.1700306. No abstract available.

24.

Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8+ T Cell Terminal Differentiation and Loss of Multipotency.

Gray SM, Amezquita RA, Guan T, Kleinstein SH, Kaech SM.

Immunity. 2017 Apr 18;46(4):596-608. doi: 10.1016/j.immuni.2017.03.012. Epub 2017 Apr 11.

25.

Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.

Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH.

J Immunol. 2017 Mar 15;198(6):2489-2499. doi: 10.4049/jimmunol.1601850. Epub 2017 Feb 8.

26.

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.

27.

Solving Immunology?

Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC.

Trends Immunol. 2017 Feb;38(2):116-127. doi: 10.1016/j.it.2016.11.006. Epub 2016 Dec 13. Review.

28.

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.

29.

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.

30.

Corrigendum: Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection.

Bohannon C, Powers R, Satyabhama L, Cui A, Tipton C, Michaeli M, Skountzou I, Mittler RS, Kleinstein SH, Mehr R, Lee FE, Sanz I, Jacob J.

Nat Commun. 2016 Aug 16;7:12687. doi: 10.1038/ncomms12687. No abstract available.

31.

Generation of Long-Lived Bone Marrow Plasma Cells Secreting Antibodies Specific for the HIV-1 gp41 Membrane-Proximal External Region in the Absence of Polyreactivity.

Donius LR, Cheng Y, Choi J, Sun ZY, Hanson M, Zhang M, Gierahn TM, Marquez S, Uduman M, Kleinstein SH, Irvine D, Love JC, Reinherz EL, Kim M.

J Virol. 2016 Sep 12;90(19):8875-90. doi: 10.1128/JVI.01089-16. Print 2016 Oct 1.

32.

RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2.

Maman Y, Teng G, Seth R, Kleinstein SH, Schatz DG.

Nucleic Acids Res. 2016 Nov 16;44(20):9624-9637. Epub 2016 Jul 19.

33.

Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection.

Bohannon C, Powers R, Satyabhama L, Cui A, Tipton C, Michaeli M, Skountzou I, Mittler RS, Kleinstein SH, Mehr R, Lee FE, Sanz I, Jacob J.

Nat Commun. 2016 Jun 7;7:11826. doi: 10.1038/ncomms11826. Erratum in: Nat Commun. 2016 Aug 16;7:12687. Lee, Francis Eun-Hyung [Lee, Frances Eun-Hyung].

34.

Age-associated vascular inflammation promotes monocytosis during atherogenesis.

Du W, Wong C, Song Y, Shen H, Mori D, Rotllan N, Price N, Dobrian AD, Meng H, Kleinstein SH, Fernandez-Hernando C, Goldstein DR.

Aging Cell. 2016 Aug;15(4):766-77. doi: 10.1111/acel.12488. Epub 2016 May 2.

35.

Recurrent genetic defects in classical Hodgkin lymphoma cell lines.

Hudnall SD, Meng H, Lozovatsky L, Li P, Strout M, Kleinstein SH.

Leuk Lymphoma. 2016 Dec;57(12):2890-2900. Epub 2016 Apr 27. Erratum in: Leuk Lymphoma. 2017 Feb;58(2):506.

PMID:
27121023
36.

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.

37.

Characterization of Diabetogenic CD8+ T Cells: IMMUNE THERAPY WITH METABOLIC BLOCKADE.

Garyu JW, Uduman M, Stewart A, Rui J, Deng S, Shenson J, Staron MM, Kaech SM, Kleinstein SH, Herold KC.

J Biol Chem. 2016 May 20;291(21):11230-40. doi: 10.1074/jbc.M115.713362. Epub 2016 Mar 18.

38.

Autoreactive T Cells from Patients with Myasthenia Gravis Are Characterized by Elevated IL-17, IFN-γ, and GM-CSF and Diminished IL-10 Production.

Cao Y, Amezquita RA, Kleinstein SH, Stathopoulos P, Nowak RJ, O'Connor KC.

J Immunol. 2016 Mar 1;196(5):2075-84. doi: 10.4049/jimmunol.1501339. Epub 2016 Jan 29.

39.

Corrigendum: NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells.

Eisenbarth SC, Williams A, Colegio OR, Meng H, Strowig T, Rongvaux A, Henao-Mejia J, Thaiss CA, Joly S, Gonzalez DG, Xu L, Zenewicz LA, Haberman AM, Elinav E, Kleinstein SH, Sutterwala FS, Flavell RA.

Nature. 2016 Feb 25;530(7591):504. doi: 10.1038/nature16074. Epub 2015 Nov 25. No abstract available.

PMID:
26605525
40.

Practical guidelines for B-cell receptor repertoire sequencing analysis.

Yaari G, Kleinstein SH.

Genome Med. 2015 Nov 20;7:121. doi: 10.1186/s13073-015-0243-2. Review.

41.

The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection.

Dominguez CX, Amezquita RA, Guan T, Marshall HD, Joshi NS, Kleinstein SH, Kaech SM.

J Exp Med. 2015 Nov 16;212(12):2041-56. doi: 10.1084/jem.20150186. Epub 2015 Oct 26.

42.

Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing.

Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC.

Integr Biol (Camb). 2015 Dec;7(12):1587-97. doi: 10.1039/c5ib00169b. Epub 2015 Oct 20.

43.

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.

Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC.

Immunity. 2015 Sep 15;43(3):605-14. doi: 10.1016/j.immuni.2015.08.014. Epub 2015 Sep 8.

44.

Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses.

Ho PC, Bihuniak JD, Macintyre AN, Staron M, Liu X, Amezquita R, Tsui YC, Cui G, Micevic G, Perales JC, Kleinstein SH, Abel ED, Insogna KL, Feske S, Locasale JW, Bosenberg MW, Rathmell JC, Kaech SM.

Cell. 2015 Sep 10;162(6):1217-28. doi: 10.1016/j.cell.2015.08.012. Epub 2015 Aug 27.

45.

Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism.

Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH.

BMC Immunol. 2015 Aug 14;16:46. doi: 10.1186/s12865-015-0107-y.

46.

Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses.

Hartmann BM, Thakar J, Albrecht RA, Avey S, Zaslavsky E, Marjanovic N, Chikina M, Fribourg M, Hayot F, Schmolke M, Meng H, Wetmur J, García-Sastre A, Kleinstein SH, Sealfon SC.

J Virol. 2015 Oct;89(20):10190-205. doi: 10.1128/JVI.01523-15. Epub 2015 Jul 29.

47.

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.

48.

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.

49.

Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease.

Di Niro R, Snir O, Kaukinen K, Yaari G, Lundin KE, Gupta NT, Kleinstein SH, Cols M, Cerutti A, Mäki M, Shlomchik MJ, Sollid LM.

Mucosal Immunol. 2016 Jan;9(1):254-64. doi: 10.1038/mi.2015.57. Epub 2015 Jul 8.

50.

Production of IL-10 by CD4(+) regulatory T cells during the resolution of infection promotes the maturation of memory CD8(+) T cells.

Laidlaw BJ, Cui W, Amezquita RA, Gray SM, Guan T, Lu Y, Kobayashi Y, Flavell RA, Kleinstein SH, Craft J, Kaech SM.

Nat Immunol. 2015 Aug;16(8):871-9. doi: 10.1038/ni.3224. Epub 2015 Jul 6.

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