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Items: 1 to 50 of 89

1.

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.

2.

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.

3.

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.

PMID:
29054998
4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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
18.

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.

19.

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.

20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

The center for expanded data annotation and retrieval.

Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O'Connor MJ, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA; CEDAR team.

J Am Med Inform Assoc. 2015 Nov;22(6):1148-52. doi: 10.1093/jamia/ocv048. Epub 2015 Jun 25.

34.

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.

35.

Analysis of gene-environment interactions in postnatal development of the mammalian intestine.

Rakoff-Nahoum S, Kong Y, Kleinstein SH, Subramanian S, Ahern PP, Gordon JI, Medzhitov R.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):1929-36. doi: 10.1073/pnas.1424886112.

36.

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):E862-70. doi: 10.1073/pnas.1417683112. Epub 2015 Feb 9.

37.

Aging-dependent alterations in gene expression and a mitochondrial signature of responsiveness to human influenza vaccination.

Thakar J, Mohanty S, West AP, Joshi SR, Ueda I, Wilson J, Meng H, Blevins TP, Tsang S, Trentalange M, Siconolfi B, Park K, Gill TM, Belshe RB, Kaech SM, Shadel GS, Kleinstein SH, Shaw AC.

Aging (Albany NY). 2015 Jan;7(1):38-52.

38.

Prolonged proinflammatory cytokine production in monocytes modulated by interleukin 10 after influenza vaccination in older adults.

Mohanty S, Joshi SR, Ueda I, Wilson J, Blevins TP, Siconolfi B, Meng H, Devine L, Raddassi K, Tsang S, Belshe RB, Hafler DA, Kaech SM, Kleinstein SH, Trentalange M, Allore HG, Shaw AC.

J Infect Dis. 2015 Apr 1;211(7):1174-84. doi: 10.1093/infdis/jiu573. Epub 2014 Nov 2.

39.

Systems immunology reveals markers of susceptibility to West Nile virus infection.

Qian F, Goel G, Meng H, Wang X, You F, Devine L, Raddassi K, Garcia MN, Murray KO, Bolen CR, Gaujoux R, Shen-Orr SS, Hafler D, Fikrig E, Xavier R, Kleinstein SH, Montgomery RR.

Clin Vaccine Immunol. 2015 Jan;22(1):6-16. doi: 10.1128/CVI.00508-14. Epub 2014 Oct 29.

40.

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.

41.

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.

42.

Shared VH1-46 gene usage by pemphigus vulgaris autoantibodies indicates common humoral immune responses among patients.

Cho MJ, Lo AS, Mao X, Nagler AR, Ellebrecht CT, Mukherjee EM, Hammers CM, Choi EJ, Sharma PM, Uduman M, Li H, Rux AH, Farber SA, Rubin CB, Kleinstein SH, Sachais BS, Posner MR, Cavacini LA, Payne AS.

Nat Commun. 2014 Jun 19;5:4167. doi: 10.1038/ncomms5167.

43.

CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype.

Zuccarino-Catania GV, Sadanand S, Weisel FJ, Tomayko MM, Meng H, Kleinstein SH, Good-Jacobson KL, Shlomchik MJ.

Nat Immunol. 2014 Jul;15(7):631-7. doi: 10.1038/ni.2914. Epub 2014 Jun 1.

44.

TLR4 ligands lipopolysaccharide and monophosphoryl lipid a differentially regulate effector and memory CD8+ T Cell differentiation.

Cui W, Joshi NS, Liu Y, Meng H, Kleinstein SH, Kaech SM.

J Immunol. 2014 May 1;192(9):4221-32. doi: 10.4049/jimmunol.1302569. Epub 2014 Mar 21.

45.

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.

46.

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.

47.

Immune markers associated with host susceptibility to infection with West Nile virus.

Qian F, Thakar J, Yuan X, Nolan M, Murray KO, Lee WT, Wong SJ, Meng H, Fikrig E, Kleinstein SH, Montgomery RR.

Viral Immunol. 2014 Mar;27(2):39-47. doi: 10.1089/vim.2013.0074.

48.

Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium.

Brusic V, Gottardo R, Kleinstein SH, Davis MM; HIPC steering committee.

Nat Biotechnol. 2014 Feb;32(2):146-8. doi: 10.1038/nbt.2777. Epub 2014 Jan 19. No abstract available.

49.

Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences.

Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH.

J Immunol. 2014 Feb 1;192(3):867-74. doi: 10.4049/jimmunol.1301551. Epub 2013 Dec 27.

50.

Mantle cell lymphoma in cyclin D1 transgenic mice with Bim-deficient B cells.

Katz SG, Labelle JL, Meng H, Valeriano RP, Fisher JK, Sun H, Rodig SJ, Kleinstein SH, Walensky LD.

Blood. 2014 Feb 6;123(6):884-93. doi: 10.1182/blood-2013-04-499079. Epub 2013 Dec 18.

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