Publications

Yaari G, Benichou JI, Vander Heiden JA, Kleinstein SH, Louzoun Y: The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5. PMID: 26194756

Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH: Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. BMC Immunol. 2015 Aug 14; 2015 Aug 14. PMID: 26272204

Laidlaw BJ, Cui W, Amezquita RA, Gray SM, Guan T, Lu Y, Kobayashi Y, Flavell RA, Kleinstein SH, Craft J, Kaech SM: Production of IL-10 by CD4(+) regulatory T cells during the resolution of infection promotes the maturation of memory CD8(+) T cells. Nat Immunol. 2015 Aug; 2015 Jul 6. PMID: 26147684

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: Human dendritic cell response signatures distinguish 1918, pandemic and seasonal H1N1 influenza viruses. J Virol. 2015 Jul 29; 2015 Jul 29. PMID: 26223639

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: Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation. Immunity. 2015 Jul 21; 2015 Jul 14. PMID: 26187411

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: Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease. Mucosal Immunol. 2015 Jul 8; 2015 Jul 8. PMID: 26153762

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: The center for expanded data annotation and retrieval. J Am Med Inform Assoc. 2015 Jun 25; 2015 Jun 25. PMID: 26112029

Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH: Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015 Jun 10; 2015 Jun 10. PMID: 26069265

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: Prolonged proinflammatory cytokine production in monocytes modulated by interleukin 10 after influenza vaccination in older adults. J Infect Dis. 2015 Apr 1; 2014 Nov 2. PMID: 25367297

Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH: Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc Natl Acad Sci U S A. 2015 Feb 24; 2015 Feb 9. PMID: 25675496

Rakoff-Nahoum S, Kong Y, Kleinstein SH, Subramanian S, Ahern PP, Gordon JI, Medzhitov R: Analysis of gene-environment interactions in postnatal development of the mammalian intestine. Proc Natl Acad Sci U S A. 2015 Feb 17. PMID: 25691701

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-dependent alterations in gene expression and a mitochondrial signature of responsiveness to human influenza vaccination. Aging (Albany NY). 2015 Jan. PMID: 25596819

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: Systems immunology reveals markers of susceptibility to West Nile virus infection. Clin Vaccine Immunol. 2015 Jan; 2014 Oct 29. PMID: 25355795

Wu YC, James LK, Vander Heiden JA, Uduman M, Durham SR, Kleinstein SH, Kipling D, Gould HJ: Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J Allergy Clin Immunol. 2014 Sep. PMID: 25171866

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: B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014 Aug 6. PMID: 25100741

Vander Heiden JA, Yaari G, Uduman M, Stern JN, O'Connor KC, Hafler DA, Vigneault F, Kleinstein SH: pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014 Jul 1; 2014 Mar 10. PMID: 24618469

Zuccarino-Catania GV, Sadanand S, Weisel FJ, Tomayko MM, Meng H, Kleinstein SH, Good-Jacobson KL, Shlomchik MJ: CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype. Nat Immunol. 2014 Jul; 2014 Jun 1. PMID: 24880458

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: Shared VH1-46 gene usage by pemphigus vulgaris autoantibodies indicates common humoral immune responses among patients. Nat Commun. 2014 Jun 19; 2014 Jun 19. PMID: 24942562

Cui W, Joshi NS, Liu Y, Meng H, Kleinstein SH, Kaech SM: TLR4 ligands lipopolysaccharide and monophosphoryl lipid a differentially regulate effector and memory CD8+ T Cell differentiation. J Immunol. 2014 May 1; 2014 Mar 21. PMID: 24659688

Bolen CR, Ding S, Robek MD, Kleinstein SH: Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression. Hepatology. 2014 Apr; 2014 Feb 18. PMID: 23929627

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: High-resolution antibody dynamics of vaccine-induced immune responses. Proc Natl Acad Sci U S A. 2014 Apr 1; 2014 Mar 17. PMID: 24639495

Qian F, Thakar J, Yuan X, Nolan M, Murray KO, Lee WT, Wong SJ, Meng H, Fikrig E, Kleinstein SH, Montgomery RR: Immune markers associated with host susceptibility to infection with West Nile virus. Viral Immunol. 2014 Mar. PMID: 24605787

Katz SG, Labelle JL, Meng H, Valeriano RP, Fisher JK, Sun H, Rodig SJ, Kleinstein SH, Walensky LD: Mantle cell lymphoma in cyclin D1 transgenic mice with Bim-deficient B cells. Blood. 2014 Feb 6; 2013 Dec 18. PMID: 24352880

Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH: Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences. J Immunol. 2014 Feb 1; 2013 Dec 27. PMID: 24376267

Brusic V, Gottardo R, Kleinstein SH, Davis MM, HIPC steering committee: Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium. Nat Biotechnol. 2014 Feb; 2014 Jan 19. PMID: 24441472

Thakar J, Schmid S, Duke JL, García-Sastre A, Kleinstein SH: Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms. J Interferon Cytokine Res. 2013 Nov; 2013 Jun 17. PMID: 23772952

Fang L, Lowther DE, Meizlish ML, Anderson RC, Bruce JN, Devine L, Huttner AJ, Kleinstein SH, Lee JY, Stern JN, Yaari G, Lovato L, Cronk KM, O'Connor KC: The immune cell infiltrate populating meningiomas is composed of mature, antigen-experienced T and B cells. Neuro Oncol. 2013 Nov; 2013 Aug 26. PMID: 23978377

Yaari G, Bolen CR, Thakar J, Kleinstein SH: Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. Nucleic Acids Res. 2013 Oct; 2013 Aug 5. PMID: 23921631

Querol L, Clark PL, Bailey MA, Cotsapas C, Cross AH, Hafler DA, Kleinstein SH, Lee JY, Yaari G, Willis SN, O'Connor KC: Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis. Neurology. 2013 Sep 10; 2013 Aug 6. PMID: 23921886

Bryniarski K, Ptak W, Jayakumar A, Püllmann K, Caplan MJ, Chairoungdua A, Lu J, Adams BD, Sikora E, Nazimek K, Marquez S, Kleinstein SH, Sangwung P, Iwakiri Y, Delgato E, Redegeld F, Blokhuis BR, Wojcikowski J, Daniel AW, Groot Kormelink T, Askenase PW: Antigen-specific, antibody-coated, exosome-like nanovesicles deliver suppressor T-cell microRNA-150 to effector T cells to inhibit contact sensitivity. J Allergy Clin Immunol. 2013 Jul; 2013 May 31. PMID: 23727037

Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG, Kleinstein SH: Multiple transcription factor binding sites predict AID targeting in non-Ig genes. J Immunol. 2013 Apr 15; 2013 Mar 20. PMID: 23514741

Qian F, Bolen CR, Jing C, Wang X, Zheng W, Zhao H, Fikrig E, Bruce RD, Kleinstein SH, Montgomery RR: Impaired toll-like receptor 3-mediated immune responses from macrophages of patients chronically infected with hepatitis C virus. Clin Vaccine Immunol. 2013 Feb; 2012 Dec 5. PMID: 23220997

Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH: Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics. 2013; 2013 Apr 17. PMID: 23734902

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: Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013; 2013 Nov 15. PMID: 24298272

Bolen CR, Robek MD, Brodsky L, Schulz V, Lim JK, Taylor MW, Kleinstein SH: The blood transcriptional signature of chronic hepatitis C virus is consistent with an ongoing interferon-mediated antiviral response. J Interferon Cytokine Res. 2013 Jan; 2012 Oct 15. PMID: 23067362

Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P: The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. PLoS Pathog. 2013; 2013 Nov 21. PMID: 24278016

Kohler KM, McDonald JJ, Duke JL, Arakawa H, Tan S, Kleinstein SH, Buerstedde JM, Schatz DG: Identification of core DNA elements that target somatic hypermutation. J Immunol. 2012 Dec 1; 2012 Oct 19. PMID: 23087403

Yaari G, Uduman M, Kleinstein SH: Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 Sep 1; 2012 May 27. PMID: 22641856

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: NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells. Nature. 2012 Apr 25; 2012 Apr 25. PMID: 22538615

Marshall HD, Chandele A, Jung YW, Meng H, Poholek AC, Parish IA, Rutishauser R, Cui W, Kleinstein SH, Craft J, Kaech SM: Differential expression of Ly6C and T-bet distinguish effector and memory Th1 CD4(+) cell properties during viral infection. Immunity. 2011 Oct 28; 2011 Oct 20. PMID: 22018471

Costa KD, Kleinstein SH, Hershberg U: Biomedical model fitting and error analysis. Sci Signal. 2011 Sep 20; 2011 Sep 20. PMID: 21954296

Frucht CS, Uduman M, Kleinstein SH, Santos-Sacchi J, Navaratnam DS: Gene expression gradients along the tonotopic axis of the chicken auditory epithelium. J Assoc Res Otolaryngol. 2011 Aug; 2011 Mar 12. PMID: 21399991

Cohen RM, Kleinstein SH, Louzoun Y: Somatic hypermutation targeting is influenced by location within the immunoglobulin V region. Mol Immunol. 2011 Jul; 2011 May 18. PMID: 21592579

Uduman M, Yaari G, Hershberg U, Stern JA, Shlomchik MJ, Kleinstein SH: Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul; 2011 Jun 10. PMID: 21665923

Bolen CR, Uduman M, Kleinstein SH: Cell subset prediction for blood genomic studies. BMC Bioinformatics. 2011 Jun 24; 2011 Jun 24. PMID: 21702940

Kerfoot SM, Yaari G, Patel JR, Johnson KL, Gonzalez DG, Kleinstein SH, Haberman AM: Germinal center B cell and T follicular helper cell development initiates in the interfollicular zone. Immunity. 2011 Jun 24. PMID: 21636295

Protiva P, Mason JB, Liu Z, Hopkins ME, Nelson C, Marshall JR, Lambrecht RW, Pendyala S, Kopelovich L, Kim M, Kleinstein SH, Laird PW, Lipkin M, Holt PR: Altered folate availability modifies the molecular environment of the human colorectum: implications for colorectal carcinogenesis. Cancer Prev Res (Phila). 2011 Apr; 2011 Feb 14. PMID: 21321062

O'Connor MJ, Hauser AE, Haberman AM, Kleinstein SH: Activated germinal centre B cells undergo directed migration. Int J Data Min Bioinform. 2011. PMID: 21805826

Frucht CS, Uduman M, Duke JL, Kleinstein SH, Santos-Sacchi J, Navaratnam DS: Gene expression analysis of forskolin treated basilar papillae identifies microRNA181a as a mediator of proliferation. PLoS One. 2010 Jul 9; 2010 Jul 9. PMID: 20634979

Pagliaccetti NE, Chu EN, Bolen CR, Kleinstein SH, Robek MD: Lambda and alpha interferons inhibit hepatitis B virus replication through a common molecular mechanism but with different in vivo activities. Virology. 2010 Jun 5; 2010 Mar 29. PMID: 20303135

Nudelman G, Ge Y, Hu J, Kumar M, Seto J, Duke JL, Kleinstein SH, Hayot F, Sealfon SC, Wetmur JG: Coregulation mapping based on individual phenotypic variation in response to virus infection. Immunome Res. 2010 Mar 18; 2010 Mar 18. PMID: 20298589

Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, Tenoever BR, Sealfon SC, Kleinstein SH: Antiviral response dictated by choreographed cascade of transcription factors. J Immunol. 2010 Mar 15; 2010 Feb 17. PMID: 20164420

Anderson SM, Khalil A, Uduman M, Hershberg U, Louzoun Y, Haberman AM, Kleinstein SH, Shlomchik MJ: Taking advantage: high-affinity B cells in the germinal center have lower death rates, but similar rates of division, compared to low-affinity cells. J Immunol. 2009 Dec 1; 2009 Nov 16. PMID: 19917681

Bruno VM, Hannemann S, Lara-Tejero M, Flavell RA, Kleinstein SH, Galán JE: Salmonella Typhimurium type III secretion effectors stimulate innate immune responses in cultured epithelial cells. PLoS Pathog. 2009 Aug; 2009 Aug 7. PMID: 19662166

Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P, Robek MD: Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication. J Biol Chem. 2008 Oct 31; 2008 Aug 29. PMID: 18757365

Kleinstein SH: Getting started in computational immunology. PLoS Comput Biol. 2008 Aug 29; 2008 Aug 29. PMID: 18769677

Hershberg U, Uduman M, Shlomchik MJ, Kleinstein SH: Improved methods for detecting selection by mutation analysis of Ig V region sequences. Int Immunol. 2008 May; 2008 Apr 7. PMID: 18397909

Liu M, Duke JL, Richter DJ, Vinuesa CG, Goodnow CC, Kleinstein SH, Schatz DG: Two levels of protection for the B cell genome during somatic hypermutation. Nature. 2008 Feb 14. PMID: 18273020

Hauser AE, Junt T, Mempel TR, Sneddon MW, Kleinstein SH, Henrickson SE, von Andrian UH, Shlomchik MJ, Haberman AM: Definition of germinal-center B cell migration in vivo reveals predominant intrazonal circulation patterns. Immunity. 2007 May. PMID: 17509908

Magori-Cohen R, Louzoun Y, Kleinstein SH: Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. Bioinformatics. 2006 Jul 15. PMID: 16873490

Kleinstein SH, Louzoun Y, Shlomchik MJ: Estimating hypermutation rates from clonal tree data. J Immunol. 2003 Nov 1. PMID: 14568938

Kleinstein SH, Singh JP: Why are there so few key mutant clones? The influence of stochastic selection and blocking on affinity maturation in the germinal center. Int Immunol. 2003 Jul. PMID: 12807826

More Publications

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