Publications

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 and O'Connor KC: B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014 Aug 6;6 (248) :248ra107. PMID: 25100741


Vander Heiden JA, Yaari G, Uduman M, Stern JN, O'Connor KC, Hafler DA, Vigneault F and Kleinstein SH: pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014 Jul 1;30 (13) :1930-2. Epub 2014 Mar 10. PMID: 24618469


Zuccarino-Catania GV, Sadanand S, Weisel FJ, Tomayko MM, Meng H, Kleinstein SH, Good-Jacobson KL and Shlomchik MJ: CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype. Nat Immunol. 2014 Jul;15 (7) :631-7. Epub 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 and Payne AS: Shared VH1-46 gene usage by pemphigus vulgaris autoantibodies indicates common humoral immune responses among patients. Nat Commun. 2014 Jun 19;5 :4167. Epub 2014 Jun 19. PMID: 24942562


Cui W, Joshi NS, Liu Y, Meng H, Kleinstein SH and Kaech SM: TLR4 ligands lipopolysaccharide and monophosphoryl lipid a differentially regulate effector and memory CD8+ T Cell differentiation. J Immunol. 2014 May 1;192 (9) :4221-32. Epub 2014 Mar 21. PMID: 24659688


Bolen CR, Ding S, Robek MD and Kleinstein SH: Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression. Hepatology. 2014 Apr;59 (4) :1262-72. Epub 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 and Church GM: High-resolution antibody dynamics of vaccine-induced immune responses. Proc Natl Acad Sci U S A. 2014 Apr 1;111 (13) :4928-33. Epub 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 and Montgomery RR: Immune markers associated with host susceptibility to infection with West Nile virus. Viral Immunol. 2014 Mar;27 (2) :39-47. PMID: 24605787


Katz SG, Labelle JL, Meng H, Valeriano RP, Fisher JK, Sun H, Rodig SJ, Kleinstein SH and Walensky LD: Mantle cell lymphoma in cyclin D1 transgenic mice with Bim-deficient B cells. Blood. 2014 Feb 6;123 (6) :884-93. Epub 2013 Dec 18. PMID: 24352880


Uduman M, Shlomchik MJ, Vigneault F, Church GM and Kleinstein SH: Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences. J Immunol. 2014 Feb 1;192 (3) :867-74. Epub 2013 Dec 27. PMID: 24376267


Brusic V, Gottardo R, Kleinstein SH and Davis MM: Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium. Nat Biotechnol. 2014 Feb;32 (2) :146-8. Epub 2014 Jan 19. PMID: 24441472

Thakar J, Schmid S, Duke JL, García-Sastre A and Kleinstein SH: Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms. J Interferon Cytokine Res. 2013 Nov;33 (11) :700-8. Epub 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 and O'Connor KC: The immune cell infiltrate populating meningiomas is composed of mature, antigen-experienced T and B cells. Neuro Oncol. 2013 Nov;15 (11) :1479-90. Epub 2013 Aug 26. PMID: 23978377


Yaari G, Bolen CR, Thakar J and 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;41 (18) :e170. Epub 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 and O'Connor KC: Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis. Neurology. 2013 Sep 10;81 (11) :956-63. Epub 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 and 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;132 (1) :170-81. Epub 2013 May 31. PMID: 23727037


Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG and Kleinstein SH: Multiple transcription factor binding sites predict AID targeting in non-Ig genes. J Immunol. 2013 Apr 15;190 (8) :3878-88. Epub 2013 Mar 20. PMID: 23514741


Qian F, Bolen CR, Jing C, Wang X, Zheng W, Zhao H, Fikrig E, Bruce RD, Kleinstein SH and 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;20 (2) :146-55. Epub 2012 Dec 5. PMID: 23220997


Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC and Kleinstein SH: Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics. 2013;14 Suppl 6 :S1. Epub 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 and Kleinstein SH: Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013;4 :358. Epub 2013 Nov 15. PMID: 24298272


Bolen CR, Robek MD, Brodsky L, Schulz V, Lim JK, Taylor MW and 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;33 (1) :15-23. Epub 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 and Poignard P: The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. PLoS Pathog. 2013;9 (11) :e1003754. Epub 2013 Nov 21. PMID: 24278016

Kohler KM, McDonald JJ, Duke JL, Arakawa H, Tan S, Kleinstein SH, Buerstedde JM and Schatz DG: Identification of core DNA elements that target somatic hypermutation. J Immunol. 2012 Dec 1;189 (11) :5314-26. Epub 2012 Oct 19. PMID: 23087403


Yaari G, Uduman M and Kleinstein SH: Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 Sep 1;40 (17) :e134. Epub 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 and Flavell RA: NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells. Nature. 2012 Apr 25;484 (7395) :510-3. Epub 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 and Kaech SM: Differential expression of Ly6C and T-bet distinguish effector and memory Th1 CD4(+) cell properties during viral infection. Immunity. 2011 Oct 28;35 (4) :633-46. Epub 2011 Oct 20. PMID: 22018471


Costa KD, Kleinstein SH and Hershberg U: Biomedical model fitting and error analysis. Sci Signal. 2011 Sep 20;4 (192) :tr9. Epub 2011 Sep 20. PMID: 21954296


Frucht CS, Uduman M, Kleinstein SH, Santos-Sacchi J and Navaratnam DS: Gene expression gradients along the tonotopic axis of the chicken auditory epithelium. J Assoc Res Otolaryngol. 2011 Aug;12 (4) :423-35. Epub 2011 Mar 12. PMID: 21399991


Cohen RM, Kleinstein SH and Louzoun Y: Somatic hypermutation targeting is influenced by location within the immunoglobulin V region. Mol Immunol. 2011 Jul;48 (12-13) :1477-83. Epub 2011 May 18. PMID: 21592579


Uduman M, Yaari G, Hershberg U, Stern JA, Shlomchik MJ and Kleinstein SH: Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39 (Web Server issue) :W499-504. Epub 2011 Jun 10. PMID: 21665923


Bolen CR, Uduman M and Kleinstein SH: Cell subset prediction for blood genomic studies. BMC Bioinformatics. 2011 Jun 24;12 :258. Epub 2011 Jun 24. PMID: 21702940


Kerfoot SM, Yaari G, Patel JR, Johnson KL, Gonzalez DG, Kleinstein SH and Haberman AM: Germinal center B cell and T follicular helper cell development initiates in the interfollicular zone. Immunity. 2011 Jun 24;34 (6) :947-60. 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 and Holt PR: Altered folate availability modifies the molecular environment of the human colorectum: implications for colorectal carcinogenesis. Cancer Prev Res (Phila). 2011 Apr;4 (4) :530-43. Epub 2011 Feb 14. PMID: 21321062


O'Connor MJ, Hauser AE, Haberman AM and Kleinstein SH: Activated germinal centre B cells undergo directed migration. Int J Data Min Bioinform. 2011;5 (3) :321-31. PMID: 21805826

Frucht CS, Uduman M, Duke JL, Kleinstein SH, Santos-Sacchi J and Navaratnam DS: Gene expression analysis of forskolin treated basilar papillae identifies microRNA181a as a mediator of proliferation. PLoS One. 2010 Jul 9;5 (7) :e11502. Epub 2010 Jul 9. PMID: 20634979


Pagliaccetti NE, Chu EN, Bolen CR, Kleinstein SH and 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;401 (2) :197-206. Epub 2010 Mar 29. PMID: 20303135


Nudelman G, Ge Y, Hu J, Kumar M, Seto J, Duke JL, Kleinstein SH, Hayot F, Sealfon SC and Wetmur JG: Coregulation mapping based on individual phenotypic variation in response to virus infection. Immunome Res. 2010 Mar 18;6 :2. Epub 2010 Mar 18. PMID: 20298589


Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, Tenoever BR, Sealfon SC and Kleinstein SH: Antiviral response dictated by choreographed cascade of transcription factors. J Immunol. 2010 Mar 15;184 (6) :2908-17. Epub 2010 Feb 17. PMID: 20164420

Anderson SM, Khalil A, Uduman M, Hershberg U, Louzoun Y, Haberman AM, Kleinstein SH and 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;183 (11) :7314-25. Epub 2009 Nov 16. PMID: 19917681


Bruno VM, Hannemann S, Lara-Tejero M, Flavell RA, Kleinstein SH and Galán JE: Salmonella Typhimurium type III secretion effectors stimulate innate immune responses in cultured epithelial cells. PLoS Pathog. 2009 Aug;5 (8) :e1000538. Epub 2009 Aug 7. PMID: 19662166

Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P and 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;283 (44) :30079-89. Epub 2008 Aug 29. PMID: 18757365


Kleinstein SH: Getting started in computational immunology. PLoS Comput Biol. 2008 Aug 29;4 (8) :e1000128. Epub 2008 Aug 29. PMID: 18769677


Hershberg U, Uduman M, Shlomchik MJ and Kleinstein SH: Improved methods for detecting selection by mutation analysis of Ig V region sequences. Int Immunol. 2008 May;20 (5) :683-94. Epub 2008 Apr 7. PMID: 18397909


Liu M, Duke JL, Richter DJ, Vinuesa CG, Goodnow CC, Kleinstein SH and Schatz DG: Two levels of protection for the B cell genome during somatic hypermutation. Nature. 2008 Feb 14;451 (7180) :841-5. PMID: 18273020

Hauser AE, Junt T, Mempel TR, Sneddon MW, Kleinstein SH, Henrickson SE, von Andrian UH, Shlomchik MJ and Haberman AM: Definition of germinal-center B cell migration in vivo reveals predominant intrazonal circulation patterns. Immunity. 2007 May;26 (5) :655-67. PMID: 17509908

Magori-Cohen R, Louzoun Y and Kleinstein SH: Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. Bioinformatics. 2006 Jul 15;22 (14) :e332-40. PMID: 16873490

Kleinstein SH, Louzoun Y and Shlomchik MJ: Estimating hypermutation rates from clonal tree data. J Immunol. 2003 Nov 1;171 (9) :4639-49. PMID: 14568938


Kleinstein SH and 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;15 (7) :871-84. PMID: 12807826