Steven H Kleinstein

Steven H Kleinstein

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Steven H Kleinstein

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

J Immunol 2019 Oct 4;203(7):1687-1692. Epub 2019 Sep 4.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511;

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http://dx.doi.org/10.4049/jimmunol.1900666DOI Listing
October 2019

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

Front Immunol 2018 26;9:1687. Epub 2018 Jul 26.

Department of Pathology, Yale School of Medicine, New Haven, CT, United States.

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http://dx.doi.org/10.3389/fimmu.2018.01687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070604PMC
September 2019

Migrant memory B cells secrete luminal antibody in the vagina.

Nature 2019 07 12;571(7763):122-126. Epub 2019 Jun 12.

Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1038/s41586-019-1285-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609483PMC
July 2019

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

PLoS Comput Biol 2019 04 2;15(4):e1006899. Epub 2019 Apr 2.

Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1006899
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http://dx.doi.org/10.1371/journal.pcbi.1006899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461294PMC
April 2019

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

BMC Bioinformatics 2019 Apr 25;20(Suppl 5):182. Epub 2019 Apr 25.

Division for Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/s12859-019-2725-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509839PMC
April 2019

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

Front Immunol 2018 7;9:1976. Epub 2018 Sep 7.

Department of Pathology, Yale School of Medicine, New Haven, CT, United States.

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http://dx.doi.org/10.3389/fimmu.2018.01976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137163PMC
September 2018

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

Cell Rep 2018 09;24(13):3367-3373.e4

Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Immunology Graduate Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183137
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http://dx.doi.org/10.1016/j.celrep.2018.08.075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192537PMC
September 2018

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

Bioinformatics 2018 07;34(13):i341-i349

Department of Pathology, Yale School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022594PMC
July 2018

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

Bioinformatics 2017 Jul;33(14):i208-i216

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870750PMC
July 2017

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

J Immunol 2017 03 8;198(6):2489-2499. Epub 2017 Feb 8.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520;

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http://dx.doi.org/10.4049/jimmunol.1601850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340603PMC
March 2017

Solving Immunology?

Trends Immunol 2017 02 13;38(2):116-127. Epub 2016 Dec 13.

Center for Advanced Research on Diagnostic Assays, Immunology Institute, Friedman Brain Institute, and Departments of Neurology, Neuroscience, Pharmacology, and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2016.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695553PMC
February 2017

Recurrent genetic defects in classical Hodgkin lymphoma cell lines.

Leuk Lymphoma 2016 12 27;57(12):2890-2900. Epub 2016 Apr 27.

a Department of Pathology, Yale School of Medicine , New Haven , CT , USA.

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http://dx.doi.org/10.1080/10428194.2016.1177179DOI Listing
December 2016

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

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

Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkw633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175335PMC
November 2016

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

J Immunol 2016 11 5;197(9):3566-3574. Epub 2016 Oct 5.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511;

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http://dx.doi.org/10.4049/jimmunol.1502263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161250PMC
November 2016

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.

J Virol 2016 10 12;90(19):8875-90. Epub 2016 Sep 12.

Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA

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http://dx.doi.org/10.1128/JVI.01089-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021391PMC
October 2016

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

J Exp Med 2015 Nov 26;212(12):2041-56. Epub 2015 Oct 26.

Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520 Howard Hughes Medical Institute, Chevy Chase, MD 20815

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http://dx.doi.org/10.1084/jem.20150186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647261PMC
November 2015

Practical guidelines for B-cell receptor repertoire sequencing analysis.

Genome Med 2015 Nov 20;7:121. Epub 2015 Nov 20.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA.

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http://dx.doi.org/10.1186/s13073-015-0243-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654805PMC
November 2015

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

Bioinformatics 2015 Oct 10;31(20):3356-8. Epub 2015 Jun 10.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA and.

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http://dx.doi.org/10.1093/bioinformatics/btv359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793929PMC
October 2015

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

J Virol 2015 Oct 29;89(20):10190-205. Epub 2015 Jul 29.

Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA

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http://dx.doi.org/10.1128/JVI.01523-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580178PMC
October 2015

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;370(1676)

Department of Mathematics, Bar-Ilan University, Ramat Gan 5290002, Israel Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 5290002, Israel

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http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rstb.2014.0242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528419PMC
September 2015

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

Cell 2015 Sep 27;162(6):1217-28. Epub 2015 Aug 27.

Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.08.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567953PMC
September 2015

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 6;16(8):871-9. Epub 2015 Jul 6.

1] Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA. [2] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

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http://www.nature.com/articles/ni.3224
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http://dx.doi.org/10.1038/ni.3224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713030PMC
August 2015

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

BMC Immunol 2015 Aug 14;16:46. Epub 2015 Aug 14.

Department of Pathology, Yale School of Medicine, New Haven, CT, 06510, USA.

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http://dx.doi.org/10.1186/s12865-015-0107-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536893PMC
August 2015

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

Immunity 2015 Jul 14;43(1):120-31. Epub 2015 Jul 14.

Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Laboratory Medicine and Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2015.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523395PMC
July 2015

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 9;112(8):E862-70. Epub 2015 Feb 9.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; Department of Pathology and Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT 06511; and

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http://dx.doi.org/10.1073/pnas.1417683112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345584PMC
February 2015

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;134(3):604-12

Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom; Medical Research Council and Asthma UK Centre, Allergic Mechanisms in Asthma, London, United Kingdom.

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http://dx.doi.org/10.1016/j.jaci.2014.07.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151999PMC
September 2014

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

Bioinformatics 2014 Jul 10;30(13):1930-2. Epub 2014 Mar 10.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USAInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, Department of Pathology, Yale School of Medicine, New Haven, CT 06511, Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, Department of Neurology, Yale School of Medicine, New Haven, CT 06511, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and AbVitro Inc., Boston, MA 02210, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071206PMC
July 2014

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

Nat Immunol 2014 Jul 1;15(7):631-7. Epub 2014 Jun 1.

1] Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA. [2] Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA. [3].

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http://www.nature.com/articles/ni.2914
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http://dx.doi.org/10.1038/ni.2914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105703PMC
July 2014

The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.

PLoS Pathog 2013 21;9(11):e1003754. Epub 2013 Nov 21.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America ; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America ; Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1003754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836729PMC
June 2014

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

J Immunol 2014 May 21;192(9):4221-32. Epub 2014 Mar 21.

Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520;

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http://dx.doi.org/10.4049/jimmunol.1302569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071140PMC
May 2014

Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression.

Hepatology 2014 Apr 18;59(4):1262-72. Epub 2014 Feb 18.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT.

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http://dx.doi.org/10.1002/hep.26657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938553PMC
April 2014

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

Blood 2014 Feb 18;123(6):884-93. Epub 2013 Dec 18.

Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA;

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http://dx.doi.org/10.1182/blood-2013-04-499079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916879PMC
February 2014

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

J Immunol 2014 Feb 27;192(3):867-74. Epub 2013 Dec 27.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520;

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http://www.jimmunol.org/cgi/doi/10.4049/jimmunol.1301551
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http://dx.doi.org/10.4049/jimmunol.1301551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363135PMC
February 2014

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

Front Immunol 2013 15;4:358. Epub 2013 Nov 15.

Bioengineering Program, Faculty of Engineering, Bar Ilan University , Ramat Gan , Israel ; Department of Pathology, Yale School of Medicine , New Haven, CT , USA.

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http://dx.doi.org/10.3389/fimmu.2013.00358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828525PMC
December 2013

Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms.

J Interferon Cytokine Res 2013 Nov 17;33(11):700-8. Epub 2013 Jun 17.

1 Department of Pathology, Yale School of Medicine , New Haven, Connecticut.

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http://dx.doi.org/10.1089/jir.2012.0113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814816PMC
November 2013

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.

Nucleic Acids Res 2013 Oct 5;41(18):e170. Epub 2013 Aug 5.

Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA, Bioengineering program, Faculty of engineering, Bar Ilan University, 5290002, Ramat Gan, Israel and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1093/nar/gkt660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794608PMC
October 2013

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.

BMC Bioinformatics 2013 17;14 Suppl 6:S1. Epub 2013 Apr 17.

Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S6-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633009PMC
September 2013

Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis.

Neurology 2013 Sep 6;81(11):956-63. Epub 2013 Aug 6.

From the Department of Neurology (L.Q., P.L.C., M.A.B., C.C., D.A.H., J.-Y.L., K.C.O.), Human and Translational Immunology Program (D.A.H., K.C.O.), Department of Genetics (C.C.), Department of Pathology (S.H.K., G.Y.), and Department of Immunobiology (D.A.H.), Yale School of Medicine, New Haven, CT; Neuromuscular Diseases Unit (L.Q.), Hospital de la Santa Creu i Sant Pau, Universitat Autónoma de Barcelona, Spain; Medical and Population Genetics (C.C.), Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (A.H.C.), Washington University School of Medicine, St. Louis, MO; Interdepartmental Program in Computational Biology and Bioinformatics (S.H.K.), Yale University, New Haven, CT; and Department of Neurology (S.N.W.), Harvard Medical School and Brigham and Women's Hospital, Boston, MA. Simon N. Willis is currently affiliated with the Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.

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http://www.neurology.org/cgi/doi/10.1212/WNL.0b013e3182a43b4
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http://dx.doi.org/10.1212/WNL.0b013e3182a43b48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888197PMC
September 2013

Multiple transcription factor binding sites predict AID targeting in non-Ig genes.

J Immunol 2013 Apr 20;190(8):3878-88. Epub 2013 Mar 20.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.4049/jimmunol.1202547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689293PMC
April 2013

The blood transcriptional signature of chronic hepatitis C virus is consistent with an ongoing interferon-mediated antiviral response.

J Interferon Cytokine Res 2013 Jan 15;33(1):15-23. Epub 2012 Oct 15.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1089/jir.2012.0037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539252PMC
January 2013

Identification of core DNA elements that target somatic hypermutation.

J Immunol 2012 Dec 19;189(11):5314-26. Epub 2012 Oct 19.

Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.4049/jimmunol.1202082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664039PMC
December 2012

Quantifying selection in high-throughput Immunoglobulin sequencing data sets.

Nucleic Acids Res 2012 Sep 27;40(17):e134. Epub 2012 May 27.

Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/nar/gks457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458526PMC
September 2012

Activated germinal centre B cells undergo directed migration.

Int J Data Min Bioinform 2011 ;5(3):321-31

University of Massachusetts Medical School, Worcester, MA 01655, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343311PMC
September 2011

Biomedical model fitting and error analysis.

Sci Signal 2011 Sep 20;4(192):tr9. Epub 2011 Sep 20.

Department of Medicine (Cardiology), Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1126/scisignal.2001983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272496PMC
September 2011

Gene expression gradients along the tonotopic axis of the chicken auditory epithelium.

J Assoc Res Otolaryngol 2011 Aug 12;12(4):423-35. Epub 2011 Mar 12.

Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1007/s10162-011-0259-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123449PMC
August 2011

Somatic hypermutation targeting is influenced by location within the immunoglobulin V region.

Mol Immunol 2011 Jul 18;48(12-13):1477-83. Epub 2011 May 18.

Math Department and Gonda Brain Research Center, Bar Ilan University, Ramat Gan 52900, Israel.

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http://dx.doi.org/10.1016/j.molimm.2011.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109224PMC
July 2011

Detecting selection in immunoglobulin sequences.

Nucleic Acids Res 2011 Jul 10;39(Web Server issue):W499-504. Epub 2011 Jun 10.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125793PMC
July 2011

Cell subset prediction for blood genomic studies.

BMC Bioinformatics 2011 Jun 24;12:258. Epub 2011 Jun 24.

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1186/1471-2105-12-258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213685PMC
June 2011

Salmonella Typhimurium type III secretion effectors stimulate innate immune responses in cultured epithelial cells.

PLoS Pathog 2009 Aug 7;5(8):e1000538. Epub 2009 Aug 7.

Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1371/journal.ppat.1000538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714975PMC
August 2009

Getting started in computational immunology.

PLoS Comput Biol 2008 Aug 29;4(8):e1000128. Epub 2008 Aug 29.

Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518523PMC
August 2008

Improved methods for detecting selection by mutation analysis of Ig V region sequences.

Int Immunol 2008 May 7;20(5):683-94. Epub 2008 Apr 7.

Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/intimm/dxn026DOI Listing
May 2008

Two levels of protection for the B cell genome during somatic hypermutation.

Nature 2008 Feb;451(7180):841-5

Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA.

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http://dx.doi.org/10.1038/nature06547DOI Listing
February 2008