Mark M Davis

Mark M Davis

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Mark M Davis

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Predicting HLA class II antigen presentation through integrated deep learning.

Nat Biotechnol 2019 Oct 14. Epub 2019 Oct 14.

Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41587-019-0280-2DOI Listing
October 2019

The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system.

Sci Data 2019 Oct 21;6(1):214. Epub 2019 Oct 21.

Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94304, USA.

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http://dx.doi.org/10.1038/s41597-019-0213-4DOI Listing
October 2019

SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses.

J Immunol 2019 Aug 14;203(3):749-759. Epub 2019 Jun 14.

Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304.

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http://dx.doi.org/10.4049/jimmunol.1900033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643048PMC
August 2019

Computational and Systems Immunology: A Student's Perspective.

Trends Immunol 2019 Aug 6;40(8):665-668. Epub 2019 Jul 6.

Department of Medicine, Center for Biomedical Research, Stanford University, Stanford, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2019.06.006DOI Listing
August 2019

Recent progress in the analysis of αβT cell and B cell receptor repertoires.

Curr Opin Immunol 2019 Aug 18;59:109-114. Epub 2019 Jul 18.

Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; The Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1016/j.coi.2019.05.012DOI Listing
August 2019

Allergen-specific CD8 T cells in peanut-allergic individuals.

J Allergy Clin Immunol 2019 May 22;143(5):1948-1952. Epub 2019 Jan 22.

Sean N. Parker Center for Allergy and Asthma Research at Stanford University School of Medicine, Stanford, Calif; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, Calif; Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University, Stanford, Calif. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2019.01.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510483PMC
May 2019

Select sequencing of clonally expanded CD8 T cells reveals limits to clonal expansion.

Proc Natl Acad Sci U S A 2019 Apr 16;116(18):8995-9001. Epub 2019 Apr 16.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1902649116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500157PMC
April 2019

Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients.

Nat Biotechnol 2019 03 18;37(3):252-258. Epub 2019 Feb 18.

Department of Surgery, Division of Cardiothoracic Surgery, Transplant and Stem Cell Immunobiology-Lab, University of California San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41587-019-0016-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419516PMC
March 2019

Histone H3 lysine 4 methylation signature associated with human undernutrition.

Proc Natl Acad Sci U S A 2018 11 12;115(48):E11264-E11273. Epub 2018 Nov 12.

Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908;

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http://dx.doi.org/10.1073/pnas.1722125115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275549PMC
November 2018

Advanced model systems and tools for basic and translational human immunology.

Genome Med 2018 09 28;10(1):73. Epub 2018 Sep 28.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13073-018-0584-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162943PMC
September 2018

Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? Seeing the Forest Rather than a Few Trees.

Cold Spring Harb Perspect Biol 2018 08 1;10(8). Epub 2018 Aug 1.

Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94304.

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http://dx.doi.org/10.1101/cshperspect.a028886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902661PMC
August 2018

Plasmablast antibody repertoires in elderly influenza vaccine responders exhibit restricted diversity but increased breadth of binding across influenza strains.

Clin Immunol 2018 08 2;193:70-79. Epub 2018 Feb 2.

Geriatric Research Education and Clinical Center (GRECC), Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA; Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.clim.2018.01.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026060PMC
August 2018

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.

Cell 2018 07;174(3):672-687.e27

Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140336PMC
July 2018

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging.

Cell 2018 05 26;173(6):1385-1397.e14. Epub 2018 Apr 26.

Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183045
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http://dx.doi.org/10.1016/j.cell.2018.03.079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984186PMC
May 2018

Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo.

Cell Stem Cell 2018 04 15;22(4):501-513.e7. Epub 2018 Feb 15.

Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.01.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6134179PMC
April 2018

Rebooting Human Immunology.

Annu Rev Immunol 2018 04 28;36:843-864. Epub 2018 Feb 28.

Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17121 Solna, Sweden.

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http://dx.doi.org/10.1146/annurev-immunol-042617-053206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677260PMC
April 2018

A Macrophage Colony-Stimulating-Factor-Producing γδ T Cell Subset Prevents Malarial Parasitemic Recurrence.

Immunity 2018 02 6;48(2):350-363.e7. Epub 2018 Feb 6.

Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2018.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5956914PMC
February 2018

can mitigate intestinal immunopathology in the context of CTLA-4 blockade.

Proc Natl Acad Sci U S A 2018 01 18;115(1):157-161. Epub 2017 Dec 18.

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1712901115
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http://dx.doi.org/10.1073/pnas.1712901115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776803PMC
January 2018

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes.

Cell 2018 01 21;172(3):549-563.e16. Epub 2017 Dec 21.

Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.11.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786495PMC
January 2018

High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization.

Immunity 2017 12 5;47(6):1037-1050.e6. Epub 2017 Dec 5.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738280PMC
December 2017

Reply to Roerink et al: Methods for recruitment, serum separation, and storage were the same for patients and controls.

Proc Natl Acad Sci U S A 2017 11 30;114(45):E9436. Epub 2017 Oct 30.

Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1714692114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5692597PMC
November 2017

Clonal Expansion and Interrelatedness of Distinct B-Lineage Compartments in Multiple Myeloma Bone Marrow.

Cancer Immunol Res 2017 09 2;5(9):744-754. Epub 2017 Aug 2.

Department of Microbiology and Immunology, Stanford University, Stanford, California.

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http://cancerimmunolres.aacrjournals.org/lookup/doi/10.1158/
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http://dx.doi.org/10.1158/2326-6066.CIR-17-0012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590392PMC
September 2017

Cytokine signature associated with disease severity in chronic fatigue syndrome patients.

Proc Natl Acad Sci U S A 2017 08 31;114(34):E7150-E7158. Epub 2017 Jul 31.

Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1710519114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576836PMC
August 2017

Continuous immunotypes describe human immune variation and predict diverse responses.

Proc Natl Acad Sci U S A 2017 07 10;114(30):E6097-E6106. Epub 2017 Jul 10.

Science for Life laboratory, Department of Medicine, Karolinska Institutet, Solna 17177, Sweden;

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http://dx.doi.org/10.1073/pnas.1705065114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544312PMC
July 2017

Systems immunology: just getting started.

Nat Immunol 2017 Jun;18(7):725-732

Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/ni.3768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790187PMC
June 2017

The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires.

BMC Bioinformatics 2017 Mar 7;18(1):155. Epub 2017 Mar 7.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305, CA, USA.

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http://dx.doi.org/10.1186/s12859-017-1556-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340033PMC
March 2017

Human immune system variation.

Nat Rev Immunol 2017 01 5;17(1):21-29. Epub 2016 Dec 5.

Department of Microbiology and Immunology, Stanford University School of Medicine.

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http://dx.doi.org/10.1038/nri.2016.125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328245PMC
January 2017

Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging.

Proc Natl Acad Sci U S A 2017 01 17;114(5):1105-1110. Epub 2017 Jan 17.

Department of Applied Physics, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1617959114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5293037PMC
January 2017

MHC-Peptide Tetramers to Visualize Antigen-Specific T Cells.

Curr Protoc Immunol 2016 11 1;115:17.3.1-17.3.44. Epub 2016 Nov 1.

Stanford University School of Medicine and The Howard Hughes Medical Institute, Palo Alto, California.

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http://dx.doi.org/10.1002/cpim.14DOI Listing
November 2016

Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.

J Immunol 2016 10 21;197(8):3086-3098. Epub 2016 Sep 21.

Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055199PMC
http://dx.doi.org/10.4049/jimmunol.1502031DOI Listing
October 2016

Antigen exposure shapes the ratio between antigen-specific Tregs and conventional T cells in human peripheral blood.

Proc Natl Acad Sci U S A 2016 10 28;113(41):E6192-E6198. Epub 2016 Sep 28.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304

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http://dx.doi.org/10.1073/pnas.1611723113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068288PMC
October 2016

Defective T Memory Cell Differentiation after Varicella Zoster Vaccination in Older Individuals.

PLoS Pathog 2016 Oct 20;12(10):e1005892. Epub 2016 Oct 20.

Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1005892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072604PMC
October 2016

Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans.

Cell Syst 2016 10 13;3(4):374-384.e4. Epub 2016 Oct 13.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://www.cell.com/cell-systems/pdf/S2405-4712(16)30299-X.p
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http://dx.doi.org/10.1016/j.cels.2016.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358544PMC
October 2016

Inhibition of T cell receptor signaling by cholesterol sulfate, a naturally occurring derivative of membrane cholesterol.

Nat Immunol 2016 07 23;17(7):844-50. Epub 2016 May 23.

The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/ni.3462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916016PMC
July 2016

In Praise of Descriptive Science: A Breath of Fresh AIRE.

Authors:
Mark M Davis

Cell 2016 Jul;166(3):530-531

Howard Hughes Medical Institute, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.07.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294994PMC
July 2016

Drug-induced mRNA signatures are enriched for the minority of genes that are highly heritable.

Pac Symp Biocomput 2015 :395-406

Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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April 2016

Successful immunotherapy induces previously unidentified allergen-specific CD4+ T-cell subsets.

Proc Natl Acad Sci U S A 2016 Mar 25;113(9):E1286-95. Epub 2016 Jan 25.

Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Pulmonary and Critical Care Medicine, Institute of Immunity, Transplantation, and Infectious Diseases, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1520180113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780622PMC
March 2016

CXCL13 is a plasma biomarker of germinal center activity.

Proc Natl Acad Sci U S A 2016 Mar 23;113(10):2702-7. Epub 2016 Feb 23.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, La Jolla, CA 92037;

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http://dx.doi.org/10.1073/pnas.1520112113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790995PMC
March 2016

Detection, phenotyping, and quantification of antigen-specific T cells using a peptide-MHC dodecamer.

Proc Natl Acad Sci U S A 2016 Mar 15;113(13):E1890-7. Epub 2016 Mar 15.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305

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http://dx.doi.org/10.1073/pnas.1602488113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822615PMC
March 2016

Human B-cell isotype switching origins of IgE.

J Allergy Clin Immunol 2016 Feb 22;137(2):579-586.e7. Epub 2015 Aug 22.

Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2015.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747810PMC
February 2016

Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus.

J Allergy Clin Immunol 2015 Nov 30;136(5):1326-36. Epub 2015 May 30.

Department of Microbiology and Immunology, Stanford University, Stanford, Calif; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, Calif; Howard Hughes Medical Institute, Stanford University, Stanford, Calif. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2015.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640970PMC
November 2015

Distinct Roles of Cytoskeletal Components in Immunological Synapse Formation and Directed Secretion.

J Immunol 2015 Nov 21;195(9):4117-25. Epub 2015 Sep 21.

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; and

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http://dx.doi.org/10.4049/jimmunol.1402175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610857PMC
November 2015

Not-So-Negative Selection.

Authors:
Mark M Davis

Immunity 2015 Nov;43(5):833-5

Howard Hughes Medical Institute; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2015.11.002DOI Listing
November 2015

William Erwin Paul (1936-2015).

Cell 2015 Oct;163(3):529-30

Howard Hughes Medical Institute, Department of Microbiology and Immunology, Institute of Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA

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https://linkinghub.elsevier.com/retrieve/pii/S00928674150133
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http://dx.doi.org/10.1016/j.cell.2015.10.024DOI Listing
October 2015

Pregnancy Does Not Attenuate the Antibody or Plasmablast Response to Inactivated Influenza Vaccine.

J Infect Dis 2015 Sep 4;212(6):861-70. Epub 2015 Mar 4.

Stanford Immunology, Stanford University School of Medicine Department of Medicine, Stanford University School of Medicine, California.

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http://dx.doi.org/10.1093/infdis/jiv138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548461PMC
September 2015

New approaches to understanding the immune response to vaccination and infection.

Vaccine 2015 Sep 29;33(40):5271-81. Epub 2015 Jul 29.

Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, United States; Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.vaccine.2015.06.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581990PMC
September 2015

mir-181a-1/b-1 Modulates Tolerance through Opposing Activities in Selection and Peripheral T Cell Function.

J Immunol 2015 Aug 10;195(4):1470-9. Epub 2015 Jul 10.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305; Achelois Pharmaceuticals, Inc., San Francisco, CA 94107

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http://dx.doi.org/10.4049/jimmunol.1401587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763610PMC
August 2015

Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma.

Cancer Immunol Res 2015 Jun 20;3(6):650-60. Epub 2015 Feb 20.

Department of Microbiology and Immunology, Stanford University, Stanford, California. Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California. The Howard Hughes Medical Institute, Stanford University, Stanford, California.

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http://dx.doi.org/10.1158/2326-6066.CIR-14-0236-TDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457663PMC
June 2015

Clonal Deletion Prunes but Does Not Eliminate Self-Specific αβ CD8(+) T Lymphocytes.

Immunity 2015 May;42(5):929-41

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2015.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455602PMC
May 2015

Distinct patterns of B-cell activation and priming by natural influenza virus infection versus inactivated influenza vaccination.

J Infect Dis 2015 Apr 21;211(7):1051-9. Epub 2014 Oct 21.

Department of Medicine Department of Microbiology and Immunology VA Palo Alto Health Care System, California.

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http://dx.doi.org/10.1093/infdis/jiu580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366605PMC
April 2015

Cytomegalovirus infection enhances the immune response to influenza.

Sci Transl Med 2015 Apr;7(281):281ra43

Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA. Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA. The Howard Hughes Medical Institute.

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http://dx.doi.org/10.1126/scitranslmed.aaa2293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4505610PMC
April 2015

The promised land of human immunology.

Cold Spring Harb Symp Quant Biol 2013 17;78:203-13. Epub 2014 Mar 17.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305 Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305

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http://dx.doi.org/10.1101/sqb.2013.78.022905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896736PMC
March 2015

The coreceptor CD4 is expressed in distinct nanoclusters and does not colocalize with T-cell receptor and active protein tyrosine kinase p56lck.

Proc Natl Acad Sci U S A 2015 Mar 17;112(13):E1604-13. Epub 2015 Mar 17.

The Howard Hughes Medical Institute and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; and

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http://dx.doi.org/10.1073/pnas.1503532112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386407PMC
March 2015

Variation in the human immune system is largely driven by non-heritable influences.

Cell 2015 Jan;160(1-2):37-47

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.12.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302727PMC
January 2015

Immunology. Flexibility for specificity.

Authors:
Mark M Davis

Science 2015 Jan;347(6220):371-2

Howard Hughes Medical Institute, Institute for Immunity, Transplantation and Infection, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1126/science.aaa5082DOI Listing
January 2015

The Split Virus Influenza Vaccine rapidly activates immune cells through Fcγ receptors.

Vaccine 2014 Oct 6;32(45):5989-97. Epub 2014 Sep 6.

The Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, United States; Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305, United States; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, United States. Electronic address:

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http://dx.doi.org/10.1016/j.vaccine.2014.07.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191649PMC
October 2014

Clinical recovery from surgery correlates with single-cell immune signatures.

Sci Transl Med 2014 Sep;6(255):255ra131

Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1126/scitranslmed.3009701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334126PMC
September 2014

Association between latent proviral characteristics and immune activation in antiretrovirus-treated human immunodeficiency virus type 1-infected adults.

J Virol 2014 Aug 21;88(15):8629-39. Epub 2014 May 21.

Department of Medicine, Stanford University School of Medicine, Stanford, California, USA Stanford Immunology, Stanford University School of Medicine, Stanford, California, USA Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA

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http://dx.doi.org/10.1128/JVI.01257-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135944PMC
August 2014

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.

PLoS Comput Biol 2014 Aug 28;10(8):e1003806. Epub 2014 Aug 28.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America; Department of Statistics, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148203PMC
August 2014

Linking T-cell receptor sequence to functional phenotype at the single-cell level.

Nat Biotechnol 2014 Jul 22;32(7):684-92. Epub 2014 Jun 22.

1] Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA. [2] Program in Computational and Systems Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA. [3] Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/nbt.2938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337815PMC
July 2014

Deconstructing the peptide-MHC specificity of T cell recognition.

Cell 2014 May;157(5):1073-87

Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.03.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071348PMC
May 2014