Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes

Human genetic variation and the gut microbiome in disease

(2017) Andrew Brantley Hall et al.   NATURE REVIEWS GENETICS

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens

(2016) Melody Y. Zeng et al.   IMMUNITY

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome ProceedsViaHigh Specificity

(2016) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

(2016) Kate L. Ormerod et al.   Microbiome

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Immune–microbiota interactions in health and disease

(2015) Noah W. Palm et al.   CLINICAL IMMUNOLOGY

Determinants of immunodominance for CD4 T cells

(2015) AeRyon Kim et al.   CURRENT OPINION IN IMMUNOLOGY

High-resolution analysis of the murine MHC class II immunopeptidome

(2015) Adriana Sofron et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Human seroreactivity to gut microbiota antigens

(2015) Benjamin S. Christmann et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS

(2015) Jan Krönke et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

(2015) Philippe Goyette et al.   NATURE GENETICS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

First Signature of Islet  -Cell-Derived Naturally Processed Peptides Selected by Diabetogenic Class II MHC Molecules

(2014) A. Suri et al.   JOURNAL OF IMMUNOLOGY

Ischemia in Tumors Induces Early and Sustained Phosphorylation Changes in Stress Kinase Pathways but Does Not Affect Global Protein Levels

(2014) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis

(2014) Matthew L Stoll et al.   ARTHRITIS RESEARCH & THERAPY

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

(2014) J. X. Binder et al.   Database-The Journal of Biological Databases and Curation

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells

(2014) Andrew McDavid et al.   PLoS Computational Biology

Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice From Salmonella Infection

(2013) Kara L. Conway et al.   GASTROENTEROLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Distinct CD4+ helper T cells involved in primary and secondary responses to infection

(2012) K. S. Weber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mechanism of HLA-DM induced peptide exchange in the MHC class II antigen presentation pathway

(2011) Monika-Sarah ED Schulze et al.   CURRENT OPINION IN IMMUNOLOGY

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

(2011) Massimo Andreatta et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy

(2009) F. R. Depontieu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A dominant, coordinated T regulatory cell-IgA response to the intestinal microbiota

(2009) Y. Cong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach

(2008) Peng Wang et al.   PLoS Computational Biology