Genomics of infection and immunity
Genome MedicineFootprints of antigen processing boost MHC class II natural ligand predictions
Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, ...Genome Medicine 2018 10:84Recent advances in immunotherapies: from infection and autoimmunity, to cancer, and back again
For at least 300 years the immune system has been targeted to improve human health. Decades of work advancing immunotherapies against infection and autoimmunity paved the way for the current explosion in cance...Genome Medicine 2018 10:79Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
The IRE1a-XBP1 pathway is a conserved adaptive mediator of the unfolded protein response. The pathway is indispensable for the development of secretory cells by facilitating protein folding and enhancing secre...Genome Medicine 2018 10:76Advanced model systems and tools for basic and translational human immunology
There are fundamental differences between humans and the animals we typically use to study the immune system. We have learned much from genetically manipulated and inbred animal models, but instances in which ...Genome Medicine 2018 10:73- Genome Medicine 2018 10:72
Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells
We have previously reported an antigen-specific protocol to induce transplant tolerance and linked suppression to human embryonic stem cell (hESC)-derived tissues in immunocompetent mice through coreceptor and...Genome Medicine 2018 10:71Exploring the pre-immune landscape of antigen-specific T cells
Adaptive immune responses to newly encountered pathogens depend on the mobilization of antigen-specific clonotypes from a vastly diverse pool of naive T cells. Using recent advances in immune repertoire sequen...Genome Medicine 2018 10:68A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle
The 2014–2016 Ebola virus (EBOV) outbreak in West Africa highlighted the need for improved therapeutic options against this virus. Approaches targeting host factors/pathways essential for the virus are advanta...Genome Medicine 2018 10:58Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines
Humoral immune responses to infectious agents or vaccination vary substantially among individuals, and many of the factors responsible for this variability remain to be defined. Current evidence suggests that ...Genome Medicine 2018 10:59Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing
Plasmodium vivax poses a significant challenge to malaria elimination due to its ability to cause relapsed infections from reactivation of dormant liver parasites called hypnozoites. We analyzed 69 P. vivax whole...Genome Medicine 2018 10:52INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance
A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and in...Genome Medicine 2018 10:46Genomic surveillance of avian-origin influenza A viruses causing human disease
Avian influenza A viruses (AIVs) pose a threat to global health because of their sporadic zoonotic transmission and potential to cause pandemics. Genomic surveillance of AIVs has become a powerful, cost-effect...Genome Medicine 2018 10:50Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease
The genetic and immunological factors that contribute to differences in susceptibility and progression between sub-types of inflammatory and autoimmune diseases continue to be elucidated. Inflammatory bowel di...Genome Medicine 2018 10:48Developing Zika vaccines: the lessons for disease X
There is an urgent need to develop vaccines against emerging diseases, including those caused by pathogens that are currently unknown to cause human disease, termed ‘disease X’. Here, Zika virus infection is c...Genome Medicine 2018 10:47KLRD1-expressing natural killer cells predict influenza susceptibility
Influenza infects tens of millions of people every year in the USA. Other than notable risk groups, such as children and the elderly, it is difficult to predict what subpopulations are at higher risk of infect...Genome Medicine 2018 10:45Antifungal immune responses: emerging host–pathogen interactions and translational implications
Understanding the complex and highly dynamic interactions between fungi and host cells in a tissue-specific manner is crucial to facilitate the development of new therapeutic approaches to infections. Here, we...Genome Medicine 2018 10:39Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes
Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple a...Genome Medicine 2018 10:34BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstr...Genome Medicine 2018 10:20
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