Genomics of infection and immunity

Genomics of infection and immunity

Genome Medicine is pleased to present a special issue on Genomics of infection and immunity, co-guest edited by Bali Pulendran and Mark Davis of Stanford School of Medicine. The issue captures recent advances made using genomic approaches toward understanding the function and diversity of the immune system, regulation of the immune response, and the underlying mechanisms of host defense against infection. It also covers pathogen adaptation and evasion strategies, as well as development of tools and approaches to monitor, protect against, and treat infectious disease.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process.

1. Content Type:Research

   Footprints 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, ...

   Authors:Carolina Barra, Bruno Alvarez, Sinu Paul, Alessandro Sette, Bjoern Peters, Massimo Andreatta, Søren Buus and Morten Nielsen

   Citation:Genome Medicine 2018 10:84

   Published on: 16 November 2018

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2. Content Type:Opinion

   Recent 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...

   Authors:Samantha L. Bucktrout, Jeffrey A. Bluestone and Fred Ramsdell

   Citation:Genome Medicine 2018 10:79

   Published on: 31 October 2018

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3. Content Type:Research

   Genome-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...

   Authors:Jhuma Pramanik, Xi Chen, Gozde Kar, Johan Henriksson, Tomás Gomes, Jong-Eun Park, Kedar Natarajan, Kerstin B. Meyer, Zhichao Miao, Andrew N. J. McKenzie, Bidesh Mahata and Sarah A. Teichmann

   Citation:Genome Medicine 2018 10:76

   Published on: 24 October 2018

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4. Content Type:Review

   Advanced 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 ...

   Authors:Lisa E. Wagar, Robert M. DiFazio and Mark M. Davis

   Citation:Genome Medicine 2018 10:73

   Published on: 28 September 2018

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5. Content Type:Editorial

   Infection and immunity: insights and therapeutic strategies through genomic analysis of the host, pathogen, and host–pathogen interaction

   Authors:Julia Simundza

   Citation:Genome Medicine 2018 10:72

   Published on: 26 September 2018

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6. Content Type:Research

   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...

   Authors:Cherry S. Leung, Kevin Y. Yang, Xisheng Li, Vicken W. Chan, Manching Ku, Herman Waldmann, Shohei Hori, Jason C. H. Tsang, Yuk Ming Dennis Lo and Kathy O. Lui

   Citation:Genome Medicine 2018 10:71

   Published on: 20 September 2018

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7. Content Type:Research

   Exploring 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...

   Authors:Mikhail V. Pogorelyy, Alla D. Fedorova, James E. McLaren, Kristin Ladell, Dmitri V. Bagaev, Alexey V. Eliseev, Artem I. Mikelov, Anna E. Koneva, Ivan V. Zvyagin, David A. Price, Dmitry M. Chudakov and Mikhail Shugay

   Citation:Genome Medicine 2018 10:68

   Published on: 25 August 2018

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8. Content Type:Research

   A 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...

   Authors:Scott Martin, Abhilash I. Chiramel, Marie Luisa Schmidt, Yu-Chi Chen, Nadia Whitt, Ari Watt, Eric C. Dunham, Kyle Shifflett, Shelby Traeger, Anne Leske, Eugen Buehler, Cynthia Martellaro, Janine Brandt, Lisa Wendt, Andreas Müller, Stephanie Peitsch…

   Citation:Genome Medicine 2018 10:58

   Published on: 7 August 2018

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9. Content Type:Research

   Human 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 ...

   Authors:Petar Scepanovic, Cécile Alanio, Christian Hammer, Flavia Hodel, Jacob Bergstedt, Etienne Patin, Christian W. Thorball, Nimisha Chaturvedi, Bruno Charbit, Laurent Abel, Lluis Quintana-Murci, Darragh Duffy, Matthew L. Albert and Jacques Fellay

   Citation:Genome Medicine 2018 10:59

   Published on: 27 July 2018

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10. Content Type:Research

    Exploration 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...

    Authors:Annie N. Cowell, Hugo O. Valdivia, Danett K. Bishop and Elizabeth A. Winzeler

    Citation:Genome Medicine 2018 10:52

    Published on: 4 July 2018

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11. Content Type:Software

    INSaFLU: 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...

    Authors:Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar and João Paulo Gomes

    Citation:Genome Medicine 2018 10:46

    Published on: 29 June 2018

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12. Content Type:Comment

    Genomic 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...

    Authors:Tommy T. Lam and Oliver G. Pybus

    Citation:Genome Medicine 2018 10:50

    Published on: 27 June 2018

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13. Content Type:Research

    Disease-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...

    Authors:Angela Mo, Urko M. Marigorta, Dalia Arafat, Lai Hin Kimi Chan, Lori Ponder, Se Ryeong Jang, Jarod Prince, Subra Kugathasan, Sampath Prahalad and Greg Gibson

    Citation:Genome Medicine 2018 10:48

    Published on: 27 June 2018

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14. Content Type:Comment

    Developing 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...

    Authors:Alan D. T. Barrett

    Citation:Genome Medicine 2018 10:47

    Published on: 26 June 2018

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15. Content Type:Research

    KLRD1-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...

    Authors:Erika Bongen, Francesco Vallania, Paul J. Utz and Purvesh Khatri

    Citation:Genome Medicine 2018 10:45

    Published on: 14 June 2018

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16. Content Type:Comment

    Antifungal 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...

    Authors:Vinod Kumar, Frank L. van de Veerdonk and Mihai G. Netea

    Citation:Genome Medicine 2018 10:39

    Published on: 25 May 2018

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17. Content Type:Method

    Simple 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...

    Authors:Praneeth Reddy Devulapally, Jörg Bürger, Thorsten Mielke, Zoltán Konthur, Hans Lehrach, Marie-Laure Yaspo, Jörn Glökler and Hans-Jörg Warnatz

    Citation:Genome Medicine 2018 10:34

    Published on: 27 April 2018

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18. Content Type:Method

    BALDR: 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...

    Authors:Amit A. Upadhyay, Robert C. Kauffman, Amber N. Wolabaugh, Alice Cho, Nirav B. Patel, Samantha M. Reiss, Colin Havenar-Daughton, Reem A. Dawoud, Gregory K. Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F. Eun-Hyung Lee, Jens Wrammert and Steven E. Bosinger

    Citation:Genome Medicine 2018 10:20

    Published on: 20 March 2018

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