Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

OMeta: an ontology-based, data-driven metadata tracking system

(2019) Indresh Singh et al.   BMC BIOINFORMATICS

Exploring the unmapped DNA and RNA reads in a songbird genome

(2019) Veronika N. Laine et al.   BMC GENOMICS

Genomic Advances in Avian Malaria Research

(2019) Elin Videvall   TRENDS IN PARASITOLOGY

Immune genes are hotspots of shared positive selection across birds and mammals

(2019) Allison J Shultz et al.   eLife

Exploring the Arctic Charr Intestinal Glycome: Evidence of Increased N-Glycolylneuraminic Acid Levels and Changed Host–Pathogen Interactions in Response to Inflammation

(2019) Vignesh Venkatakrishnan et al.   JOURNAL OF PROTEOME RESEARCH

Integrative Genomics Reveals the Genetics and Evolution of the Honey Bee’s Social Immune System

(2019) Brock A Harpur et al.   Genome Biology and Evolution

Adaptation to Host-Specific Bacterial Pathogens Drives Rapid Evolution of a Human Innate Immune Receptor

(2019) Jonas Adrian et al.   CURRENT BIOLOGY

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Ancient pathogen genomics as an emerging tool for infectious disease research

(2019) Maria A. Spyrou et al.   NATURE REVIEWS GENETICS

High-Throughput Sequencing for Understanding the Ecology of Emerging Infectious Diseases at the Wildlife-Human Interface

(2019) Georgia C. Titcomb et al.   Frontiers in Ecology and Evolution

Avian MHC Evolution in the Era of Genomics: Phase 1.0

(2019) Emily A. O’Connor et al.   Cells

Non-mammalian Toll-like receptor 18 (Tlr18) recognizes bacterial pathogens in common carp ( Cyprinus carpio L.): Indications for a role of participation in the NF-κB signaling pathway

(2018) Shijuan Shan et al.   FISH & SHELLFISH IMMUNOLOGY

Helicobacter suis binding to carbohydrates on human and porcine gastric mucins and glycolipids occurs via two modes

(2018) Médea Padra et al.   Virulence

Detection of Emerging Zoonotic Pathogens: An Integrated One Health Approach

(2018) Brian H. Bird et al.   Annual Review of Animal Biosciences

Two host gut-derived lactic acid bacteria activate the proPO system and increase resistance to an AHPND-causing strain of Vibrio parahaemolyticus in the shrimp Litopenaeus vannamei

(2018) Sudarat Chomwong et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

How complete are “complete” genome assemblies?-An avian perspective

(2018) Valentina Peona et al.   Molecular Ecology Resources

Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages

(2018) Aaron F. Carlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers

(2018) Melissa K. Takahashi et al.   Nature Communications

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans

(2018) David Enard et al.   CELL

Evolution of Copy Number at the MHC Varies across the Avian Tree of Life

(2018) Piotr Minias et al.   Genome Biology and Evolution

Experimental evolution of a fungal pathogen into a gut symbiont

(2018) Gloria Hoi Wan Tso et al.   SCIENCE

Avian Toll-like receptor allelic diversity far exceeds human polymorphism: an insight from domestic chicken breeds

(2018) Zuzana Świderská et al.   Scientific Reports

Analysis validation has been neglected in the Age of Reproducibility

(2018) Kathleen E. Lotterhos et al.   PLOS BIOLOGY

Dual Transcriptomics of Host-Pathogen Interaction of Cystic Fibrosis Isolate Pseudomonas aeruginosa PASS1 With Zebrafish

(2018) Sheemal S. Kumar et al.   Frontiers in Cellular and Infection Microbiology

The role of the microbiota in infectious diseases

(2018) Josie Libertucci et al.   Nature Microbiology

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

Parasitism drives host genome evolution: Insights from thePasteuria ramosa-Daphnia magnasystem

(2017) Yann Bourgeois et al.   EVOLUTION

Host effects on microbiota community assembly

(2017) Kathrin Näpflin et al.   JOURNAL OF ANIMAL ECOLOGY

Parasite life-cycle studies: a plea to resurrect an old parasitological tradition

(2017) I. Blasco-Costa et al.   JOURNAL OF HELMINTHOLOGY

Brachyspira hyodysenteriae Infection Regulates Mucin Glycosylation Synthesis Inducing an Increased Expression of Core-2 O-Glycans in Porcine Colon

(2017) Vignesh Venkatakrishnan et al.   JOURNAL OF PROTEOME RESEARCH

Genomic evolution of bacterial populations under coselection by antibiotics and phage

(2017) Johannes Cairns et al.   MOLECULAR ECOLOGY

Proteomics and integrative omic approaches for understanding host–pathogen interactions and infectious diseases

(2017) Pierre M Jean Beltran et al.   Molecular Systems Biology

Announcement: Towards greater reproducibility for life-sciences research in Nature

(2017)   NATURE

Frequency dependence limits divergent evolution by favouring rare immigrants over residents

(2017) Daniel I. Bolnick et al.   NATURE

Host and viral traits predict zoonotic spillover from mammals

(2017) Kevin J. Olival et al.   NATURE

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

(2017) N. R. Faria et al.   NATURE

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh et al.   NATURE

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

The Evolutionary Consequences of Stepwise Infection Processes

(2017) Matthew D. Hall et al.   TRENDS IN ECOLOGY & EVOLUTION

BabA dependent binding of Helicobacter pylori to human gastric mucins cause aggregation that inhibits proliferation and is regulated via ArsS

(2017) Emma C. Skoog et al.   Scientific Reports

Resolving host–pathogen interactions by dual RNA-seq

(2017) Alexander J. Westermann et al.   PLoS Pathogens

Pathogen metadata platform: software for accessing and analyzing pathogen strain information

(2016) Wenling E. Chang et al.   BMC BIOINFORMATICS

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

(2016) Hélène Quach et al.   CELL

Immunotoxic effects of environmental pollutants in marine mammals

(2016) Jean-Pierre W. Desforges et al.   ENVIRONMENT INTERNATIONAL

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

(2016) Mohammad R. Hasan et al.   JOURNAL OF CLINICAL MICROBIOLOGY

House Finch (Haemorhous mexicanus) Conjunctivitis, and Mycoplasma spp. Isolated from North American Wild Birds, 1994–2015

(2016) David H. Ley et al.   JOURNAL OF WILDLIFE DISEASES

EuPathDB: the eukaryotic pathogen genomics database resource

(2016) Cristina Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

When pathogenic bacteria meet the intestinal microbiota

(2016) Nathalie Rolhion et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Human drivers of ecological and evolutionary dynamics in emerging and disappearing infectious disease systems

(2016) Mary A. Rogalski et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers

(2016) Ryan S. Schwarz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composition of the gut microbiota modulates the severity of malaria

(2016) Nicolas F. Villarino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host–pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies

(2016) Daniel G. Streicker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immune response and gut microbial community structure in bumblebees after microbiota transplants

(2016) Kathrin Näpflin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

(2016) Pauline L. Kamath et al.   Nature Communications

Protocols.io: Virtual Communities for Protocol Development and Discussion

(2016) Leonid Teytelman et al.   PLOS BIOLOGY

The Legacy of Past Pandemics: Common Human Mutations That Protect against Infectious Disease

(2016) Kelly J. Pittman et al.   PLoS Pathogens

Viruses are a dominant driver of protein adaptation in mammals

(2016) David Enard et al.   eLife

Genomic Analysis of Viral Outbreaks

(2016) Shirlee Wohl et al.   Annual Review of Virology

PCB pollution continues to impact populations of orcas and other dolphins in European waters

(2016) Paul D. Jepson et al.   Scientific Reports

Understanding the ecology and evolution of host-parasite interactions across scales

(2015) Rachel M. Penczykowski et al.   Evolutionary Applications

A world without parasites: exploring the hidden ecology of infection

(2015) Chelsea L Wood et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

RNA-seq based transcriptomic analysis of single bacterial cells

(2015) Jiangxin Wang et al.   Integrative Biology

Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome

(2015) Yinfeng Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations

(2015) Pauline D. Scanlan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A novel locus of resistance to severe malaria in a region of ancient balancing selection

(2015)   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

The O-Linked Glycome and Blood Group Antigens ABO on Mucin-Type Glycoproteins in Mucinous and Serous Epithelial Ovarian Tumors

(2015) Varvara Vitiazeva et al.   PLoS One

Hidden costs of infection: Chronic malaria accelerates telomere degradation and senescence in wild birds

(2015) M. Asghar et al.   SCIENCE

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

(2015) Claire L. Webster et al.   PLOS BIOLOGY

Closing the genotype-phenotype gap: Emerging technologies for evolutionary genetics in ecological model vertebrate systems

(2014) Claudius F. Kratochwil et al.   BIOESSAYS

A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines

(2014) Qu Zhang et al.   BMC GENOMICS

Aeromonas salmonicida Binds Differentially to Mucins Isolated from Skin and Intestinal Regions of Atlantic Salmon in anN-Acetylneuraminic Acid-Dependent Manner

(2014) János T. Padra et al.   INFECTION AND IMMUNITY

Parasite biodiversity revisited: frontiers and constraints

(2014) Robert Poulin   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata)

(2014) Jackie Lighten et al.   Molecular Ecology Resources

Gut microbiota–generated metabolites in animal health and disease

(2014) Won-Jae Lee et al.   Nature Chemical Biology

Natural selection and infectious disease in human populations

(2014) Elinor K. Karlsson et al.   NATURE REVIEWS GENETICS

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Differences in susceptibility and immune responses of three-spined sticklebacks (Gasterosteus aculeatus) from lake and river ecotypes to sequential infections with the eye fluke Diplostomum pseudospathaceum

(2014) Jörn Scharsack et al.   Parasites & Vectors

Bat Distribution Size or Shape as Determinant of Viral Richness in African Bats

(2014) Gaël D. Maganga et al.   PLoS One

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

(2014) Vivien G. Dugan et al.   PLoS One

Viewing forests through the lens of complex systems science

(2014) Elise Filotas et al.   Ecosphere

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Control of pathogens and pathobionts by the gut microbiota

(2013) Nobuhiko Kamada et al.   NATURE IMMUNOLOGY

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

(2013) D. M. de Vienne et al.   NEW PHYTOLOGIST

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

(2013) S. Franzenburg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymorphisms at the innate immune receptor TLR2 are associated with Borrelia infection in a wild rodent population

(2013) B. Tschirren et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

(2013) István Bartha et al.   eLife

Host mucin glycosylation plays a role in bacterial adhesion in lungs of individuals with cystic fibrosis

(2013) Vignesh Venkatakrishnan et al.   Expert Review of Respiratory Medicine

Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC

(2012) Yuanyuan Cheng et al.   BMC GENOMICS

A new method for isolation of purified genomic DNA from haemosporidian parasites inhabiting nucleated red blood cells

(2012) Vaidas Palinauskas et al.   EXPERIMENTAL PARASITOLOGY

The changing face of pathogen discovery and surveillance

(2012) W. Ian Lipkin   NATURE REVIEWS MICROBIOLOGY

Epigenetics of Host–Pathogen Interactions: The Road Ahead and the Road Behind

(2012) Elena Gómez-Díaz et al.   PLoS Pathogens

Signatures of historical demography and pathogen richness on MHC class I genes

(2011) Nouar Qutob et al.   IMMUNOGENETICS

The expression of virulence during double infections by different parasites with conflicting host exploitation and transmission strategies

(2011) F. BEN-AMI et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Increased migration in host–pathogen metapopulations can cause host extinction

(2011) K.C. Harding et al.   JOURNAL OF THEORETICAL BIOLOGY

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Mucin dynamics and enteric pathogens

(2011) Michael A. McGuckin et al.   NATURE REVIEWS MICROBIOLOGY

MHC genotypes associate with resistance to a frog-killing fungus

(2011) A. E. Savage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Susceptibility to winter vomiting disease: a sweet matter

(2011) Gustaf E. Rydell et al.   REVIEWS IN MEDICAL VIROLOGY

Animal Migration and Infectious Disease Risk

(2011) S. Altizer et al.   SCIENCE

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Hybrid selection for sequencing pathogen genomes from clinical samples

(2011) Alexandre Melnikov et al.   GENOME BIOLOGY

Gene duplication and fragmentation in the zebra finch major histocompatibility complex

(2010) Christopher N Balakrishnan et al.   BMC BIOLOGY

Role of Mucin Lewis Status in Resistance to Helicobacter pylori Infection in Pediatric Patients

(2010) Sara Lindén et al.   HELICOBACTER

From Structure to Function: the Ecology of Host-Associated Microbial Communities

(2010) C. J. Robinson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings

(2010) L. G. Spurgin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Species Interactions in a Parasite Community Drive Infection Risk in a Wildlife Population

(2010) Sandra Telfer et al.   SCIENCE

MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochromeblineages

(2009) STAFFAN BENSCH et al.   Molecular Ecology Resources

Major histocompatibility complex (MHC) heterozygote superiority to natural multi-parasite infections in the water vole (Arvicola terrestris)

(2009) M.K Oliver et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Poverty trap formed by the ecology of infectious diseases

(2009) M. H. Bonds et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MUC1 Limits Helicobacter pylori Infection both by Steric Hindrance and by Acting as a Releasable Decoy

(2009) Sara K. Lindén et al.   PLoS Pathogens

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

(2008) P.C.Y. Woo et al.   CLINICAL MICROBIOLOGY AND INFECTION

Causal inference in disease ecology: investigating ecological drivers of disease emergence

(2008) Raina K Plowright et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Mucins in the mucosal barrier to infection

(2008) S K Linden et al.   Mucosal Immunology

Ecosystem energetic implications of parasite and free-living biomass in three estuaries

(2008) Armand M. Kuris et al.   NATURE

Global trends in emerging infectious diseases

(2008) Kate E. Jones et al.   NATURE

Role of ABO Secretor Status in Mucosal Innate Immunity and H. pylori Infection

(2008) Sara Lindén et al.   PLoS Pathogens

Ecological rules governing helminth microparasite coinfection

(2008) A. L. Graham   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homage to Linnaeus: How many parasites? How many hosts?

(2008) A. Dobson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics

Climate‐Driven Spatial Dynamics of Plague among Prairie Dog Colonies

(2007) T. Snäll et al.   AMERICAN NATURALIST