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

Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure

(2018) Kristine Bohmann et al.   Molecular Ecology Resources

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis

(2018) Luis E. M. Villegas et al.   PLoS One

The Global Virome Project

(2018) Dennis Carroll et al.   SCIENCE

Novel viruses in birds: Flying through the roof or is a cage needed?

(2018) R. Bodewes   VETERINARY JOURNAL

Geospatial distribution of viromes in tropical freshwater ecosystems

(2018) Xiaoqiong Gu et al.   WATER RESEARCH

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants

(2018) Simon H. Williams et al.   mBio

MPD: a pathogen genome and metagenome database

(2018) Tingting Zhang et al.   Database-The Journal of Biological Databases and Curation

Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

(2018) Erin K. Grey et al.   Scientific Reports

Detailed ecological associations of triatomines revealed by metabarcoding and next-generation sequencing: implications for triatomine behavior and Trypanosoma cruzi transmission cycles

(2018) Eric Dumonteil et al.   Scientific Reports

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia

(2018) Bruce A. Rosa et al.   Microbiome

Pandemics: spend on surveillance, not prediction

(2018) Edward C. Holmes et al.   NATURE

Investigating diversity of pathogenic microbes in commercial bait trade water

(2018) Andrew R. Mahon et al.   PeerJ

The use of nemabiome metabarcoding to explore gastro-intestinal nematode species diversity and anthelmintic treatment effectiveness in beef calves

(2017) Russell W. Avramenko et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Parasite-microbiota interactions potentially affect intestinal communities in wild mammals

(2017) Tuomas Aivelo et al.   JOURNAL OF ANIMAL ECOLOGY

iDNA screening: Disease vectors as vertebrate samplers

(2017) Arthur Kocher et al.   MOLECULAR ECOLOGY

Interacting effects of land use and climate on rodent-borne pathogens in central Kenya

(2017) Hillary S. Young et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Interacting effects of wildlife loss and climate on ticks and tick-borne disease

(2017) Georgia Titcomb et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Urbanization and Disease Emergence: Dynamics at the Wildlife–Livestock–Human Interface

(2017) James M. Hassell et al.   TRENDS IN ECOLOGY & EVOLUTION

New Technologies for Detection of Enteric Parasites

(2017) Una Ryan et al.   TRENDS IN PARASITOLOGY

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases

(2017) Panpim Thongsripong et al.   Ecology and Evolution

Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats

(2017) Maria Augusta Dario et al.   PLoS Neglected Tropical Diseases

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases

(2017) David F. Nieuwenhuijse et al.   Frontiers in Microbiology

Surveillance for highly pathogenic influenza A viruses in California during 2014–2015 provides insights into viral evolutionary pathways and the spatiotemporal extent of viruses in the Pacific Americas Flyway

(2017) Andrew M Ramey et al.   Emerging Microbes & Infections

Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen

(2017) Jerome Bouquet et al.   Scientific Reports

Barcoding the food chain: from Sanger to high-throughput sequencing

(2016) Joanne E. Littlefair et al.   GENOME

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

Estimating species richness using environmental DNA

(2016) Brett P. Olds et al.   Ecology and Evolution

Bunyaviruses are common in male and femaleIxodes scapularisticks in central Pennsylvania

(2016) Joyce M. Sakamoto et al.   PeerJ

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships’ Ballast Water: Implications for Biogeography and Infectious Diseases

(2015) K. M. Pagenkopp Lohan et al.   MICROBIAL ECOLOGY

Interactions between the intestinal microbiome and helminth parasites

(2015) M. M. Zaiss et al.   PARASITE IMMUNOLOGY

Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods

(2015) Marcia Gumiel et al.   Parasites & Vectors

Diverse Applications of Environmental DNA Methods in Parasitology

(2015) David Bass et al.   TRENDS IN PARASITOLOGY

Bats as reservoirs of severe emerging infectious diseases

(2015) Hui-Ju Han et al.   VIRUS RESEARCH

Long duration, room temperature preservation of filtered eDNA samples

(2015) Benjamin J. Wegleitner et al.   Conservation Genetics Resources

A Review of the Role of Food and the Food System in the Transmission and Spread of Ebolavirus

(2015) Erin Mann et al.   PLoS Neglected Tropical Diseases

Interesting Open Questions in Disease Ecology and Evolution

(2014) Curtis M. Lively et al.   AMERICAN NATURALIST

Gut Microbiota of the Tick Vector Ixodes scapularis Modulate Colonization of the Lyme Disease Spirochete

(2014) Sukanya Narasimhan et al.   Cell Host & Microbe

Distribution, diversity and drivers of blood-borne parasite co-infections in Alaskan bird populations

(2014) Khouanchy S. Oakgrove et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection?

(2014) Sarah Temmam et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

The Pathogen-Host Interactions database (PHI-base): additions and future developments

(2014) Martin Urban et al.   NUCLEIC ACIDS RESEARCH

Detection and characterization of zoonotic pathogens of free-ranging non-human primates from Zambia

(2014) Jesca Nakayima et al.   Parasites & Vectors

Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens

(2014) Yongjin Qiu et al.   PLoS One

Zoonosis emergence linked to agricultural intensification and environmental change

(2013) B. A. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomics for pathogen detection in public health

(2013) Ruth R Miller et al.   Genome Medicine

Prediction and prevention of the next pandemic zoonosis

(2012) Stephen S Morse et al.   LANCET

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What can we predict about viral evolution and emergence?

(2012) Edward C Holmes   Current Opinion in Virology

From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments

(2011) John A. Darling et al.   ENVIRONMENTAL RESEARCH

From superspreaders to disease hotspots: linking transmission across hosts and space

(2011) Sara H Paull et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

Raw Sewage Harbors Diverse Viral Populations

(2011) P. G. Cantalupo et al.   mBio

Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission

(2011) S. Baker et al.   Open Biology

Advancing ecological understandings through technological transformations in noninvasive genetics

(2009) ALBANO BEJA-PEREIRA et al.   Molecular Ecology Resources

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

Global trends in emerging infectious diseases

(2008) Kate E. Jones et al.   NATURE