Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity

Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples

(2019) Adrian C. Paskey et al.   BMC GENOMICS

Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak

(2019) Irina Maljkovic Berry et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Aerosol Transmission of Gull-Origin Iceland Subtype H10N7 Influenza A Virus in Ferrets

(2019) Minhui Guan et al.   JOURNAL OF VIROLOGY

Whole Genome Sequencing of Extended Spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae Isolated from Hospitalized Patients in KwaZulu-Natal, South Africa

(2019) Raspail Carrel Founou et al.   Scientific Reports

The Burden of Dengue Fever and Chikungunya in Southern Coastal Ecuador: Epidemiology, Clinical Presentation, and Phylogenetics from the First Two Years of a Prospective Study

(2018) Anna M. Stewart-Ibarra et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance

(2018) Eldin Talundzic et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development

(2018) S. Pollett et al.   INFECTION GENETICS AND EVOLUTION

Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China

(2018) Jiafa Liu et al.   Scientific Reports

Stochastic processes constrain the within and between host evolution of influenza virus

(2018) John T McCrone et al.   eLife

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

(2018) Walid Mottawea et al.   Frontiers in Microbiology

Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda

(2018) Matthew J Cummings et al.   CLINICAL INFECTIOUS DISEASES

Pandemics: spend on surveillance, not prediction

(2018) Edward C. Holmes et al.   NATURE

Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing

(2018) Briana R. Flaherty et al.   Microbiome

The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses

(2018) Tracey Goldstein et al.   Nature Microbiology

Conjugative Transfer of a Novel Staphylococcal Plasmid Encoding the Biocide Resistance Gene, qacA

(2018) Patrick T. LaBreck et al.   Frontiers in Microbiology

Antiviral resistance markers in influenza virus sequences in Mexico, 2000–2017

(2018) William Toledo-Rueda et al.   Infection and Drug Resistance

A novel flavivirus detected in two Aedes spp. collected near the demilitarized zone of the Republic of Korea

(2017) Achareeya Korkusol et al.   JOURNAL OF GENERAL VIROLOGY

Species and genotype diversity of Plasmodium in malaria patients from Gabon analysed by next generation sequencing

(2017) Albert Lalremruata et al.   MALARIA JOURNAL

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity

(2017) Chris Wymant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics

(2017) Simon Dellicour et al.   MOLECULAR BIOLOGY AND EVOLUTION

Zika virus evolution and spread in the Americas

(2017) Hayden C. Metsky 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

Dengue diversity across spatial and temporal scales: Local structure and the effect of host population size

(2017) Henrik Salje et al.   SCIENCE

Evolution of selective-sequencing approaches for virus discovery and virome analysis

(2017) Arvind Kumar et al.   VIRUS RESEARCH

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

(2016) Dingchen Li et al.   Biology Direct

Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread

(2016) Irina Maljkovic Berry et al.   BMC BIOLOGY

Real time application of whole genome sequencing for outbreak investigation – What is an achievable turnaround time?

(2016) Patrick McGann et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country

(2016) S. Pollett et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories

(2016) Amy S. Gargis et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel

(2016) Erin H. Graf et al.   JOURNAL OF CLINICAL MICROBIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

(2016) Michael Worobey et al.   NATURE

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

(2016) Po-E Li et al.   NUCLEIC ACIDS RESEARCH

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Zika virus in the Americas: Early epidemiological and genetic findings

(2016) N. R. Faria et al.   SCIENCE

Recent advances in malaria genomics and epigenomics

(2016) Sebastian Kirchner et al.   Genome Medicine

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

(2016) Ignacio Mena et al.   eLife

Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome

(2016) Robert P. Dickson et al.   Nature Microbiology

Antimicrobial Resistance Prediction in PATRIC and RAST

(2016) James J. Davis et al.   Scientific Reports

Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer

(2016) Hong Kai Lee et al.   Scientific Reports

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

(2015) Andy Kilianski et al.   BMC BIOINFORMATICS

BEACON: automated tool for Bacterial GEnome Annotation ComparisON

(2015) Manal Kalkatawi et al.   BMC GENOMICS

Enhanced virome sequencing using targeted sequence capture

(2015) Todd N. Wylie et al.   GENOME RESEARCH

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

(2015) Jason C. Kwong et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2015)   NATURE

Genetic architecture of artemisinin-resistant Plasmodium falciparum

(2015) Olivo Miotto et al.   NATURE GENETICS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Molecular Evidence of Sexual Transmission of Ebola Virus

(2015) Suzanne E. Mate et al.   NEW ENGLAND JOURNAL OF MEDICINE

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Virus evolution and transmission in an ever more connected world

(2015) Oliver G. Pybus et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management

(2015) Mark E. J. Woolhouse et al.   Science Translational Medicine

Human Adenovirus Diversity in Water Samples Using a Next-Generation Amplicon Sequencing Approach

(2015) Leslie Ogorzaly et al.   Food and Environmental Virology

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

Bioinformatics in Africa: The Rise of Ghana?

(2015) Thomas K. Karikari   PLoS Computational Biology

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Population genomics of intrapatient HIV-1 evolution

(2015) Fabio Zanini et al.   eLife

Curation, integration and visualization of bacterial virulence factors in PATRIC

(2014) Chunhong Mao et al.   BIOINFORMATICS

Automated ensemble assembly and validation of microbial genomes

(2014) Sergey Koren et al.   BMC BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Real-time investigation of a Legionella pneumophila outbreak using whole genome sequencing

(2014) R. M. A. GRAHAM et al.   EPIDEMIOLOGY AND INFECTION

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors

(2014) X.-C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

(2013) Frédéric Ariey et al.   NATURE

Evolutionary epidemiology: preparing for an age of genomic plenty

(2013) O. G. Pybus et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Detection of novel viruses in porcine fecal samples from China

(2013) Jie-mei Yu et al.   Virology Journal

Whole-Genome Sequencing of Trypanosoma brucei Reveals Introgression between Subspecies That Is Associated with Virulence

(2013) I. Goodhead et al.   mBio

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum

(2012) Daniel E Neafsey et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Consensus Rules in Variant Detection from Next-Generation Sequencing Data

(2012) Peilin Jia et al.   PLoS One

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation

(2012) J. C. Stack et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sexual Development in Plasmodium: Lessons from Functional Analyses

(2012) David S. Guttery et al.   PLoS Pathogens

A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

(2012) Gilda Grard et al.   PLoS Pathogens

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

(2011) T. Downing et al.   GENOME RESEARCH

Cross-Species Transmission of a Novel Adenovirus Associated with a Fulminant Pneumonia Outbreak in a New World Monkey Colony

(2011) Eunice C. Chen et al.   PLoS Pathogens

Hepatitis C Virus Infections from Unsafe Injection Practices at an Endoscopy Clinic in Las Vegas, Nevada, 2007–2008

(2010) Gayle E. Fischer et al.   CLINICAL INFECTIOUS DISEASES

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

(2008) Jane M. Carlton et al.   NATURE