Zika virus evolution and spread in the Americas

Vital Signs: Update on Zika Virus–Associated Birth Defects and Evaluation of All U.S. Infants with Congenital Zika Virus Exposure — U.S. Zika Pregnancy Registry, 2016

(2017) Megan R. Reynolds et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

(2016) Silvia I. Sardi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

missMDA: A Package for Handling Missing Values in Multivariate Data Analysis

(2016) Julie Josse et al.   Journal of Statistical Software

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

(2016) Michael Worobey et al.   NATURE

Zika Virus in the Americas — Yet Another Arbovirus Threat

(2016) Anthony S. Fauci et al.   NEW ENGLAND JOURNAL OF MEDICINE

Zika virus in the Americas: Early epidemiological and genetic findings

(2016) N. R. Faria et al.   SCIENCE

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models

(2015) Sebastián Duchêne et al.   BMC EVOLUTIONARY BIOLOGY

Emergence and potential for spread of Chikungunya virus in Brazil

(2015) Marcio Roberto Teixeira Nunes et al.   BMC Medicine

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

(2015) Daniel J. Park et al.   CELL

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Functions of the 3′ and 5′ genome RNA regions of members of the genus Flavivirus

(2015) Margo A. Brinton et al.   VIRUS RESEARCH

Beta Regression inR

(2015) Francisco Cribari-Neto et al.   Journal of Statistical Software

First case of laboratory-confirmed Zika virus infection imported into Europe, November 2013

(2014) D Tappe et al.   Eurosurveillance

Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone

(2014) John S. Schieffelin et al.   NEW ENGLAND JOURNAL OF MEDICINE

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

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

(2014) S. K. Gire et al.   SCIENCE

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dengue Virus Type 3 Adaptive Changes during Epidemics in São Jose de Rio Preto, Brazil, 2006–2007

(2013) Christian Julian Villabona-Arenas et al.   PLoS One

Quantitative real-time PCR detection of Zika virus and evaluation with field-caught Mosquitoes

(2013) Oumar Faye et al.   Virology Journal

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

A diagnostic polymerase chain reaction assay for Zika virus

(2012) Michelle N.D. Balm et al.   JOURNAL OF MEDICAL VIROLOGY

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Bayesian analysis of elapsed times in continuous-time Markov chains

(2010) Marco A. R. Ferreira et al.   CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

(2010) B. Shapiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

HIV-1 evolution in gag and env is highly correlated but exhibits different relationships with viral load and the immune response

(2009) Anne Piantadosi et al.   AIDS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Dengue Virus Pathogenesis: an Integrated View

(2009) B. E. E. Martina et al.   CLINICAL MICROBIOLOGY REVIEWS

Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus

(2009) A. A. Sall et al.   JOURNAL OF VIROLOGY

One-step RT-PCR for detection of Zika virus

(2008) Oumar Faye et al.   JOURNAL OF CLINICAL VIROLOGY

PlasmoDB: a functional genomic database for malaria parasites

(2008) C. Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY