List of works - Timothy B Stockwell

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

scientific article

A draft genome sequence for the Ixodes scapularis cell line, ISE6.

scientific article

A host subtraction database for virus discovery in human cell line sequencing data

ANDES: Statistical tools for the ANalyses of DEep Sequencing

scientific article

Analysis of recombinant H7N9 wild-type and mutant viruses in pigs shows that the Q226L mutation in HA is important for transmission

scientific article

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation

scientific article published on 10 January 2018

Author Correction: Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens

scholarly article published by Susmita Shrivastava in 2018

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

scientific article

Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem

scholarly article by Divya Venkatesh published in August 2018

Characterization of uncultivable bat influenza virus using a replicative synthetic virus

scientific article published in October 2014

Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination.

scientific article published on September 2017

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome

scientific article

Complete genomic sequence for an avian group G rotavirus from South Africa

scientific article

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification

scientific article published on 05 October 2016

Deep sequencing identifies noncanonical editing of Ebola and Marburg virus RNAs in infected cells

scientific article

Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance

scientific article

Degenerate primer design for highly variable genomes

scientific article published on January 2015

Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential

scientific article

Evaluation of next generation sequencing platforms for population targeted sequencing studies

scientific article published on 27 March 2009

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas

scientific article published on 3 August 2017

Evolution of a reassortant North American gull influenza virus lineage: drift, shift and stability.

scientific article published on 06 June 2013

Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community

scientific article

First Complete Genome Sequences of Two Keystone Viruses from Florida

scientific article

Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

scientific article published in February 2018

Genetic variation in an individual human exome

scientific article

Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens

scientific article published on 7 February 2018

Genomic reassortment of influenza A virus in North American swine, 1998-2011.

scientific article

Identification of Dezidougou Virus in a DAK AR 41524 Zika Virus Stock

scientific article published on 27 July 2017

Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing

scientific article

Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data

scientific article

Influenza a virus migration and persistence in North American wild birds

scientific article

Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid

scientific article published on 17 May 2017

Isolation and characterization of a novel gammaherpesvirus from a microbat cell line

scientific article

Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4B

scientific article published on 16 May 2019

Large scale complete genome sequencing and phylodynamic analysis of eastern equine encephalitis virus reveal source-sink transmission dynamics in the United States.

scientific article published on 4 April 2018

Long-term surveillance of H7 influenza viruses in American wild aquatic birds: are the H7N3 influenza viruses in wild birds the precursors of highly pathogenic strains in domestic poultry?

scientific article published on 17 June 2015

Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

scientific article published on 18 October 2011

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

scientific article published on 9 December 2015

Molecular epidemiology of human enterovirus 71 at the origin of an epidemic of fatal hand, foot and mouth disease cases in Cambodia

scientific article published on 21 September 2016

Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses

scientific article published on 4 October 2017

Nanoliter reactors improve multiple displacement amplification of genomes from single cells

scientific article

North Atlantic migratory bird flyways provide routes for intercontinental movement of avian influenza viruses

scientific article

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

scientific article

Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam.

scientific article published on 17 June 2015

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.

scientific article

Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-13.

scientific article published on 20 February 2018

Quantifying influenza virus diversity and transmission in humans

scientific article

Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene

scientific article published on 23 May 2016

Reversion of Cold-Adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus

scientific article

SISPA-Seq for rapid whole genome surveys of bacterial isolates

scientific article published on 19 March 2015

Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus

scientific article

Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway

scientific article

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

Synthetic generation of influenza vaccine viruses for rapid response to pandemics

scientific article

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

scientific article

The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing

scientific article

The HuRef Browser: a web resource for individual human genomics

scientific article published on 26 November 2008

The contrasting phylodynamics of human influenza B viruses.

scientific article

The diploid genome sequence of an individual human

scientific article published on 4 September 2007

The effective rate of influenza reassortment is limited during human infection

scientific article

The evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, Nicaragua

scientific article published on 22 June 2014

The soft palate is an important site of adaptation for transmissible influenza viruses

scientific article

Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics

scientific article published on 05 February 2014

VariantClassifier: A hierarchical variant classifier for annotated genomes

scientific article

Whole genome analyses of G1P[8] rotavirus strains from vaccinated and non-vaccinated South African children presenting with diarrhea.

scientific article published on 20 May 2014

Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa

scientific article

Whole-genome analyses of DS-1-like human G2P[4] and G8P[4] rotavirus strains from Eastern, Western and Southern Africa

scientific article

List of works by Timothy B Stockwell

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

A draft genome sequence for the Ixodes scapularis cell line, ISE6.

A host subtraction database for virus discovery in human cell line sequencing data

A host subtraction database for virus discovery in human cell line sequencing data

ANDES: Statistical tools for the ANalyses of DEep Sequencing

Analysis of recombinant H7N9 wild-type and mutant viruses in pigs shows that the Q226L mutation in HA is important for transmission

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation

Author Correction: Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem

Characterization of uncultivable bat influenza virus using a replicative synthetic virus

Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination.

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome

Complete genomic sequence for an avian group G rotavirus from South Africa

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification

Deep sequencing identifies noncanonical editing of Ebola and Marburg virus RNAs in infected cells

Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance

Degenerate primer design for highly variable genomes

Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential

Evaluation of next generation sequencing platforms for population targeted sequencing studies

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas

Evolution of a reassortant North American gull influenza virus lineage: drift, shift and stability.

Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community

First Complete Genome Sequences of Two Keystone Viruses from Florida

Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

Genetic variation in an individual human exome

Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens

Genomic reassortment of influenza A virus in North American swine, 1998-2011.

Identification of Dezidougou Virus in a DAK AR 41524 Zika Virus Stock

Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing

Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data

Influenza a virus migration and persistence in North American wild birds

Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid

Isolation and characterization of a novel gammaherpesvirus from a microbat cell line

Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4B

Large scale complete genome sequencing and phylodynamic analysis of eastern equine encephalitis virus reveal source-sink transmission dynamics in the United States.

Long-term surveillance of H7 influenza viruses in American wild aquatic birds: are the H7N3 influenza viruses in wild birds the precursors of highly pathogenic strains in domestic poultry?

Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Molecular epidemiology of human enterovirus 71 at the origin of an epidemic of fatal hand, foot and mouth disease cases in Cambodia

Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses

Nanoliter reactors improve multiple displacement amplification of genomes from single cells

North Atlantic migratory bird flyways provide routes for intercontinental movement of avian influenza viruses

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam.

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.

Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-13.

Quantifying influenza virus diversity and transmission in humans

Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene

Reversion of Cold-Adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus

SISPA-Seq for rapid whole genome surveys of bacterial isolates

Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus

Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway

Standardized metadata for human pathogen/vector genomic sequences

Synthetic generation of influenza vaccine viruses for rapid response to pandemics

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing

The HuRef Browser: a web resource for individual human genomics

The contrasting phylodynamics of human influenza B viruses.

The diploid genome sequence of an individual human

The effective rate of influenza reassortment is limited during human infection

The evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, Nicaragua

The soft palate is an important site of adaptation for transmissible influenza viruses

Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics

VariantClassifier: A hierarchical variant classifier for annotated genomes

Whole genome analyses of G1P[8] rotavirus strains from vaccinated and non-vaccinated South African children presenting with diarrhea.

Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa

Whole-genome analyses of DS-1-like human G2P[4] and G8P[4] rotavirus strains from Eastern, Western and Southern Africa