R. Halpin

Timothy B. Stockwell, T. Stockwell, K. Schmader, 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Large-Scale Complete-Genome Sequencing and Phylodynamic Analysis of Eastern Equine Encephalitis Virus Reveals Source-Sink Transmission Dynamics in the United States

T. Stockwell, T. Lam, R. Tesh, 2018, Journal of Virology.

Molecular characterization of a new species in the genus Alphacoronavirus associated with mink epizootic catarrhal gastroenteritis.

E. Ghedin, D. Spiro, A. Vlasova, 2011, The Journal of general virology.

Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015

L. Kramer, B. Pickett, S. Zink, 2019, Virus evolution.

Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic

L. Kramer, E. Harris, V. Puri, 2018, PLoS neglected tropical diseases.

PB2 Residue 158 Is a Pathogenic Determinant of Pandemic H1N1 and H5 Inﬂuenza A Viruses in Mice (cid:1) ‡

D. Spiro, E. Hine, R. Halpin, 2010 .

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

Timothy B. Stockwell, T. Stockwell, D. Seto, 2018, Emerging Microbes & Infections.

Individual variation in ballooning dispersal by black widow spiderlings: The effects of family and social rearing

Dale R. Stevens, J. C. Johnson, R. Halpin, 2015 .

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.

S. Yooseph, K. Nelson, L. Anderson, 2016, The Journal of infectious diseases.

Spike Protein Fusion Peptide and Feline Coronavirus Virulence

D. Spiro, P. Rottier, Hui-Wen Chang, 2012, Emerging infectious diseases.

Intermediate turbidity elicits the greatest antipredator response and generates repeatable behaviour in mosquitofish

Sean M. Ehlman, A. Sih, R. Halpin, 2019, Animal Behaviour.

Biologic, Antigenic, and Full-Length Genomic Characterization of a Bovine-Like Coronavirus Isolated from a Giraffe

Anastasia Vlasova, David Spiro, Elodie Ghedin, 2007, Journal of Virology.

Bovine-Like Coronaviruses Isolated from Four Species of Captive Wild Ruminants Are Homologous to Bovine Coronaviruses, Based on Complete Genomic Sequences

David Spiro, Elodie Ghedin, Linda J. Saif, 2006, Journal of Virology.

Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus

Daniel Janies, David Spiro, Elodie Ghedin, 2006, Virology.

Equine Influenza A(H3N8) Virus Isolated from Bactrian Camel, Mongolia

Sarah K White, M. Nelson, G. Gray, 2014, Emerging infectious diseases.

Amino Acid Substitutions in Positions 385 and 393 of the Hydrophobic Region of VP4 May Be Associated with Rotavirus Attenuation and Cell Culture Adaptation

A. Vlasova, L. Saif, R. Halpin, 2020, Viruses.

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

Timothy B. Stockwell, T. Stockwell, V. Puri, 2016, Scientific Reports.

Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan

V. Puri, M. Nelson, M. Shilts, 2019, Microbial genomics.

Comparative Genomics of Emerging Human Ehrlichiosis Agents

Jonathan Crabtree, Jaideep P. Sundaram, Rekha Seshadri, 2006, PLoS genetics.

Transposition Pathovars in Genes Involved in Virulence 1448 A Reveals Divergence among pv . phaseolicola Pseudomonas syringae Whole-Genome Sequence Analysis of

O. White, T. Creasy, C. Fraser, 2005 .

Adaptation of Pandemic H2N2 Influenza A Viruses in Humans

Thomas P. Fabrizio, Gavin J. D. Smith, R. Webby, 2014, Journal of Virology.

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

Timothy B. Stockwell, Gavin J. D. Smith, Rob Lambkin-Williams, 2016, Journal of Virology.

Quantifying influenza virus diversity and transmission in humans

Timothy B. Stockwell, T. Stockwell, R. Rosenfeld, 2016, Nature Genetics.

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

Timothy B. Stockwell, T. Stockwell, K. Ndiaye, 2015, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Influenza A Virus Migration and Persistence in North American Wild Birds

Timothy B. Stockwell, Gavin J. D. Smith, T. Stockwell, 2013, PLoS pathogens.

North Atlantic Migratory Bird Flyways Provide Routes for Intercontinental Movement of Avian Influenza Viruses

Jeffrey S. Hall, Timothy B. Stockwell, T. Stockwell, 2014, PloS one.

Viral genome sequencing by random priming methods

A. Djikeng, N. Anderson, E. Ghedin, 2008 .

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

Timothy B. Stockwell, Sergei L. Kosakovsky Pond, A. P. Adams, 2017, PLoS neglected tropical diseases.

Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing

Timothy B. Stockwell, Xiaotao Lu, Kelvin Li, 2010, PLoS pathogens.

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

Timothy B. Stockwell, Hoang Minh Tu Van, T. Stockwell, 2015, Journal of Virology.

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

Timothy B. Stockwell, Elodie Ghedin, Xudong Lin, 2011, The Journal of infectious diseases.

The contrasting phylodynamics of human influenza B viruses

Timothy B. Stockwell, Gavin J. D. Smith, T. Stockwell, 2015, eLife.

The effective rate of influenza reassortment is limited during human infection

Christopher J. R. Illingworth, Timothy B. Stockwell, Gavin J. D. Smith, 2017, PLoS pathogens.

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

T. Stockwell, Anushka Brownley, Kelvin Li, 2012, Virology Journal.

Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery

K. Nelson, M. Torralba, L. Anderson, 2015, Microbial Ecology.

Multiple Introductions and Antigenic Mismatch with Vaccines May Contribute to Increased Predominance of G12P[8] Rotaviruses in the United States

K. Edwards, C. Fonnesbeck, M. Shilts, 2018, Journal of Virology.

Sequencing and Analysis of Globally Obtained Human Respiratory Syncytial Virus A and B Genomes

Christopher D. Town, Daniel E. Noyola, Cristina Videla, 2015, PloS one.

Avian influenza viruses in wild birds: virus evolution in a multi-host 1 ecosystem 2

T. Stockwell, H. van Bakel, T. Bestebroer, 2018 .

Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States

Cecile Viboud, Mark A. Miller, Edward C. Holmes, 2008, PLoS pathogens.

Mixed Infection and the Genesis of Influenza Virus Diversity

Edward C. Holmes, Elodie Ghedin, Kirsten St. George, 2009, Journal of Virology.

Molecular Signature of High Yield (Growth) Influenza A Virus Reassortants Prepared as Candidate Vaccine Seeds

D. Spiro, E. Hine, R. Halpin, 2013, PloS one.

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

T. Stockwell, E. Holmes, A. Vincent, 2012, The Journal of general virology.

Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes

C. Town, M. Nelson, K. Henrickson, 2019, PloS one.

Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl

O. Pybus, R. Fouchier, B. Olsen, 2021, bioRxiv.

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

Eric J. Ma, Timothy B. Stockwell, Gavin J. D. Smith, 2016, PLoS pathogens.

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

Timothy B. Stockwell, T. Stockwell, T. Lam, 2012, Ecology letters.

Evolution of Influenza B Virus in Kuala Lumpur, Malaysia, between 1995 and 2008

Gavin J. D. Smith, E. Ghedin, I. Sam, 2015, Journal of Virology.

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

Yi Guan, Timothy B. Stockwell, Edward C. Holmes, 2011, Proceedings of the National Academy of Sciences.

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

Timothy B. Stockwell, Gavin J. D. Smith, T. Stockwell, 2015, The Journal of general virology.

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

Timothy B. Stockwell, Uma S. Kamaraj, T. Stockwell, 2017, Journal of Clinical Microbiology.

The early diversification of influenza A/H1N1pdm

Timothy B. Stockwell, T. Stockwell, C. Viboud, 2009, PLoS currents.

Where do all the subtypes go? Temporal dynamics of H8–H12 influenza A viruses in waterfowl

O. Pybus, R. Fouchier, J. Raghwani, 2018, Virus evolution.

Complete Genome Sequence of a Reassortant H14N2 Avian Influenza Virus from California

L. L. Lindsay, W. Boyce, S. Schobel, 2013, Genome Announcements.

Whole-genome sequencing and analyses identify high genetic heterogeneity, diversity and endemicity of rotavirus genotype P[6] strains circulating in Africa.

B. Pickett, Susmita Shrivastava, R. Halpin, 2018, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

Kelvin Li, Anushka Brownley, T. Stockwell, 2012, Virology Journal.

Genomic and Protein Structural Maps of Adaptive Evolution of Human Influenza A Virus to Increased Virulence in the Mouse

Timothy B. Stockwell, Samar K Dankar, T. Stockwell, 2011, PloS one.

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

Timothy B. Stockwell, T. Stockwell, S. Schultz-Cherry, 2016, Journal of Virology.

Chemically Defined, High-Density Insect Cell-Based Expression System for Scalable AAV Vector Production

Y. Ikeda, A. Tovchigrechko, Changshou Gao, 2020, Molecular therapy. Methods & clinical development.

PB2 Residue 158 Is a Pathogenic Determinant of Pandemic H1N1 and H5 Influenza A Viruses in Mice

D. Spiro, Bin Zhou, E. Hine, 2010, Journal of Virology.

Despite egg-adaptive mutations, the 2012-13 H3N2 influenza vaccine induced comparable antibody titers to the intended strain

Timothy B. Stockwell, T. Stockwell, K. Schmader, 2017, bioRxiv.

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

T. Stockwell, Sunando Roy, R. Halpin, 2014, Virus Genes.

Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation

Daniel Janies, Anastasia Vlasova, David Spiro, 2007, Virology.

Influence of Sex on Respiratory Syncytial Virus Genotype Infection Frequency and Nasopharyngeal Microbiome

V. Puri, T. Hartert, R. Peebles, 2023, Journal of virology.

Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy

K. Nelson, L. Anderson, S. Schobel, 2018, The Journal of allergy and clinical immunology.

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

Timothy B. Stockwell, Ram Sasisekharan, Xudong Lin, 2015, Nature.

Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination.

G. Sims, C. Town, K. Holmes, 2012, The Journal of general virology.

Universal Influenza B Virus Genomic Amplification Facilitates Sequencing, Diagnostics, and Reverse Genetics

Timothy B. Stockwell, T. Stockwell, I. Barr, 2014, Journal of Clinical Microbiology.

Extensive Geographical Mixing of 2009 Human H1N1 Influenza A Virus in a Single University Community

Timothy B. Stockwell, Kimberly C. Brouwer, T. Stockwell, 2011, Journal of Virology.

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment

R. Haselkorn, J. Badger, I. Paulsen, 2006, Proceedings of the National Academy of Sciences.

Dual infection of novel influenza viruses A/H1N1 and A/H3N2 in a cluster of Cambodian patients.

P. Blair, D. Spiro, R. Halpin, 2011, The American journal of tropical medicine and hygiene.

Extreme developmental synchrony reduces sibling cannibalism in the black widow spider, Latrodectus hesperus

Dale R. Stevens, J. C. Johnson, R. Halpin, 2016, Animal Behaviour.

Decreased Serologic Response in Vaccinated Military Recruits during 2011 Correspond to Genetic Drift in Concurrent Circulating Pandemic A/H1N1 Viruses

Christopher D. Clagett, P. Blair, Angelia A. Eick-Cost, 2012, PloS one.

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

K. Nelson, B. Methé, Indresh Singh, 2020, Nature Communications.

Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents

Jaideep P. Sundaram, Samuel V. Angiuoli, O. White, 2006, PLoS Genetics.

Migration and Persistence of Human Influenza A Viruses, Vietnam, 2001–2008

P. Horby, T. Lam, M. F. Boni, 2013, Emerging infectious diseases.

First Complete Genome Sequences of Two Keystone Viruses from Florida

Timothy B. Stockwell, T. Stockwell, L. Kramer, 2015, Genome Announcements.

Time of Eclosion and Mating Success of Male Sagebrush Crickets

J. C. Johnson, J. Adams, R. Halpin, 2012 .

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

Timothy B. Stockwell, T. Stockwell, E. Holmes, 2015, Emerging infectious diseases.

Reassortment of Influenza A Viruses in Wild Birds in Alaska before H5 Clade 2.3.4.4 Outbreaks

Eric J. Ma, W. Boyce, D. Suarez, 2017, Emerging infectious diseases.

Molecular Analysis of H7 Avian Influenza Viruses from Australia and New Zealand: Genetic Diversity and Relationships from 1976 to 2007

Daniel Janies, Dieter Bulach, David Spiro, 2010, Journal of Virology.

Haemagglutinin mutations and glycosylation changes shaped the 2012/13 influenza A(H3N2) epidemic, Houston, Texas.

Timothy B. Stockwell, T. Stockwell, R. Olsen, 2015, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

K. Nelson, B. Methé, Indresh Singh, 2020, Nature Communications.

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in analog hosts

K. Nelson, B. Methé, Indresh Singh, 2018, bioRxiv.

Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses.

C. Town, Amy Ransier, Zhaohui Qian, 2014, The Journal of general virology.

Using Clinical Research Networks to Assess Severity of an Emerging Influenza Pandemic

Henrik Nielsen, L. Mathiesen, C. Leen, 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Timothy B. Stockwell, T. Stockwell, A. Bowman, 2015, Journal of Virology.

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

Timothy B. Stockwell, T. Stockwell, E. Harris, 2014, Virology.