Publications by authors named "Samuel S Shepard"

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Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment.
Jordan T Ort, Samuel S Shepard, Sonja A Zolnoski, Tommy T-Y Lam, C Todd Davis

Virus Evol· August 2025

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Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections.
David VanInsberghe, Dillon S McBride, Juliana DaSilva, Thomas J Stark, Max S Y Lau, Samuel S Shepard

PLoS Pathog· April 2024

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Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections.
David VanInsberghe, Dillon S McBride, Juliana DaSilva, Thomas J Stark, Max S Y Lau, Samuel S Shepard

bioRxiv· October 2023

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Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.
Kevin C Ma, Philip Shirk, Anastasia S Lambrou, Norman Hassell, Xiao-Yu Zheng, Samuel S Shepard

MMWR Morb Mortal Wkly Rep· June 2023

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SARS-CoV-2 Delta-Omicron Recombinant Viruses, United States.
Kristine A Lacek, Benjamin L Rambo-Martin, Dhwani Batra, Xiao-Yu Zheng, Norman Hassell, Samuel S Shepard

Emerg Infect Dis· July 2022

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Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.
Jiani Chen, Xueting Qiu, Vasanthi Avadhanula, Samuel S Shepard, Do-Kyun Kim

Influenza Other Respir Viruses· May 2022

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Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.
Anastasia S Lambrou, Philip Shirk, Molly K Steele, Prabasaj Paul, Clinton R Paden, Samuel S Shepard

MMWR Morb Mortal Wkly Rep· February 2022

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Impact of Immune Priming, Vaccination, and Infection on Influenza A(H3N2) Antibody Landscapes in Children.
Michael Hinojosa, Samuel S Shepard, Jessie R Chung, Jennifer P King, Huong Q McLean

J Infect Dis· August 2021

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Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals.
Ketaki Ganti, Anish Bagga, Juliana DaSilva, Samuel S Shepard, John R Barnes

Viruses· March 2021

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Author Correction: Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome.
Matthew W Keller, Benjamin L Rambo-Martin, Malania M Wilson, Callie A Ridenour, Samuel S Shepard

Sci Rep· October 2018

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Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome.
Matthew W Keller, Benjamin L Rambo-Martin, Malania M Wilson, Callie A Ridenour, Samuel S Shepard

Sci Rep· September 2018

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Antigenic characterization of highly pathogenic avian influenza A(H5N1) viruses with chicken and ferret antisera reveals clade-dependent variation in hemagglutination inhibition profiles.
Diep Thi Nguyen, Samuel S Shepard, David Francis Burke, Joyce Jones, Sharmi Thor

Emerg Microbes Infect· May 2018

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Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors.
Shannon L M Whitmer, Jason T Ladner, Michael R Wiley, Ketan Patel, Gytis Dudas, Samuel S Shepard

Cell Rep· January 2018

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Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015.
Diep T Nguyen, Yunho Jang, Tho D Nguyen, Joyce Jones, Samuel S Shepard

J Virol· March 2017

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Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences.
Shannon L M Whitmer, César Albariño, Samuel S Shepard, Gytis Dudas, Mili Sheth

J Infect Dis· October 2016

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Erratum to: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler.
Samuel S Shepard, Sarah Meno, Justin Bahl, Malania M Wilson, John Barnes

BMC Genomics· October 2016

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Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler.
Samuel S Shepard, Sarah Meno, Justin Bahl, Malania M Wilson, John Barnes

BMC Genomics· September 2016

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Improving pandemic influenza risk assessment.
Colin A Russell, Peter M Kasson, Ruben O Donis, Steven Riley, John Dunbar, Samuel S Shepard

Elife· October 2014

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LABEL: fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins.
Samuel S Shepard, C Todd Davis, Justin Bahl, Pierre Rivailler, Ian A York

PLoS One· September 2014

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Structural and antigenic variation among diverse clade 2 H5N1 viruses.
David A Shore, Hua Yang, Amanda L Balish, Samuel S Shepard, Paul J Carney

PLoS One· July 2014

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Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models.
Samuel S Shepard, Andrew McSweeny, Gursel Serpen, Alexei Fedorov

Nucleic Acids Res· June 2012

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Critical association of ncRNA with introns.
David Rearick, Ashwin Prakash, Andrew McSweeny, Samuel S Shepard, Larisa Fedorova

Nucleic Acids Res· March 2011

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Evolution of genomic sequence inhomogeneity at mid-range scales.
Ashwin Prakash, Samuel S Shepard, Jie He, Benjamin Hart, Miao Chen

BMC Genomics· November 2009

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