Publications by authors named "Dustin Machi"

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BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.
Maulik Shukla, Alice R Wattam, Antonio Aleman, Roshni Bhattacharya, Nicole Bowers, Dustin Machi

Nucleic Acids Res· November 2025

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Epihiper-A high performance computational modeling framework to support epidemic science.
Jiangzhuo Chen, Stefan Hoops, Henning S Mortveit, Bryan L Lewis, Dustin Machi

PNAS Nexus· January 2025

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Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread.
Parantapa Bhattacharya, Dustin Machi, Jiangzhuo Chen, Stefan Hoops, Bryan Lewis

J Parallel Distrib Comput· September 2024

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Role of heterogeneity: National scale data-driven agent-based modeling for the US COVID-19 Scenario Modeling Hub.
Jiangzhuo Chen, Parantapa Bhattacharya, Stefan Hoops, Dustin Machi, Abhijin Adiga

Epidemics· September 2024

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Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance.
Alice R Wattam, Nicole Bowers, Thomas Brettin, Neal Conrad, Clark Cucinell, Dustin Machi

Methods Mol Biol· May 2024

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Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub.
Sung-Mok Jung, Sara L Loo, Emily Howerton, Lucie Contamin, Claire P Smith, Dustin Machi

PLoS Med· April 2024

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Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub.
Sung-Mok Jung, Sara L Loo, Emily Howerton, Lucie Contamin, Claire P Smith, Dustin Machi

medRxiv· November 2023

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Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty.
Emily Howerton, Lucie Contamin, Luke C Mullany, Michelle Qin, Nicholas G Reich, Dustin Machi

Nat Commun· November 2023

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Informing pandemic response in the face of uncertainty. .
Emily Howerton, Lucie Contamin, Luke C Mullany, Michelle Qin, Nicholas G Reich, Dustin Machi

medRxiv· July 2023

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Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.
Robert D Olson, Rida Assaf, Thomas Brettin, Neal Conrad, Clark Cucinell, Dustin Machi

Nucleic Acids Res· January 2023

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Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: A multi-model study.
Rebecca K Borchering, Luke C Mullany, Emily Howerton, Matteo Chinazzi, Claire P Smith, Dustin Machi

Lancet Reg Health Am· January 2023

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Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support.
Parantapa Bhattacharya, Jiangzhuo Chen, Stefan Hoops, Dustin Machi, Bryan Lewis

Int J High Perform Comput Appl· January 2023

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COVID's collateral damage: likelihood of measles resurgence in the United States.
Mugdha Thakur, Richard Zhou, Mukundan Mohan, Achla Marathe, Jiangzhuo Chen, Dustin Machi

BMC Infect Dis· September 2022

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Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination.
Shaun Truelove, Claire P Smith, Michelle Qin, Luke C Mullany, Rebecca K Borchering, Dustin Machi

Elife· June 2022

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Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study.
Rebecca K Borchering, Luke C Mullany, Emily Howerton, Matteo Chinazzi, Claire P Smith, Dustin Machi

medRxiv· March 2022

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A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.
Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas Brettin, Emily M Dietrich, Dustin Machi

Brief Bioinform· November 2021

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Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination.
Shaun Truelove, Claire P Smith, Michelle Qin, Luke C Mullany, Rebecca K Borchering, Dustin Machi

medRxiv· September 2021

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Scalable Epidemiological Workflows to Support COVID-19 Planning and Response.
Dustin Machi, Parantapa Bhattacharya, Stefan Hoops, Jiangzhuo Chen, Henning Mortveit

medRxiv· February 2021

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Data analysis and modeling pipelines for controlled networked social science experiments.
Vanessa Cedeno-Mieles, Zhihao Hu, Yihui Ren, Xinwei Deng, Noshir Contractor, Dustin Machi

PLoS One· January 2021

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From 5Vs to 6Cs: Operationalizing Epidemic Data Management with COVID-19 Surveillance.
Akhil Sai Peddireddy, Dawen Xie, Pramod Patil, Mandy L Wilson, Dustin Machi

medRxiv· October 2020

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Evaluating the impact of international airline suspensions on the early global spread of COVID-19.
Aniruddha Adiga, Srinivasan Venkatramanan, James Schlitt, Akhil Peddireddy, Allan Dickerman, Dustin Machi

medRxiv· February 2020

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The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.
James J Davis, Alice R Wattam, Ramy K Aziz, Thomas Brettin, Ralph Butler, Dustin Machi

Nucleic Acids Res· January 2020

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PATRIC as a unique resource for studying antimicrobial resistance.
Dionysios A Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas Brettin, Christopher Bun, Dustin Machi

Brief Bioinform· July 2019

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Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
Alice R Wattam, Thomas Brettin, James J Davis, Svetlana Gerdes, Ronald Kenyon, Dustin Machi

Methods Mol Biol· November 2018

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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Alice R Wattam, James J Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Dustin Machi

Nucleic Acids Res· January 2017

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