Search Results - "Machi, Dustin"

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities by Davis, James J, Wattam, Alice R, Aziz, Ramy K, Brettin, Thomas, Butler, Ralph, Butler, Rory M, Chlenski, Philippe, Conrad, Neal, Dickerman, Allan, Dietrich, Emily M, Gabbard, Joseph L, Gerdes, Svetlana, Guard, Andrew, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Murphy-Olson, Dan, Nguyen, Marcus, Nordberg, Eric K, Olsen, Gary J, Olson, Robert D, Overbeek, Jamie C, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Shukla, Maulik, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S, Xia, Fangfang, Xie, Dawen, Yoo, Hyunseung, Stevens, Rick

“…Abstract The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and…”
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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center by Wattam, Alice R, Davis, James J, Assaf, Rida, Boisvert, Sébastien, Brettin, Thomas, Bun, Christopher, Conrad, Neal, Dietrich, Emily M, Disz, Terry, Gabbard, Joseph L, Gerdes, Svetlana, Henry, Christopher S, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Nordberg, Eric K, Olsen, Gary J, Murphy-Olson, Daniel E, Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Shukla, Maulik, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung, Stevens, Rick L

“…The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC…”
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PATRIC, the bacterial bioinformatics database and analysis resource by Wattam, Alice R, Abraham, David, Dalay, Oral, Disz, Terry L, Driscoll, Timothy, Gabbard, Joseph L, Gillespie, Joseph J, Gough, Roger, Hix, Deborah, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Nordberg, Eric K, Olson, Robert, Overbeek, Ross, Pusch, Gordon D, Shukla, Maulik, Schulman, Julie, Stevens, Rick L, Sullivan, Daniel E, Vonstein, Veronika, Warren, Andrew, Will, Rebecca, Wilson, Meredith J C, Yoo, Hyun Seung, Zhang, Chengdong, Zhang, Yan, Sobral, Bruno W

“…The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by…”
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COVID's collateral damage: likelihood of measles resurgence in the United States by Thakur, Mugdha, Zhou, Richard, Mohan, Mukundan, Marathe, Achla, Chen, Jiangzhuo, Hoops, Stefan, Machi, Dustin, Lewis, Bryan, Vullikanti, Anil

“…Lockdowns imposed throughout the US to control the COVID-19 pandemic led to a decline in all routine immunizations rates, including the MMR (measles, mumps,…”
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PATRIC as a unique resource for studying antimicrobial resistance by Antonopoulos, Dionysios A, Assaf, Rida, Aziz, Ramy Karam, Brettin, Thomas, Bun, Christopher, Conrad, Neal, Davis, James J, Dietrich, Emily M, Disz, Terry, Gerdes, Svetlana, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Murphy-Olson, Daniel E, Nordberg, Eric K, Olsen, Gary J, Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Santerre, John, Shukla, Maulik, Stevens, Rick L, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S, Wattam, Alice R, Xia, Fangfang, Yoo, Hyunseung

“…Abstract The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need…”
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Role of heterogeneity: National scale data-driven agent-based modeling for the US COVID-19 Scenario Modeling Hub by Chen, Jiangzhuo, Bhattacharya, Parantapa, Hoops, Stefan, Machi, Dustin, Adiga, Abhijin, Mortveit, Henning, Venkatramanan, Srinivasan, Lewis, Bryan, Marathe, Madhav

“…UVA-EpiHiper is a national scale agent-based model to support the US COVID-19 Scenario Modeling Hub (SMH). UVA-EpiHiper uses a detailed representation of the…”
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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 by Truelove, Shaun, Smith, Claire P, Qin, Michelle, Mullany, Luke C, Borchering, Rebecca K, Lessler, Justin, Shea, Katriona, Howerton, Emily, Contamin, Lucie, Levander, John, Kerr, Jessica, Hochheiser, Harry, Kinsey, Matt, Tallaksen, Kate, Wilson, Shelby, Shin, Lauren, Rainwater-Lovett, Kaitlin, Lemairtre, Joseph C, Dent, Juan, Kaminsky, Joshua, Lee, Elizabeth C, Perez-Saez, Javier, Hill, Alison, Karlen, Dean, Chinazzi, Matteo, Davis, Jessica T, Mu, Kunpeng, Xiong, Xinyue, Pastore Y Piontti, Ana, Vespignani, Alessandro, Srivastava, Ajitesh, Porebski, Przemyslaw, Venkatramanan, Srinivasan, Adiga, Aniruddha, Lewis, Bryan, Klahn, Brian, Outten, Joseph, Orr, Mark, Harrison, Galen, Hurt, Benjamin, Chen, Jiangzhuo, Vullikanti, Anil, Marathe, Madhav, Hoops, Stefan, Bhattacharya, Parantapa, Machi, Dustin, Chen, Shi, Paul, Rajib, Janies, Daniel, Thill, Jean-Claude, Galanti, Marta, Yamana, Teresa K, Pei, Sen, Shaman, Jeffrey L, Healy, Jessica M, Slayton, Rachel B, Biggerstaff, Matthew, Johansson, Michael A, Runge, Michael C, Viboud, Cecile

“…In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United…”
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Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support by Bhattacharya, Parantapa, Chen, Jiangzhuo, Hoops, Stefan, Machi, Dustin, Lewis, Bryan, Venkatramanan, Srinivasan, Wilson, Mandy L., Klahn, Brian, Adiga, Aniruddha, Hurt, Benjamin, Outten, Joseph, Adiga, Abhijin, Warren, Andrew, Baek, Young Yun, Porebski, Przemyslaw, Marathe, Achla, Xie, Dawen, Swarup, Samarth, Vullikanti, Anil, Mortveit, Henning, Eubank, Stephen, Barrett, Christopher L., Marathe, Madhav

“…This paper describes an integrated, data-driven operational pipeline based on national agent-based models to support federal and state-level pandemic planning…”
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Data analysis and modeling pipelines for controlled networked social science experiments by Cedeno-Mieles, Vanessa, Hu, Zhihao, Ren, Yihui, Deng, Xinwei, Contractor, Noshir, Ekanayake, Saliya, Epstein, Joshua M, Goode, Brian J, Korkmaz, Gizem, Kuhlman, Chris J, Machi, Dustin, Macy, Michael, Marathe, Madhav V, Ramakrishnan, Naren, Saraf, Parang, Self, Nathan

“…There is large interest in networked social science experiments for understanding human behavior at-scale. Significant effort is required to perform data…”
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Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR by Olson, Robert D, Assaf, Rida, Brettin, Thomas, Conrad, Neal, Cucinell, Clark, Davis, James J, Dempsey, Donald M, Dickerman, Allan, Dietrich, Emily M, Kenyon, Ronald W, Kuscuoglu, Mehmet, Lefkowitz, Elliot J, Lu, Jian, Machi, Dustin, Macken, Catherine, Mao, Chunhong, Niewiadomska, Anna, Nguyen, Marcus, Olsen, Gary J, Overbeek, Jamie C, Parrello, Bruce, Parrello, Victoria, Porter, Jacob S, Pusch, Gordon D, Shukla, Maulik, Singh, Indresh, Stewart, Lucy, Tan, Gene, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Wallace, Zachary S, Warren, Andrew S, Wattam, Alice R, Xia, Fangfang, Yoo, Hyunseung, Zhang, Yun, Zmasek, Christian M, Scheuermann, Richard H, Stevens, Rick L

“…The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with…”
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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 by Bhattacharya, Parantapa, Machi, Dustin, Chen, Jiangzhuo, Hoops, Stefan, Lewis, Bryan, Mortveit, Henning, Venkatramanan, Srinivasan, Wilson, Mandy L., Marathe, Achla, Porebski, Przemyslaw, Klahn, Brian, Outten, Joseph, Vullikanti, Anil, Xie, Dawen, Adiga, Abhijin, Brown, Shawn, Barrett, Christopher, Marathe, Madhav

“…We present MacKenzie, a HPC-driven multi-cluster workflow system that was used repeatedly to configure and execute fine-grained US national-scale epidemic…”
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A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes by VanOeffelen, Margo, Nguyen, Marcus, Aytan-Aktug, Derya, Brettin, Thomas, Dietrich, Emily M, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Olson, Robert, Pusch, Gordon D, Shukla, Maulik, Stevens, Rick, Vonstein, Veronika, Warren, Andrew S, Wattam, Alice R, Yoo, Hyunseung, Davis, James J

“…Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the global research…”
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Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub by Jung, Sung-Mok, Loo, Sara L, Howerton, Emily, Contamin, Lucie, Smith, Claire P, Carcelén, Erica C, Yan, Katie, Bents, Samantha J, Levander, John, Espino, Jessi, Lemaitre, Joseph C, Sato, Koji, McKee, Clifton D, Hill, Alison L, Chinazzi, Matteo, Davis, Jessica T, Mu, Kunpeng, Vespignani, Alessandro, Rosenstrom, Erik T, Rodriguez-Cartes, Sebastian A, Ivy, Julie S, Mayorga, Maria E, Swann, Julie L, España, Guido, Cavany, Sean, Moore, Sean M, Perkins, T Alex, Chen, Shi, Paul, Rajib, Janies, Daniel, Thill, Jean-Claude, Srivastava, Ajitesh, Aawar, Majd Al, Bi, Kaiming, Bandekar, Shraddha Ramdas, Bouchnita, Anass, Fox, Spencer J, Meyers, Lauren Ancel, Porebski, Przemyslaw, Venkatramanan, Srini, Adiga, Aniruddha, Hurt, Benjamin, Klahn, Brian, Outten, Joseph, Chen, Jiangzhuo, Mortveit, Henning, Wilson, Amanda, Hoops, Stefan, Bhattacharya, Parantapa, Machi, Dustin, Vullikanti, Anil, Lewis, Bryan, Marathe, Madhav, Hochheiser, Harry, Runge, Michael C, Shea, Katriona, Truelove, Shaun, Viboud, Cécile, Lessler, Justin

“…Coronavirus Disease 2019 (COVID-19) continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of…”
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Networked experiments and modeling for producing collective identity in a group of human subjects using an iterative abduction framework by Cedeno-Mieles, Vanessa, Hu, Zhihao, Ren, Yihui, Deng, Xinwei, Adiga, Abhijin, Barrett, Christopher, Contractor, Noshir, Ekanayake, Saliya, Epstein, Joshua M., Goode, Brian J., Korkmaz, Gizem, Kuhlman, Chris J., Machi, Dustin, Macy, Michael W., Marathe, Madhav V., Ramakrishnan, Naren, Ravi, S. S., Saraf, Parang, Self, Nathan

“…Group or collective identity is an individual’s cognitive, moral, and emotional connection with a broader community, category, practice, or institution. There…”
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ExecutionManager: A Software System to Control Execution of Third-Party Software that Performs Network Computations by Carscadden, Henry L., Machi, Lucas, Kishore, Aparna, Kuhlman, Chris J., Machi, Dustin, Ravi, S. S.

“…We describe a software system called ExecutionManager (abbreviated EM) that controls the execution of third-party software (TPS) for analyzing networks. Based…”
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GraphTrans: A Software System for Network Conversions for Simulation, Structural Analysis, and Graph Operations by Carscadden, Henry L., Machi, Lucas, Kuhlman, Chris J., Machi, Dustin, Ravi, S. S.

“…Network representations of socio-physical systems are ubiquitous, examples being social (media) networks and infrastructure networks like power transmission…”
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CSonNet: An Agent-Based Modeling Software System for Discrete Time Simulation by Priest, Joshua D., Kishore, Aparna, Machi, Lucas, Kuhlman, Chris J., Machi, Dustin, Ravi, S. S.

“…Contagion dynamics on networks are used to study many problems, including disease and virus epidemics, incarceration, obesity, protests and rebellions, needle…”
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Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance by Wattam, Alice R, Bowers, Nicole, Brettin, Thomas, Conrad, Neal, Cucinell, Clark, Davis, James J, Dickerman, Allan W, Dietrich, Emily M, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Nguyen, Marcus, Olson, Robert D, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Shukla, Maulik, Stevens, Rick L, Vonstein, Veronika, Warren, Andrew S

“…As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The…”
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RNA-Rocket: an RNA-Seq analysis resource for infectious disease research by Warren, Andrew S, Aurrecoechea, Cristina, Brunk, Brian, Desai, Prerak, Emrich, Scott, Giraldo-Calderón, Gloria I, Harb, Omar, Hix, Deborah, Lawson, Daniel, Machi, Dustin, Mao, Chunhong, McClelland, Michael, Nordberg, Eric, Shukla, Maulik, Vosshall, Leslie B, Wattam, Alice R, Will, Rebecca, Yoo, Hyun Seung, Sobral, Bruno

“…RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study…”
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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 studyResearch in context by Rebecca K. Borchering, Luke C. Mullany, Emily Howerton, Matteo Chinazzi, Claire P. Smith, Michelle Qin, Nicholas G. Reich, Lucie Contamin, John Levander, Jessica Kerr, J. Espino, Harry Hochheiser, Kaitlin Lovett, Matt Kinsey, Kate Tallaksen, Shelby Wilson, Lauren Shin, Joseph C. Lemaitre, Juan Dent Hulse, Joshua Kaminsky, Elizabeth C. Lee, Alison L. Hill, Jessica T. Davis, Kunpeng Mu, Xinyue Xiong, Ana Pastore y Piontti, Alessandro Vespignani, Ajitesh Srivastava, Przemyslaw Porebski, Srini Venkatramanan, Aniruddha Adiga, Bryan Lewis, Brian Klahn, Joseph Outten, Benjamin Hurt, Jiangzhuo Chen, Henning Mortveit, Amanda Wilson, Madhav Marathe, Stefan Hoops, Parantapa Bhattacharya, Dustin Machi, Shi Chen, Rajib Paul, Daniel Janies, Jean-Claude Thill, Marta Galanti, Teresa Yamana, Sen Pei, Jeffrey Shaman, Guido España, Sean Cavany, Sean Moore, Alex Perkins, Jessica M. Healy, Rachel B. Slayton, Michael A. Johansson, Matthew Biggerstaff, Katriona Shea, Shaun A. Truelove, Michael C. Runge, Cécile Viboud, Justin Lessler

“…Background: The COVID-19 Scenario Modeling Hub convened nine modeling teams to project the impact of expanding SARS-CoV-2 vaccination to children aged 5–11…”
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