The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities von 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

Volltext

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center von 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

Volltext

PATRIC, the bacterial bioinformatics database and analysis resource von 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

Volltext

Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center von Wattam, Alice R., Brettin, Thomas, Davis, James J., Gerdes, Svetlana, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Olson, Robert, Overbeek, Ross, Pusch, Gordon D., Shukla, Maulik P., Stevens, Rick, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung

Volltext

COVID's collateral damage: likelihood of measles resurgence in the United States von Thakur, Mugdha, Zhou, Richard, Mohan, Mukundan, Marathe, Achla, Chen, Jiangzhuo, Hoops, Stefan, Machi, Dustin, Lewis, Bryan, Vullikanti, Anil

Volltext

PATRIC as a unique resource for studying antimicrobial resistance von 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

Volltext

Role of heterogeneity: National scale data-driven agent-based modeling for the US COVID-19 Scenario Modeling Hub von Chen, Jiangzhuo, Bhattacharya, Parantapa, Hoops, Stefan, Machi, Dustin, Adiga, Abhijin, Mortveit, Henning, Venkatramanan, Srinivasan, Lewis, Bryan, Marathe, Madhav

Volltext

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 von 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

Volltext

Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support von 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

Volltext

Data analysis and modeling pipelines for controlled networked social science experiments von 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

Volltext

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR von 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

Volltext

Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread von 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

Volltext

Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub von 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

Volltext

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes von 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.

Volltext

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes von 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.

Volltext

Networked experiments and modeling for producing collective identity in a group of human subjects using an iterative abduction framework von 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

Volltext

A Framework for Simulating Multiple Contagions Over Multiple Networks von Kishore, Aparna, Machi, Lucas, Kuhlman, Chris J., Machi, Dustin, Ravi, S. S.

Volltext

Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance von 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.

Volltext

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research von 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

Volltext

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... von 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

Volltext