Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota

Autor: Mary E. Petrone, Jessica E. Rothman, Mallery I. Breban, Isabel M. Ott, Alexis Russell, Erica Lasek-Nesselquist, Hamada Badr, Kevin Kelly, Greg Omerza, Nicholas Renzette, Anne E. Watkins, Chaney C. Kalinich, Tara Alpert, Anderson F. Brito, Rebecca Earnest, Irina R. Tikhonova, Christopher Castaldi, John P. Kelly, Matthew Shudt, Jonathan Plitnick, Erasmus Schneider, Steven Murphy, Caleb Neal, Eva Laszlo, Ahmad Altajar, Claire Pearson, Anthony Muyombwe, Randy Downing, Jafar Razeq, Linda Niccolai, Madeline S. Wilson, Margaret L. Anderson, Jianhui Wang, Chen Liu, Pei Hui, Shrikant Mane, Bradford P. Taylor, William P. Hanage, Marie L. Landry, David R. Peaper, Kaya Bilguvar, Joseph R. Fauver, Chantal B. F. Vogels, Lauren M. Gardner, Virginia E. Pitzer, Kirsten St. George, Mark D. Adams, Nathan D. Grubaugh

Publikováno v: Communications Biology, Vol 5, Iss 1, Pp 1-10 (2022)

The Alpha and Iota SARS-CoV-2 variants exhibit up to 50% greater transmissibility compared to other circulating variants in Connecticut in early 2021.

Externí odkaz: https://doaj.org/article/028dafa93b3d4984824dfc01b20e2df0

saks-nf: A json solution for Nextflow pipeline construction

Autor: Xinming Zhuo, Nicholas Renzette, Gregory Omerza

To address the increasing complexity of data in scientific research, researchers have developed many workflow manager tools. Nextflow is one of the most widely used tools, enabling scalability and reproducibility of scientific workflows across variou

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::df80e92750bb499d51310cf18fc7cc7c
https://doi.org/10.1101/2022.09.19.508305

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

Autor: Rebecca Earnest, Rockib Uddin, Nicholas Matluk, Nicholas Renzette, Sarah E. Turbett, Katherine J. Siddle, Christine Loreth, Gordon Adams, Christopher H. Tomkins-Tinch, Mary E. Petrone, Jessica E. Rothman, Mallery I. Breban, Robert Tobias Koch, Kendall Billig, Joseph R. Fauver, Chantal B.F. Vogels, Kaya Bilguvar, Bony De Kumar, Marie L. Landry, David R. Peaper, Kevin Kelly, Greg Omerza, Heather Grieser, Sim Meak, John Martha, Hannah B. Dewey, Susan Kales, Daniel Berenzy, Kristin Carpenter-Azevedo, Ewa King, Richard C. Huard, Vlad Novitsky, Mark Howison, Josephine Darpolor, Akarsh Manne, Rami Kantor, Sandra C. Smole, Catherine M. Brown, Timelia Fink, Andrew S. Lang, Glen R. Gallagher, Virginia E. Pitzer, Pardis C. Sabeti, Stacey Gabriel, Bronwyn L. MacInnis, Ryan Tewhey, Mark D. Adams, Daniel J. Park, Jacob E. Lemieux, Nathan D. Grubaugh, Ahmad Altajar, Alexandra DeJesus, Anderson Brito, Anne E. Watkins, Anthony Muyombwe, Brendan S. Blumenstiel, Caleb Neal, Chaney C. Kalinich, Chen Liu, Christopher Castaldi, Claire Pearson, Clare Bernard, Corey M. Nolet, David Ferguson, Erika Buzby, Eva Laszlo, Faye L. Reagan, Gina Vicente, Heather M. Rooke, Heidi Munger, Hillary Johnson, Irina R. Tikhonova, Isabel M. Ott, Jafar Razeq, James C. Meldrim, Jessica Brown, Jianhui Wang, Johanna Vostok, John P. Beauchamp, Jonna L. Grimsby, Joshua Hall, Katelyn S. Messer, Katie L. Larkin, Kyle Vernest, Lawrence C. Madoff, Lisa M. Green, Lori Webber, Luc Gagne, Maesha A. Ulcena, Marianne C. Ray, Marissa E. Fisher, Mary Barter, Matthew D. Lee, Matthew T. DeFelice, Michelle C. Cipicchio, Natasha L. Smith, Niall J. Lennon, Nicholas A. Fitzgerald, Nicholas Kerantzas, Pei Hui, Rachel Harrington, Randy Downing, Rashida Haye, Ryan Lynch, Scott E. Anderson, Scott Hennigan, Sean English, Seana Cofsky, Selina Clancy, Shrikant Mane, Stephanie Ash, Stephanie Baez, Steve Fleming, Steven Murphy, Sushma Chaluvadi, Tara Alpert, Trevor Rivard, Wade Schulz, Zoe M. Mandese

Publikováno v: medRxiv
article-version (status) pre
article-version (number) 1

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% mor

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b52ebf3f526fa0d741135b86555fe0db
http://europepmc.org/articles/PMC8509091

Influenza virus drug resistance: a time-sampled population genetics perspective.

Autor: Matthieu Foll, Yu-Ping Poh, Nicholas Renzette, Anna Ferrer-Admetlla, Claudia Bank, Hyunjin Shim, Anna-Sapfo Malaspinas, Gregory Ewing, Ping Liu, Daniel Wegmann, Daniel R Caffrey, Konstantin B Zeldovich, Daniel N Bolon, Jennifer P Wang, Timothy F Kowalik, Celia A Schiffer, Robert W Finberg, Jeffrey D Jensen

Publikováno v: PLoS Genetics, Vol 10, Iss 2, p e1004185 (2014)

The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for distinguishing these processes, and we here propose approximate Bayesian, maximum likelihoo

Externí odkaz: https://doaj.org/article/c83d55bae4ba41bfac40d6f845e6e97e

Reduced subgenomic RNA expression is a molecular indicator of asymptomatic SARS-CoV-2 infection

Autor: Edison T. Liu, Chee Hong Wong, Rachel L. Goldfeder, Gregory Omerza, Nicholas Renzette, Chia-Lin Wei, Jennifer Idol, Kevin Kelly, Frederick A. Browne, Chris Kuhlberg, Francine De Abreu, Chew Yee Ngan, Rahul Maurya, Lei Li

Publikováno v: Communications medicine. 1

It is estimated that up to 80% of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are asymptomatic and asymptomatic patients can still effectively transmit the virus and cause disease. While much of the effort has be

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::05d114fbad61d09ffee32ebb1c41cf5c
https://pubmed.ncbi.nlm.nih.gov/35602196