Search Results - "Wertheim, Joel O"

Detecting individual sites subject to episodic diversifying selection by Murrell, Ben, Wertheim, Joel O, Moola, Sasha, Weighill, Thomas, Scheffler, Konrad, Kosakovsky Pond, Sergei L

“…The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects…”
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The emergence of SARS-CoV-2 in Europe and North America by Worobey, Michael, Pekar, Jonathan, Larsen, Brendan B, Nelson, Martha I, Hill, Verity, Joy, Jeffrey B, Rambaut, Andrew, Suchard, Marc A, Wertheim, Joel O, Lemey, Philippe

“…Accurate understanding of the global spread of emerging viruses is critical for public health responses and for anticipating and preventing future outbreaks…”
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The origins of SARS-CoV-2: A critical review by Holmes, Edward C., Goldstein, Stephen A., Rasmussen, Angela L., Robertson, David L., Crits-Christoph, Alexander, Wertheim, Joel O., Anthony, Simon J., Barclay, Wendy S., Boni, Maciej F., Doherty, Peter C., Farrar, Jeremy, Geoghegan, Jemma L., Jiang, Xiaowei, Leibowitz, Julian L., Neil, Stuart J.D., Skern, Tim, Weiss, Susan R., Worobey, Michael, Andersen, Kristian G., Garry, Robert F., Rambaut, Andrew

“…Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest…”
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Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection by Smith, Martin D, Wertheim, Joel O, Weaver, Steven, Murrell, Ben, Scheffler, Konrad, Kosakovsky Pond, Sergei L

“…Over the past two decades, comparative sequence analysis using codon-substitution models has been honed into a powerful and popular approach for detecting…”
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RELAX: detecting relaxed selection in a phylogenetic framework by Wertheim, Joel O, Murrell, Ben, Smith, Martin D, Kosakovsky Pond, Sergei L, Scheffler, Konrad

“…Relaxation of selective strength, manifested as a reduction in the efficiency or intensity of natural selection, can drive evolutionary innovation and presage…”
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Social and Genetic Networks of HIV-1 Transmission in New York City by Wertheim, Joel O, Kosakovsky Pond, Sergei L, Forgione, Lisa A, Mehta, Sanjay R, Murrell, Ben, Shah, Sharmila, Smith, Davey M, Scheffler, Konrad, Torian, Lucia V

“…Sexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify,…”
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Purifying Selection Can Obscure the Ancient Age of Viral Lineages by Wertheim, Joel O., Kosakovsky Pond, Sergei L.

“…Statistical methods for molecular dating of viral origins have been used extensively to infer the time of most common recent ancestor for many rapidly evolving…”
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Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment by Mazrouee, Sepideh, Little, Susan J, Wertheim, Joel O

“…HIV molecular epidemiology estimates the transmission patterns from clustering genetically similar viruses. The process involves connecting genetically similar…”
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Using HIV networks to inform real time prevention interventions by Little, Susan J, Kosakovsky Pond, Sergei L, Anderson, Christy M, Young, Jason A, Wertheim, Joel O, Mehta, Sanjay R, May, Susanne, Smith, Davey M

“…To reconstruct the local HIV-1 transmission network from 1996 to 2011 and use network data to evaluate and guide efforts to interrupt transmission. HIV-1 pol…”
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Evolutionary origins of human herpes simplex viruses 1 and 2 by Wertheim, Joel O, Smith, Martin D, Smith, Davey M, Scheffler, Konrad, Kosakovsky Pond, Sergei L

“…Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this…”
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Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2 by Wertheim, Joel O, Worobey, Michael

“…Great strides have been made in understanding the evolutionary history of simian immunodeficiency virus (SIV) and the zoonoses that gave rise to HIV-1 and…”
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Natural selection favoring more transmissible HIV detected in United States molecular transmission network by Wertheim, Joel O., Oster, Alexandra M., Switzer, William M., Zhang, Chenhua, Panneer, Nivedha, Campbell, Ellsworth, Saduvala, Neeraja, Johnson, Jeffrey A., Heneine, Walid

“…HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV transmission. These variable transmission rates are primarily driven…”
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Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa by Havens, Jennifer L., Calvignac-Spencer, Sébastien, Merkel, Kevin, Burrel, Sonia, Boutolleau, David, Wertheim, Joel O.

“…Human herpes simplex virus 2 (HSV-2) is a ubiquitous, slowly evolving DNA virus. HSV-2 has two primary lineages, one found in West and Central Africa and the…”
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A Case for the Ancient Origin of Coronaviruses by Wertheim, Joel O, Chu, Daniel K W, Peiris, Joseph S M, Kosakovsky Pond, Sergei L, Poon, Leo L M

“…Article Usage Stats Services JVI Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021 by Yakovleva, Anna, Kovalenko, Ganna, Redlinger, Matthew, Liulchuk, Mariia G., Bortz, Eric, Zadorozhna, Viktoria I., Scherbinska, Alla M., Wertheim, Joel O., Goodfellow, Ian, Meredith, Luke, Vasylyeva, Tetyana I.

“…The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),…”
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Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020 by Yakovleva, Anna, Kovalenko, Ganna, Redlinger, Matthew, Smyrnov, Pavlo, Tymets, Olga, Korobchuk, Anna, Kotlyk, Lyudmyla, Kolodiazieva, Anna, Podolina, Anna, Cherniavska, Svitlana, Antonenko, Petro, Strathdee, Steffanie A, Friedman, Samuel R, Goodfellow, Ian, Wertheim, Joel O, Bortz, Eric, Meredith, Luke, Vasylyeva, Tetyana I

“…Due to practical challenges associated with genetic sequencing in low-resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people…”
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The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021 by Vasylyeva, Tetyana I, Havens, Jennifer L, Wang, Jade C, Luoma, Elizabeth, Hassler, Gabriel W, Amin, Helly, Di Lonardo, Steve, Taki, Faten, Omoregie, Enoma, Hughes, Scott, Wertheim, Joel O

“…Socio-economic disparities were associated with disproportionate viral incidence between neighborhoods of New York City (NYC) during the first wave of…”
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HIV Transmission Dynamics Among Foreign-Born Persons in the United States by Valverde, Eduardo E, Oster, Alexandra M, Xu, Songli, Wertheim, Joel O, Hernandez, Angela L

“…In the United States (US), foreign-born persons are disproportionately affected by HIV and differ epidemiologically from US-born persons with diagnosed HIV…”
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Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection by Mazrouee, Sepideh, Hallmark, Camden J., Mora, Ricardo, Del Vecchio, Natascha, Carrasco Hernandez, Rocio, Carr, Michelle, McNeese, Marlene, Fujimoto, Kayo, Wertheim, Joel O.

“…Detection of viral transmission clusters using molecular epidemiology is critical to the response pillar of the Ending the HIV Epidemic initiative. Here, we…”
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Establishing a framework towards monitoring HCV microelimination among men who have sex with men living with HIV in Germany: A modeling analysis by Marquez, Lara K, Ingiliz, Patrick, Boesecke, Christoph, Krznaric, Ivanka, Schewe, Knud, Lutz, Thomas, Mauss, Stefan, Christensen, Stefan, Rockstroh, Jürgen K, Jain, Sonia, He, Feng, Wertheim, Joel O, Martin, Natasha K

“…Prior to direct-acting antivirals (DAAs), HCV incidence rose among men who have sex with men (MSM) living with HIV infection in Germany despite high hepatitis…”
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