5 Works

Data from: Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions

Michael G. Buhnerkempe, Katherine C. Prager, Christopher C. Strelioff, Denise J. Greig, Jeff L. Laake, Sharon R. Melin, Robert L. DeLong, Frances M. D. Gulland & James O. Lloyd-Smith
Identifying mechanisms driving pathogen persistence is a vital component of wildlife disease ecology and control. Asymptomatic, chronically infected individuals are an oft-cited potential reservoir of infection but demonstrations of the importance of chronic shedding to pathogen persistence at the population level remain scarce. Studying chronic shedding using commonly collected disease data is hampered by numerous challenges, including short-term surveillance that focuses on single epidemics and acutely ill individuals, the subtle dynamical influence of chronic shedding...

Data from: Genome-wide evolutionary dynamics of influenza B viruses on a global scale

Pinky Langat, Jayna Raghwani, Gytis Dudas, Thomas A. Bowden, Stephanie Edwards, Astrid Gall, Trevor Bedford, Andrew Rambaut, Rodney S. Daniels, Colin A. Russell, Oliver G. Pybus, John McCauley, Paul Kellam & Simon J. Watson
The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genes

Vanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....

Data from: Tracing the origin of the early wet-season Anopheles coluzzii in the Sahel

Tovi Lehmann, David Weetman, Diana L. Huestis, Alpha S. Yaro, Yaya Kassogue, Moussa Diallo, Martin J. Donnelly & Adama Dao
In arid environments the source of the malaria mosquito populations that re-establish soon after first rains remains a puzzle and alternative explanations have been proposed. Using genetic data, we evaluated whether the early Rainy Season (RS) population of Anopheles coluzzii is descended from the preceding late-RS generation at the same locality, consistent with dry season (DS) dormancy (aestivation), or from migrants from distant locations. Distinct predictions derived from these two hypotheses were assessed, based on...

Registration Year

  • 2017

Resource Types

  • Dataset


  • National Institutes of Health
  • Fred Hutchinson Cancer Research Center
  • University of Washington
  • Columbia University
  • Duke University
  • University of North Carolina
  • University of Cambridge
  • University of California, Berkeley
  • Alaska Fisheries Science Center
  • Duke University School of Medicine