Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: outbreaker
https://packages.ecosyste.ms/registries/pypi.org/packages/outbreaker
Explore WHO Disease Outbreak News
5 versions
Latest release: over 3 years ago
8 downloads last month
Papers Mentioning outbreaker 8
10.1016/j.epidem.2014.04.003
OutbreakTools: A new platform for disease outbreak analysis using the R softwareCited by: 37
Author(s): Thibaut Jombart, David M. Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Caitlin Collins, Anne Cori, Xavier Didelot, Christophe Fraser, Simon D. W. Frost, Niel Hens, Joseph Hugues, Michael Höhle, Lulla Opatowski, Andrew Rambaut, Oliver Ratmann, Samuel Soubeyrand, Marc A. Suchard, Jacco Wallinga, Rolf J. F. Ypma, Neil M. Ferguson
Software Mentions: 11
Published: over 10 years ago
10.1186/s12859-018-2330-z
outbreaker2: a modular platform for outbreak reconstructionCited by: 50
Author(s): Finlay Campbell, Xavier Didelot, Richard G. FitzJohn, Neil Ferguson, Anne Cori, Thibaut Jombart
Software Mentions: 6
Published: almost 6 years ago
10.1371/journal.pcbi.1003457
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic DataCited by: 207
Author(s): Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil M. Ferguson
Software Mentions: 5
Published: over 10 years ago
10.1098/rsif.2020.0084
Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance dataCited by: 7
Author(s): Alexis Robert, Adam J. Kucharski, Paul A. Gastañaduy, Prabasaj Paul, Sebastian Funk
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0129745
'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in PathogensCited by: 23
Author(s): Colin J. Worby, Timothy D. Read
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pcbi.1006748
A dynamic power-law sexual network model of gonorrhoea outbreaksCited by: 22
Author(s): Lilith K Whittles, Peter J White, Xavier Didelot
Software Mentions: 2
Published: over 5 years ago
10.3389/fpubh.2021.667337
Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source CasesCited by: 2
Author(s): Kathryn Winglee, Clinton J. McDaniel, Lauren Linde, Steve Kammerer, Martin Cilnis, Kala M. Raz, Wendy S. Noboa, Jillian Knorr, Lauren S. Cowan, Sue Reynolds, James E. Posey, Jeanne Sullivan Meissner, Shameer Poonja, Tambi Shaw, Sarah Talarico, Benjamin J. Silk
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pbio.3000611
Combining genomics and epidemiology to track mumps virus transmission in the United StatesCited by: 34
Author(s): Shirlee Wohl, Hayden C. Metsky, Stephen F. Schaffner, Anne Piantadosi, Meagan Burns, Joseph A Lewnard, Bridget Chak, Lydia A. Krasilnikova, Katherine J. Siddle, Christian B. Matranga, Bettina Bankamp, Scott Hennigan, Brandon Sabina, Elizabeth H. Byrne, Rebecca J. McNall, Rickey R. Shah, James Qu, Daniel J. Park, Soheyla D. Gharib, Susan Fitzgerald, Paul Barreira, Stephen B. Fleming, Susan M. Lett, Paul A. Rota, Lawrence C. Madoff, Nathan L. Yozwiak, Bronwyn MacInnis, Sandra Smole, Yonatan H. Grad
Software Mentions: 2
Published: over 4 years ago