cran: TransPhylo | Projects | Ecosyste.ms: Papers

10.1002/cpz1.60

Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo
Cited by: 24
Author(s): Xavier Didelot, Michaela Kendall, Yuanwei Xu, Peter J White, Noel D. McCarthy
Software Mentions: 7
Published: over 3 years ago

10.1093/molbev/msz058

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling
Cited by: 14
Author(s): Matthew Hall, Caroline Colijn
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-018-2330-z

outbreaker2: a modular platform for outbreak reconstruction
Cited 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.1009300

MicrobeTrace: Retooling molecular epidemiology for rapid public health response
Cited by: 17
Author(s): Ellsworth Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, S. P. Knyazev, Roxana Cintrón, William M. Switzer
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-019-41103-6

Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models
Cited by: 30
Author(s): Simon M. Firestone, Yoko Hayama, Richard Bradhurst, Takehisa Yamamoto, Toshiyuki Tsutsui, Mark Stevenson
Software Mentions: 5
Published: over 5 years ago

10.1099/mgen.0.000539

Population structure and transmission of Mycobacterium bovis in Ethiopia
Cited by: 8
Author(s): Gizat Almaw, Getnet Abie Mekonnen, Adane Mihret, Abraham Aseffa, Hawult Taye, Andrew J. K. Conlan, Balako Gumi, Aboma Zewude, Abde Aliy, Mekdes Tamiru, Abebe Olani, Matios Lakew, Melaku Sombo, Solomon Gebre, Colette Diguimbaye, Markus Hilty, Adama Fané, Borna Müller, R. Glyn Hewinson, Richard J. Ellis, Javier Núñez-García, Eleftheria Palkopoulou, Tamrat Abebe, Gobena Ameni, Julian Parkhill, James Wood, Stefan Berg, Andries J. van Tonder
Software Mentions: 5
Published: over 3 years ago

10.1099/mgen.0.000418

Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
Cited by: 16
Author(s): Katharine S. Walter, Caroline Colijn, Ted Cohen, Barun Mathema, Qingyun Liu, Jolene R. Bowers, David M. Engelthaler, Apurva Narechania, Darrin Lemmer, Júlio Croda, Jason R Andrews
Software Mentions: 4
Published: about 4 years ago

10.1099/mgen.0.000263

Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains
Cited by: 18
Author(s): Lucy van Dorp, Qi Wang, Liam Shaw, Mislav Acman, Ola Brønstad Brynildsrud, Vegard Eldholm, Ruobing Wang, Hua Gao, Yuyao Yin, Hongbin Chen, Chuling Ding, Rhys A. Farrer, Xavier Didelot, François Balloux, Hui Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1005495

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
Cited by: 89
Author(s): Don Klinkenberg, J.A. Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga
Software Mentions: 4
Published: over 7 years ago

10.1099/mgen.0.000361

Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants
Cited by: 16
Author(s): Benjamin Sobkowiak, Louis Banda, Themba Mzembe, Amelia C. Crampin, Judith R. Glynn, Taane G. Clark
Software Mentions: 3
Published: over 4 years ago

10.1099/mgen.0.000219

Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population
Cited by: 10
Author(s): Diepreye Ayabina, Janne O. Rønning, Kristian Alfsnes, Nadia Debech, Ola Brønstad Brynildsrud, Trude Margrete Arnesen, Gunnstein Norheim, Anne Torunn Mengshoel, Rikard Rykkvin, Ulf R. Dahle, Caroline Colijn, Vegard Eldholm
Software Mentions: 3
Published: almost 6 years ago

10.3389/fpubh.2021.667337

Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source Cases
Cited 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

10.7717/peerj.4210

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
Cited by: 58
Author(s): Jason C Kwong, Courtney R Lane, Finn Romanes, Anders Gonçalves da Silva, Marion Easton, Katie Cronin, Mary Jo Waters, Takehiro Tomita, Kerrie Stevens, Mark B. Schultz, Sarah L. Baines, Norelle L Sherry, Glen P. Carter, Andre Mu, Michelle Sait, Susan A Ballard, Torsten Seemann, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1006748

A dynamic power-law sexual network model of gonorrhoea outbreaks
Cited by: 22
Author(s): Lilith K Whittles, Peter J White, Xavier Didelot
Software Mentions: 2
Published: over 5 years ago

10.1099/mgen.0.000480

Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway
Cited by: 11
Author(s): Magnus N Osnes, Xavier Didelot, Jolinda de Korne-Elenbaas, Kristian Alfsnes, Ola Brønstad Brynildsrud, Gaute Syversen, Ø Nilsen, Birgitte Freiesleben de Blasio, Dominique A. Caugant, Vegard Eldholm
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms21124546

Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic
Cited by: 35
Author(s): Alejandro Llanes, Carlos M. Restrepo, Zuleima Caballero, Sreekumari Rajeev, Melissa Kennedy, Ricardo Lleonart
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pmed.1002961

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain
Cited by: 50
Author(s): Yuanwei Xu, Irving Cancino-Muñoz, Manuela Torres-Puente, Luis M Villamayor, Rafael Borrás, María Borrás-Máñez, Montserrat Bosque, Juan J. Camarena, Ester Colomer-Roig, Javier Colomina, Isabel Escribano, Oscar Esparcia-Rodríguez, Ana Gil-Brusola, Concepción Gimeno, Adelina Gimeno-Gascón, Bárbara Gomila-Sard, Damiana González-Granda, Nieves Gonzalo-Jiménez, María Remedio Guna-Serrano, José Luís López-Hontangas, Coral Martín-González, Rosario Moreno-Muñoz, David Navarro, Marı́a Luisa Navarro, Nieves Orta, Elvira Pérez Pérez, Josep Morera Prat, Juan Carlos Rodrı́guez, María Montserrat Ruiz-García, Herme Vanaclocha, Caroline Colijn, Iñaki Comas
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-019-47740-1

Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada
Cited by: 17
Author(s): Patrick J. Stapleton, Alireza Eshaghi, Chi Yon Seo, Sarah E. Wilson, Tara Harris, Shelley L. Deeks, Shelly Bolotin, Lee W. Goneau, Jonathan B. Gubbay, Samir N. Patel
Software Mentions: 2
Published: about 5 years ago

10.1093/molbev/msw275

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
Cited by: 104
Author(s): Xavier Didelot, Christophe Fraser, Jennifer L. Gardy, Caroline Colijn
Software Mentions: 1
Published: over 7 years ago

10.1099/mgen.0.000450

Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data
Cited by: 8
Author(s): Yuanwei Xu, Jessica E. Stockdale, Vijay Naidu, Hollie Hatherell, James A. Stimson, Helen R. Stagg, Ibrahim Abubakar, Caroline Colijn
Software Mentions: 1
Published: almost 4 years ago

10.1099/mgen.0.000060

Declaring a tuberculosis outbreak over with genomic epidemiology
Cited by: 20
Author(s): Hollie-Ann Hatherell, Xavier Didelot, Sue Pollock, Patrick Tang, Anamaria Crisan, James C. Johnston, Caroline Colijn, Jennifer L. Gardy
Software Mentions: 1
Published: over 8 years ago

10.3390/microorganisms8020196

Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort
Cited by: 7
Author(s): Lauren Mak, Deshan Perera, Raynell Lang, Pathum Kossinna, Jingni He, M. John Gill, Quan Long, Guido van Marle
Software Mentions: 1
Published: over 4 years ago

10.4269/ajtmh.17-0700

Genomic Investigation of a Mycobacterium tuberculosis Outbreak Involving Prison and Community Cases in Florida, United States
Cited by: 14
Author(s): Marie Nancy Séraphin, Xavier Didelot, David J. Nolan, Justin R. May, Shafiqul Islam Khan, Ellen R. Murray, Marco Salemi, J. Glenn Morris, Michael Lauzardo
Software Mentions: 1
Published: almost 6 years ago

10.3389/fgene.2018.00376

Diagnosing Emerging Fungal Threats: A One Health Perspective
Cited by: 17
Author(s): Pria Ghosh, Matthew C. Fisher, Kieran A. Bates
Software Mentions: 1
Published: about 6 years ago

10.2196/19170

A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis
Cited by: 43
Author(s): Carla Mavian, Simone Marini, Mattia Prosperi, Marco Salemi
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: cran: TransPhylo

Papers Mentioning TransPhylo 25