David Welch

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Alexei J. DrummondProfessor of Computational Biology, University of AucklandVerified email at cs.auckland.ac.nz
Tanja StadlerETH ZurichVerified email at env.ethz.ch
Alexandra "Sasha" GavryushkinaPostdoctoral fellow at University of OtagoVerified email at otago.ac.nz
Tina ToniImperial College London, Massachusetts Institute of TechnologyVerified email at mit.edu
Michael P H StumpfProfessor of Theoretical Systems Biology, University of MelbourneVerified email at unimelb.edu.au
Timothy G VaughanDepartment of Biosystems Science and Engineering, ETH Zürich, SwitzerlandVerified email at bsse.ethz.ch
Geoff NichollsAssociate Professor of Statistics, University of OxfordVerified email at stats.ox.ac.uk
David HunterProfessor of Statistics, Penn State UniversityVerified email at psu.edu
Jordan DouglasUniversity of AucklandVerified email at auckland.ac.nz
Jemma L GeogheganUniversity of Otago; ESR; Rutherford Discovery FellowVerified email at otago.ac.nz
Colin R SimpsonProfessor of Population Health, Victoria University of Wellington, Wellington, New ZealandVerified email at vuw.ac.nz
Xiaoyun RenInstitute of Environmental Science and ResearchVerified email at esr.cri.nz
Nigel FrenchDistinguished Professor of Veterinary Public Health, Massey University.Verified email at massey.ac.nz
Tracy A. HeathAssistant Professor, Iowa State UniversityVerified email at iastate.edu
Daniel KsepkaCurator, Bruce MuseumVerified email at brucemuseum.org
Joep de LigtLead - Bioinformatics and Genomics @ ESR, NZVerified email at esr.cri.nz
Edward C HolmesUniversity of SydneyVerified email at sydney.edu.au
Sue HuangInstitute of Environmental Science and ResearchVerified email at esr.cri.nz
Quentin AtkinsonUniversity of AucklandVerified email at auckland.ac.nz
Denise KühnertMax Planck Institute for the Science of Human HistoryVerified email at shh.mpg.de

David Welch

Senior Lecturer, Computational Evolution Group, Dept of Computer Science, University of Auckland

Verified email at auckland.ac.nz - Homepage

Bayesian statistics epidemiology phylogenetics networks sampling algorithms


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Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems T Toni, D Welch, N Strelkowa, A Ipsen, MPH Stumpf Journal of the Royal Society Interface 6 (31), 187-202, 2009	1297	2009
Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration A Gavryushkina, D Welch, T Stadler, AJ Drummond PLoS Comput Biol 10 (12), e1003919, 2014	212	2014
Bayesian total-evidence dating reveals the recent crown radiation of penguins A Gavryushkina, TA Heath, DT Ksepka, T Stadler, D Welch, AJ Drummond Systematic biology 66 (1), 57-73, 2017	186	2017
From words to dates: water into wine, mathemagic or phylogenetic inference? Q Atkinson, G Nicholls, D Welch, R Gray Transactions of the Philological Society 103 (2), 193-219, 2005	116	2005
Efficient Bayesian inference under the structured coalescent TG Vaughan, D Kühnert, A Popinga, D Welch, AJ Drummond Bioinformatics 30 (16), 2272-2279, 2014	92	2014
Bayesian inference for contact networks given epidemic data C Groendyke, D Welch, DR Hunter Scandinavian Journal of Statistics 38 (3), 600-616, 2011	79	2011
Statistical inference to advance network models in epidemiology D Welch, S Bansal, DR Hunter Epidemics 3 (1), 38-45, 2011	74	2011
A network‐based analysis of the 1861 Hagelloch measles data C Groendyke, D Welch, DR Hunter Biometrics 68 (3), 755-765, 2012	65	2012
Protocols for sampling viral sequences to study epidemic dynamics JC Stack, JD Welch, MJ Ferrari, BU Shapiro, BT Grenfell Journal of the Royal Society Interface 7 (48), 1119-1127, 2010	58	2010
Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand JL Geoghegan, X Ren, M Storey, J Hadfield, L Jelley, S Jefferies, ... Nature communications 11 (1), 1-7, 2020	38	2020
Inferring ancestral recombination graphs from bacterial genomic data TG Vaughan, D Welch, AJ Drummond, PJ Biggs, T George, NP French Genetics 205 (2), 857-870, 2017	25	2017
Estimating Epidemic Incidence and Prevalence from Genomic Data TG Vaughan, GE Leventhal, DA Rasmussen, AJ Drummond, D Welch, ... Molecular Biology and Evolution, 2019	22	2019
Estimating epidemic incidence and prevalence from genomic data TG Vaughan, GE Leventhal, DA Rasmussen, AJ Drummond, D Welch, ... bioRxiv, 142570, 2017	22	2017
Integrating genealogy and epidemiology: the ancestral infection and selection graph as a model for reconstructing host virus histories D Welch, GK Nicholls, A Rodrigo, W Solomon Theoretical population biology 68 (1), 65-75, 2005	21	2005
Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing T Swadi, JL Geoghegan, T Devine, C McElnay, J Sherwood, P Shoemack, ... Emerging Infectious Diseases 27 (3), 2021	17*	2021
Is network clustering detectable in transmission trees? D Welch Viruses 3 (6), 659-676, 2011	17	2011
Demographic inference under the coalescent in a spatial continuum S Guindon, H Guo, D Welch Theoretical population biology 111, 43-50, 2016	14	2016
Recursive algorithms for phylogenetic tree counting A Gavryushkina, D Welch, AJ Drummond Algorithms for Molecular Biology 8 (1), 1-13, 2013	13	2013
epinet: An R Package to Analyze Epidemics Spread across Contact Networks C Groendyke, D Welch Journal of Statistical Software 83 (11), 1-22, 2018	11	2018
The transmission process: A combinatorial stochastic process for the evolution of transmission trees over networks R Sainudiin, D Welch Journal of theoretical biology 410, 137-170, 2016	10*	2016

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