David Welch

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Alexei J. DrummondProfessor of Computational Biology, University of AucklandVerified email at cs.auckland.ac.nz
Jemma L GeogheganAssociate Professor, University of Otago; ESR; Rutherford Discovery FellowVerified email at otago.ac.nz
Nigel FrenchDistinguished Professor of Infectious Disease Epidemiology and Public Health, Massey University.Verified email at massey.ac.nz
Joep de LigtSenior Science Lead - Bioinformatics and Genomics @ ESR, NZVerified email at esr.cri.nz
Jordan DouglasUniversity of AucklandVerified email at auckland.ac.nz
Xiaoyun RenInstitute of Environmental Science and ResearchVerified email at esr.cri.nz
Tanja StadlerETH ZurichVerified email at env.ethz.ch
Colin R SimpsonVictoria University of WellingtonVerified email at vuw.ac.nz
Alexandra "Sasha" GavryushkinaPostdoctoral fellow at Canterbury UniversityVerified email at canterbury.ac.nz
Sue HuangInstitute of Environmental Science and ResearchVerified email at esr.cri.nz
Timothy G VaughanDepartment of Biosystems Science and Engineering, ETH Zürich, SwitzerlandVerified email at bsse.ethz.ch
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
Andrew SporleiNZight Analytics LtdVerified email at auckland.ac.nz
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
Christophe GroendykeVerified email at rmu.edu
Edward C HolmesUniversity of SydneyVerified email at sydney.edu.au
Fábio Kuriki MendesPostdoctoral fellow, Washington University in St. LouisVerified email at wustl.edu
Quentin AtkinsonUniversity of AucklandVerified email at auckland.ac.nz

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	1618	2009
Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration A Gavryushkina, D Welch, T Stadler, AJ Drummond PLoS computational biology 10 (12), e1003919, 2014	285	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	256	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	127	2005
Efficient Bayesian inference under the structured coalescent TG Vaughan, D Kühnert, A Popinga, D Welch, AJ Drummond Bioinformatics 30 (16), 2272-2279, 2014	120	2014
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), 6351, 2020	116	2020
Bayesian inference for contact networks given epidemic data C Groendyke, D Welch, DR Hunter Scandinavian Journal of Statistics 38 (3), 600-616, 2011	86	2011
Statistical inference to advance network models in epidemiology D Welch, S Bansal, DR Hunter Epidemics 3 (1), 38-45, 2011	82	2011
A network‐based analysis of the 1861 Hagelloch measles data C Groendyke, D Welch, DR Hunter Biometrics 68 (3), 755-765, 2012	71	2012
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	69*	2021
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	62	2010
Estimating Epidemic Incidence and Prevalence from Genomic Data TG Vaughan, GE Leventhal, DA Rasmussen, AJ Drummond, D Welch, ... Molecular Biology and Evolution, 2019	41	2019
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	39	2017
Use of genomics to track coronavirus disease outbreaks, New Zealand JL Geoghegan, J Douglas, X Ren, M Storey, J Hadfield, OK Silander, ... Emerging infectious diseases 27 (5), 1317, 2021	32	2021
Real-time genomics for tracking severe acute respiratory syndrome coronavirus 2 border incursions after virus elimination, New Zealand J Douglas, JL Geoghegan, J Hadfield, R Bouckaert, M Storey, X Ren, ... Emerging infectious diseases 27 (9), 2361, 2021	28	2021
Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations J Douglas, FK Mendes, R Bouckaert, D Xie, CL Jiménez-Silva, ... Virus evolution 7 (2), veab052, 2021	26	2021
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	22	2005
Demographic inference under the coalescent in a spatial continuum S Guindon, H Guo, D Welch Theoretical population biology 111, 43-50, 2016	21	2016
Is network clustering detectable in transmission trees? D Welch Viruses 3 (6), 659-676, 2011	19	2011
epinet: An R Package to Analyze Epidemics Spread across Contact Networks C Groendyke, D Welch Journal of Statistical Software 83 (11), 1-22, 2018	14	2018

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