Dr Sam Clifford

B AppSc PhD

Assistant Professor
in Machine (Statistical) Learning


Keppel Street
United Kingdom

Sam obtained a Bachelors Degree in Applied Science (with Honours) from Queensland University of Technology (QUT, Brisbane, Australia), majoring in Applied and Computational Mathematics. After a short break teaching mathematics to video game developers at Krome Studios, Sam undertook his Doctoral studies at the International Laboratory for Air Quality and Health (ILAQH), a WHO Collaborating Centre, at QUT.

Under Professors Lidia Morawska and Kerrie Mengersen and Dr Samantha Low-Choy, Sam's thesis investigated spatio-temporal modelling of ultrafine particles in Brisbane, Australia. After five and a half years of postdoctoral work at QUT (ILAQH and the ARC Centre of Excellence for Mathematical and Statistical Frontiers), Sam joined the London School of Hygiene and Tropical Medicine for 2.5 years as a postdoctoral fellow.

In 2020 Sam was promoted to Assistant Professor, where he continues his work on streptococcus pneumoniae, SARS-CoV-2/COVID-19 and Dengue.


Faculty of Epidemiology and Population Health
Department of Infectious Disease Epidemiology


Centre for the Mathematical Modelling of Infectious Diseases (CMMID)


Sam's current teaching at LSHTM includes the following short courses:

and the following MSc modules:

Sam is currently enrolled in the Postgraduate Certificate in Learning and Teaching at LSHTM.

Prior to joining LSHTM, Sam lectured mathematics and statistics to first year Bachelor of Science students at QUT in the core unit SEB113 - Quantitative Methods for Science. His teaching makes use of blended learning approaches to prepare students for lecture material, and collaborative workshops with project-based learning.

In 2015, Sam and his team were awarded a Vice Chancellor's Award for Innovation on the basis of their work transforming SEB113.



Sam's research at LSHTM includes the following:

  • Traveller screening, contact tracing and quarantine for SARS-CoV-2/COVID-19
  • Spatio-temporal variation in Streptococcus pneumoniae serotypes
  • Maternal colonisation of Group B Streptococcus
  • Modelling the health and economic impact of dengue vaccination

In addition to his doctoral thesis on spatio-temporal modelling of ultrafine particle number concentration, Sam's research interests include

  • exposure assessment
  • personal monitoring equipment for air pollution
  • non-parametric regression
  • jaguar conservation
  • Great Barrier Reef conservation
  • machine learning for spatial data
  • Bayesian hierarchical modelling
  • data visualisation
  • mathematics and statistics education
Research Area
Statistical methods
Bayesian Analysis
Environmental Health
Mobile technologies
Spatial analysis
Mathematical modelling
Disease and Health Conditions
Respiratory disease

Selected Publications

Strategies to reduce the risk of SARS-CoV-2 importation from international travellers: modelling estimations for the United Kingdom, July 2020.
Clifford S; Quilty BJ; Russell TW; Liu Y; Chan Y-WD; Pearson CAB; Eggo RM; Endo A; CMMID COVID-19 Working Group; Flasche S
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Contact tracing is an imperfect tool for controlling COVID-19 transmission and relies on population adherence.
Davis EL; Lucas TCD; Borlase A; Pollington TM; Abbott S; Ayabina D; Crellen T; Hellewell J; Pi L; CMMID COVID-19 Working Group
Nature communications
Implementation strategies for the first licensed dengue vaccine: A meeting report.
Fongwen N; Delrieu I; Ham LH; Gubler DJ; Durbin A; Ooi E-E; Peeling RW; Flasche S; Hartigan-Go K; Clifford S
Estimation of country-level incidence of early-onset invasive Group B Streptococcus disease in infants using Bayesian methods.
Gonçalves BP; Procter SR; Clifford S; Koukounari A; Paul P; Lewin A; Jit M; Lawn J
PLoS computational biology
Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data.
Munday JD; Jarvis CI; Gimma A; Wong KLM; van Zandvoort K; CMMID COVID-19 Working Group; Funk S; Edmunds WJ
BMC medicine
SARS-CoV-2 infection risk during delivery of childhood vaccination campaigns: a modelling study.
Procter SR; Abbas K; Flasche S; Griffiths U; Hagedorn B; O'Reilly KM; CMMID COVID-19 Working Group; Jit M
BMC Medicine
Pneumococcal exposure routes for infants, a nested cross-sectional survey in Nha Trang, Vietnam
Qian G; Toizumi M; Clifford S; Le LT; Papastylianou T; Quilty B; Iwasaki C; Kitamura N; Takegata M; Nguyen TM
Quarantine and testing strategies to reduce transmission risk from imported SARS-CoV-2 infections: a global modelling study
Quilty B; Russell T; Clifford S; Flasche S; Pickering S; Neil SJD; Galão RP; Edmunds J; CMMID COVID-19 Working Group
See more Publications