Dr Sam Clifford


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.


Department of Infectious Disease Epidemiology
Faculty of Epidemiology and Population Health


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 has completed 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

Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era.
Barnard RC; Davies NG; Centre for Mathematical Modelling of Infectious Diseases COVID-1; Jit M; Edmunds WJ
Nature Communications
Using trained dogs and organic semi-conducting sensors to identify asymptomatic and mild SARS-CoV-2 infections: an observational study.
Guest C; Dewhirst SY; Lindsay SW; Allen DJ; Aziz S; Baerenbold O; Bradley J; Chabildas U; Chen-Hussey V; Clifford S
Journal of travel medicine
The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.
McCarthy CV; O'Mara O; van Leeuwen E; CMMID COVID-19 Working Group; Jit M; Sandmann F
BMC Public Health
Using high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events.
Pung R; Firth JA; Spurgin LG; Singapore CruiseSafe working group; CMMID COVID-19 working group; Lee VJ; Kucharski AJ
Nature Communications
Association of pneumococcal carriage in infants with the risk of carriage among their contacts in Nha Trang, Vietnam: A nested cross-sectional survey.
Qian G; Toizumi M; Clifford S; Le LT; Papastylianou T; Satzke C; Quilty B; Iwasaki C; Kitamura N; Takegata M
PLoS medicine
Ultrafine particle exposure and biomarkers of effect on small airways in children.
Robinson PD; Salimi F; Cowie CT; Clifford S; King GG; Thamrin C; Hardaker K; Mazaheri M; Morawska L; Toelle BG
Environmental research
Optimal age targeting for pneumococcal vaccination in older adults; a modelling study
Thindwa D; Clifford S; Kleynhans J; Gottberg AV; Walaza S; Meiring S; Swarthout TD; Miller E; McIntyre P; Andrews N
Cold Spring Harbor Laboratory
Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK.
Waites W; Pearson CAB; Gaskell KM; House T; Pellis L; Johnson M; Gould V; Hunt A; Stone NRH; Kasstan B
Scientific Reports
See more Publications