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.


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 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

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7.
Davies NG; Jarvis CI; CMMID COVID-19 Working Group; Edmunds WJ; Jewell NP; Diaz-Ordaz K; Keogh RH
The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.
Jarvis CI; Gimma A; van Zandvoort K; Wong KLM; CMMID COVID-19 working group; Edmunds WJ
BMC medicine
Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England.
Leclerc QJ; Nightingale ES; Abbott S; CMMID COVID-19 Working Group; Jombart T
Scientific reports
The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories.
Liu Y; Morgenstern C; Kelly J; Lowe R; CMMID COVID-19 Working Group; Jit M
BMC Medicine
The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya.
Mburu CN; Ojal J; Chebet R; Akech D; Karia B; Tuju J; Sigilai A; Abbas K; Jit M; Funk S
BMC medicine
Global and national estimates of the number of healthcare workers at high risk of SARS-CoV-2 infection.
McCarthy CV; Sandmann FG; CMMID COVID-19 Working Group; Jit M
The Journal of hospital infection
Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England.
Munday JD; Sherratt K; Meakin S; Endo A; Pearson CAB; Hellewell J; Abbott S; Bosse NI; CMMID COVID-19 Working Group; Atkins KE
Nature communications
Quarantine and testing strategies in contact tracing for SARS-CoV-2: a modelling study.
Quilty BJ; Clifford S; Hellewell J; Russell TW; Kucharski AJ; Flasche S; Edmunds WJ; Centre for the Mathematical Modelling of Infectious Diseases COV
The Lancet Public Health
See more Publications