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

Measuring the effects of COVID-19-related disruption on dengue transmission in southeast Asia and Latin America: a statistical modelling study.
Chen Y; Li N; Lourenço J; Wang L; Cazelles B; Dong L; Li B; Liu Y; Jit M; Bosse NI
The Lancet. Infectious diseases
SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort.
Finch E; Lowe R; Fischinger S; de St Aubin M; Siddiqui SM; Dayal D; Loesche MA; Rhee J; Beger S; Hu Y
PLoS biology
Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey: A repeated cross-sectional study.
Gimma A; Munday JD; Wong KLM; Coletti P; van Zandvoort K; Prem K; CMMID COVID-19 working group; Klepac P; Rubin GJ; Funk S
PLoS medicine
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
Travel measures in the SARS-CoV-2 variant era need clear objectives.
Kucharski AJ; Jit M; Logan JG; Cotten M; Clifford S; Quilty BJ; Russell TW; Peeling RW; Antonio M; Heymann DL
Lancet (London, England)
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
Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission: a prospective cohort study in England
Clifford S; Waight P; Hackman J; Hué S; Gower C; Kirsebom FCM; Skarnes C; Letley L; Bernal JL; Andrews N
The importance of saturating density dependence for population-level predictions of SARS-CoV-2 resurgence compared with density-independent or linearly density-dependent models, England, 23 March to 31 July 2020.
Nightingale ES; Brady OJ; CMMID Covid-19 working group; Yakob L
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
See more Publications