Simon Lam
Bioinformatician, data scientist, research associate
Research Associate at University of Cambridge
PhD in Systems Biology, King’s College London
Activities
I empower bench scientists to do whatever analysis they want without worrying about how they’re going to analyse it. I enable computational scientists to do data science with open-source code and publicly available web resources.
Bioinformatics
Trained in systems biology at King’s College London, I work with experimental scientists and analyse any type of biological data, from deep sequencing and genomics to mathematical modelling and molecular dynamics.
Statistics
Statistics tells us whether the trend we see is important. I advise on and implement standard and custom statistical tests, to assess probability of observation due to chance and calculation of effect size.
Data science
Data are meant to be reused. I use big data techniques to maintain large databases and probe them in meta-analysis to infer trends that can’t be concluded from individual datasets in isolation.
Data visualisation
Visualisation makes data both accessible and beautiful. Using ggplot2 and Adobe Illustrator, my figures are designed for scientists and laypeople alike. Interactive data viz with plotly makes for a truly powerful and pleasant experience.
Web design
International scientific communities benefit from web services providing access to data and software for free. I design websites with UI/UX in mind, deploying services as Shiny and Dash apps.
Software development
Transparent, open, and consistent code is essential for reproducible science. I script in R, Python, MATLAB, Perl, SQL, Docker, HTML, CSS, Bash, PowerShell, and LOLCODE.
System administrator
I maintain and monitor web servers, understanding how users interact with services with analytics from nginx, lighttpd, and ShinyProxy. I’m experienced in self-hosting web services, including this website.
Artificial intelligence
Big data are amenable to analysis with artificial intelligence and machine learning techniques. I explore how our databases can leverage AI/ML to uncover novel findings and drive health sciences forward.
Biology
Having performed western blots, light microscopy, PCR, PAGE, and IHC in teaching labs, I can follow a protocol and I have the appreciation for where biological data come from. I work with bench scientists and am used to being the responsible person for their data.
Eternal scholar
It is fascinating to be at the cutting edge of both biology and bioinformatics. Every day is a learning day, learning from bench scientists, the scientific literature, and my own curiosity.
Selected works
Simple, thoughtful web resources bridge the gap between data generation and interpretation.
The DNA damage response (DDR) CRISPR screen (DDRcs) database is a data science and visualisation tool. It is an ongoing literature search for CRISPR screens investigating the DDR in human and mouse cell lines. DDRcs provides visualisation tools both within and between screens. All data were re-analysed from raw counts or sequencing data to ensure consistency across datasets.
Systematic profiling of interactions in DNA repair (SPIDR) is a dual CRISPR interference screen silencing pairs of DDR genes simultaneously. Over 150,000 pairwise interactions were probed for synergy and suppressing behaviours. SPIDRweb is a portal that lets you explore the results of this screen.
Oligonucleotide libraries designed from a reference genome but then used on a cell line with a genome or expression profile that does not represent that reference can cause a problem when making inferences from the results. Exome-guided reannotation of nucleotide sequences (Exorcise) uses alignment and set theory to apply reannotations to oligonucleotides, bridging the gap between reference and the cell line under investigation.
Education
A foundation in science and a background in experimental methods give me the awareness for where data come from.
2019-2023
PhD in Systems Biology
King’s College London, London, United Kingdom
Associateship of King’s College London
King’s College London, London, United Kingdom
2017
Certificate in Teaching English to Speakers of Other Languages
Library of Birmingham, Birmingham, United Kingdom
2013-2017
MSci (Hons) Natural Sciences
University of Cambridge, Cambridge, United Kingdom
BA (Hons) Natural Sciences
University of Cambridge, Cambridge, United Kingdom
2008-2013
A-Level: Biology, Chemistry, Physics, Mathematics
AS-Level: Further Mathematics
9 GCSEs
Publications
Widely published in diverse fields in biology from neurology and cancer to bioinformatics and software.
2025
2024
2021
2020
Conferences
Always looking to expand and transfer knowledge.
2025
CRISPR and Beyond: Perturbations at Scale to Understand Genomes, Wellcome Genome Campus, Hinxton, United Kingdom. Attendee.
2024
European Bioconductor Conference, University of Oxford, Oxford, United Kingdom. Poster presenter.
2023
CRUK RadNet: Enabling Research with Complex Technologies, Cancer Research UK Manchester Institute, Manchester, United Kingdom. Oral presenter.
Genome Stability Network, University of Cambridge, Cambridge, United Kingdom. Attendee.
2022
Cell Symposia: Metabolites in Signalling and Disease, Altis Grand Hotel, Lisbon, Portugal. Poster presenter.
2021
Harvard Chan Microbiome in Public Health Center Symposium: The Microbiome and Infectious Diseases, Harvard University, Boston, MA, United States. Attendee.
2020
Neurodegenerative Diseases: Biology and Therapeutics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States. Attendee.
2019
Turkish Medical World Congress VI, Renaissance Polat Hotel Istanbul, Istanbul, Türkiye. Oral presenter.
2016
The Chemistry and Biology of Natural Products Symposium X, University of Warwick, Coventry, United Kingdom. Attendee.
Work history
A career in science.
2022-
Research Associate, University of Cambridge, Cambridge, United Kingdom.
Responsible for bioinformatics, statistics, and data analysis demands from bench scientists. Develop and maintain data science web services.
2021-2023
Graduate Teaching Assistant, King’s College London, London, United Kingdom.
Supported lecturers on MSc course and moderated sessions delivered online.
2021
King’s Experience Assessor, King’s College London, London, United Kingdom.
Marked students’ work for the Undergraduate Research Fellowship, providing constructive feedback.
2020-
Peer Reviewer, online.
Peer-review manuscripts for various journals.
2019-2023
PhD Candidate in Systems Biology, King’s College London, London, United Kingdom.
PhD candidate.
2018-2019
Teacher of English as a Foreign Language, Huazhong Agricultural University, Wuhan, China.
Design and deliver English lessons and examinations for undergraduate and postgraduate students.
2016-2017
MSci Student Researcher, University of Cambridge, Cambridge, United Kingdom.
MSci student.
2016
Visiting Researcher, University of Birmingham, Birmingham, United Kingdom.
Visiting researcher.
2016
BA Student Researcher, University of Cambridge, Cambridge, United Kingdom.
BA student.
2015
Visiting Research Intern, University of Birmingham, Birmingham, United Kingdom.
Visiting research intern.
2012-2016
STEM Ambassador, University of Worcester, United Kingdom.
Delivered and supervised an inorganic chemistry lesson at a local high school. Volunteered at open days and careers fairs for secondary school pupils.