{"id":29,"date":"2023-11-19T22:37:39","date_gmt":"2023-11-19T22:37:39","guid":{"rendered":"https:\/\/simonlammmm.ddns.net\/?page_id=29"},"modified":"2025-12-03T14:00:12","modified_gmt":"2025-12-03T14:00:12","slug":"curriculum-vitae","status":"publish","type":"page","link":"https:\/\/simonlammmm.ddns.net\/index.php\/curriculum-vitae\/","title":{"rendered":"Curriculum vitae"},"content":{"rendered":"\n
<\/span>
\n

Simon Lam<\/p>\n\n\n\n

Bioinformatician, data scientist, research associate<\/p>\n\n\n\n

Research Associate at University of Cambridge<\/p>\n\n\n\n

PhD in Systems Biology, King’s College London<\/p>\n<\/div><\/div>\n\n\n\n

\n\n\n\n

Activities<\/h2>\n\n\n\n

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.<\/p>\n\n\n\n

\n
\n

Bioinformatics<\/h3>\n\n\n\n

Trained in systems biology at King’s College London, I work with experimental scientists and analyse any type of biological data, from deep sequencing<\/strong> and genomics<\/strong> to mathematical modelling<\/strong> and molecular dynamics<\/strong>.<\/p>\n<\/div>\n\n\n\n

\n

Statistics<\/h3>\n\n\n\n

Statistics tells us whether the trend we see is important. I advise on and implement standard and custom statistical tests<\/strong>, to assess probability of observation due to chance<\/strong> and calculation of effect size<\/strong>.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

Data science<\/h3>\n\n\n\n

Data are meant to be reused. I use big data<\/strong> techniques to maintain large databases<\/strong> and probe them in meta-analysis<\/strong> to infer trends that can’t be concluded from individual datasets in isolation.<\/p>\n<\/div>\n\n\n\n

\n

Data visualisation<\/h3>\n\n\n\n

Visualisation makes data both accessible<\/strong> and beautiful. Using ggplot2<\/strong> and Adobe Illustrator<\/strong>, my figures are designed for scientists and laypeople alike. Interactive data viz with plotly<\/strong> makes for a truly powerful and pleasant experience.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

Web design<\/h3>\n\n\n\n

International scientific communities benefit from web services providing access to data and software for free. I design websites with UI\/UX<\/strong> in mind, deploying services as Shiny<\/strong> and Dash<\/strong> apps.<\/p>\n<\/div>\n\n\n\n

\n

Software development<\/h3>\n\n\n\n

Transparent, open, and consistent code is essential for reproducible<\/strong> science. I script in R<\/strong>, Python<\/strong>, MATLAB<\/strong>, Perl<\/strong>, SQL<\/strong>, Docker<\/strong>, HTML<\/strong>, CSS<\/strong>, Bash<\/strong>, PowerShell<\/strong>, and LOLCODE.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

System administrator<\/h3>\n\n\n\n

I maintain and monitor web servers, understanding how users interact with services with analytics from nginx<\/strong>, lighttpd<\/strong>, and ShinyProxy<\/strong>. I’m experienced in self-hosting web services, including this website.<\/p>\n<\/div>\n\n\n\n

\n

Artificial intelligence<\/h3>\n\n\n\n

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.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

Biology<\/h3>\n\n\n\n

Having performed western blots<\/strong>, light microscopy<\/strong>, PCR<\/strong>, PAGE<\/strong>, and IHC<\/strong> 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.<\/p>\n<\/div>\n\n\n\n

\n

Eternal scholar<\/h3>\n\n\n\n

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.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n\n\n\n

Selected works<\/h2>\n\n\n\n

Simple, thoughtful web resources bridge the gap between data generation and interpretation.<\/p>\n\n\n\n

\n
\n
\n
DDRcs<\/a><\/div>\n<\/div>\n<\/div>\n\n\n\n
\n

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.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n
\n
SPIDRweb<\/a><\/div>\n<\/div>\n<\/div>\n\n\n\n
\n

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.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n
\n
Exorcise<\/a><\/div>\n<\/div>\n<\/div>\n\n\n\n
\n

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.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n\n\n\n

Education<\/h2>\n\n\n\n

A foundation in science and a background in experimental methods give me the awareness for where data come from.<\/p>\n\n\n\n

\n
\n

2019-2023<\/p>\n<\/div>\n\n\n\n

\n

PhD in Systems Biology
King’s College London, London, United Kingdom<\/p>\n\n\n\n

Associateship of King’s College London
King’s College London, London, United Kingdom<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2017<\/p>\n<\/div>\n\n\n\n

\n

Certificate in Teaching English to Speakers of Other Languages
Library of Birmingham, Birmingham, United Kingdom<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2013-2017<\/p>\n<\/div>\n\n\n\n

\n

MSci (Hons) Natural Sciences
University of Cambridge, Cambridge, United Kingdom<\/p>\n\n\n\n

BA (Hons) Natural Sciences
University of Cambridge, Cambridge, United Kingdom<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2008-2013<\/p>\n<\/div>\n\n\n\n

\n

A-Level: Biology, Chemistry, Physics, Mathematics
AS-Level: Further Mathematics
9 GCSEs<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n\n\n\n

Publications<\/h2>\n\n\n\n

Widely published in diverse fields in biology from neurology and cancer to bioinformatics and software. <\/p>\n\n\n\n

\n
\n

Preprints<\/p>\n<\/div>\n\n\n\n

\n

Schlapansky et al. “Cell-stereotyped DNA repair outcomes are widespread during genome editing\u201d. bioRxiv.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2025<\/p>\n<\/div>\n\n\n\n

\n

Wilson et al. “WEE1 inhibitors synergise with mRNA translation defects via activation of the kinase GCN2.” Nature Communications. 16: 8983.<\/a><\/p>\n\n\n\n

Kochenova et al. “USP37 prevents premature disassembly of stressed replisomes by TRAIP.” Nature Communications. 16: 5333.<\/a><\/p>\n\n\n\n

Fielden et al. \u201cComprehensive interrogation of synthetic lethality in the DNA damage response.\u201d Nature. 640: 1093-1102.<\/a><\/p>\n\n\n\n

Awwad et al. \u201cKLF5 loss sensitizes to ATR inhibition and is synthetic lethal with ARID1A deficiency.\u201d Nature Communications. 16(1): 480.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2024<\/p>\n<\/div>\n\n\n\n

\n

Lewis et al. \u201cPlastid translocon recycling in dinoflagellates demonstrates the portability of complex plastids between hosts.\u201d Current Biology, 34(23): 5494\u20135506.e3.<\/a><\/p>\n\n\n\n

Lam et al. \u201cGenome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens.\u201d Genome Medicine, 16: 139.<\/a><\/p>\n\n\n\n

Carnie et al. \u201cThe dCMP deaminase DCTD and the E3 ligase TOPORS mediate decitabine cytotoxicity.\u201d EMBO Journal, 43(12): 2397\u20132423.<\/a><\/p>\n\n\n\n

Carnie et al. \u201cTranscription-coupled repair of DNA\u2013protein cross-links depends on CSA and CSB.\u201d Nature Cell Biology, 26(5): 797\u2013810.<\/a><\/p>\n\n\n\n

Mohammadi et al. \u201cDrug repositioning for immunotherapy in breast cancer using single-cell analysis.\u201d npj Systems Biology and Applications, 10: 37.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2022<\/p>\n<\/div>\n\n\n\n

\n

Lam et al. \u201cMachine learning analysis reveals biomarkers for the detection of neurological diseases\u201d. Frontiers in Molecular Neuroscience. 15: 889728.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2021<\/p>\n<\/div>\n\n\n\n

\n

Bayraktar et al. \u201cRevealing the molecular mechanisms of Alzheimer\u2019s disease based on network analysis.\u201d International Journal of Molecular Sciences. 22(21): 11556.<\/a><\/p>\n\n\n\n

Mohammadi et al. \u201cImprovement of the performance of anticancer peptides using a drug repositioning pipeline.\u201d Biotechnol<\/a>ogy Journal. e2100417.<\/a><\/p>\n\n\n\n

Lam et al. \u201cSystems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer\u2019s and Parkinson\u2019s diseases.\u201d Biomedicines. 9(10): 1310.<\/a><\/p>\n\n\n\n

Doran et al. \u201cMulti-omics approaches for revealing the complexity of cardiovascular disease.\u201d Briefings in Bioinformatics. bbab061.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2020<\/p>\n<\/div>\n\n\n\n

\n

Altay et al. \u201cCurrent status of COVID-19 therapies and drug repositioning applications.\u201d iScience. 25(7): 101303.<\/a><\/p>\n\n\n\n

Lam et al. \u201cA systems biology approach for studying neurodegenerative diseases.\u201d Drug Discovery Today. 25 (7): 1146\u20131159.<\/a><\/p>\n\n\n\n

Ozcan et al. \u201cImprovement in the current therapies for hepatocellular carcinoma using a systems medicine approach.\u201d Advanced Biosystems. 4(6): 2000030.<\/a><\/p>\n\n\n\n

Lam et al. \u201cAddressing the heterogeneity in liver diseases using biological networks.\u201d Briefings in Bioinformatics. 22 (2): 1751\u20131766.<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

\n\n\n\n

Conferences<\/h2>\n\n\n\n

Always looking to expand and transfer knowledge.<\/p>\n\n\n\n

\n
\n

2025<\/p>\n<\/div>\n\n\n\n

\n

CRISPR and Beyond: Perturbations at Scale to Understand Genomes<\/a>, Wellcome Genome Campus, Hinxton, United Kingdom. Attendee.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2024<\/p>\n<\/div>\n\n\n\n

\n

European Bioconductor Conference<\/a>, University of Oxford, Oxford, United Kingdom. Poster presenter.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2023<\/p>\n<\/div>\n\n\n\n

\n

CRUK RadNet: Enabling Research with Complex Technologies<\/a>, Cancer Research UK Manchester Institute, Manchester, United Kingdom. Oral presenter.<\/p>\n\n\n\n

Genome Stability Network<\/a>, University of Cambridge, Cambridge, United Kingdom. Attendee.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2022<\/p>\n<\/div>\n\n\n\n

\n

Cell Symposia: Metabolites in Signalling and Disease<\/a>, Altis Grand Hotel, Lisbon, Portugal. Poster presenter.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2021<\/p>\n<\/div>\n\n\n\n

\n

Harvard Chan Microbiome in Public Health Center Symposium: The Microbiome and Infectious Diseases<\/a>, Harvard University, Boston, MA, United States. Attendee.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2020<\/p>\n<\/div>\n\n\n\n

\n

Neurodegenerative Diseases: Biology and Therapeutics<\/a>, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States. Attendee.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2019<\/p>\n<\/div>\n\n\n\n

\n

Turkish Medical World Congress VI<\/a>, Renaissance Polat Hotel Istanbul, Istanbul, T\u00fcrkiye. Oral presenter.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2016<\/p>\n<\/div>\n\n\n\n

\n

The Chemistry and Biology of Natural Products Symposium X<\/a>, University of Warwick, Coventry, United Kingdom. Attendee.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n\n\n\n

Work history<\/h2>\n\n\n\n

A career in science.<\/p>\n\n\n\n

\n
\n

2022-<\/p>\n<\/div>\n\n\n\n

\n

Research Associate, University of Cambridge, Cambridge, United Kingdom.<\/p>\n\n\n\n

Responsible for bioinformatics, statistics, and data analysis demands from bench scientists. Develop and maintain data science web services.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2021-2023<\/p>\n<\/div>\n\n\n\n

\n

Graduate Teaching Assistant, King’s College London, London, United Kingdom.<\/p>\n\n\n\n

Supported lecturers on MSc course and moderated sessions delivered online. <\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2021<\/p>\n<\/div>\n\n\n\n

\n

King’s Experience Assessor, King’s College London, London, United Kingdom.<\/p>\n\n\n\n

Marked students’ work for the Undergraduate Research Fellowship, providing constructive feedback.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2020-<\/p>\n<\/div>\n\n\n\n

\n

Peer Reviewer, online.<\/p>\n\n\n\n

Peer-review manuscripts for various journals.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2019-2023<\/p>\n<\/div>\n\n\n\n

\n

PhD Candidate in Systems Biology, King’s College London, London, United Kingdom.<\/p>\n\n\n\n

PhD candidate.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2018-2019<\/p>\n<\/div>\n\n\n\n

\n

Teacher of English as a Foreign Language, Huazhong Agricultural University, Wuhan, China.<\/p>\n\n\n\n

Design and deliver English lessons and examinations for undergraduate and postgraduate students.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2016-2017<\/p>\n<\/div>\n\n\n\n

\n

MSci Student Researcher, University of Cambridge, Cambridge, United Kingdom.<\/p>\n\n\n\n

MSci student.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2016<\/p>\n<\/div>\n\n\n\n

\n

Visiting Researcher, University of Birmingham, Birmingham, United Kingdom.<\/p>\n\n\n\n

Visiting researcher.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2016<\/p>\n<\/div>\n\n\n\n

\n

BA Student Researcher, University of Cambridge, Cambridge, United Kingdom. <\/p>\n\n\n\n

BA student.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2015<\/p>\n<\/div>\n\n\n\n

\n

Visiting Research Intern, University of Birmingham, Birmingham, United Kingdom.<\/p>\n\n\n\n

Visiting research intern.<\/p>\n<\/div>\n<\/div>\n\n\n\n

\n
\n

2012-2016<\/p>\n<\/div>\n\n\n\n

\n

STEM Ambassador, University of Worcester, United Kingdom.<\/p>\n\n\n\n

Delivered and supervised an inorganic chemistry lesson at a local high school. Volunteered at open days and careers fairs for secondary school pupils.<\/p>\n<\/div>\n<\/div>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

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 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-29","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/pages\/29","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/comments?post=29"}],"version-history":[{"count":13,"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/pages\/29\/revisions"}],"predecessor-version":[{"id":92,"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/pages\/29\/revisions\/92"}],"wp:attachment":[{"href":"https:\/\/simonlammmm.ddns.net\/index.php\/wp-json\/wp\/v2\/media?parent=29"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}