Ong, Swee Hoe
Initially trained as a bench scientist, I have been a computational biologist for many years working in fields as diverse as small-molecule antiviral drug discovery, molecular diagnostic development, bacterial metagenomics and cancer genomics. I am most interested in research that can lead to better diagnostics and therapeutics.
Initially my role in the Virus Genomics group at the Sanger Institute was to make sense out of virus genomic sequence data, e.g. to understand the origins, diversity, transmission, and evolutionary dynamics of important viral infectious agents such as HIV, HCV, MERS-CoV et cetera. I looked after the in-house bioinformatics pipepline for large-scale de novo genome assembly, quality checking and classification of HIV-1 genomes for three major international collaborative projects: BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe), ICONIC (Infection Response through Virus Genomics), and PANGEA (Phylogenetics and Networks for Generalised HIV Epidemics in Africa) which is funded by the Bill and Melinda Gates Foundation.
I moved to the Stem Cell Genetics group under the Cellular Genetics Programme in 2016, and I have been supporting the group on whole-genome CRISPR/Cas9 guide RNA library design and optimisation, and analysis of genome-scale CRISPR/Cas9 knockout genetic screening data.
In September 2017 I joined the Jones group to work on characterising mutations in the early stages of cancer evolution.
Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3.
BMC genomics 2019;20;1;272
Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations.
Cell stem cell 2018;23;5;687-699.e8
Genome-wide CRISPR-KO Screen Uncovers mTORC1-Mediated Gsk3 Regulation in Naive Pluripotency Maintenance and Dissolution.
Cell reports 2018;24;2;489-502
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Virus evolution 2018;4;1;vey007
Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries.
Scientific reports 2017;7;1;7384
From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.
Virus research 2017;239;10-16
Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
PLoS biology 2017;15;6;e2001855
Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes.
BMC genomics 2017;18;1;419
IVA: accurate de novo assembly of RNA virus genomes.
Bioinformatics (Oxford, England) 2015;31;14;2374-6
Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.
Journal of virology 2014;88;19;11056-69
Systems consequences of amplicon formation in human breast cancer.
Genome research 2014;24;10;1559-71
Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus.
Patient-based transcriptome-wide analysis identify interferon and ubiquination pathways as potential predictors of influenza A disease severity.
PloS one 2014;9;11;e111640
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
PloS one 2013;8;4;e60811
Plasmablasts generated during repeated dengue infection are virus glycoprotein-specific and bind to multiple virus serotypes.
Journal of immunology (Baltimore, Md. : 1950) 2012;189;12;5877-85
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.
Nucleic acids research 2012;40;22;11189-201
A method for full genome sequencing of all four serotypes of the dengue virus.
Journal of virological methods 2010;169;1;202-6
Genomic epidemiology of a dengue virus epidemic in urban Singapore.
Journal of virology 2009;83;9;4163-73
Periodic re-emergence of endemic strains with strong epidemic potential-a proposed explanation for the 2004 Indonesian dengue epidemic.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2008;8;2;191-204
IDBD: infectious disease biomarker database.
Nucleic acids research 2008;36;Database issue;D455-60
DengueInfo: A web portal to dengue information resources.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2007;7;4;540-1
A genomics approach to understanding host response during dengue infection.
Novartis Foundation symposium 2006;277;206-14; discussion 214-7, 251-3