Swee Hoe Ong | Principal Software Developer

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.


  • RNAmut: robust identification of somatic mutations in acute myeloid leukemia using RNA-seq.

    Gu M, Zwiebel M, Ong SH, Boughton N, Nomdedeu J et al.

    Haematologica 2019

  • Outcompeting p53-Mutant Cells in the Normal Esophagus by Redox Manipulation.

    Fernandez-Antoran D, Piedrafita G, Murai K, Ong SH, Herms A et al.

    Cell stem cell 2019;25;3;329-341.e6

  • Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3.

    Bassano I, Ong SH, Sanz-Hernandez M, Vinkler M, Kebede A et al.

    BMC genomics 2019;20;1;272

  • Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations.

    Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V et al.

    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.

    Li M, Yu JSL, Tilgner K, Ong SH, Koike-Yusa H and Yusa K

    Cell reports 2018;24;2;489-502

  • Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

    Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M et al.

    Virus evolution 2018;4;1;vey007

  • Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries.

    Ong SH, Li Y, Koike-Yusa H and Yusa K

    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.

    Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š et al.

    Virus research 2017;239;10-16

  • Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.

    Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M et al.

    PLoS biology 2017;15;6;e2001855

  • Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes.

    Bassano I, Ong SH, Lawless N, Whitehead T, Fife M and Kellam P

    BMC genomics 2017;18;1;419

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B et al.

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

  • Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.

    Cotten M, Petrova V, Phan MV, Rabaa MA, Watson SJ et al.

    Journal of virology 2014;88;19;11056-69

  • Systems consequences of amplicon formation in human breast cancer.

    Inaki K, Menghi F, Woo XY, Wagner JP, Jacques PÉ et al.

    Genome research 2014;24;10;1559-71

  • Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus.

    Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL et al.

    mBio 2014;5;1

  • Patient-based transcriptome-wide analysis identify interferon and ubiquination pathways as potential predictors of influenza A disease severity.

    Hoang LT, Tolfvenstam T, Ooi EE, Khor CC, Naim AN et al.

    PloS one 2014;9;11;e111640

  • Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

    Ong SH, Kukkillaya VU, Wilm A, Lay C, Ho EX et al.

    PloS one 2013;8;4;e60811

  • Plasmablasts generated during repeated dengue infection are virus glycoprotein-specific and bind to multiple virus serotypes.

    Xu M, Hadinoto V, Appanna R, Joensson K, Toh YX et al.

    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.

    Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH et al.

    Nucleic acids research 2012;40;22;11189-201

  • A method for full genome sequencing of all four serotypes of the dengue virus.

    Christenbury JG, Aw PP, Ong SH, Schreiber MJ, Chow A et al.

    Journal of virological methods 2010;169;1;202-6

  • Genomic epidemiology of a dengue virus epidemic in urban Singapore.

    Schreiber MJ, Holmes EC, Ong SH, Soh HS, Liu W et al.

    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.

    Ong SH, Yip JT, Chen YL, Liu W, Harun S et al.

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2008;8;2;191-204

  • IDBD: infectious disease biomarker database.

    Yang IS, Ryu C, Cho KJ, Kim JK, Ong SH et al.

    Nucleic acids research 2008;36;Database issue;D455-60

  • DengueInfo: A web portal to dengue information resources.

    Schreiber MJ, Ong SH, Holland RC, Hibberd ML, Vasudevan SG et al.

    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.

    Hibberd ML, Ling L, Tolfvenstam T, Mitchell W, Wong C et al.

    Novartis Foundation symposium 2006;277;206-14; discussion 214-7, 251-3

Ong, Swee Hoe
Swee Hoe's Timeline

Joined the WTSI as Senior Computational Biologist.


Joined the Genome Institute of Singapore as Postdoctoral Fellow.

Graduated with a Ph.D. from the Department of Public Health and Epidemiology, Swiss Tropical Institute, University of Basel, Switzerland.


Joined the Dengue Unit of the Novartis Institute for Tropical Diseases in Singapore as a Graduate Research Associate/Ph.D. candidate.


Joined the Genome Institute of Singapore as Bioinformatics Specialist.

Graduated with an M.Sc. in Bioinformatics from the Faculty of Medicine, National University of Singapore.


Joined the A*STAR Bioinformatics Institute as Graduate Research Associate/M.Sc. candidate.


Graduated with a B.Sc. in Cell and Molecular Biology from the Department of Biochemistry, Faculty of Life Sciences, National University of Malaysia.