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Dr Sara Ballouz

Dr Sara Ballouz

Senior Lecturer

Education

2013 - PhD, Victor Chang Cardiac Research Institute and the University of New South Wales, Sydney - Australia
2008 - BE Bioinformatics First Class Honours, University of New South Wales, Sydney – Australia
2008 - BSc Genetics, University of New South Wales, Sydney – Australia

Engineering
Computer Science and Engineering

My central scientific interest has been to understand the genetic architecture of disease. With data from the genome, transcriptome, epigenome and proteome increasing exponentially, robust tools and practices need to be established to analyse this deluge, in particular if to be applied to personalized medicine.

I obtained my PhD from the University of New South Wales and the Victor Chang Cardiac Research Institute in 2013, working with Drs Merridee Wouters and Bruno Gaeta. I then moved to Cold Spring Harbor Laboratory for my postdoctoral training with Dr Jesse Gillis. In 2020, I started my own group at the Garvan-Weizmann Centre for Cellular Genomics at the Garvan Institute of Medical Research. In 2023, I moved to the School of Computer Science and Engineering at UNSW where I am continuing my research and teaching the next generation of Bioinformaticians. 

 
E-mail
s.ballouz@unsw.edu.au
Location
Garvan
  • Book Chapters | 2011
    Oti M; Ballouz S; Wouters MA, 2011, 'Web tools for the prioritization of candidate disease genes', in , pp. 189 - 206, http://dx.doi.org/10.1007/978-1-61779-176-5_12
  • Journal articles | 2026
    Dewa G; Munier CML; Ballouz S; Louie R, 2026, 'Machine learning approaches for biomarker discovery using single-cell RNA sequencing', Frontiers in Bioinformatics, 6, pp. 1767362, http://dx.doi.org/10.3389/fbinf.2026.1767362
    Journal articles | 2026
    Gray LG; Telfser A; Hu H; Kane A; Deenick EK; Phan TG; Ballouz S, 2026, 'Machine learning reveals X chromosome transcriptional signatures that classify systemic lupus erythematosus in females.', BMC Rheumatol, http://dx.doi.org/10.1186/s41927-026-00669-1
    Journal articles | 2026
    Sopena-Rios M; Ripoll-Cladellas A; Omidi F; Ballouz S; Alquicira-Hernandez J; Oelen R; Hewitt AW; Franke L; van der Wijst MGP; Powell JE; Melé M, 2026, 'Single-cell analysis of the human immune system reveals sex-specific dynamics of immunosenescence', Nature Aging, 6, pp. 932 - 949, http://dx.doi.org/10.1038/s43587-026-01099-x
    Journal articles | 2026
    Yazar S; Alquicira-Hernandez J; Wing K; Senabouth A; Andersen S; Fairfax KA; Hewitt AW; Powell JE; Ballouz S, 2026, 'The impact of sex on the immune system explored at the single-cell level', American Journal of Human Genetics, 113, pp. 1006 - 1023, http://dx.doi.org/10.1016/j.ajhg.2026.04.003
    Journal articles | 2024
    Phetsouphanh C; Jacka B; Ballouz S; Jackson KJL; Wilson DB; Manandhar B; Klemm V; Tan HX; Wheatley A; Aggarwal A; Akerman A; Milogiannakis V; Starr M; Cunningham P; Turville SG; Kent SJ; Byrne A; Brew BJ; Darley DR; Dore GJ; Kelleher AD; Matthews GV, 2024, 'Improvement of immune dysregulation in individuals with long COVID at 24-months following SARS-CoV-2 infection', Nature Communications, 15, pp. 3315, http://dx.doi.org/10.1038/s41467-024-47720-8
    Journal articles | 2023
    Ballouz S; Kawaguchi RK; Pena MT; Fischer S; Crow M; French L; Knight FM; Adams LB; Gillis J, 2023, 'The transcriptional legacy of developmental stochasticity', Nature Communications, 14, pp. 7226 - 7226, http://dx.doi.org/10.1038/s41467-023-43024-5
    Journal articles | 2023
    Stavrou MR; So SS; Finch AM; Ballouz S; Smith NJ, 2023, 'Gene expression analyses of TAS1R taste receptors relevant to the treatment of cardiometabolic disease', Chemical Senses, 48, http://dx.doi.org/10.1093/chemse/bjad027
    Journal articles | 2022
    Kaminow B; Ballouz S; Gillis J; Dobin A, 2022, 'Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses', Genome Research, 32, pp. 738 - 750, http://dx.doi.org/10.1101/gr.275613.121
    Journal articles | 2022
    Werner JM; Ballouz S; Hover J; Gillis J, 2022, 'Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events', Developmental Cell, 57, pp. 1995 - 2008.e5, http://dx.doi.org/10.1016/j.devcel.2022.07.007
    Journal articles | 2021
    Ballouz S; Mangala MM; Perry MD; Heitmann S; Gillis JA; Hill AP; Vandenberg JI, 2021, 'Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events', Cardiovascular Research, 117, pp. 2216 - 2227, http://dx.doi.org/10.1093/cvr/cvaa280
    Journal articles | 2021
    Lee J; Shah M; Ballouz S; Crow M; Gillis J, 2021, 'CoCoCoNet: Conserved and comparative co-expression across a diverse set of species', Nucleic Acids Research, 48, pp. W566 - W571, http://dx.doi.org/10.1093/NAR/GKAA348
    Journal articles | 2020
    Ballouz S, 2020, 'Single-Cell Transcriptomics', eLS, pp. 1 - 10, http://dx.doi.org/10.1002/9780470015902.a0028528
    Journal articles | 2020
    Pang CNI; Ballouz S; Weissberger D; Thibaut LM; Hamey JJ; Gillis J; Wilkins MR; Hart-Smith G, 2020, 'Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes', Molecular and Cellular Proteomics, 19, pp. 1876 - 1895, http://dx.doi.org/10.1074/mcp.RA120.002154
    Journal articles | 2019
    Ballouz S; Dobin A; Gillis JA, 2019, 'Is it time to change the reference genome?', Genome Biology, 20, pp. 159, http://dx.doi.org/10.1186/s13059-019-1774-4
    Journal articles | 2019
    Crow M; Lim N; Ballouz S; Pavlidis P; Gillis J, 2019, 'Predictability of human differential gene expression', Proceedings of the National Academy of Sciences of the United States of America, 116, pp. 6491 - 6500, http://dx.doi.org/10.1073/pnas.1802973116
    Journal articles | 2018
    Ballouz S; Dobin A; Gingeras TR; Gillis J, 2018, 'The fractured landscape of RNA-seq alignment: The default in our STARs', Nucleic Acids Research, 46, pp. 5125 - 5138, http://dx.doi.org/10.1093/nar/gky325
    Journal articles | 2018
    Crow M; Paul A; Ballouz S; Huang ZJ; Gillis J, 2018, 'Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor', Nature Communications, 9, pp. 884, http://dx.doi.org/10.1038/s41467-018-03282-0
    Journal articles | 2017
    Ballouz S; Dörfel M; Crow M; Crain J; Faivre L; Keegan C; Kitsiou-Tzeli S; Tzetis M; Lyon G; Gillis J, 2017, 'Not by systems alone: replicability assessment of disease expression signals', , http://dx.doi.org/10.1101/128439
    Journal articles | 2017
    Ballouz S; Gillis J, 2017, 'Strength of functional signature correlates with effect size in autism', Genome Medicine, 9, pp. 64, http://dx.doi.org/10.1186/s13073-017-0455-8
    Journal articles | 2017
    Ballouz S; Pavlidis P; Gillis J, 2017, 'Using predictive specificity to determine when gene set analysis is biologically meaningful', Nucleic acids research, 45, pp. e20 - e20, http://dx.doi.org/10.1093/nar/gkw957
    Journal articles | 2017
    Ballouz S; Weber M; Pavlidis P; Gillis J, 2017, 'EGAD: Ultra-fast functional analysis of gene networks', Bioinformatics, 33, pp. 612 - 614, http://dx.doi.org/10.1093/bioinformatics/btw695
    Journal articles | 2016
    Ballouz S; Gillis J, 2016, 'AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression', Plos Computational Biology, 12, pp. e1004868, http://dx.doi.org/10.1371/journal.pcbi.1004868
    Journal articles | 2016
    Crow M; Paul A; Ballouz S; Huang ZJ; Gillis J, 2016, 'Exploiting single-cell expression to characterize co-expression replicability', Genome Biology, 17, pp. 101, http://dx.doi.org/10.1186/s13059-016-0964-6
    Journal articles | 2016
    O'Meara MJ; Ballouz S; Shoichet BK; Gillis JG, 2016, 'Ligand similarity complements sequence, physical interaction, and Co-Expression for gene function prediction', Plos One, 11, pp. e0160098, http://dx.doi.org/10.1371/journal.pone.0160098
    Journal articles | 2016
    Verleyen W; Ballouz S; Gillis J, 2016, 'Positive and negative forms of replicability in gene network analysis', Bioinformatics, 32, pp. 1065 - 1073, http://dx.doi.org/10.1093/bioinformatics/btv734
    Journal articles | 2015
    Ballouz S; Verleyen W; Gillis J, 2015, 'Guidance for RNA-seq co-expression network construction and analysis: Safety in numbers', Bioinformatics, 31, pp. 2123 - 2130, http://dx.doi.org/10.1093/bioinformatics/btv118
    Journal articles | 2015
    Verleyen W; Ballouz S; Gillis J, 2015, 'Measuring the wisdom of the crowds in network-based gene function inference', Bioinformatics, 31, pp. 745 - 752, http://dx.doi.org/10.1093/bioinformatics/btu715
    Journal articles | 2014
    Ballouz S; Liu JY; Oti M; Gaeta B; Fatkin D; Bahlo M; Wouters MA, 2014, 'Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease.', Mol Genet Genomic Med, 2, pp. 44 - 57, http://dx.doi.org/10.1002/mgg3.40
    Journal articles | 2014
    Gillis J; Ballouz S; Pavlidis P, 2014, 'Bias tradeoffs in the creation and analysis of protein-protein interaction networks', Journal of Proteomics, 100, pp. 44 - 54, http://dx.doi.org/10.1016/j.jprot.2014.01.020
    Journal articles | 2013
    Ballouz S; Liu JY; George RA; Bains N; Liu A; Oti M; Gaeta B; Fatkin D; Wouters MA, 2013, 'Gentrepid V2.0: A web server for candidate disease gene prediction', BMC Bioinformatics, 14, pp. 249, http://dx.doi.org/10.1186/1471-2105-14-249
  • Working Papers |
    Ballouz S; Mangala MM; Perry MD; Heitmann S; Gillis JA; Hill AP; Vandenberg JI, Co-expression of calcium channels and delayed rectifier potassium channels protects the heart from proarrhythmic events, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/659821
  • Preprints | 2026
    Gray LG; Telfser A; Hu H; Kane A; Deenick EK; Phan TG; Ballouz S, 2026, Machine learning reveals X chromosome transcriptional signatures that predict systemic lupus erythematosus in females, http://dx.doi.org/10.21203/rs.3.rs-8991344/v1
    Preprints | 2026
    Kawaguchi RK; Ballouz S; Pena MT; French L; Knight FM; Adams LB; Gillis J, 2026, Monocyte Lineage Expansion Drives Transcriptomic Individuality in Genetically Identical Armadillo Quadruplets., http://dx.doi.org/10.64898/2026.03.30.715171
    Preprints | 2025
    Sopena-Rios M; Ripoll-Cladellas A; Omidi F; Ballouz S; Alquicira-Hernandez J; Oelen R; Franke L; Wijst MVD; Powell J, 2025, Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence, http://dx.doi.org/10.21203/rs.3.rs-6784948/v1
    Conference Papers | 2023
    Stavrou MM; So S; Ballouz S; Finch A; Smith NJ, 2023, 'Tasteless organs: why the taste receptors are exclusive to the tongue', in BRITISH JOURNAL OF PHARMACOLOGY, WILEY, SCOTLAND, Glasgow, pp. 694 - 695, presented at 19th World Congress of Basic and Clinical Pharmacology (WCP), SCOTLAND, Glasgow, 02 July 2023 - 07 July 2023
    Conference Papers | 2022
    Muzumdar S; Ballouz S; Lam F; Degrange M; Kreuzburg S; Chong H; Zerbe C; Jongco A; Gillis J, 2022, 'A granular view of X-linked chronic granulomatous disease exploiting single-cell transcriptomics', in JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS, OR, Portland, presented at Immunology Meeting, OR, Portland, 06 May 2022 - 10 May 2022, http://dx.doi.org/10.4049/jimmunol.208.Supp.159.04
    Preprints | 2021
    Werner JM; Ballouz S; Hover J; Gillis J, 2021, Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development, http://dx.doi.org/10.1101/2021.09.13.460075
    Preprints | 2018
    Lihm J; Ahrens S; Ballouz S; Lee H; Crow M; Tollkuhn J; McCarthy S; Li B; McCombie WR; Gillis J, 2018, How Low Can You Go? Calling Robust ATAC-Seq Peaks Through Read Down-Sampling, http://dx.doi.org/10.2139/ssrn.3266868
    Preprints | 2016
    Ballouz S; Gillis J, 2016, Strength of functional signature correlates with effect size in autism, http://dx.doi.org/10.1101/043422
    Conference Papers | 2014
    Grover MP; Ballouz S; Mohanasundaram KA; George RA; Goscinski A; Crowley TM; Sherman CDH; Wouters MA, 2014, 'Novel therapeutics for coronary artery disease from genome-wide association study data', in BMC Medical Genomics, Springer Nature, PEOPLES R CHINA, Qingdao, pp. s1, presented at 4th Annual Translational Bioinformatics Conference (TBC) / 8th International Conference on Systems Biology (ISB), PEOPLES R CHINA, Qingdao, 24 October 2014 - 27 October 2014, http://dx.doi.org/10.1186/1755-8794-8-S2-S1
    Conference Presentations | 2013
    Grover MP; Ballouz S; Mohanasundaram KA; George RA; H Sherman CD; Crowley TM; Wouters MA, 2013, 'Identification of novel therapeutics for complex diseases from genome-wide association data', presented at 3rd Annual Translational Bioinformatics Conference (TBC) / ISCB-Asia, SOUTH KOREA, Seoul, 02 October 2013 - 04 October 2013, http://dx.doi.org/10.1186/1755-8794-7-S1-S8
    Preprints |
    Ballouz S; Dobin A; Gillis J, Is it time to change the reference genome?, http://dx.doi.org/10.1101/533166
    Preprints |
    Ballouz S; Dörfel M; Crow M; Crain J; Faivre L; Keegan CE; Kitsiou-Tzeli S; Tzetis M; Lyon GJ; Gillis J, Not by systems alone: replicability assessment of disease expression signals, http://dx.doi.org/10.1101/128439
    Preprints |
    Ballouz S; Gillis J, AuPairWise: a method to estimate RNA-seq replicability through co-expression, http://dx.doi.org/10.1101/044669
    Preprints |
    Ballouz S; Pavlidis P; Gillis J, Using predictive specificity to determine when gene set analysis is biologically meaningful, http://dx.doi.org/10.1101/080127
    Preprints |
    Ballouz S; Weber M; Pavlidis P; Gillis J, EGAD: Ultra-fast functional analysis of gene networks, http://dx.doi.org/10.1101/053868
    Preprints |
    Crow M; Paul A; Ballouz S; Huang ZJ; Gillis J, Addressing the looming identity crisis in single cell RNA-seq, http://dx.doi.org/10.1101/150524
    Preprints |
    Kaminow B; Ballouz S; Gillis J; Dobin A, Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses, http://dx.doi.org/10.1101/2020.12.22.423111
    Preprints |
    Lee J; Shah M; Ballouz S; Crow M; Gillis J, CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species, http://dx.doi.org/10.1101/2020.04.21.053900
    Preprints |
    Phetsouphanh C; Jacka B; Ballouz S; Jackson KJ; Wilson DB; Manandhar B; Klemm V; Tan H-X; Wheatley A; Aggarwal A; Akerman A; Milogiannakis V; Starr M; Cunningham P; Turville SG; Kent SJ; Byrne A; Brew BJ; Darley DR; Dore GJ; Kelleher AD; Matthews GV, Improvement of immune dysregulation and health-related quality of life in individuals with long COVID at 24-months following SARS-CoV-2 infection, http://dx.doi.org/10.1101/2023.08.27.23294704
    Preprints |
    Sopena-Rios M; Ripoll-Cladellas A; Omidi F; Ballouz S; Hernandez JA; Oelen R; Franke L; van der Wijst MGP; Powell JE; Melé M, Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence, http://dx.doi.org/10.1101/2024.11.06.622096
    Preprints |
    Yazar S; Alquicira-Hernandez J; Wing K; Senabouth A; Andersen S; Fairfax KA; Hewitt AW; Powell JE; Ballouz S, The impact of sex on the immune system explored at the single-cell level, http://dx.doi.org/10.1101/2025.07.27.667062

• Transcriptomics (single-cell and bulk)

• Co-expression

• X-linked disorders

• Sex differences in disease

• Meta-analysis

• Personalized medicine

My Teaching

Convening and teaching:

Introduction to Bioinformatics BINF2010

Computational Bioinformatics BINF3020 

Guest lecturing:

Applied Bioinformatics BINF3010

Molecular Biology of Proteins BIOC3111