By Dr Sara Ballouz

Preprints

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

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

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

Ballouz S; Gillis J, AuPairWise: a method to estimate RNA-seq replicability through co-expression, http://dx.doi.org/10.1101/044669

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

Ballouz S; Weber M; Pavlidis P; Gillis J, EGAD: Ultra-fast functional analysis of gene networks, http://dx.doi.org/10.1101/053868

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

Ballouz S; Dobin A; Gillis J, Is it time to change the reference genome?, http://dx.doi.org/10.1101/533166

Gray LG; Telfser A; Hu H; Kane A; Deenick EK; Phan TG; Ballouz S, 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

Kawaguchi RK; Ballouz S; Pena MT; French L; Knight FM; Adams LB; Gillis J, Monocyte Lineage Expansion Drives Transcriptomic Individuality in Genetically Identical Armadillo Quadruplets, http://dx.doi.org/10.64898/2026.03.30.715171

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

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

Melé M; Sopena-Rios M; Ripoll-Cladellas A; Omidi F; Ballouz S; Alquicira-Hernandez J; Oelen R; Franke L; van der Wijst M; Powell J, 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

Ballouz S; Gillis J, Strength of functional signature correlates with effect size in autism, http://dx.doi.org/10.1101/043422

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

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

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

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