By Dr Sara Ballouz

Book Chapters

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

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, http://dx.doi.org/10.1038/s41467-024-47720-8

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, http://dx.doi.org/10.1038/s41467-023-43024-5

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

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

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

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

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

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

Ballouz S, 2020, 'Single-Cell Transcriptomics', eLS, pp. 1 - 10, http://dx.doi.org/10.1002/9780470015902.a0028528

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Ballouz S; Liu JY; Oti M; Gaeta B; Fatkin D; Bahlo M; Wouters MA, 2014, 'Candidate disease gene prediction using : application to a genome-wide association study on coronary artery disease', Molecular Genetics & Genomic Medicine, 2, pp. 44 - 57, http://dx.doi.org/10.1002/mgg3.40

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

Conference Papers

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, http://dx.doi.org/10.4049/jimmunol.208.Supp.159.04

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

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

Working Papers

Ballouz S; Mangala M; Perry M; Heitmann S; Gillis J; Hill A; Vandenberg J, 2019, Co-expression of calcium channels and delayed rectifier potassium channels protects the heart from proarrhythmic events, http://dx.doi.org10.1101/659821

Preprints

Phetsouphanh C; Jacka B; Ballouz S; Jackson KJL; Wilson D; Manandhar B; Klemm V; Tan H-X; Wheatley A; Aggarwal A; Akerman A; Milogiannakis V; Starr M; Cunningham P; Turville S; Kent S; Byrne A; Brew B; Darley D; Dore G; Kelleher A; Matthews G, 2023, 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

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

Kaminow B; Ballouz S; Gillis J; Dobin A, 2020, 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

Lee J; Shah M; Ballouz S; Crow M; Gillis J, 2020, CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species, http://dx.doi.org/10.1101/2020.04.21.053900

Ballouz S; Dobin A; Gillis J, 2019, Is it time to change the reference genome?, http://dx.doi.org/10.1101/533166

Crow M; Paul A; Ballouz S; Huang ZJ; Gillis J, 2017, Addressing the looming identity crisis in single cell RNA-seq, http://dx.doi.org/10.1101/150524

Ballouz S; Pavlidis P; Gillis J, 2016, Using predictive specificity to determine when gene set analysis is biologically meaningful, http://dx.doi.org/10.1101/080127

Ballouz S; Weber M; Pavlidis P; Gillis J, 2016, EGAD: Ultra-fast functional analysis of gene networks, http://dx.doi.org/10.1101/053868

Ballouz S; Gillis J, 2016, AuPairWise: a method to estimate RNA-seq replicability through co-expression, http://dx.doi.org/10.1101/044669

Ballouz S; Gillis J, 2016, Strength of functional signature correlates with effect size in autism, http://dx.doi.org/10.1101/043422

Lihm J; Ahrens S; Ballouz S; Lee H; Crow M; Tollkuhn J; McCarthy S; Li B; McCombie WR; Gillis J, How Low Can You Go? Calling Robust ATAC-Seq Peaks Through Read Down-Sampling, http://dx.doi.org/10.2139/ssrn.3266868

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