User profiles for S. Ballouz

Sara Ballouz

UNSW
Verified email at unsw.edu.au
Cited by 1442

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

S Ballouz, W Verleyen, J Gillis - Bioinformatics, 2015 - academic.oup.com
… We then measured a network’s functional significance in its ability to capture functional
information as encoded by GO using a cross-validation approach; essentially asking if a genes’ …

[HTML][HTML] Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

M Crow, A Paul, S Ballouz, ZJ Huang, J Gillis - Nature communications, 2018 - nature.com
… Thus, to address the impact of rarity on MetaNeighbor’s performance, we alter the incidence
of excitatory neurons to be within our observed range of subtype incidences, repeatedly …

[HTML][HTML] Is it time to change the reference genome?

S Ballouz, A Dobin, JA Gillis - Genome biology, 2019 - Springer
… After 20 May 2019, the kilogram (Le Grand K) was redefined in reference to Planck’s constant
(6.626070150 × 10 − 34 kg∙m 2 /s [1]) and this will not change for the foreseeable future. …

Predictability of human differential gene expression

M Crow, N Lim, S Ballouz… - Proceedings of the …, 2019 - National Acad Sciences
… Here, we reanalyze more than 600 studies and find that knowledge of a gene’s prior probability
of differential expression (DE) allows for accurate prediction of DE hit lists, regardless of …

EGAD: ultra-fast functional analysis of gene networks

S Ballouz, M Weber, P Pavlidis, J Gillis - Bioinformatics, 2017 - academic.oup.com
Evaluating gene networks with respect to known biology is a common task but often a
computationally costly one. Many computational experiments are difficult to apply exhaustively in …

[HTML][HTML] Exploiting single-cell expression to characterize co-expression replicability

M Crow, A Paul, S Ballouz, ZJ Huang, J Gillis - Genome biology, 2016 - Springer
… sum of the gene’s edge weights within the function divided by the gene’s node degree). This
… A network’s performance is the average score for each GO function and is reported as the …

Bias tradeoffs in the creation and analysis of protein–protein interaction networks

J Gillis, S Ballouz, P Pavlidis - Journal of proteomics, 2014 - Elsevier
Networks constructed from aggregated protein–protein interaction data are commonplace in
biology. But the studies these data are derived from were conducted with their own …

CoCoCoNet: conserved and comparative co-expression across a diverse set of species

J Lee, M Shah, S Ballouz, M Crow… - Nucleic acids …, 2020 - academic.oup.com
… Next, we compute the Spearman’s correlation between each sample in each dataset and
this global average (Supplementary Figures S3 and S4). If the average of the worst 10 …

[PDF][PDF] Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events

JM Werner, S Ballouz, J Hover, J Gillis - Developmental cell, 2022 - cell.com
… We apply Fisher’s method to aggregate each test gene’s distribution of empirical p values to
calculate a meta-analytic p value to determine significance (ARHGAP4 meta-analytic p value…

[HTML][HTML] Conditions for the evolution of gene clusters in bacterial genomes

S Ballouz, AR Francis, R Lan… - PLoS computational …, 2010 - journals.plos.org
Genes encoding proteins in a common pathway are often found near each other along bacterial
chromosomes. Several explanations have been proposed to account for the evolution of …