User profiles for S. Ballouz
Sara BallouzUNSW Verified email at unsw.edu.au Cited by 1442 |
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
… 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’ …
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
… 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 …
of excitatory neurons to be within our observed range of subtype incidences, repeatedly …
[HTML][HTML] Is it time to change the reference genome?
… 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. …
(6.626070150 × 10 − 34 kg∙m 2 /s [1]) and this will not change for the foreseeable future. …
Predictability of human differential gene expression
… 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 …
of differential expression (DE) allows for accurate prediction of DE hit lists, regardless of …
EGAD: ultra-fast functional analysis of gene networks
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 …
computationally costly one. Many computational experiments are difficult to apply exhaustively in …
[HTML][HTML] Exploiting single-cell expression to characterize co-expression replicability
… 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 …
… 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
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 …
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
… 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 …
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
… 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…
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
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 …
chromosomes. Several explanations have been proposed to account for the evolution of …