Sara Ballouz
Sara Ballouz
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2
Strength of functional signature correlates with effect size in autism
BACKGROUND: Disagreements over genetic signatures associated with disease have been particularly prominent in the field of psychiatric …
Sara Ballouz
,
Jesse Gillis
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DOI
Using predictive specificity to determine when gene set analysis is biologically meaningful
Gene set analysis, which translates gene lists into enriched functions, is among the most common bioinformatic methods. Yet few would …
Sara Ballouz
,
Paul Pavlidis
,
Jesse Gillis
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DOI
Exploiting single-cell expression to characterize co-expression replicability
BACKGROUND: Co-expression networks have been a useful tool for functional genomics, providing important clues about the cellular and …
Megan Crow
,
Anirban Paul
,
Sara Ballouz
,
Z. Josh Huang
,
Jesse Gillis
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DOI
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater …
Sara Ballouz
,
Jesse Gillis
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DOI
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction
The expansion of protein-ligand annotation databases has enabled large-scale networking of proteins by ligand similarity. These …
Matthew J. O'Meara
,
Sara Ballouz
,
Brian K. Shoichet
,
Jesse Gillis
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DOI
Positive and negative forms of replicability in gene network analysis
MOTIVATION: Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This …
Wim Verleyen
,
Sara Ballouz
,
Jesse Gillis
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DOI
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
MOTIVATION: RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of …
Sara Ballouz
,
Wim Verleyen
,
Jesse Gillis
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DOI
Measuring the wisdom of the crowds in network-based gene function inference
MOTIVATION: Network-based gene function inference methods have proliferated in recent years, but measurable progress remains elusive. …
Wim Verleyen
,
Sara Ballouz
,
Jesse Gillis
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DOI
Novel therapeutics for coronary artery disease from genome-wide association study data
BACKGROUND: Coronary artery disease (CAD), one of the leading causes of death globally, is influenced by both environmental and genetic …
Mani P. Grover
,
Sara Ballouz
,
Kaavya A. Mohanasundaram
,
Richard A. George
,
Andrzej Goscinski
,
Tamsyn M. Crowley
,
Craig D. H. Sherman
,
Merridee A. Wouters
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DOI
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 …
Jesse Gillis
,
Sara Ballouz
,
Paul Pavlidis
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DOI
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