Sara Ballouz
Sara Ballouz
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Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events
{X-chromosome inactivation (XCI) is a random, permanent, and developmentally early epigenetic event that occurs during mammalian …
Jonathan Werner
,
Sara Ballouz
,
John Hover
,
Jesse Gillis
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DOI
Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately …
Benjamin Kaminow
,
Sara Ballouz
,
Jesse Gillis
,
Alexander Dobin
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DOI
Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes
Co-fractionation MS (CF-MS) is a technique with potential to characterize endogenous and unmanipulated protein complexes on an …
Chi Nam Ignatius Pang
,
Sara Ballouz
,
Daniel Weissberger
,
Loïc M Thibaut
,
Joshua J Hamey
,
Jesse Gillis
,
Marc R Wilkins
,
Gene Hart-Smith
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DOI
CoCoCoNet: conserved and comparative co-expression across a diverse set of species
Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species …
John Lee
,
Manthan Shah
,
Sara Ballouz
,
Megan Crow
,
Jesse Gillis
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DOI
Single-cell Transcriptomics
Single‐cell transcriptomics is an emerging field with a variety of applications, from revealing tissue heterogeneity and cell identity …
Sara Ballouz
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Is it time to change the reference genome?
The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating …
Sara Ballouz
,
Alexander Dobin
,
Jesse A. Gillis
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DOI
Predictability of human differential gene expression
Differential expression (DE) is commonly used to explore molecular mechanisms of biological conditions. While many studies report …
Megan Crow
,
Nathaniel Lim
,
Sara Ballouz
,
Paul Pavlidis
,
Jesse Gillis
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DOI
The fractured landscape of RNA-seq alignment: the default in our STARs
Many tools are available for RNA-seq alignment and expression quantification, with comparative value being hard to establish. …
Sara Ballouz
,
Alexander Dobin
,
Thomas R. Gingeras
,
Jesse Gillis
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DOI
Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor
Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover and characterize cell types; however, the …
Megan Crow
,
Anirban Paul
,
Sara Ballouz
,
Z. Josh Huang
,
Jesse Gillis
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DOI
EGAD: ultra-fast functional analysis of gene networks
Summary: Evaluating gene networks with respect to known biology is a common task but often a computationally costly one. Many …
Sara Ballouz
,
Melanie Weber
,
Paul Pavlidis
,
Jesse Gillis
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DOI
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