Computational Biology

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 …
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Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events
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 …
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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 …
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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 …
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Single-cell Transcriptomics
Single‐cell transcriptomics is an emerging field with a variety of applications, from revealing tissue heterogeneity and cell identity …
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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 …
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Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor
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 …
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EGAD: ultra-fast functional analysis of gene networks
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 …
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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 …
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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. …
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