Single-Molecule Studies of Actin Assembly and Disassembly Factors
Published in Methods in Enzymology
Single-Molecule Studies of Actin Assembly and Disassembly Factors
ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid recep...
Published in Genome Research
The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction of bound genomic regions. To identify sequences responsible for recruitment of this transcription factor (TF) to individual loci, we turned to the high-resolution ChIP-exo approach. We exploited this signal by determining footprint pr...
Alignathon: a competitive assessment of whole-genome alignment methods.
...Published in Genome research
Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same...
A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection.
...Published in Genome research
MicroRNAs (miRNAs) are critical regulators of gene expression, and their role in a wide variety of biological processes, including host antimicrobial defense, is increasingly well described. Consistent with their diverse functional effects, miRNA expression is highly context dependent and shows marked changes upon cellular activation. However, the ...
Frac-seq reveals isoform-specific recruitment to polyribosomes.
Published in Genome research
Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here, we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of ...
Proteome-wide discovery of mislocated proteins in cancer.
...Published in Genome research
Several studies have sought systematically to identify protein subcellular locations, but an even larger task is to map which of these proteins conditionally relocates in disease (the mislocalizome). Here, we report an integrative computational framework for mapping conditional location and mislocation of proteins on a proteome-wide scale, called a...
Genome-scale coestimation of species and gene trees.
Published in Genome Research
Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss. Because current methods to reconstruct phylogenies fail to model the two-way dependency between gene trees and the species tree, they often misrepresent gene and species histories. We present a new probabilisti...
GENCODE: the reference human genome annotation for The ENCODE Project.
...Published in Genome research
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadil...
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
...Published in Genome research
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technolo...
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.
Published in Genome research
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were exam...
