Smith, Benjamin A. Gelles, Jeff Goode, Bruce L.
Published in
Methods in Enzymology
The actin cytoskeleton is very dynamic and highly regulated by multiple associated proteins in vivo. Understanding how this system of proteins functions in the processes of actin network assembly and disassembly requires methods to dissect the mechanisms of activity of individual factors and of multiple factors acting in concert. The advent of sing...
Pérez-Rico, Yuvia A. Valentina Boeva Mallory, Allison C. Bitetti, Angelo Majello, Sara Barillot, Emmanuel Shkumatava, Alena
Published in
Genome Research
Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide hist...
Starick, S.R. Ibn-Salem, J. Jurk, M. Celine Hernandez Love, M.I. Chung, H.-R. Vingron, M. Thomas-Chollier, M. Meijsing, S.H.
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...
Earl, Dent Nguyen, Ngan Hickey, Glenn Harris, Robert S Fitzgerald, Stephen Beal, Kathryn Seledtsov, Igor Molodtsov, Vladimir Raney, Brian J Clawson, Hiram
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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...
Siddle, Katherine J Deschamps, Matthieu Tailleux, Ludovic Nédélec, Yohann Pothlichet, Julien Lugo-Villarino, Geanncarlo Libri, Valentina Gicquel, Brigitte Neyrolles, Olivier Laval, Guillaume
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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 ...
Sterne-Weiler, Timothy Martinez-Nunez, Rocio Teresa Howard, Jonathan M Cvitovik, Ivan Katzman, Sol Tariq, Muhammad A Pourmand, Nader Sanford, Jeremy R
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 ...
Lee, KiYoung Byun, Kyunghee Hong, Wonpyo Chuang, Han-Yu Pack, Chan-Gi Bayarsaikhan, Enkhjargal Paek, Sun Ha Kim, Hyosil Shin, Hye Young Ideker, Trey
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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...
Boussau, Bastien Szöllosi, Gergely J Duret, Laurent Gouy, Manolo Tannier, Eric Daubin, Vincent
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...
Harrow, Jennifer Frankish, Adam Gonzalez, Jose M Tapanari, Electra Diekhans, Mark Kokocinski, Felix Aken, Bronwen L Barrell, Daniel Zadissa, Amonida Searle, Stephen
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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...
Earl, Dent Bradnam, Keith St John, John Darling, Aaron Lin, Dawei Fass, Joseph Yu, Hung On Ken Buffalo, Vince Zerbino, Daniel R Diekhans, Mark
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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...