Energy-driven genome regulation by ATP-dependent chromatin remodellers
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …
Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Genomic nucleosome organization reconstituted with pure proteins
N Krietenstein, M Wal, S Watanabe, B Park… - Cell, 2016 - cell.com
Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but
their individual contributions are obfuscated by the complex in vivo milieu of factor …
their individual contributions are obfuscated by the complex in vivo milieu of factor …
A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated
much excitement in recent years owing to its ability to manipulate targeted genes and …
much excitement in recent years owing to its ability to manipulate targeted genes and …
Quantum annealing versus classical machine learning applied to a simplified computational biology problem
Transcription factors regulate gene expression, but how these proteins recognize and
specifically bind to their DNA targets is still debated. Machine learning models are effective …
specifically bind to their DNA targets is still debated. Machine learning models are effective …
MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding
Polycomb-mediated repression of gene expression is essential for development, with a
pivotal role played by trimethylation of histone H3 lysine 27 (H3K27me3), which is deposited …
pivotal role played by trimethylation of histone H3 lysine 27 (H3K27me3), which is deposited …
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
Q He, J Johnston, J Zeitlinger - Nature biotechnology, 2015 - nature.com
Understanding how eukaryotic enhancers are bound and regulated by specific
combinations of transcription factors is still a major challenge. To better map transcription …
combinations of transcription factors is still a major challenge. To better map transcription …
Quantitative modeling of transcription factor binding specificities using DNA shape
DNA binding specificities of transcription factors (TFs) are a key component of gene
regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs …
regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs …
Protein–DNA binding: complexities and multi-protein codes
Binding of proteins to particular DNA sites across the genome is a primary determinant of
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …
Massively parallel assays and quantitative sequence–function relationships
JB Kinney, DM McCandlish - Annual review of genomics and …, 2019 - annualreviews.org
Over the last decade, a rich variety of massively parallel assays have revolutionized our
understanding of how biological sequences encode quantitative molecular phenotypes …
understanding of how biological sequences encode quantitative molecular phenotypes …