Insight into dynamic genome imaging: Canonical framework identification and high-throughput analysis.
Sign Up to like & getrecommendations! Published in 2017 at "Methods"
DOI: 10.1016/j.ymeth.2017.04.022
Abstract: The human genome is dynamic in structure, complicating researcher's attempts at fully understanding it. Time series "Fluorescent in situ Hybridization" (FISH) imaging has increased our ability to observe genome structure, but due to cell type… read more here.
Keywords: genome imaging; framework; analysis; canonical framework ... See more keywords
A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization
Sign Up to like & getrecommendations! Published in 2024 at "Molecular Systems Biology"
DOI: 10.1038/s44320-024-00038-5
Abstract: Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level… read more here.
Keywords: native chromatin; chromatin; dynamic genome; genome organization ... See more keywords
PHi-C2: interpreting Hi-C data as the dynamic 3D genome state
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac613
Abstract: Hi-C is a widely used assay for studying three-dimensional (3D) genome organization across the whole genome. Here, we present PHi-C2, a Python package supported by mathematical and biophysical polymer modeling, that converts an input Hi-C… read more here.
Keywords: python package; genome state; phi; phi interpreting ... See more keywords
A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii
Sign Up to like & getrecommendations! Published in 2023 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.03519-22
Abstract: Nonconventional yeasts promise to provide new metabolic pathways for producing industrially relevant compounds and tolerating specific stressors such as cold temperatures. The mechanisms behind the cold tolerance of S. kudriavzevii or its sympatric relationship with… read more here.
Keywords: genome scale; tolerance; dynamic genome; model ... See more keywords