CANA v1.0.0: efficient quantification of canalization in automata networks
Sign Up to like & getrecommendations! Published in 2025 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaf461
Abstract: Abstract Summary The biomolecular networks underpinning cell function exhibit canalization, or the buffering of fluctuations required to function in a noisy environment. We present a new major release of CANA, v1.0.0, an open-source Python package… read more here.
Keywords: https github; canalization automata; symmetry; cana ... See more keywords
Haplotype-aware graph indexes
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz575
Abstract: Abstract Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes. Results We augment… read more here.
Keywords: haplotype aware; https github; github com; haplotype ... See more keywords
Applying rearrangement distances to enable plasmid epidemiology with pling
Sign Up to like & getrecommendations! Published in 2024 at "Microbial Genomics"
DOI: 10.1101/2024.06.12.598623
Abstract: Plasmids are a key vector of antibiotic resistance, but the current bioinformatics toolkit is not well suited to tracking them. The rapid structural changes seen in plasmid genomes present considerable challenges to evolutionary and epidemiological… read more here.
Keywords: epidemiology; rearrangement distances; https github; https ... See more keywords