885 days ago
A guide to machine learning for biologists
Because of the increasing size and inherent complexity of biological data, there has been an increase in the application of machine learning in biology to create useful and predicti...871 days ago
oGNM:Conformational dynamics based on contact topology in a coarse-grained presentation
Gaussian Network Model (GNM) is a powerful tool to sample conformational dynamics based...normal modes are the same as those in unperturbed systems (in the absence of the envir...efficient (saving 3/4 time, assuming equal size of system...851 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single...835 days ago
Tiara: deep learning-based classification system for eukaryotic sequences
With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.794 days ago
Ten quick tips for deep learning in biology
By taking a comprehensive and careful approach to deep learning based on critical thinking about research questions, planning to maintain rigor, and discerning how work...783 days ago
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431 days ago
Proksee: in-depth characterization and visualization of bacterial genomes
Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.373 days ago
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
This tutorial describes the usage of homologizer to phase gene copies into...an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for ma...348 days ago