Published in Bioinformatics (Oxford, England)
Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nano...
Published in Bioinformatics (Oxford, England)
RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering to enhance the analysis and visualization of the conformational complexity. It combines precise calculation of n...
Published in Bioinformatics (Oxford, England)
The transition from evaluating a single time point to examining the entire dynamic evolution of a system is possible only in the presence of the proper framework. The strong variability of dynamic evolution makes the definition of an explanatory procedure for data fitting and clustering challenging. We developed CONNECTOR, a data-driven framework a...
Published in Bioinformatics (Oxford, England)
Various computational biology calculations require a probabilistic optimization protocol to determine the parameters that capture the system at a desired state in the configurational space. Many existing methods excel at certain scenarios, but fail in others due, in part, to an inefficient exploration of the parameter space and easy trapping into l...
Published in Bioinformatics (Oxford, England)
While conventional flow cytometry is limited to dozens of markers, new experimental and computational strategies, such as Infinity Flow, allow for the generation and imputation of hundreds of cell surface protein markers in millions of cells. Here, we describe an end-to-end analysis workflow for Infinity Flow data in Python. pyInfinityFlow enables ...
Published in Bioinformatics (Oxford, England)
As an important group of proteins discovered in phages, anti-CRISPR inhibits the activity of the immune system of bacteria (i.e. CRISPR-Cas), offering promise for gene editing and phage therapy. However, the prediction and discovery of anti-CRISPR are challenging due to their high variability and fast evolution. Existing biological studies rely on ...
Published in Bioinformatics (Oxford, England)
From a systematic perspective, it is crucial to infer and analyze gene regulatory network (GRN) from high-throughput single-cell RNA sequencing data. However, most existing GRN inference methods mainly focus on the network topology, only few of them consider how to explicitly describe the updated logic rules of regulation in GRNs to obtain their dy...
Published in Bioinformatics (Oxford, England)
Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome sequencing data are collected for n genes across p conditions at r occasions. Matrix variate distributions offer a na...
Published in Bioinformatics (Oxford, England)
Genome-wide association studies (GWASs) have identified numerous genetic variants associated with complex disease risk; however, most of these associations are non-coding, complicating identifying their proximal target gene. Transcriptome-wide association studies (TWASs) have been proposed to mitigate this gap by integrating expression quantitative...
Published in Bioinformatics
Motivation Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype–phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that requir...
