Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics...
SUMMARY: TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable...
MOTIVATION: Structure-based drug discovery methods exploit protein structural information to design small molecules binding to given protein pockets. This work proposes a purely data driven, structure-based approach for imaging ligands as spatial fie...
Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host. It is critical to study VFs for better understanding microbial pathogenesis and host defense mechanisms. Victors (ht...
Database : the journal of biological databases and curation
Jan 1, 2019
The automatic extraction of meaningful relations from biomedical literature or clinical records is crucial in various biomedical applications. Most of the current deep learning approaches for medical relation extraction require large-scale training d...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
In the analysis of protein-ligand interactions, two abstractions have been widely employed to build a systematic approach to analyze these complexes: protein and chemical spaces. The pioneering idea of the protein space dates back to 1970, and the ch...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
Recent progress in the development of scientific libraries with machine-learning techniques paved the way for the implementation of integrated computational tools to predict ligand-binding affinity. The prediction of binding affinity uses the atomic ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
Molecular docking enables large-scale prediction of whether and how small molecules bind to a macromolecular target. Machine-learning scoring functions are particularly well suited to predict the strength of this interaction. Here we describe how to ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
Segmentation is one of the most ubiquitous problems in biological image analysis. Here we present a machine learning-based solution to it as implemented in the open source ilastik toolkit. We give a broad description of the underlying theory and demo...
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