BOL

In a lot of my work in bioinformatics, I have been using hidden Markov models (HMMs). As a postdoc with David Haussler at UCSC we developed the so-called profile HMMs (refs). Since then I have applied HMMs to membrane proteins (refs) and gene...

The main subject of interest in our laboratory is the study of the relationship among sequence, structure, and function in proteins and nucleic acids. Our research can be divided in two major topics: the study of the sequence-structure...

A new optogenetic protein gives neuroscientists more control over brain circuits.

bioinformatics.oxfordjournals.org - An ultra–high-performance protein–protein docking software for heterogeneous supercomputers Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics...

an R package for analysing ontologies and protein domain annotations

MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable...

abi.inf.uni-tuebingen.de - Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and...

Predicting the structure of protein–protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes....

github.com - A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...

pasapipeline.github.io - PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation...