Hidden Markov models (HMMs) have been extensively used in biological sequence
analysis. In this paper, we give a tutorial review of HMMs and their applications in a variety …

Protein function prediction is one of the most challenging problems in the post-genomic era.
The number of newly identified proteins has been exponentially increasing with the …

Today's genomic experiments have to process the so-called “biological big data” that is now
reaching the size of Terabytes and Petabytes. To process this huge amount of data …

Background Small Heat Shock Proteins (sHSPs) are chaperone-like proteins involved in the
prevention of the irreversible aggregation of misfolded proteins. Although many studies have …

Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and
dispersal during diversification. In temperate regions, repeated distributional shifts driven by …

Protein modeling has been a very challenging problem in drug discovery and computational
biology. The latest advances and progress in computational power have helped to solve this …

Protein structure alignment methods are essential for many different challenges in protein
science, such as the determination of relations between proteins in the fold space or the …

Recognition is considered to be a basic human mental ability in psychology [Myers and
DeWall (2018); Reisberg (2013)]. It consists of identifying the objects (systems, processes …

Phylogenetic analysis and multiple sequence alignment (MSA) are closely related
bioinformatics fields. Phylogenetic analysis makes extensive use of MSA in the construction …

In the bacterial reaction center (bRC) of Rhodobacter sphaeroides, the key residues of
proton transfer to the secondary quinone (QB) are known. Also, several possible proton …