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At any time humans need accurate information to solve different problems. For example, how to perform a task, what happens in the news, what the hundreds of tweets say, etc. On the other hand, electronic information has ...

This thesis, entitled €High Performance Computing for solving large sparse systems. Optical Diffraction Tomography as a case of study€ investigates the computational issues related to the resolution of linear systems o...

Digital technologies have revolutionized studying, analyzing, and interpreting human culture, history, and society. Digital humanities (DH) combine traditional disciplines such as literature, history, and philosophy with...

We introduce and discuss a new computational model for the HermiteLagrange interpolation with nonlinear classes of polynomial interpolants. We distinguish between an interpolation problem and an algorithm that solves it....

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a st...

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been...

Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis p...

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use....

MOTIVATION: Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missi...

The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystal...

Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it ...

It is known that the Minimum Weight Triangulation problem is NP-hard. Also the complexity of Minimum Weight Pseudo-Triangulation problem is unknown, suspecting that it is also a NP-hard problem. Therefore we focused on ...

MOTIVATION: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. m...

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, i...

BACKGROUND: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issu...

Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, an...

Subjects / keywords: Transmembrane protein; Signal peptide; Computational biology; Protein Sorting Signals; SIGNAL (programming language); Cell biology; Chemistry; Biology; Biophysics; Computer science; Biochemistry; Peptide sequence