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16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers...

Two extended basis sets (termed 5–31G and 6–31G) consisting of atomic orbitals expressed as fixed linear combinations of Gaussian functions are presented for the first row atoms carbon to fluorine. These basis functi...

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (b...

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolut...

Materias / palabras clave: Population stratification; Spurious relationship; Biology; Principal component analysis; Allele frequency; Genetic association; Genome-wide association study; Population; Evolutionary biology; Computational biology; Geno...

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for informatio...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3 , implementing new features including drawing the exte...

SUMMARY: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis ta...

First-principles simulation, meaning density-functional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensed-matter theory. Here I look at the basics of the suject, give a...

BACKGROUND: Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis...

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method ...

There is increasing evidence that genome-wide association (GWA) studies represent a powerful approach to the identification of genes involved in common human diseases. We describe a joint GWA study (using the Affymetrix ...

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing...

UNLABELLED: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, i...

Infiltrating stromal and immune cells form the major fraction of normal cells in tumour tissue and not only perturb the tumour signal in molecular studies but also have an important role in cancer biology. Here we descri...

A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of ...

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...

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagen...

Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not cor...

The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor ...

Abstract Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be dep...

The prefrontal cortex has long been suspected to play an important role in cognitive control, in the ability to orchestrate thought and action in accordance with internal goals. Its neural basis, however, has remained a ...

High entropy alloys (HEAs) are barely 12 years old. The field has stimulated new ideas and has inspired the exploration of the vast composition space offered by multi-principal element alloys (MPEAs). Here we present a c...