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Stimulated Raman scattering (SRS) microscopy is a fast Raman imaging technique that combines the molecular specificity of vibrational spectroscopy with the high spatial resolution and speed of laser-scanning microscopy. ...

Background - Plants in over one hundred families in habitats worldwide bear extrafloral nectaries (EFNs). EFNs display a remarkable diversity of evolutionary origins, as well as diverse morphology and location on the pla...

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesi...

Programmed cell death (PCD) plays a key role in developmental biology and in maintenance of the steady state in continuously renewing tissues. Currently, its existence is inferred mainly from gel electrophoresis of a poo...

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...

Materias / palabras clave: Similarity (geometry); Amino acid; Homology (biology); Sequence (biology); TRACE (psycholinguistics); Mathematics; Computational biology; Computer science; Algorithm; Biology; Genetics; Artificial intelligence

The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order to discover biologically important changes ...

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...

BACKGROUND: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, a...

Materias / palabras clave: Microvesicles; RNA; Cell biology; Exosome; microRNA; Biology; Messenger RNA; Endocytic cycle; Mast cell; Cell; Molecular biology; Gene

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have con...

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been...

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organism...

We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to imp...

In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replic...

Materias / palabras clave: Competition (biology); Selection (genetic algorithm); Inclusive fitness; Kin selection; Genetic Fitness; Biology; Darwinism; Wright; Mathematical economics; Social evolution; Replica; Evolutionary biology

TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produ...

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU ...

Fil: Ledesma Mateos, Ismael. Universidad Nacional Autónoma de México. Facultad de Estudios Superiores Iztacala; México. La medicina es una práctica que se desarrolla desde tiempos inmemoriales, que trasciende el espa...

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...

The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, k...

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated ...

Materias / palabras clave: Angiogenesis; Cancer; Function (biology); Cancer therapy; Clinical trial; Medicine; Computational biology; Biology; Bioinformatics; Cancer research; Internal medicine; Cell biology

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems...