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Materias / palabras clave: RNA; Sequence (biology); Molecule; Chemistry; In vitro; Riboswitch; Binding site; Computational biology; Population; Biology; Biochemistry; Non-coding RNA

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available ...

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a...

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...

A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two popula...

Materias / palabras clave: Biology; Stem cell; Cell biology; Elasticity (physics); Matrix (chemical analysis); Cell lineage; Computational biology; Evolutionary biology; Cellular differentiation; Genetics; Gene; Physics

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...

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simu...

Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes cal...

Materias / palabras clave: Metagenomics; Biology; Phylogenetic tree; 16S ribosomal RNA; Gene; Computational biology; Phylogenetics; Microbiome; Genetics; Ribosomal RNA; Genome; Evolutionary biology

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...

BACKGROUND: The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of g...

A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measureme...

Materias / palabras clave: Enumeration; Biology; Haematopoiesis; RNA; Gene; Computational biology; Hematopoietic cell; Cell; Gene expression; Molecular biology; Messenger RNA; Cell biology

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and sim...

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...

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not b...

Materias / palabras clave: Biology; Transcription factor; Cell type; Genetics; DNA binding site; Cell biology; Cell; Gene; Computational biology; Promoter; Gene expression

Materias / palabras clave: Sequence assembly; De novo transcriptome assembly; Transcriptome; Computational biology; RNA-Seq; Computer science; Set (abstract data type); Biology; Sequence (biology); Software; Gene; Genetics

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic a...

Materias / palabras clave: microRNA; Biology; Haematopoiesis; Computational biology; Gene; Regulation of gene expression; Messenger RNA; Nervous system; Genetics; Cell biology; Stem cell; Neuroscience

Materias / palabras clave: Histone code; Nucleosome; Chromatin; Histone; Computational biology; Cell biology; Histone H1; Biology; Epigenomics; Histone methyltransferase; Histone H2A; Histone-modifying enzymes