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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...

Materias / palabras clave: Phylogenetic tree; Selection (genetic algorithm); Computational biology; Evolutionary biology; Model selection; Biology; Phylogenetics; Computer science; Genetics; Artificial intelligence; Gene

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: Linkage (software); Genetic association; Genome-wide association study; Association (psychology); Set (abstract data type); Genetics; Population; Biology; Computational biology; Association mapping; Evolutionary biology;...

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...

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...

Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also for a variety of research once the phylogenies are estimated. ...

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 ...

Genomic and darwinian medicine deal with the application of hereditary and evolutionary principles for the understanding of health and disease. The progress in molecular and bioinformatic knowledge is making possible thr...

El objetivo de este trabajo es describir los patrones de variación del tamaño corporal de las poblaciones del Holoceno tardío de Pampa y Patagonia Continental con el fin de discutir los procesos evolutivos que los hab...

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although di...

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are imp...

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months fr...

Abstract In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, wh...

Materias / palabras clave: evolution, genetics, genomics, proteomics; Science: Biology (General): Evolution

Materias / palabras clave: molecular epidemiology, evolutionary genetics, infectious diseases, coevolution, host-pathogen interactions; Science: Biology (General): Genetics; Medicine: Internal medicine: Infectious and parasitic diseases

Materias / palabras clave: zoology, evolutionary biology, population genetics, systematic zoology; Science: Zoology; Science: Biology (General): Evolution

Materias / palabras clave: evolutionary biology, evolutionary genetics, evolutionary dynamics, phylogenetics, adaptation; Science: Biology (General): Evolution

Materias / palabras clave: evolutionary biology, genomics, molecular biology; Science: Biology (General): Evolution; Science: Biology (General): Genetics

Materias / palabras clave: genome sequencing and analysis, functional genomics, comparative and evolutionary genomics, bioinformatics and computational genomics, regulatory and epigenomic genomics, genomic methods and technology development; Scien...

Materias / palabras clave: history of biology, biology, genetics, social history, evolutionary theory; History (General) and history of Europe: History (General); Science: Biology (General)