Buscar recursos académicos

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-...

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...

We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genom...

Materias / palabras clave: Computational biology; Evolutionary biology; Biology

Materias / palabras clave: Missing heritability problem; Heritability; Genome-wide association study; Genetic architecture; Genetic association; Biology; Genetics; Disease; Evolutionary biology; Computational biology; Data science; Genetic variant...

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...

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...

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...

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 ...

A framework is developed to explore the connection between effective optimization algorithms and the problems they are solving. A number of "no free lunch" (NFL) theorems are presented which establish that for any algori...

The particle swarm is an algorithm for finding optimal regions of complex search spaces through the interaction of individuals in a population of particles. This paper analyzes a particle's trajectory as it moves in disc...

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...

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...

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 new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= nei...