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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: Mendelian randomization; Pleiotropy; Biology; Genetics; Trait; Mendelian inheritance; Outlier; Evolutionary biology; Statistics; Phenotype; Mathematics; Genetic variants

The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are devel...

Page 108, last line of text, for P/P″ read P′/P″. Page 120, last line, for δ v read δ y . Page 123, line 10, for 4Nn read 4Nu. Page 125, line 1, for q read q. Page 126, line 12, for q read q. Page 135, line 5 fro...

Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transve...

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...

A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance ...

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: Oxidative stress; Ageing; Reactive oxygen species; Life span; Oxygen; Biology; Chemistry; Cell biology; Evolutionary biology; Biochemistry; Genetics; Organic chemistry

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...

We need scarcely add that the contemplation in natural science of a wider domain than the actual leads to a far better understanding of the actual.' (p. 267,The, Nature of the Physical World.)x PREFACE evolutionary theor...