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Method

Next-generation sequencing identifies the natural killer cell microRNA transcriptome

  • First Published October 8, 2010
Research

Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines

  • First Published October 5, 2010
Research

Drosophila and mammals" > Conservation of an RNA regulatory map between Drosophila and mammals

  • First Published October 4, 2010
Research

Young proteins experience more variable selection pressures than old proteins

  • First Published October 4, 2010
Research

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution

  • First Published September 28, 2010
Research

RNA synthesis precision is regulated by preinitiation complex turnover

  • First Published September 20, 2010
Research

Overlapping codes within protein-coding sequences

  • First Published September 14, 2010
Research

A unique H3K4me2 profile marks tissue-specific gene regulation

  • First Published September 14, 2010
Research

De novo rates and selection of large copy number variation

  • First Published September 14, 2010
Method

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

  • First Published September 14, 2010
Research

Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites" > Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites

  • First Published September 9, 2010
Research

Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species

  • First Published September 4, 2010
Research

Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging

  • First Published September 1, 2010
Method

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing

  • First Published September 1, 2010
Resource

Candida albicans using RNA-seq" > Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

  • First Published September 1, 2010
Resource

Detecting copy number variation with mated short reads

  • First Published August 30, 2010
Method

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

  • First Published August 27, 2010
Research

Drosophila" > Age-dependent chromosomal distribution of male-biased genes in Drosophila

  • First Published August 26, 2010
Research

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

  • First Published August 24, 2010
Research

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

  • First Published August 24, 2010
Research

A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness

  • First Published August 18, 2010
Research

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy

  • First Published August 17, 2010
Research

Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer

  • First Published August 17, 2010
Research

Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis

  • First Published August 13, 2010
Research

cis-regulatory architecture of mouse photoreceptors" > CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

  • First Published August 6, 2010
Method

Optimization of de novo transcriptome assembly from next-generation sequencing data

  • First Published August 6, 2010
Research

Massive turnover of functional sequence in human and other mammalian genomes

  • First Published August 6, 2010
Research

Signatures of positive selection apparent in a small sample of human exomes

  • First Published August 6, 2010
Research

CACNG2" > Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2

  • First Published August 5, 2010
Research

Genomic signatures of germline gene expression

  • First Published August 4, 2010
Review

Origins, evolution, and phenotypic impact of new genes

  • First Published July 22, 2010
Resource

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

  • First Published July 20, 2010
Research

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain

  • First Published July 20, 2010
Resource

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

  • First Published July 19, 2010
Research

Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure

  • First Published July 14, 2010
Method

Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

  • First Published July 14, 2010
Research

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

  • First Published July 13, 2010
Method

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples

  • First Published July 13, 2010
Research

TATA is a modular component of synthetic promoters

  • First Published July 13, 2010
Method

Saccharomyces cerevisiae deletion collection" > High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection

  • First Published July 7, 2010
Research

Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts

  • First Published July 6, 2010
Research

Drosophila" > Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila

  • First Published July 2, 2010
Resource

Geobacter sulfurreducens genome" > Structural and operational complexity of the Geobacter sulfurreducens genome

  • First Published June 30, 2010
Research

The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia

  • First Published June 29, 2010
Research

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

  • First Published June 21, 2010
Research

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

  • First Published June 15, 2010
Resource

Phenotypic annotation of the mouse X chromosome

  • First Published June 14, 2010
Research

Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver

  • First Published June 10, 2010
Method

Predicting genetic modifier loci using functional gene networks

  • First Published June 9, 2010
Research

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences

  • First Published June 9, 2010
Research

Patching gaps in plant genomes results in gene movement and erosion of colinearity

  • First Published June 7, 2010
Research

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

  • First Published June 7, 2010
Method

Strand-specific deep sequencing of the transcriptome

  • First Published June 2, 2010
Research

Coccidioides fungi reveals recent hybridization and transposon control" > Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

  • First Published June 1, 2010
ERRATUM

Erratum

  • First Published June 1, 2010
Research

Genome-wide misexpression of X-linked versus autosomal genes associated with hybrid male sterility

  • First Published May 28, 2010
Method

Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome

  • First Published May 27, 2010
Method

A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes

  • First Published May 27, 2010
Perspective

Assembly of large genomes using second-generation sequencing

  • First Published May 27, 2010
Research

A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells

  • First Published May 27, 2010
Research

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

  • First Published May 27, 2010
Research

Sequence features that drive human promoter function and tissue specificity

  • First Published May 25, 2010
Research

The mutational spectrum of non-CpG DNA varies with CpG content

  • First Published May 24, 2010
Research

C. elegans" > Genome-wide gene expression regulation as a function of genotype and age in C. elegans

  • First Published May 20, 2010
Method

Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

  • First Published May 20, 2010
Method

Drosophila melanogaster using genomic capture sequencing" > Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing

  • First Published May 14, 2010
Research

A global network of coexisting microbes from environmental and whole-genome sequence data

  • First Published May 10, 2010
Method

mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain

  • First Published May 7, 2010
Research

cis and trans regulation in yeasts" > Natural selection on cis and trans regulation in yeasts

  • First Published May 5, 2010
Research

Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping

  • First Published May 4, 2010
Research

Reprogramming of miRNA networks in cancer and leukemia

  • First Published May 3, 2010
Perspective

Neanderthal genomics and the evolution of modern humans

  • First Published May 3, 2010
Research

Drosophila genome" > Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome

  • First Published April 30, 2010
Method

Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families

  • First Published April 29, 2010
Research

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

  • First Published April 29, 2010
Research

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

  • First Published April 29, 2010
Research

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

  • First Published April 23, 2010
COMMENTARY

Ethical challenges in genotype-driven research recruitment

  • First Published April 23, 2010
Research

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

  • First Published April 22, 2010
Research

Orcinus orca) indicates multiple species" > Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

  • First Published April 22, 2010
Research

Characterization of the RNA content of chromatin

  • First Published April 19, 2010
Research

Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program

  • First Published April 15, 2010
Method

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

  • First Published April 8, 2010
Research

Rickettsia prowazekii reveals its adaptive mutation capabilities" > Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities

  • First Published April 5, 2010
Research

Global survey of escape from X inactivation by RNA-sequencing in mouse

  • First Published April 2, 2010
Research

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

  • First Published April 2, 2010
Research

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus

  • First Published April 1, 2010
Research

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

  • First Published March 31, 2010
Research

Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome

  • First Published March 31, 2010
Research

Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds

  • First Published March 31, 2010
Research

Taeniopygia guttata genome" > The recombination landscape of the zebra finch Taeniopygia guttata genome

  • First Published March 31, 2010
Research

Drosophila revealed by mRNA-seq" > Regulatory divergence in Drosophila revealed by mRNA-seq

  • First Published March 30, 2010
Research

Natural selection drives the accumulation of amino acid tandem repeats in human proteins

  • First Published March 24, 2010
Research

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

  • First Published March 22, 2010
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