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Research

Canonical nucleosome organization at promoters forms during genome activation

  • First Published November 27, 2013
Method

cis-regulatory landscapes in vertebrates" > A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates

  • First Published November 25, 2013
Research

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

  • First Published November 21, 2013
Method

Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases

  • First Published November 19, 2013
Method

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

  • First Published November 19, 2013
Research

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

  • First Published November 18, 2013
Research

Genomic and transcriptomic plasticity in treatment-naïve ovarian cancer

  • First Published November 12, 2013
Method

Discovery of recurrent structural variants in nasopharyngeal carcinoma

  • First Published November 8, 2013
Research

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

  • First Published November 7, 2013
Research

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

  • First Published November 6, 2013
Method

Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair

  • First Published October 31, 2013
Method

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

  • First Published October 31, 2013
Perspective

Functional transcriptomics in the post-ENCODE era

  • First Published October 30, 2013
Resource

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

  • First Published October 29, 2013
Method

A unified model for yeast transcript definition

  • First Published October 29, 2013
Research

The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

  • First Published October 29, 2013
Resource

Variation Ontology for annotation of variation effects and mechanisms

  • First Published October 25, 2013
Resource

Improved exome prioritization of disease genes through cross-species phenotype comparison

  • First Published October 25, 2013
Research

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

  • First Published October 24, 2013
Resource

Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize

  • First Published October 16, 2013
Research

Gene duplication and neofunctionalization: POLR3G and POLR3GL

  • First Published October 9, 2013
Method

Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma

  • First Published October 8, 2013
Research

Maize centromeres expand and adopt a uniform size in the genetic background of oat

  • First Published October 7, 2013
Research

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

  • First Published October 3, 2013
Research

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

  • First Published October 2, 2013
Research

Hominoid fission of chromosome 14/15 and the role of segmental duplications

  • First Published September 27, 2013
Research

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

  • First Published September 27, 2013
Research

The evolution of evolvability in microRNA target sites in vertebrates

  • First Published September 27, 2013
Research

3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

  • First Published September 26, 2013
Research

Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization

  • First Published September 25, 2013
Research

Random replication of the inactive X chromosome

  • First Published September 24, 2013
Research

Monodelphis domestica" > Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica

  • First Published September 24, 2013
Research

Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements" > Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements

  • First Published September 24, 2013
Method

Single-cell mutational profiling and clonal phylogeny in cancer

  • First Published September 20, 2013
Research

Heliconius butterflies" > Genome-wide evidence for speciation with gene flow in Heliconius butterflies

  • First Published September 17, 2013
Research

Derived variants at six genes explain nearly half of size reduction in dog breeds

  • First Published September 11, 2013
Research

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

  • First Published September 11, 2013
Research

Alu elements during B-cell activation" > DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation

  • First Published September 6, 2013
Research

Identifying multiple causative genes at a single GWAS locus

  • First Published September 4, 2013
Research

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

  • First Published September 3, 2013
Resource

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

  • First Published September 3, 2013
Research

HOXD13 mutations" > Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations

  • First Published August 30, 2013
Research

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

  • First Published August 29, 2013
Research

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

  • First Published August 29, 2013
Research

The shared genomic architecture of human nucleolar organizer regions

  • First Published August 29, 2013
Research

Multiple RNA recognition patterns during microRNA biogenesis in plants

  • First Published August 29, 2013
Method

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

  • First Published August 15, 2013
Method

Defining cell-type specificity at the transcriptional level in human disease

  • First Published August 15, 2013
Resource

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

  • First Published August 15, 2013
Research

Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

  • First Published August 12, 2013
Method

Analysis and correction of crosstalk effects in pathway analysis

  • First Published August 9, 2013
Method

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

  • First Published August 6, 2013
Method

Drosophila genomes" > Efficient identification of Y chromosome sequences in the human and Drosophila genomes

  • First Published August 6, 2013
Resource

Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators

  • First Published August 6, 2013
Research

RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

  • First Published August 2, 2013
Research

DNA methylation contributes to natural human variation

  • First Published August 1, 2013
Research

Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

  • First Published August 1, 2013
Erratum

Erratum

  • First Published August 1, 2013
Research

Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation

  • First Published July 26, 2013
Method

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

  • First Published July 22, 2013
Resource

Honey bee protein atlas at organ-level resolution

  • First Published July 22, 2013
Resource

Coelacanth genomes reveal signatures for evolutionary transition from water to land

  • First Published July 22, 2013
Research

GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination

  • First Published July 18, 2013
Research

Meta-analyses of studies of the human microbiota

  • First Published July 16, 2013
Method

FST: The impact of rare variants" > Estimating and interpreting FST: The impact of rare variants

  • First Published July 16, 2013
Research

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins

  • First Published July 16, 2013
Research

Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes

  • First Published July 16, 2013
Method

Pathoscope: Species identification and strain attribution with unassembled sequencing data" > Pathoscope: Species identification and strain attribution with unassembled sequencing data

  • First Published July 10, 2013
Research

Evolution and diversity of copy number variation in the great ape lineage

  • First Published July 3, 2013
Method

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

  • First Published July 1, 2013
Perspective

From human genome to cancer genome: The first decade

  • First Published July 1, 2013
Perspective

Understanding the regulatory and transcriptional complexity of the genome through structure

  • First Published July 1, 2013
Perspective

Insights into neural crest development and evolution from genomic analysis

  • First Published July 1, 2013
Perspective

Comparative genomics as a tool to understand evolution and disease

  • First Published July 1, 2013
Commentary

Hypothesis-generating research and predictive medicine

  • First Published July 1, 2013
Research

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

  • First Published June 28, 2013
Research

Caenorhabditis elegans" > Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans

  • First Published June 28, 2013
Method

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

  • First Published June 26, 2013
Method

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

  • First Published June 26, 2013
Research

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions

  • First Published June 26, 2013
Research

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

  • First Published June 26, 2013
Resource

Caenorhabditis elegans" > The million mutation project: A new approach to genetics in Caenorhabditis elegans

  • First Published June 25, 2013
Research

The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

  • First Published June 25, 2013
Research

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer" > CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

  • First Published June 24, 2013
Research

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

  • First Published June 20, 2013
Research

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

  • First Published June 20, 2013
Research

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast

  • First Published June 20, 2013
Research

The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

  • First Published June 19, 2013
Research

Frac-seq reveals isoform-specific recruitment to polyribosomes

  • First Published June 19, 2013
Research

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

  • First Published June 13, 2013
Method

Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations

  • First Published June 6, 2013
Research

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

  • First Published June 5, 2013
Research

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

  • First Published June 5, 2013
Research

Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers

  • First Published June 4, 2013
Research

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

  • First Published June 3, 2013
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