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Research

Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons

  • First Published April 5, 2011
Research

Transcriptional consequences of genomic structural aberrations in breast cancer

  • First Published April 5, 2011
Research

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

  • First Published April 5, 2011
Research

Natural genetic variation caused by small insertions and deletions in the human genome

  • First Published April 1, 2011
Resource

Low-coverage sequencing: Implications for design of complex trait association studies

  • First Published April 1, 2011
Method

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

  • First Published April 1, 2011
Resource

MicroRNA programs in normal and aberrant stem and progenitor cells

  • First Published March 30, 2011
Method

Detection of common single nucleotide polymorphisms synthesizing quantitative trait association of rarer causal variants

  • First Published March 25, 2011
Method

Revealing the genetic structure of a trait by sequencing a population under selection

  • First Published March 21, 2011
Research

Genetic analysis of complex traits in the emerging Collaborative Cross

  • First Published March 15, 2011
Research

RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology" > RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology

  • First Published March 10, 2011
Research

Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH

  • First Published March 7, 2011
Research

Drosophila embryos: Efficient functional analysis and evolutionary conservation" > High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

  • First Published March 7, 2011
Research

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

  • First Published March 7, 2011
Resource

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

  • First Published March 3, 2011
Research

C. elegans" > Core promoter T-blocks correlate with gene expression levels in C. elegans

  • First Published March 2, 2011
Method

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

  • First Published March 2, 2011
Research

Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

  • First Published March 1, 2011
Method

High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome

  • First Published March 1, 2011
Resource

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

  • First Published February 24, 2011
Method

Biome representational in silico karyotyping

  • First Published February 10, 2011
Resource

Maximum-likelihood estimation of recent shared ancestry (ERSA)

  • First Published February 8, 2011
Resource

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

  • First Published February 7, 2011
Method

A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes

  • First Published February 7, 2011
Perspective

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

  • First Published February 4, 2011
Research

Coordinated histone modifications are associated with gene expression variation within and between species

  • First Published February 4, 2011
Research

Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch

  • First Published February 3, 2011
Method

Sequence-based physical mapping of complex genomes by whole genome profiling

  • First Published February 1, 2011
Research

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

  • First Published February 1, 2011
Research

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

  • First Published January 26, 2011
Research

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

  • First Published January 26, 2011
Research

Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles

  • First Published January 20, 2011
Method

Efficient storage of high throughput DNA sequencing data using reference-based compression

  • First Published January 18, 2011
Research

Drosophila melanogaster TORC1–S6K pathway signaling" > Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1–S6K pathway signaling

  • First Published January 14, 2011
Research

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

  • First Published January 13, 2011
Method

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

  • First Published January 13, 2011
Research

Nucleotide composition-linked divergence of vertebrate core promoter architecture

  • First Published January 10, 2011
Resource

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

  • First Published January 6, 2011
Resource

Adaptive seeds tame genomic sequence comparison

  • First Published January 5, 2011
Erratum

Erratum

  • First Published January 4, 2011
Research

Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes

  • First Published January 4, 2011
Research

Developmental control of the DNA replication and transcription programs

  • First Published December 22, 2010
Research

C. elegans trans-splicing" > A global analysis of C. elegans trans-splicing

  • First Published December 22, 2010
Resource

Drosophila melanogaster transcriptome by paired-end RNA sequencing" > The Drosophila melanogaster transcriptome by paired-end RNA sequencing

  • First Published December 22, 2010
Method

Drosophila melanogaster and Caenorhabditis elegans" > Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans

  • First Published December 22, 2010
Research

Drosophila melanogaster" > Genome-wide analysis of promoter architecture in Drosophila melanogaster

  • First Published December 22, 2010
Resource

Drosophila cell lines" > The transcriptional diversity of 25 Drosophila cell lines

  • First Published December 22, 2010
Research

C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

  • First Published December 22, 2010
Research

C. elegans" > Broad chromosomal domains of histone modification patterns in C. elegans

  • First Published December 22, 2010
Research

C. elegans" > High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

  • First Published December 22, 2010
Resource

Caenorhabditis elegans" > Genome-wide analysis of alternative splicing in Caenorhabditis elegans

  • First Published December 22, 2010
Research

Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence" > Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

  • First Published December 22, 2010
Resource

C. elegans gene expression" > A spatial and temporal map of C. elegans gene expression

  • First Published December 22, 2010
Research

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

  • First Published December 22, 2010
Method

C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

  • First Published December 22, 2010
Research

Drosophila heterochromatin" > Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

  • First Published December 22, 2010
Research

Drosophila replication program" > Chromatin signatures of the Drosophila replication program

  • First Published December 22, 2010
Research

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

  • First Published December 20, 2010
Method

Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I–induced DNA damage

  • First Published December 20, 2010
Research

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

  • First Published December 20, 2010
Research

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease

  • First Published December 16, 2010
Research

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

  • First Published December 16, 2010
Research

Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer

  • First Published December 14, 2010
Research

LSH and G9a/GLP complex are required for developmentally programmed DNA methylation

  • First Published December 13, 2010
Research

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

  • First Published December 13, 2010
Research

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors

  • First Published December 8, 2010
Research

cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts" > Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts

  • First Published December 8, 2010
Research

High-throughput sequencing of complete human mtDNA genomes from the Philippines

  • First Published December 8, 2010
Research

Alu repeat discovery and characterization within human genomes" > Alu repeat discovery and characterization within human genomes

  • First Published December 3, 2010
Erratum

Erratum

  • First Published December 1, 2010
Reviewer Index

Reviewer Index, Volume 20, 2010

  • First Published December 1, 2010
Author Index

Author Index, Volume 20, 2010

  • First Published December 1, 2010
Method

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

  • First Published November 24, 2010
Method

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

  • First Published November 24, 2010
Research

Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation

  • First Published November 18, 2010
Research

Copy number variation modifies expression time courses

  • First Published November 17, 2010
Method

Genome-wide characterization of centromeric satellites from multiple mammalian genomes

  • First Published November 16, 2010
Research

AK005651) and contributes to type 1 diabetes susceptibility" > A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility

  • First Published November 4, 2010
Method

Gene expression profiling of human breast tissue samples using SAGE-Seq

  • First Published November 2, 2010
Method

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

  • First Published November 2, 2010
Research

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

  • First Published November 2, 2010
Method

High-throughput discovery of rare insertions and deletions in large cohorts

  • First Published November 1, 2010
Perspective

Transgenerational epigenetic inheritance: More questions than answers

  • First Published November 1, 2010
Research

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

  • First Published October 29, 2010
Research

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

  • First Published October 29, 2010
Research

Caenorhabditis elegans" > Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans

  • First Published October 29, 2010
Resource

Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans

  • First Published October 27, 2010
Method

Caenorhabditis nematode genome with RNA-seq" > Scaffolding a Caenorhabditis nematode genome with RNA-seq

  • First Published October 27, 2010
Resource

Dindel: Accurate indel calls from short-read data

  • First Published October 27, 2010
Resource

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

  • First Published October 27, 2010
Resource

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

  • First Published October 27, 2010
Research

Adaptive selection of an incretin gene in Eurasian populations

  • First Published October 26, 2010
Research

Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps

  • First Published October 26, 2010
Research

trans and cis mutations" > Coevolution within a transcriptional network by compensatory trans and cis mutations

  • First Published October 26, 2010
Research

Localized hypermutation and associated gene losses in legume chloroplast genomes

  • First Published October 26, 2010
Research

OPA1 links human mitochondrial genome maintenance to mtDNA replication and distribution

  • First Published October 25, 2010
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