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Research

Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4

  • First Published March 3, 2016
Research

Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest

  • First Published March 3, 2016
Method

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

  • First Published March 2, 2016
Research

Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes

  • First Published March 2, 2016
Research

Callithrix jacchus genome" > Discovery of a new repeat family in the Callithrix jacchus genome

  • First Published February 25, 2016
Research

Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

  • First Published February 25, 2016
Method

Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes

  • First Published February 24, 2016
Research

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

  • First Published February 23, 2016
Research

PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network" > Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network

  • First Published February 18, 2016
Research

Neurospora tetrasperma" > Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma

  • First Published February 18, 2016
Research

Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

  • First Published February 17, 2016
Research

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

  • First Published February 17, 2016
Research

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

  • First Published February 17, 2016
Research

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal

  • First Published February 16, 2016
Method

A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1

  • First Published February 9, 2016
Method

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

  • First Published February 4, 2016
Method

Models of human core transcriptional regulatory circuitries

  • First Published February 3, 2016
Research

Gene regulation and speciation in house mice

  • First Published February 1, 2016
Method

Degradation dynamics of microRNAs revealed by a novel pulse-chase approach

  • First Published January 28, 2016
Method

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

  • First Published January 26, 2016
Research

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha

  • First Published January 21, 2016
Method

Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

  • First Published January 19, 2016
Method

Assessment of megabase-scale somatic copy number variation using single-cell sequencing

  • First Published January 15, 2016
Method

Mapping nucleosome positions using DNase-seq

  • First Published January 15, 2016
Research

Pervasive polymorphic imprinted methylation in the human placenta

  • First Published January 14, 2016
Research

ZAK as a cause of limb defects in humans and mice" > Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice

  • First Published January 11, 2016
Research

APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication

  • First Published January 11, 2016
Research

Concerted activities of Mcm4, Sld3, and Dbf4 in control of origin activation and DNA replication fork progression

  • First Published January 5, 2016
Method

Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase

  • First Published January 4, 2016
Research

The life history of retrocopies illuminates the evolution of new mammalian genes

  • First Published January 4, 2016
Research

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

  • First Published January 4, 2016
Research

TP53 regulates miRNA association with AGO2 to remodel the miRNA–mRNA interaction network

  • First Published December 23, 2015
Research

Worldwide patterns of genomic variation and admixture in gray wolves

  • First Published December 17, 2015
Research

Nasonia" > DNA methylation changes induced by long and short photoperiods in Nasonia

  • First Published December 15, 2015
Resource

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

  • First Published December 15, 2015
Resource

Ciona intestinalis" > Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

  • First Published December 14, 2015
Method

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

  • First Published December 2, 2015
Resource

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

  • First Published December 1, 2015
Author Index

Author Index, Volume 25, 2015

  • First Published December 1, 2015
Reviewer Index

Reviewer Index, Volume 25, 2015

  • First Published December 1, 2015
Research

Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

  • First Published November 24, 2015
Research

EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos

  • First Published November 17, 2015
Method

cis-regulatory analysis in the mammalian central nervous system" > Massively parallel cis-regulatory analysis in the mammalian central nervous system

  • First Published November 17, 2015
Research

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

  • First Published November 13, 2015
Research

RNA structure replaces the need for U2AF2 in splicing

  • First Published November 13, 2015
Resource

The pig X and Y Chromosomes: structure, sequence, and evolution

  • First Published November 11, 2015
Research

The chromatin environment shapes DNA replication origin organization and defines origin classes

  • First Published November 11, 2015
Method

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

  • First Published November 10, 2015
Method

Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens" > RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens

  • First Published November 9, 2015
Research

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

  • First Published November 6, 2015
Research

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

  • First Published November 4, 2015
Research

Nascent RNA folding mitigates transcription-associated mutagenesis

  • First Published October 30, 2015
Research

Tribolium castaneum" > MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum

  • First Published October 30, 2015
Research

Daphnia pulex" > High mutational rates of large-scale duplication and deletion in Daphnia pulex

  • First Published October 30, 2015
Research

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

  • First Published October 30, 2015
Research

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

  • First Published October 30, 2015
Research

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

  • First Published October 28, 2015
Research

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

  • First Published October 20, 2015
Research

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

  • First Published October 20, 2015
Method

A probabilistic method for testing and estimating selection differences between populations

  • First Published October 13, 2015
Research

An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function

  • First Published October 8, 2015
Method

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

  • First Published October 7, 2015
Research

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

  • First Published October 1, 2015
Perspective

The path to routine use of genomic biomarkers in the cancer clinic

  • First Published October 1, 2015
Perspective

Defining cell types and states with single-cell genomics

  • First Published October 1, 2015
Research

Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer

  • First Published October 1, 2015
Perspective

The first five years of single-cell cancer genomics and beyond

  • First Published October 1, 2015
Perspective

The Mendelian disorders of the epigenetic machinery

  • First Published October 1, 2015
Perspective

Epigenomics and the structure of the living genome

  • First Published October 1, 2015
Perspective

Genomic approaches for understanding the genetics of complex disease

  • First Published October 1, 2015
Perspective

Enabling functional genomics with genome engineering

  • First Published October 1, 2015
Perspective

Biological data sciences in genome research

  • First Published October 1, 2015
Perspective

Linking RNA biology to lncRNAs

  • First Published October 1, 2015
Perspective

Parlez-vous VUS?

  • First Published October 1, 2015
Perspective

A vision for ubiquitous sequencing

  • First Published October 1, 2015
Perspective

Functional genomics bridges the gap between quantitative genetics and molecular biology

  • First Published October 1, 2015
Preface

Genome Research" > 20 Years of Genome Research

  • First Published October 1, 2015
Method

Enhanced virome sequencing using targeted sequence capture

  • First Published September 22, 2015
Research

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

  • First Published September 21, 2015
Research

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background

  • First Published September 16, 2015
Resource

Chlorocebus aethiops sabaeus)" > The genome of the vervet (Chlorocebus aethiops sabaeus)

  • First Published September 16, 2015
Research

Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B

  • First Published September 10, 2015
Research

Replication timing is regulated by the number of MCMs loaded at origins

  • First Published September 10, 2015
Research

Noise in gene expression is coupled to growth rate

  • First Published September 9, 2015
Research

Ficedula flycatchers" > Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

  • First Published September 9, 2015
Method

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

  • First Published September 9, 2015
Research

Ribosome profiling reveals an important role for translational control in circadian gene expression

  • First Published September 3, 2015
Research

Drosophila zygotic genome activation" > Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

  • First Published September 2, 2015
Research

Drosophila embryo" > Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo

  • First Published September 2, 2015
Research

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

  • First Published September 1, 2015
Corrigendum

Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site

  • First Published September 1, 2015
Corrigendum

Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

  • First Published September 1, 2015
Method

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

  • First Published August 27, 2015
Research

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

  • First Published August 21, 2015
Resource

Drosophila by 56 RNA binding proteins" > Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

  • First Published August 20, 2015
Research

DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts

  • First Published August 20, 2015
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