Published in BMC Genomics on April 15, 2014
Genome-wide characterization of the routes to pluripotency. Nature (2014) 2.34
Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol (2014) 1.88
SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene (2015) 1.65
Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature (2015) 1.39
Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature (2015) 1.32
β-catenin mediates stress resilience through Dicer1/microRNA regulation. Nature (2014) 1.21
A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis. Cell (2015) 1.09
deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res (2016) 1.07
High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma. Oncogene (2015) 1.01
Integrator mediates the biogenesis of enhancer RNAs. Nature (2015) 1.01
ACF chromatin-remodeling complex mediates stress-induced depressive-like behavior. Nat Med (2015) 0.99
Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol (2015) 0.98
High mobility group protein-mediated transcription requires DNA damage marker γ-H2AX. Cell Res (2015) 0.97
Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Min (2015) 0.96
DNA methylation changes in plasticity genes accompany the formation and maintenance of memory. Nat Neurosci (2015) 0.96
Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci (2014) 0.94
Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability. Science (2016) 0.92
ΔNp63α induces the expression of FAT2 and Slug to promote tumor invasion. Oncotarget (2016) 0.92
Alu element-containing RNAs maintain nucleolar structure and function. EMBO J (2015) 0.91
DNA break mapping reveals topoisomerase II activity genome-wide. Int J Mol Sci (2014) 0.91
Altered chromatin occupancy of master regulators underlies evolutionary divergence in the transcriptional landscape of erythroid differentiation. PLoS Genet (2014) 0.90
Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes. Oncotarget (2016) 0.89
Trimethylation of Lys36 on H3 restricts gene expression change during aging and impacts life span. Genes Dev (2015) 0.87
Repression of the soma-specific transcriptome by Polycomb-repressive complex 2 promotes male germ cell development. Genes Dev (2014) 0.86
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res (2014) 0.86
A Cbx8-containing polycomb complex facilitates the transition to gene activation during ES cell differentiation. PLoS Genet (2014) 0.86
Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer. PLoS One (2015) 0.85
UTX demethylase activity is required for satellite cell-mediated muscle regeneration. J Clin Invest (2016) 0.85
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience (2015) 0.85
Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family. Mob DNA (2015) 0.85
Structural analysis of human KDM5B guides histone demethylase inhibitor development. Nat Chem Biol (2016) 0.84
ColoWeb: a resource for analysis of colocalization of genomic features. BMC Genomics (2015) 0.84
Histone H3 globular domain acetylation identifies a new class of enhancers. Nat Genet (2016) 0.84
TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer. Sci Rep (2015) 0.84
The transcriptional regulator Aire binds to and activates super-enhancers. Nat Immunol (2017) 0.84
Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis. Cell (2016) 0.83
SIRT1-FOXO3a regulate cocaine actions in the nucleus accumbens. J Neurosci (2015) 0.83
Alteration in 5-hydroxymethylcytosine-mediated epigenetic regulation leads to Purkinje cell vulnerability in ATM deficiency. Brain (2015) 0.83
Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes. Plant Cell (2015) 0.83
Characterization of the direct targets of FOXO transcription factors throughout evolution. Aging Cell (2016) 0.82
MMP-9 facilitates selective proteolysis of the histone H3 tail at genes necessary for proficient osteoclastogenesis. Genes Dev (2016) 0.82
Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell (2016) 0.82
Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes. Arthritis Rheumatol (2015) 0.81
Superenhancer reprogramming drives a B-cell-epithelial transition and high-risk leukemia. Genes Dev (2016) 0.81
Selective suppression of antisense transcription by Set2-mediated H3K36 methylation. Nat Commun (2016) 0.81
Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal. EMBO J (2017) 0.80
Oncofetal Epigenetic Bivalency in Breast Cancer Cells: H3K4 and H3K27 Tri-Methylation as a Biomarker for Phenotypic Plasticity. J Cell Physiol (2016) 0.80
Cooperative Binding of Transcription Factors Orchestrates Reprogramming. Cell (2017) 0.80
Different molecular complexes that mediate transcriptional induction and repression by FoxP3. Nat Immunol (2017) 0.80
AKT phosphorylates H3-threonine 45 to facilitate termination of gene transcription in response to DNA damage. Nucleic Acids Res (2015) 0.80
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. Biomed Res Int (2015) 0.80
Multivalent Histone and DNA Engagement by a PHD/BRD/PWWP Triple Reader Cassette Recruits ZMYND8 to K14ac-Rich Chromatin. Cell Rep (2016) 0.80
Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders. Genome Biol (2016) 0.80
Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins. Cell Rep (2016) 0.79
Shifting transcriptional machinery is required for long-term memory maintenance and modification in Drosophila mushroom bodies. Nat Commun (2016) 0.79
TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemia. Leukemia (2014) 0.79
LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PLoS One (2016) 0.79
Enhancer of Zeste Homolog 2 Inhibition Stimulates Bone Formation and Mitigates Bone Loss Caused by Ovariectomy in Skeletally Mature Mice. J Biol Chem (2016) 0.79
Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms. BMC Genomics (2016) 0.79
DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies. PeerJ (2016) 0.79
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Nucleic Acids Res (2015) 0.79
Semiconductor-based sequencing of genome-wide DNA methylation states. Epigenetics (2015) 0.79
Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. Nat Commun (2016) 0.79
Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells. Sci Rep (2016) 0.78
DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy. Nat Commun (2016) 0.78
metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. PLoS Comput Biol (2016) 0.78
Satb2 determines miRNA expression and long-term memory in the adult central nervous system. Elife (2016) 0.78
Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res (2016) 0.78
Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nat Genet (2017) 0.78
Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality. Nucleic Acids Res (2016) 0.77
Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters. PLoS One (2016) 0.77
Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol (2016) 0.77
Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress. Sci Rep (2015) 0.76
Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1(+) pre-B ALL. J Exp Med (2017) 0.76
Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation. Cell Discov (2016) 0.76
Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features. Biomed Res Int (2016) 0.76
Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. Sci Data (2016) 0.76
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget (2016) 0.76
An EWS-FLI1-Induced Osteosarcoma Model Unveiled a Crucial Role of Impaired Osteogenic Differentiation on Osteosarcoma Development. Stem Cell Reports (2016) 0.76
Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development. Epigenetics Chromatin (2016) 0.76
Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin. Proc Natl Acad Sci U S A (2016) 0.76
Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome. PLoS Genet (2016) 0.76
Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells. PLoS One (2015) 0.76
iTagPlot: an accurate computation and interactive drawing tool for tag density plot. Bioinformatics (2015) 0.75
Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res (2016) 0.75
Transcriptional Selectivity of Epigenetic Therapy in Cancer. Cancer Res (2016) 0.75
Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data. Bio Protoc (2017) 0.75
The chromatin remodeling factor CHD7 controls cerebellar development by regulating reelin expression. J Clin Invest (2017) 0.75
Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. BMC Bioinformatics (2016) 0.75
REST regulation of gene networks in adult neural stem cells. Nat Commun (2016) 0.75
Expression of Ribosomal RNA and Protein Genes in Human Embryonic Stem Cells Is Associated With the Activating H3K4me3 Histone Mark. J Cell Physiol (2016) 0.75
5-Hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human. Hum Mol Genet (2016) 0.75
AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors. Nat Commun (2016) 0.75
Dpy30 is critical for maintaining the identity and function of adult hematopoietic stem cells. J Exp Med (2016) 0.75
Comprehensive mapping of 5-hydroxymethylcytosine epigenetic dynamics in axon regeneration. Epigenetics (2016) 0.75
Neuronal activity modifies the chromatin accessibility landscape in the adult brain. Nat Neurosci (2017) 0.75
Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Res (2016) 0.75
Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors. Nat Commun (2016) 0.75
Transient ectopic expression of the histone demethylase JMJD3 accelerates the differentiation of human pluripotent stem cells. Development (2016) 0.75
Chromatin binding of Gcn5 in Drosophila is largely mediated by CP190. Nucleic Acids Res (2016) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
The human genome browser at UCSC. Genome Res (2002) 168.23
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (2009) 32.97
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res (2008) 26.04
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science (2002) 24.31
HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (2014) 23.22
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science (2011) 14.29
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell (2013) 9.55
BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (2010) 9.11
The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res (2012) 9.02
A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature (2011) 8.31
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Regulation of alternative splicing by histone modifications. Science (2010) 7.98
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell (2011) 7.41
Applications of next-generation sequencing technologies in functional genomics. Genomics (2008) 6.50
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature (2011) 6.48
A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell (1981) 6.43
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics (2011) 5.86
Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell (2011) 4.89
RSeQC: quality control of RNA-seq experiments. Bioinformatics (2012) 4.31
CEAS: cis-regulatory element annotation system. Bioinformatics (2009) 4.26
Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet (2011) 4.25
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Essential role of the histone methyltransferase G9a in cocaine-induced plasticity. Science (2010) 3.97
Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res (2009) 3.95
Retinoic acid induces embryonal carcinoma cells to differentiate into neurons and glial cells. J Cell Biol (1982) 3.85
seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res (2010) 3.74
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol (2011) 3.48
DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. Proc Natl Acad Sci U S A (1981) 3.39
The next-generation sequencing revolution and its impact on genomics. Cell (2013) 3.35
CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development (2009) 3.34
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat Rev Genet (2012) 3.29
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol (2013) 3.18
rtracklayer: an R package for interfacing with genome browsers. Bioinformatics (2009) 3.16
Human postmortem tissue: what quality markers matter? Brain Res (2006) 2.92
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet (2011) 2.87
ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol (2012) 2.51
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell (2013) 2.17
diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One (2013) 1.58
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res (2012) 1.46
Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics (2010) 1.45
Spark: a navigational paradigm for genomic data exploration. Genome Res (2012) 1.10
Comparison of human (and other) genome browsers. Hum Genomics (2006) 1.09
A brief introduction to web-based genome browsers. Brief Bioinform (2012) 1.08
Morphine epigenomically regulates behavior through alterations in histone H3 lysine 9 dimethylation in the nucleus accumbens. J Neurosci (2012) 1.07
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics (2011) 1.04
Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics Inform (2013) 0.81
STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (2013) 0.78
Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol (2014) 1.88
diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One (2013) 1.58
In need of high-throughput behavioral systems. Drug Discov Today (2002) 1.29
Norbin is an endogenous regulator of metabotropic glutamate receptor 5 signaling. Science (2009) 1.22
Behavioral epigenetics. Ann N Y Acad Sci (2011) 1.14
The use of animal models in psychiatric research and treatment. Am J Psychiatry (2008) 1.08
WebLab: a data-centric, knowledge-sharing bioinformatic platform. Nucleic Acids Res (2009) 1.00
Essential role of SIRT1 signaling in the nucleus accumbens in cocaine and morphine action. J Neurosci (2013) 0.95
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies. Nucleic Acids Res (2010) 0.95
Telomere and telomerase as targets for cancer therapy. Appl Biochem Biotechnol (2009) 0.89
LSD 2.0: an update of the leaf senescence database. Nucleic Acids Res (2013) 0.85
Regulation of CART peptide expression by CREB in the rat nucleus accumbens in vivo. Brain Res (2008) 0.85
Cholesteryl ester transfer protein levels and gene deficiency in Chinese patients with cardio-cerebrovascular diseases. Chin Med J (Engl) (2002) 0.81
Thin-film microextraction. Anal Chem (2003) 0.78
G-quadruplex structure: a target for anticancer therapy and a probe for detection of potassium. Biochemistry (Mosc) (2008) 0.77
A Conversation with Eric Nestler. Cold Spring Harb Symp Quant Biol (2014) 0.75
Stranded in the web of evidence and ethics. J Pak Med Assoc (2010) 0.75
NOTES: 'pre-dilatation' as a remedy for technical issues during transgastric access. J Pak Med Assoc (2012) 0.75