Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
Authors
Keywords
-
Journal
PLoS One
Volume 12, Issue 1, Pages e0169249
Publisher
Public Library of Science (PLoS)
Online
2017-01-10
DOI
10.1371/journal.pone.0169249
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- High-throughput mapping of regulatory DNA
- (2016) Nisha Rajagopal et al. NATURE BIOTECHNOLOGY
- TT-seq maps the human transient transcriptome
- (2016) Björn Schwalb et al. SCIENCE
- Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence
- (2015) T. Org et al. EMBO JOURNAL
- Integrative analysis of 111 reference human epigenomes
- (2015) Anshul Kundaje et al. NATURE
- Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
- (2015) Jason Ernst et al. NATURE BIOTECHNOLOGY
- The selection and function of cell type-specific enhancers
- (2015) Sven Heinz et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
- (2015) Lucas D. Ward et al. NUCLEIC ACIDS RESEARCH
- Functional annotation of HOT regions in the human genome: implications for human disease and cancer
- (2015) Hao Li et al. Scientific Reports
- The Ensembl Regulatory Build
- (2015) Daniel R Zerbino et al. GENOME BIOLOGY
- Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome
- (2015) Alessandro Mammana et al. GENOME BIOLOGY
- Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model
- (2014) Robin Andersson BIOESSAYS
- High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
- (2014) Michal Rabani et al. CELL
- High-throughput functional testing of ENCODE segmentation predictions
- (2014) Jamie C. Kwasnieski et al. GENOME RESEARCH
- Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle
- (2014) B. Zacher et al. Molecular Systems Biology
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- A promoter-level mammalian expression atlas
- (2014) NATURE
- Genome-wide analysis of noncoding regulatory mutations in cancer
- (2014) Nils Weinhold et al. NATURE GENETICS
- Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
- (2014) Leighton J Core et al. NATURE GENETICS
- Transcriptional enhancers: from properties to genome-wide predictions
- (2014) Daria Shlyueva et al. NATURE REVIEWS GENETICS
- DEEP: a general computational framework for predicting enhancers
- (2014) Dimitrios Kleftogiannis et al. NUCLEIC ACIDS RESEARCH
- Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- (2013) P. Kheradpour et al. GENOME RESEARCH
- Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
- (2013) J. Ernst et al. GENOME RESEARCH
- Comparative annotation of functional regions in the human genome using epigenomic data
- (2013) Kyoung-Jae Won et al. NUCLEIC ACIDS RESEARCH
- The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
- (2013) Danielle Welter et al. NUCLEIC ACIDS RESEARCH
- Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
- (2013) C. D. Arnold et al. SCIENCE
- RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
- (2013) Nisha Rajagopal et al. PLoS Computational Biology
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- Normalization of ChIP-seq data with control
- (2012) Kun Liang et al. BMC BIOINFORMATICS
- A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
- (2012) M.-A. Dillies et al. BRIEFINGS IN BIOINFORMATICS
- HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
- (2012) E. Z. Kvon et al. GENES & DEVELOPMENT
- Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- (2012) J. Wang et al. GENOME RESEARCH
- Architecture of the human regulatory network derived from ENCODE data
- (2012) Mark B. Gerstein et al. NATURE
- Chromatin marks identify critical cell types for fine mapping complex trait variants
- (2012) Gosia Trynka et al. NATURE GENETICS
- Unsupervised pattern discovery in human chromatin structure through genomic segmentation
- (2012) Michael M Hoffman et al. NATURE METHODS
- ChromHMM: automating chromatin-state discovery and characterization
- (2012) Jason Ernst et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Integrative annotation of chromatin elements from ENCODE data
- (2012) Michael M. Hoffman et al. NUCLEIC ACIDS RESEARCH
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
- (2012) Kevin Y Yip et al. GENOME BIOLOGY
- Discriminative prediction of mammalian enhancers from DNA sequence
- (2011) D. Lee et al. GENOME RESEARCH
- Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
- (2011) Gabriel E. Zentner et al. GENOME RESEARCH
- Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
- (2011) C. Miller et al. Molecular Systems Biology
- A high-resolution map of human evolutionary constraint using 29 mammals
- (2011) Kerstin Lindblad-Toh et al. NATURE
- Mapping and analysis of chromatin state dynamics in nine human cell types
- (2011) Jason Ernst et al. NATURE
- Nascent transcript sequencing visualizes transcription at nucleotide resolution
- (2011) L. Stirling Churchman et al. NATURE
- Large-scale discovery of enhancers from human heart tissue
- (2011) Dalit May et al. NATURE GENETICS
- Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
- (2010) Peter V. Kharchenko et al. NATURE
- Widespread transcription at neuronal activity-regulated enhancers
- (2010) Tae-Kyung Kim et al. NATURE
- Discovery and characterization of chromatin states for systematic annotation of the human genome
- (2010) Jason Ernst et al. NATURE BIOTECHNOLOGY
- rtracklayer: an R package for interfacing with genome browsers
- (2009) M. Lawrence et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- ChIP-seq accurately predicts tissue-specific activity of enhancers
- (2009) Axel Visel et al. NATURE
- An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
- (2009) Daniel Ramsköld et al. PLoS Computational Biology
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search