4.3 Review

Regulatory elements in molecular networks

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Oncology

CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas

Yanwen Jiang et al.

CANCER DISCOVERY (2017)

Article Biochemistry & Molecular Biology

Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality

Han-Yu Shih et al.

Article Biochemistry & Molecular Biology

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes

Peter van Galen et al.

MOLECULAR CELL (2016)

Article Biotechnology & Applied Microbiology

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

Gozde Korkmaz et al.

NATURE BIOTECHNOLOGY (2016)

Article Genetics & Heredity

Genetic dissection of the α-globin super-enhancer in vivo

Deborah Hay et al.

NATURE GENETICS (2016)

Review Cell Biology

Genome-wide mapping and analysis of chromosome architecture

Anthony D. Schmitt et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)

Review Cell Biology

Applying CRISPR-Cas9 tools to identify and characterize transcriptional enhancers

Rui Lopes et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)

Article Multidisciplinary Sciences

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

Feng Liu et al.

SCIENTIFIC REPORTS (2016)

Article Endocrinology & Metabolism

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

Amanda M. Ackermann et al.

MOLECULAR METABOLISM (2016)

Article Biochemistry & Molecular Biology

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Zhonghui Tang et al.

Article Biochemistry & Molecular Biology

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

Zhi-Ping Liu

CURRENT GENOMICS (2015)

Article Biochemistry & Molecular Biology

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

Denes Hnisz et al.

MOLECULAR CELL (2015)

Article Multidisciplinary Sciences

Integrative analysis of 111 reference human epigenomes

Anshul Kundaje et al.

NATURE (2015)

Article Multidisciplinary Sciences

Single-cell chromatin accessibility reveals principles of regulatory variation

Jason D. Buenostro et al.

NATURE (2015)

Article Multidisciplinary Sciences

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

Matthew C. Canver et al.

NATURE (2015)

Article Biotechnology & Applied Microbiology

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Babak Alipanahi et al.

NATURE BIOTECHNOLOGY (2015)

Editorial Material Genetics & Heredity

What are super-enhancers?

Sebastian Pott et al.

NATURE GENETICS (2015)

Article Biochemical Research Methods

Functional annotation of native enhancers with a Cas9-histone demethylase fusion

Nicola A. Kearns et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Predicting effects of noncoding variants with deep learning-based sequence model

Jian Zhou et al.

NATURE METHODS (2015)

Review Cell Biology

The selection and function of cell type-specific enhancers

Sven Heinz et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Medicine, General & Internal

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

Melina Claussnitzer et al.

NEW ENGLAND JOURNAL OF MEDICINE (2015)

Article Multidisciplinary Sciences

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Darren A. Cusanovich et al.

SCIENCE (2015)

Article Mathematical & Computational Biology

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

Zhi-Ping Liu et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)

Article Biochemistry & Molecular Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S. P. Rao et al.

Article Biotechnology & Applied Microbiology

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

Richard I. Sherwood et al.

NATURE BIOTECHNOLOGY (2014)

Article Genetics & Heredity

Genome-wide analysis of noncoding regulatory mutations in cancer

Nils Weinhold et al.

NATURE GENETICS (2014)

Article Biochemical Research Methods

Motif-based analysis of large nucleotide data sets using MEME-ChIP

Wenxiu Ma et al.

NATURE PROTOCOLS (2014)

Review Genetics & Heredity

Transcriptional enhancers: from properties to genome-wide predictions

Daria Shlyueva et al.

NATURE REVIEWS GENETICS (2014)

Article Biochemistry & Molecular Biology

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Warren A. Whyte et al.

Article Biochemistry & Molecular Biology

Super-Enhancers in the Control of Cell Identity and Disease

Denes Hnisz et al.

Review Biochemistry & Molecular Biology

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

Matthias Merkenschlager et al.

Article Biochemistry & Molecular Biology

Inferring chromatin-bound protein complexes from genome-wide binding assays

Eugenia G. Giannopoulou et al.

GENOME RESEARCH (2013)

Article Multidisciplinary Sciences

TERT Promoter Mutations in Familial and Sporadic Melanoma

Susanne Horn et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Highly Recurrent TERT Promoter Mutations in Human Melanoma

Franklin W. Huang et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

Cosmas D. Arnold et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Ekta Khurana et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

The mutational landscape of phosphorylation signaling in cancer

Jueri Reimand et al.

SCIENTIFIC REPORTS (2013)

Article Biochemical Research Methods

The Next Generation of Transcription Factor Binding Site Prediction

Anthony Mathelier et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Multidisciplinary Sciences

An expansive human regulatory lexicon encoded in transcription factor footprints

Shane Neph et al.

NATURE (2012)

Article Multidisciplinary Sciences

Architecture of the human regulatory network derived from ENCODE data

Mark B. Gerstein et al.

NATURE (2012)

Review Biotechnology & Applied Microbiology

Transcriptional enhancers in development and disease

Noboru Jo Sakabe et al.

GENOME BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

Matthew Slattery et al.

Article Biochemistry & Molecular Biology

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Ho Sung Rhee et al.

Review Cell Biology

Pioneer transcription factors: establishing competence for gene expression

Kenneth S. Zaret et al.

GENES & DEVELOPMENT (2011)

Article Multidisciplinary Sciences

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

Daniel S. Lieber et al.

PLOS ONE (2010)

Article Biochemistry & Molecular Biology

Revealing Global Regulatory Perturbations across Human Cancers

Hani Goodarzi et al.

MOLECULAR CELL (2009)

Article Multidisciplinary Sciences

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Nathaniel D. Heintzman et al.

NATURE (2009)

Article Multidisciplinary Sciences

The role of DNA shape in protein-DNA recognition

Remo Rohs et al.

NATURE (2009)

Article Biochemistry & Molecular Biology

MEME SUITE: tools for motif discovery and searching

Timothy L. Bailey et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Article Biochemistry & Molecular Biology

High-resolution mapping and characterization of open chromatin across the genome

Alan P. Boyle et al.

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

A universal framework for regulatory element discovery across all Genomes and data types

Olivier Elemento et al.

MOLECULAR CELL (2007)

Article Multidisciplinary Sciences

Genome-wide mapping of in vivo protein-DNA interactions

David S. Johnson et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

Identification of molecular apocrine breast tumours by microarray analysis

P Farmer et al.

ONCOGENE (2005)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Article Genetics & Heredity

Regulatory element detection using correlation with expression

HJ Bussemaker et al.

NATURE GENETICS (2001)