4.7 Article

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

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 Biochemistry & Molecular Biology

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

Luis de la Torre-Ubieta et al.

Article Multidisciplinary Sciences

Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

Hong Sook Kim et al.

NATURE (2018)

Article Multidisciplinary Sciences

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Fidel Ramirez et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

The cis-regulatory dynamics of embryonic development at single-cell resolution

Darren A. Cusanovich et al.

NATURE (2018)

Article Biochemistry & Molecular Biology

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

Aaron C. Daugherty et al.

GENOME RESEARCH (2017)

Article Genetics & Heredity

Promoter shape varies across populations and affects promoter evolution and expression noise

Ignacio E. Schor et al.

NATURE GENETICS (2017)

Article Biochemical Research Methods

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

Charles Girardot et al.

BMC BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

Falong Lu et al.

Article Genetics & Heredity

Histone H3 globular domain acetylation identifies a new class of enhancers

Madapura M. Pradeepa et al.

NATURE GENETICS (2016)

Article Biochemistry & Molecular Biology

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos

Youqiong Ye et al.

SCIENTIFIC REPORTS (2016)

Article Multidisciplinary Sciences

Integrative analysis of 111 reference human epigenomes

Anshul Kundaje et al.

NATURE (2015)

Article Biochemistry & Molecular Biology

RSAT 2015: Regulatory Sequence Analysis Tools

Alejandra Medina-Rivera et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Cell Biology

A conserved role for Snail as a potentiator of active transcription

Martina Rembold et al.

GENES & DEVELOPMENT (2014)

Article Multidisciplinary Sciences

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

Evgeny Z. Kvon et al.

NATURE (2014)

Article Multidisciplinary Sciences

Chromatin state dynamics during blood formation

David Lara-Astiaso et al.

SCIENCE (2014)

Article Biochemical Research Methods

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

Mahmoud Ghandi et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

Andrew B. Stergachis et al.

Article Cell Biology

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

Daniel J. McKay et al.

DEVELOPMENTAL CELL (2013)

Article Biochemical Research Methods

Software for Computing and Annotating Genomic Ranges

Michael Lawrence et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

Guillaume Junion et al.

Article Biochemistry & Molecular Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Stephen G. Landt et al.

GENOME RESEARCH (2012)

Article Multidisciplinary Sciences

The accessible chromatin landscape of the human genome

Robert E. Thurman et al.

NATURE (2012)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

Stefan Bonn et al.

NATURE PROTOCOLS (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Statistics & Probability

MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS

Qunhua Li et al.

ANNALS OF APPLIED STATISTICS (2011)

Article Multidisciplinary Sciences

The developmental transcriptome of Drosophila melanogaster

Brenton R. Graveley et al.

NATURE (2011)

Article Biochemical Research Methods

The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana

Roger B. Deal et al.

NATURE PROTOCOLS (2011)

Article Biochemistry & Molecular Biology

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

Steven M. Gallo et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biotechnology & Applied Microbiology

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

Sean Thomas et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

Robert C. McLeay et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Robert P. Zinzen et al.

NATURE (2009)

Article Biochemical Research Methods

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

Jay R. Hesselberth et al.

NATURE METHODS (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 Biotechnology & Applied Microbiology

Quantifying similarity between motifs

Shobhit Gupta et al.

GENOME BIOLOGY (2007)

Article Biochemical Research Methods

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

Peter J. Sabo et al.

NATURE METHODS (2006)

Article Cell Biology

Highly sensitive, fluorescent transformation marker for Drosophila transgenesis

C Horn et al.

DEVELOPMENT GENES AND EVOLUTION (2000)