High-resolution TADs reveal DNA sequences underlying genome organization in flies
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
High-resolution TADs reveal DNA sequences underlying genome organization in flies
Authors
Keywords
-
Journal
Nature Communications
Volume 9, Issue 1, Pages -
Publisher
Springer Nature
Online
2018-01-09
DOI
10.1038/s41467-017-02525-w
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts
- (2017) Pau Pascual-Garcia et al. MOLECULAR CELL
- Evolutionarily Conserved Principles Predict 3D Chromatin Organization
- (2017) M. Jordan Rowley et al. MOLECULAR CELL
- Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach
- (2017) Raphaël Mourad et al. PLoS Computational Biology
- Chromatin Domains: The Unit of Chromosome Organization
- (2016) Jesse R. Dixon et al. MOLECULAR CELL
- Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
- (2016) Mihaela Pertea et al. Nature Protocols
- deepTools2: a next generation web server for deep-sequencing data analysis
- (2016) Fidel Ramírez et al. NUCLEIC ACIDS RESEARCH
- Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture
- (2016) Caelin Cubeñas-Potts et al. NUCLEIC ACIDS RESEARCH
- Formation of Chromosomal Domains by Loop Extrusion
- (2016) Geoffrey Fudenberg et al. Cell Reports
- A CTCF Code for 3D Genome Architecture
- (2015) Michael H. Nichols et al. CELL
- Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
- (2015) Darío G. Lupiáñez et al. CELL
- CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
- (2015) Ya Guo et al. CELL
- Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
- (2015) Sergey V. Ulianov et al. GENOME RESEARCH
- Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes
- (2015) Osamu Iwasaki et al. MOLECULAR CELL
- High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila
- (2015) Fidel Ramírez et al. MOLECULAR CELL
- Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing
- (2015) Li Li et al. MOLECULAR CELL
- Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments
- (2015) Dhawal Jain et al. NUCLEIC ACIDS RESEARCH
- Standardizing chromatin research: a simple and universal method for ChIP-seq
- (2015) Laura Arrigoni et al. NUCLEIC ACIDS RESEARCH
- TopDom: an efficient and deterministic method for identifying topological domains in genomes
- (2015) Hanjun Shin et al. NUCLEIC ACIDS RESEARCH
- Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
- (2015) Adrian L. Sanborn et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation
- (2015) Varun Narendra et al. SCIENCE
- Regularization Paths for Generalized Linear Models via Coordinate Descent
- (2015) Jerome Friedman et al. Journal of Statistical Software
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2014) Suhas S.P. Rao et al. CELL
- Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function
- (2014) S. Cuartero et al. EMBO JOURNAL
- Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin
- (2014) Oksana Maksimenko et al. GENOME RESEARCH
- UpSet: Visualization of Intersecting Sets
- (2014) Alexander Lex et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation
- (2014) Muhammad A. Zabidi et al. NATURE
- Motif-based analysis of large nucleotide data sets using MEME-ChIP
- (2014) Wenxiu Ma et al. Nature Protocols
- CTCF: an architectural protein bridging genome topology and function
- (2014) Chin-Tong Ong et al. NATURE REVIEWS GENETICS
- Insulator function and topological domain border strength scale with architectural protein occupancy
- (2014) Kevin Van Bortle et al. GENOME BIOLOGY
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- (2013) Y. Liao et al. BIOINFORMATICS
- Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle
- (2013) B Gurudatta et al. CELL CYCLE
- Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor
- (2013) Jian Li et al. EMBO JOURNAL
- Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
- (2012) Tom Sexton et al. CELL
- Nature and function of insulator protein binding sites in the Drosophila genome
- (2012) Y. B. Schwartz et al. GENOME RESEARCH
- Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains
- (2012) K. Van Bortle et al. GENOME RESEARCH
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- (2012) S. G. Landt et al. GENOME RESEARCH
- Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
- (2012) Chunhui Hou et al. MOLECULAR CELL
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Iterative correction of Hi-C data reveals hallmarks of chromosome organization
- (2012) Maxim Imakaev et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Identifying ChIP-seq enrichment using MACS
- (2012) Jianxing Feng et al. Nature Protocols
- Self-organization of domain structures by DNA-loop-extruding enzymes
- (2012) E. Alipour et al. NUCLEIC ACIDS RESEARCH
- The NSL Complex Regulates Housekeeping Genes in Drosophila
- (2012) Kin Chung Lam et al. PLoS Genetics
- DREME: motif discovery in transcription factor ChIP-seq data
- (2011) Timothy L. Bailey BIOINFORMATICS
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- Regulation of Chromatin Organization and Inducible Gene Expression by a Drosophila Insulator
- (2011) Ashley M. Wood et al. MOLECULAR CELL
- Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
- (2011) Reza Kalhor et al. NATURE BIOTECHNOLOGY
- Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
- (2011) Morgane Thomas-Chollier et al. Nature Protocols
- The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset
- (2011) Christian Feller et al. NUCLEIC ACIDS RESEARCH
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
- (2010) Robert C McLeay et al. BMC BIOINFORMATICS
- Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
- (2010) Guillaume J. Filion et al. CELL
- The developmental transcriptome of Drosophila melanogaster
- (2010) Brenton R. Graveley et al. NATURE
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
- (2010) Jeremy Goecks et al. GENOME BIOLOGY
- Unlocking the secrets of the genome
- (2009) Susan E. Celniker et al. NATURE
- Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
- (2008) S. Cuddapah et al. GENOME RESEARCH
- BEAF Regulates Cell-Cycle Genes through the Controlled Deposition of H3K9 Methylation Marks into Its Conserved Dual-Core Binding Sites
- (2008) Eldon Emberly et al. PLOS BIOLOGY
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now