Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling
出版年份 2019 全文链接
标题
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling
作者
关键词
-
出版物
GENES & DEVELOPMENT
Volume 33, Issue 21-22, Pages 1591-1612
出版商
Cold Spring Harbor Laboratory
发表日期
2019-10-11
DOI
10.1101/gad.328971.119
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
- (2019) Yad Ghavi-Helm et al. NATURE GENETICS
- Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs
- (2018) Maria Samata et al. Annual Review of Biochemistry
- FMLRC: Hybrid long read error correction using an FM-index
- (2018) Jeremy R. Wang et al. BMC BIOINFORMATICS
- Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- (2018) Nathan H. Lazar et al. GENOME RESEARCH
- High-resolution TADs reveal DNA sequences underlying genome organization in flies
- (2018) Fidel Ramírez et al. Nature Communications
- MUMmer4: A fast and versatile genome alignment system
- (2018) Guillaume Marçais et al. PLoS Computational Biology
- Genomes of Diptera
- (2018) Brian M Wiegmann et al. Current Opinion in Insect Science
- Evolutionary stability of topologically associating domains is associated with conserved gene regulation
- (2018) Jan Krefting et al. BMC BIOLOGY
- Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells
- (2018) Claudia Isabelle Keller Valsecchi et al. Nature Communications
- RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation
- (2018) Maria Kim et al. PLoS Genetics
- 3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments
- (2017) Pengfei Dong et al. Molecular Plant
- A chromosome conformation capture ordered sequence of the barley genome
- (2017) Martin Mascher et al. NATURE
- Hidden genetic variation shapes the structure of functional elements in Drosophila
- (2017) Mahul Chakraborty et al. NATURE GENETICS
- Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
- (2017) Derek M Bickhart et al. NATURE GENETICS
- Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map
- (2017) Kyle P. Eagen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
- (2017) Olga Dudchenko et al. SCIENCE
- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
- (2016) Heng Li BIOINFORMATICS
- Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
- (2016) Jeffrey J. Quinn et al. GENES & DEVELOPMENT
- Dosage Compensation in Drosophila--a Model for the Coordinate Regulation of Transcription
- (2016) M. I. Kuroda et al. GENETICS
- deepTools2: a next generation web server for deep-sequencing data analysis
- (2016) Fidel Ramírez et al. NUCLEIC ACIDS RESEARCH
- Heatmapper: web-enabled heat mapping for all
- (2016) Sasha Babicki et al. NUCLEIC ACIDS RESEARCH
- Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
- (2016) Neva C. Durand et al. Cell Systems
- DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
- (2016) Chengxi Ye et al. Scientific Reports
- BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
- (2015) Felipe A. Simão et al. BIOINFORMATICS
- 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
- Condensin-driven remodelling of X chromosome topology during dosage compensation
- (2015) Emily Crane et al. NATURE
- Standardizing chromatin research: a simple and universal method for ChIP-seq
- (2015) Laura Arrigoni et al. NUCLEIC ACIDS RESEARCH
- Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
- (2015) Matteo Vietri Rudan et al. Cell Reports
- Numerous Transitions of Sex Chromosomes in Diptera
- (2015) Beatriz Vicoso et al. PLOS BIOLOGY
- Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila
- (2015) Qi Zhou et al. PLoS Genetics
- Repbase Update, a database of repetitive elements in eukaryotic genomes
- (2015) Weidong Bao et al. Mobile DNA
- Imaging Fos-Jun Transcription Factor Mobility and Interaction in Live Cells by Single Plane Illumination-Fluorescence Cross Correlation Spectroscopy
- (2015) Agata Pernuš et al. PLoS One
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2014) Suhas S.P. Rao et al. CELL
- High-quality genome (re)assembly using chromosomal contact data
- (2014) Hervé Marie-Nelly et al. Nature Communications
- Drosophila Embryogenesis Scales Uniformly across Temperature in Developmentally Diverse Species
- (2014) Steven G. Kuntz et al. PLoS Genetics
- 3D imaging of Sox2 enhancer clusters in embryonic stem cells
- (2014) Zhe Liu et al. eLife
- Insulator function and topological domain border strength scale with architectural protein occupancy
- (2014) Kevin Van Bortle et al. GENOME BIOLOGY
- The MaSuRCA genome assembler
- (2013) Aleksey V. Zimin et al. BIOINFORMATICS
- CrossMap: a versatile tool for coordinate conversion between genome assemblies
- (2013) Hao Zhao et al. BIOINFORMATICS
- Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila
- (2013) A. A. Alekseyenko et al. GENES & DEVELOPMENT
- High-throughput genome scaffolding from in vivo DNA interaction frequency
- (2013) Noam Kaplan et al. NATURE BIOTECHNOLOGY
- Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
- (2013) Joshua N Burton et al. NATURE BIOTECHNOLOGY
- Genome assembly and haplotyping with Hi-C
- (2013) Jan O Korbel et al. NATURE BIOTECHNOLOGY
- Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network
- (2013) C. E. Ellison et al. SCIENCE
- Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)
- (2013) Claudia A. M. Russo et al. ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
- (2012) Jia-Ming Chang et al. BMC BIOINFORMATICS
- Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
- (2012) Tom Sexton et al. CELL
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq
- (2012) T. Straub et al. GENOME RESEARCH
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Spatial partitioning of the regulatory landscape of the X-inactivation centre
- (2012) Elphège P. Nora et al. NATURE
- Iterative correction of Hi-C data reveals hallmarks of chromosome organization
- (2012) Maxim Imakaev et al. NATURE METHODS
- Fiji: an open-source platform for biological-image analysis
- (2012) Johannes Schindelin et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Facilitated Diffusion on Mobile DNA: Configurational Traps and Sequence Heterogeneity
- (2012) C. A. Brackley et al. PHYSICAL REVIEW LETTERS
- Faster-X Evolution of Gene Expression in Drosophila
- (2012) Richard P. Meisel et al. PLoS Genetics
- The NSL Complex Regulates Housekeeping Genes in Drosophila
- (2012) Kin Chung Lam et al. PLoS Genetics
- Defining the Role of Essential Genes in Human Disease
- (2011) Jonathan E. Dickerson et al. PLoS One
- 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
- Phylogenetic relationships and macro-evolutionary patterns within the Drosophila tripunctata “radiation” (Diptera: Drosophilidae)
- (2010) Lizandra J. Robe et al. GENETICA
- A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates
- (2010) Jessica A. Thomas et al. MOLECULAR BIOLOGY AND EVOLUTION
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Unlocking the secrets of the genome
- (2009) Susan E. Celniker et al. NATURE
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- A Sequence Motif within Chromatin Entry Sites Directs MSL Establishment on the Drosophila X Chromosome
- (2008) Artyom A. Alekseyenko et al. CELL
- Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes
- (2008) A. Bhutkar et al. GENETICS
- Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
- (2008) Da Wei Huang et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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