Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

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