Anopheles mosquitoes reveal new principles of 3D genome organization in insects

Order and stochasticity in the folding of individual Drosophila genomes

(2021) Sergey V. Ulianov et al.   Nature Communications

Predicting Genome Architecture: Challenges and Solutions

(2021) Polina Belokopytova et al.   Frontiers in Genetics

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly

(2021) Mahul Chakraborty et al.   BMC BIOLOGY

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila

(2021) Yi Liao et al.   GENOME RESEARCH

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

(2021) Anjali Kaushal et al.   Nature Communications

Erythrocytes 3D genome organization in vertebrates

(2021) Anastasia Ryzhkova et al.   Scientific Reports

H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization

(2021) Bobbie Pelham-Webb et al.   MOLECULAR CELL

A cookbook for DNase Hi-C

(2021) Maria Gridina et al.   Epigenetics & Chromatin

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

(2021) Anton Zamyatin et al.   GigaScience

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

(2020) Robert M. Waterhouse et al.   BMC BIOLOGY

Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes

(2020) Phillip George et al.   Cells

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity

(2020) Xiaotian Zhang et al.   MOLECULAR CELL

Regulation of single-cell genome organization into TADs and chromatin nanodomains

(2020) Quentin Szabo et al.   NATURE GENETICS

The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere

(2020) Austin Compton et al.   G3-Genes Genomes Genetics

3D genome evolution and reorganization in the Drosophila melanogaster species group

(2020) Nicole S. Torosin et al.   PLoS Genetics

A Near-Chromosome Level Genome Assembly of Anopheles stephensi

(2020) Afiya Razia Chida et al.   Frontiers in Genetics

Chromatin Structure and Function in Mosquitoes

(2020) Óscar M. Lezcano et al.   Frontiers in Genetics

Divide and Rule: Phase Separation in Eukaryotic Genome Functioning

(2020) Sergey V. Razin et al.   Cells

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization

(2019) M. Jordan Rowley et al.   Cell Reports

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

C-InterSecture – a computational tool for interspecies comparison of genome architecture

(2019) M Nuriddinov et al.   BIOINFORMATICS

Recurrent Losses and Rapid Evolution of the Condensin II Complex in Insects

(2019) Thomas D King et al.   MOLECULAR BIOLOGY AND EVOLUTION

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

(2019) Jay Ghurye et al.   GigaScience

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

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

(2019) Gina Renschler et al.   GENES & DEVELOPMENT

Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing

(2019) Russell B. Corbett-Detig et al.   GENETICS

A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

(2019) Sarah B Kingan et al.   GigaScience

Quantitative prediction of enhancer–promoter interactions

(2019) Polina S. Belokopytova et al.   GENOME RESEARCH

Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome

(2018) Gleb N. Artemov et al.   BMC GENOMICS

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional and chromatin changes accompanying de novo formation of transgenic piRNA clusters

(2018) Natalia Akulenko et al.   RNA

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex

(2018) Yuttapong Thawornwattana et al.   MOLECULAR BIOLOGY AND EVOLUTION

3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin

(2018) Veniamin Fishman et al.   NUCLEIC ACIDS RESEARCH

New Approaches for Genome Assembly and Scaffolding

(2018) Edward S. Rice et al.   Annual Review of Animal Biosciences

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

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

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

(2017) Nathan Harmston et al.   Nature Communications

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles

(2016) Gleb N. Artemov et al.   G3-Genes Genomes Genetics

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions

(2015) Camille Berthelot et al.   Cell Reports

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Gene density and chromosome territory shape

(2014) Nitasha Sehgal et al.   CHROMOSOMA

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

(2014) Gloria I. Giraldo-Calderón et al.   NUCLEIC ACIDS RESEARCH

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

(2014) D. E. Neafsey et al.   SCIENCE

Adaptation through chromosomal inversions in Anopheles

(2014) Diego Ayala et al.   Frontiers in Genetics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion

(2013) Emmanuel Paradis   MOLECULAR PHYLOGENETICS AND EVOLUTION

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Evolutionary Conservation of Histone Modifications in Mammals

(2012) Y. H. Woo et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

An Integrated Chromosome Map of Microsatellite Markers and Inversion Breakpoints for an Asian Malaria Mosquito, Anopheles stephensi

(2011) Maryam Kamali et al.   JOURNAL OF HEREDITY

A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber

(2011) I. Comet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Physical Map for an Asian Malaria Mosquito, Anopheles stephensi

(2010) Maria V. Sharakhova et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

Genome mapping and characterization of the Anopheles gambiae heterochromatin

(2010) Maria V Sharakhova et al.   BMC GENOMICS

High-resolution cytogenetic map for the African malaria vector Anopheles gambiae

(2010) P. George et al.   INSECT MOLECULAR BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Dual effects of TNFα on nerve fiber formation from ventral mesencephalic organotypic tissue cultures

(2008) Franziska Marschinke et al.   BRAIN RESEARCH

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology