3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Local rewiring of genome–nuclear lamina interactions by transcription

(2020) Laura Brueckner et al.   EMBO JOURNAL

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

(2020) Vinícius G Contessoto et al.   NUCLEIC ACIDS RESEARCH

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

(2020) Austin B. Mudd et al.   Communications Biology

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

(2019) Ferdinand Marlétaz et al.   CURRENT BIOLOGY

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs

(2019) Christ Leemans et al.   CELL

The Whole-Genome Sequence of the Coral Acropora millepora

(2019) Hua Ying et al.   Genome Biology and Evolution

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

(2019) David J. Bertioli et al.   NATURE GENETICS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

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

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Direct arene C–H fluorination with 18F− via organic photoredox catalysis

(2019) Wei Chen et al.   SCIENCE

Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

(2019) Eoin O'Connor et al.   G3-Genes Genomes Genetics

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

(2019) Yutaka Satou et al.   Genome Biology and Evolution

Highly structured homolog pairing reflects functional organization of the Drosophila genome

(2019) Jumana AlHaj Abed et al.   Nature Communications

Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles

(2019) Ratchaphol Thongchum et al.   Scientific Reports

Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation

(2019) Ahmed M.O. Elbatsh et al.   MOLECULAR CELL

OUP accepted manuscript

(2018)   BIOINFORMATICS

Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis : Biotechnological implications

(2018) Daxi Wang et al.   BIOTECHNOLOGY ADVANCES

Ki-67 and condensins support the integrity of mitotic chromosomes through distinct mechanisms

(2018) Masatoshi Takagi et al.   JOURNAL OF CELL SCIENCE

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Condensin II drives large-scale folding and spatial partitioning of interphase chromosomes in Drosophila nuclei

(2018) Leah F. Rosin et al.   PLoS Genetics

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

(2018) James T. Robinson et al.   Cell Systems

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

(2018) Yuichiro Hara et al.   Nature Ecology & Evolution

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

(2018) Holly C. Betts et al.   Nature Ecology & Evolution

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

Improved reference genome of Aedes aegypti informs arbovirus vector control

(2018) Benjamin J. Matthews et al.   NATURE

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging

(2017) Tadasu Nozaki et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Xenbase: a genomic, epigenomic and transcriptomic model organism database

(2017) Kamran Karimi et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

(2017) Yuki Yoshida et al.   PLOS BIOLOGY

The dynamic three-dimensional organization of the diploid yeast genome

(2017) Seungsoo Kim et al.   eLife

Condensin-Based Chromosome Organization from Bacteria to Vertebrates

(2016) Tatsuya Hirano   CELL

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

Identification of peanut (Arachis hypogaea)chromosomes using a fluorescencein situhybridization system reveals multiple hybridization events during tetraploid peanut formation

(2016) Laining Zhang et al.   NEW PHYTOLOGIST

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome

(2016) Bin Zhang et al.   PHYSICAL REVIEW LETTERS

Transferable model for chromosome architecture

(2016) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

(2015) Christopher E. Laumer et al.   CURRENT BIOLOGY

Balancing Acts of Two HEAT Subunits of Condensin I Support Dynamic Assembly of Chromosome Axes

(2015) Kazuhisa Kinoshita et al.   DEVELOPMENTAL CELL

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

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

(2014) Suhas S.P. Rao et al.   CELL

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

(2014) Patrick Essletzbichler et al.   GENOME RESEARCH

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Overlapping and Non-overlapping Functions of Condensins I and II in Neural Stem Cell Divisions

(2014) Kenji Nishide et al.   PLoS Genetics

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization

(2013) Jean Ollion et al.   BIOINFORMATICS

The Arabidopsis CAP-D proteins are required for correct chromatin organisation, growth and fertility

(2013) Veit Schubert et al.   CHROMOSOMA

The Nucleoplasmin Homolog NLP Mediates Centromere Clustering and Anchoring to the Nucleolus

(2013) Jan Padeken et al.   MOLECULAR CELL

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum)

(2013) T. K. Mehta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

(2013) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Contrasting roles of condensin I and condensin II in mitotic chromosome formation

(2012) L. C. Green et al.   JOURNAL OF CELL SCIENCE

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

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

(2012) E. Morin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condensin II Promotes the Formation of Chromosome Territories by Inducing Axial Compaction of Polyploid Interphase Chromosomes

(2012) Christopher R. Bauer et al.   PLoS Genetics

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

(2011) Chenwei Wang et al.   BMC GENETICS

The relative ratio of condensin I to II determines chromosome shapes

(2011) K. Shintomi et al.   GENES & DEVELOPMENT

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

High frequency, cell type-specific visualization of fluorescent-tagged genomic sites in interphase and mitotic cells of living Arabidopsis plants

(2010) Antonius JM Matzke et al.   Plant Methods

Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

(2010) P. Arensburger et al.   SCIENCE

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length

(2009) John F. Marko   PHYSICAL REVIEW E

Comparative gene mapping in cattle, Indian muntjac, and Chinese muntjac by fluorescence in situ hybridization

(2008) Andrea E. Murmann et al.   GENETICA

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE