Chromosomics: Bridging the Gap between Genomes and Chromosomes

Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development

(2019) Kris G. Alavattam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

(2019) Lucas Patel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

(2019) Covadonga Vara et al.   Cell Reports

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

(2018) Lukas F. K. Kuderna et al.   Nature Communications

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

Evolution of Sex Chromosome Dosage Compensation in Animals: A Beautiful Theory, Undermined by Facts and Bedeviled by Details

(2017) Luiqi Gu et al.   Genome Biology and Evolution

Landscape of DNA Methylation on the Marsupial X

(2017) Shafagh A Waters et al.   MOLECULAR BIOLOGY AND EVOLUTION

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

Reconstruction and evolutionary history of eutherian chromosomes

(2017) Jaebum Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic variation in chromosome Y regulates susceptibility to influenza A virus infection

(2017) Dimitry N. Krementsov 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

Y and W Chromosome Assemblies: Approaches and Discoveries

(2017) Marta Tomaszkiewicz et al.   TRENDS IN GENETICS

Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis)

(2017) Zhongkai Cui et al.   Scientific Reports

Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing

(2016) Alexey I. Makunin et al.   BMC GENOMICS

Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

(2016) Janine E. Deakin et al.   BMC GENOMICS

Nucleolar organizer regions: genomic ‘dark matter’ requiring illumination

(2016) Brian McStay   GENES & DEVELOPMENT

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia

(2016) L Capilla et al.   Genome Biology and Evolution

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

(2016) Joana Damas et al.   GENOME RESEARCH

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

(2016) Marta Tomaszkiewicz et al.   GENOME RESEARCH

Interspecific Y chromosome variation is sufficient to rescue hybrid male sterility and is influenced by the grandparental origin of the chromosomes

(2016) L O Araripe et al.   HEREDITY

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

An Integrative Breakage Model of genome architecture, reshuffling and evolution

(2015) Marta Farré et al.   BIOESSAYS

Advanced microscopy methods for visualizing chromatin structure

(2015) Melike Lakadamyali et al.   FEBS LETTERS

The pig X and Y Chromosomes: structure, sequence, and evolution

(2015) Benjamin M. Skinner et al.   GENOME RESEARCH

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Chromosome Scaffold is a Double-Stranded Assembly of Scaffold Proteins

(2015) Rawin Poonperm et al.   Scientific Reports

High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps

(2015) Arthur Georges et al.   GigaScience

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

(2014) Anna Ullastres et al.   BMC GENOMICS

The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation

(2014) Silvia Garagna et al.   CHROMOSOMA

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Epigenetic modification and inheritance in sexual reversal of fish

(2014) C. Shao et al.   GENOME RESEARCH

Fluorescence In Situ Hybridization and Optical Mapping to Correct Scaffold Arrangement in the Tomato Genome

(2014) Lindsay A. Shearer et al.   G3-Genes Genomes Genetics

Marsupial X chromosome inactivation: past, present and future

(2013) Janine E. Deakin   AUSTRALIAN JOURNAL OF ZOOLOGY

Efficient high-throughput sequencing of a laser microdissected chromosome arm

(2013) Eva Seifertova et al.   BMC GENOMICS

High-throughput sequencing of a single chromosome: a moth W chromosome

(2013) Walther Traut et al.   CHROMOSOME RESEARCH

Meta-Analysis Reveals that Genes Regulated by the Y Chromosome in Drosophila melanogaster Are Preferentially Localized to Repressive Chromatin

(2013) Timothy B. Sackton et al.   Genome Biology and Evolution

The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

(2013) L. K. Case et al.   GENOME RESEARCH

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Independent Evolution of Transcriptional Inactivation on Sex Chromosomes in Birds and Mammals

(2013) Alexandra M. Livernois et al.   PLoS Genetics

Nuclear Organization and Genome Function

(2012) Kevin Van Bortle et al.   Annual Review of Cell and Developmental Biology

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory

(2012) Marta Farré et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

(2010) Jennifer F. Hughes et al.   NATURE

Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict

(2010) B. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

(2009) Claire Lemaitre et al.   BMC GENOMICS

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

(2009) D. M. Larkin et al.   GENOME RESEARCH

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

The Status of Dosage Compensation in the Multiple X Chromosomes of the Platypus

(2008) Janine E. Deakin et al.   PLoS Genetics