Genomic architecture constrained placental mammal X Chromosome evolution

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

An improved pig reference genome sequence to enable pig genetics and genomics research

(2020) Amanda Warr et al.   GigaScience

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

(2020) Reuben M. Buckley et al.   PLoS Genetics

Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis)

(2020) Kevin R Bredemeyer et al.   JOURNAL OF HEREDITY

Recombination-aware phylogenomics reveals the structured genomic landscape of hybridizing cat species

(2019) Gang Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

(2019) Mark S. Springer et al.   Frontiers in Genetics

SMCHD1 Merges Chromosome Compartments and Assists Formation of Super-Structures on the Inactive X

(2018) Chen-Yu Wang et al.   CELL

Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

(2018) Elise A. Lucotte et al.   GENETICS

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

(2018) G. Bonora et al.   Nature Communications

Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

(2018) Elise A. Lucotte et al.   GENETICS

Characterization of the ICCE Repeat in Mammals Reveals an Evolutionary Relationship with the DXZ4 Macrosatellite through Conserved CTCF Binding Motifs

(2018) Natalia Westervelt et al.   Genome Biology and Evolution

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci inDrosophila melanogaster

(2017) Daniel E. Khost et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Landscape of X chromosome inactivation across human tissues

(2017) Taru Tukiainen et al.   NATURE

The X chromosome in space

(2017) Teddy Jégu et al.   NATURE REVIEWS GENETICS

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

High-Resolution Maps of Mouse Reference Populations

(2017) Petr Simecek et al.   G3-Genes Genomes Genetics

X Chromosome Evolution in Cetartiodactyla

(2017) Anastasia Proskuryakova et al.   Genes

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

(2017) Henrique V. Figueiró et al.   Science Advances

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

(2016) Gang Li 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

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Extreme selective sweeps independently targeted the X chromosomes of the great apes

(2015) Kiwoong Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence

(2015) Julien Y. Dutheil et al.   PLoS Genetics

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

(2015) Fan Yang et al.   GENOME BIOLOGY

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

(2014) Suhas S.P. Rao et al.   CELL

A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome

(2014) Emily M. Darrow et al.   CHROMOSOME RESEARCH

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

(2014) Michael J. Montague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acceleration of X-chromosome gene order evolution in the cattle lineage

(2013) Woncheoul Park et al.   BMB Reports

Large, Male Germ Cell-Specific Hypomethylated DNA Domains With Unique Genomic and Epigenomic Features on the Mouse X Chromosome

(2013) R. Ikeda et al.   DNA RESEARCH

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

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

Independent specialization of the human and mouse X chromosomes for the male germ line

(2013) Jacob L Mueller et al.   NATURE GENETICS

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome

(2012) Andrea H. Horakova et al.   HUMAN MOLECULAR GENETICS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Chromosome X-encoded cancer/testis antigens show distinctive expression patterns in developing gonads and in testicular seminoma

(2011) Y.-T. Chen et al.   HUMAN REPRODUCTION

The biology of cancer testis antigens: Putative function, regulation and therapeutic potential

(2011) Elisabetta Fratta et al.   Molecular Oncology

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

(2010) Junwu Ma et al.   BMC GENOMICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years

(2009) Claudia Leticia Rodríguez Delgado et al.   CHROMOSOME RESEARCH

A Comprehensive Linkage Map of the Dog Genome

(2009) A. K. Wong et al.   GENETICS

DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts

(2008) B. P. Chadwick   GENOME RESEARCH

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS