An Integrative Breakage Model of genome architecture, reshuffling and evolution

Inching toward the 3D genome

(2015) E. Pennisi   SCIENCE

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

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

(2014) Michael N Romanov et al.   BMC GENOMICS

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

(2014) Suhas S.P. Rao et al.   CELL

Unraveling architecture of the pluripotent genome

(2014) Jennifer E Phillips-Cremins   CURRENT OPINION IN CELL BIOLOGY

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background

(2014) L. Capilla et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recombination initiation maps of individual human genomes

(2014) F. Pratto et al.   SCIENCE

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Inference of the Protokaryotypes of Amniotes and Tetrapods and the Evolutionary Processes of Microchromosomes from Comparative Gene Mapping

(2013) Yoshinobu Uno et al.   PLoS One

Ancient cis-regulatory constraints and the evolution of genome architecture

(2013) Manuel Irimia et al.   TRENDS IN GENETICS

Molecular Basis for the Regulation of the H3K4 Methyltransferase Activity of PRDM9

(2013) Hong Wu et al.   Cell Reports

Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution

(2012) Adriana Muñoz et al.   BMC BIOINFORMATICS

Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

(2012) Yolanda Guillén et al.   BMC GENOMICS

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

(2012) O. Capozzi et al.   GENOME RESEARCH

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

Genetic recombination is directed away from functional genomic elements in mice

(2012) Kevin Brick et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip

(2012) Tom Sexton et al.   Nature Protocols

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

(2012) Craig B. Lowe et al.   PLoS One

Chromosome Fragile Sites in Arabidopsis Harbor Matrix Attachment Regions That May Be Associated with Ancestral Chromosome Rearrangement Events

(2012) Joelle S. dela Paz et al.   PLoS Genetics

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

(2011) Amélie S Véron et al.   BMC GENOMICS

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

(2011) E. Gazave et al.   GENOME RESEARCH

Molecular cytogenetic and genomic insights into chromosomal evolution

(2011) A Ruiz-Herrera et al.   HEREDITY

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes

(2011) Marta Farré et al.   PLoS One

Immunostaining of modified histones defines high-level features of the human metaphase epigenome

(2011) Edith Terrenoire et al.   GENOME BIOLOGY

Selection against Robertsonian fusions involving housekeeping genes in the house mouse: integrating data from gene expression arrays and chromosome evolution

(2010) Aurora Ruiz-Herrera et al.   CHROMOSOME RESEARCH

Copy number variation modifies expression time courses

(2010) E. Chaignat et al.   GENOME RESEARCH

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

(2010) E. M. Kvikstad et al.   GENOME RESEARCH

The Red Queen theory of recombination hotspots

(2010) F. ÚBEDA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

(2010) Neil F Lobo et al.   MALARIA JOURNAL

DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo

(2010) S. Gangadharan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosomal speciation revisited: rearranging theory with pieces of evidence

(2010) Rui Faria et al.   TRENDS IN ECOLOGY & EVOLUTION

Chromosome Territories

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

Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes

(2010) Fátima Al-Shahrour et al.   PLoS Computational Biology

Comparative genomics reveals birth and death of fragile regions in mammalian evolution

(2010) Max A Alekseyev et al.   GENOME BIOLOGY

Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

(2009) Claus Kemkemer et al.   BMC EVOLUTIONARY BIOLOGY

Long-range regulation is a major driving force in maintaining genome integrity

(2009) Emmanuel Mongin et al.   BMC EVOLUTIONARY BIOLOGY

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

(2009) Mark S Longo et al.   BMC GENOMICS

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

(2009) Claire Lemaitre et al.   BMC GENOMICS

Non-B DNA structure-induced genetic instability and evolution

(2009) Junhua Zhao et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transposable elements in gene regulation and in the evolution of vertebrate genomes

(2009) Guillaume Bourque   CURRENT OPINION IN GENETICS & DEVELOPMENT

Recovering genome rearrangements in the mammalian phylogeny

(2009) H. Zhao et al.   GENOME RESEARCH

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

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

Copy number variation influences gene expression and metabolic traits in mice

(2009) Luz D. Orozco et al.   HUMAN MOLECULAR GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

(2009) Asaf Levy et al.   NUCLEIC ACIDS RESEARCH

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The origins and impact of primate segmental duplications

(2009) Tomas Marques-Bonet et al.   TRENDS IN GENETICS

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

(2009) Lucia Carbone et al.   PLoS Genetics

Histones: Annotating Chromatin

(2008) Eric I. Campos et al.   Annual Review of Genetics

Molecular mechanisms of chromosomal rearrangement during primate evolution

(2008) Hildegard Kehrer-Sawatzki et al.   CHROMOSOME RESEARCH

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

(2008) A. Bacolla et al.   GENOME RESEARCH

Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

(2008) Jungnam Lee et al.   PLoS One

A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase

(2008) O. Mihola et al.   SCIENCE

Dynamics of Genome Rearrangement in Bacterial Populations

(2008) Aaron E. Darling et al.   PLoS Genetics