The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Direct recognition of homology between double helices of DNA in Neurospora crassa

(2014) Eugene Gladyshev et al.   Nature Communications

Evolution of Alu Elements toward Enhancers

(2014) Ming Su et al.   Cell Reports

Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression

(2014) Daudi Jjingo et al.   Mobile DNA

The ENCODE project: Missteps overshadowing a success

(2013) Sean R. Eddy   CURRENT BIOLOGY

Genetic and epigenetic determinants of DNA replication origins, position and activation

(2013) Marcel Méchali et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

(2013) F. S. J. de Souza et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

Normalization of a chromosomal contact map

(2012) Axel Cournac et al.   BMC GENOMICS

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

(2012) Tom Sexton et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

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

(2012) Dominic Schmidt et al.   CELL

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

3C-based technologies to study the shape of the genome

(2012) Wouter de Laat et al.   METHODS

Epigenetic Regulation of Condensin-Mediated Genome Organization during the Cell Cycle and upon DNA Damage through Histone H3 Lysine 56 Acetylation

(2012) Atsunari Tanaka et al.   MOLECULAR CELL

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

(2012) Daniela M. Witten et al.   NUCLEIC ACIDS RESEARCH

Genomic impact of eukaryotic transposable elements

(2012) Irina R Arkhipova et al.   Mobile DNA

Genomic relationship between SINE retrotransposons, Pol III–Pol II transcription, and chromatin organization: the journey from junk to jewel

(2011) Victoria V. Lunyak et al.   Biochemistry and Cell Biology

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Repeat performance: how do genome packaging and regulation depend on simple sequence repeats?

(2010) Ram Parikshan Kumar et al.   BIOESSAYS

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide

(2010) Marco Botta et al.   Molecular Systems Biology

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

(2010) Hideki Tanizawa et al.   NUCLEIC ACIDS RESEARCH

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

OrthoClusterDB: an online platform for synteny blocks

(2009) Man-Ping Ng et al.   BMC BIOINFORMATICS

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

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

(2009) Guillaume Bourque   CURRENT OPINION IN GENETICS & DEVELOPMENT

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Self-organization in the genome

(2009) T. Misteli   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single molecule detection of direct, homologous, DNA/DNA pairing

(2009) C. Danilowicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes

(2009) Aristotelis Tsirigos et al.   PLoS Computational Biology

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

(2008) Effie Apostolou et al.   CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

(2008) G.-F. Richard et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS