Genome-wide profiling of S/MAR-based replicon contact sites

Genome-wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4+ T Cells

(2016) Andreas Gogol-Döring et al.   MOLECULAR THERAPY

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Distinct epigenetic features of differentiation-regulated replication origins

(2016) Owen K. Smith et al.   Epigenetics & Chromatin

Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture

(2014) Job Dekker   Epigenetics & Chromatin

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

(2013) Ralph Stadhouders et al.   Nature Protocols

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle

(2013) Haiqing Fu et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genomic cis-acting Sequences Improve Expression and Establishment of a Nonviral Vector

(2013) Claudia Hagedorn et al.   Molecular Therapy-Nucleic Acids

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

(2012) Guoliang Li et al.   CELL

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

(2012) Argyris Papantonis et al.   EMBO JOURNAL

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Genetic Modification of Cancer Cells Using Non-Viral, Episomal S/MAR Vectors for In Vivo Tumour Modelling

(2012) Orestis Argyros et al.   PLoS One

Variegated gene expression caused by cell-specific long-range DNA interactions

(2011) Daan Noordermeer et al.   NATURE CELL BIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

pEPito: a significantly improved non-viral episomal expression vector for mammalian cells

(2010) Rudolf Haase et al.   BMC BIOTECHNOLOGY

Controlled removal of a nonviral episomal vector from transfected cells

(2010) Sina Rupprecht et al.   GENE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Boundary sequences stabilize transgene expression from subtle position effects in retroviral vectors

(2009) Rafael Moreno et al.   BLOOD CELLS MOLECULES AND DISEASES

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Cell cycle dependent histone dynamics of an episomal non-viral vector

(2009) Sina Rupprecht et al.   GENE

The Latent Origin of Replication of Epstein-Barr Virus Directs Viral Genomes to Active Regions of the Nucleus

(2009) M. J. Deutsch et al.   JOURNAL OF VIROLOGY

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Similar active genes cluster in specialized transcription factories

(2008) Meng Xu et al.   JOURNAL OF CELL BIOLOGY

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

(2008) Lars Guelen et al.   NATURE

High-resolution circular chromosome conformation capture assay

(2008) Anita Göndör et al.   Nature Protocols