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List of works by Job Dekker

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

scientific article published on 04 November 2019

A closer look at long-range chromosomal interactions

scientific article

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

scientific article (publication date: 7 April 2011)

A pathway for mitotic chromosome formation.

scientific article published on 18 January 2018

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

scientific article

An encyclopedia of mouse DNA elements (Mouse ENCODE).

scientific article

Analysis of long-range chromatin interactions using Chromosome Conformation Capture ⬇️

scientific article published on August 15, 2012

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

scientific article

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

scholarly article

Author Correction: Perspectives on ENCODE

scholarly article

CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning

scientific article published on 17 January 2019

Capturing chromosome conformation

scientific article (publication date: 15 February 2002)

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

scientific article

Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease

scientific article

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

scientific article

Chromosome Conformation Capture (3C) in Budding Yeast

scientific article published on June 2015

Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast

scientific article published on June 2015

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

scientific article

Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation

scientific article published on 05 September 2019

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

scientific article published on 03 September 2013

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

scientific article published on 12 October 2014

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

scientific article (publication date: 9 October 2009)

Condensin-driven remodelling of X chromosome topology during dosage compensation.

scientific article

Defining functional DNA elements in the human genome

scientific article

Detecting chromatin interactions between and along sister chromatids with SisterC

scientific article published on 23 September 2020

Determining spatial chromatin organization of large genomic regions using 5C technology

scientific article

Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening

scientific article

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.

scientific article published on 30 October 2011

Epigenetic characteristics of the mitotic chromosome in 1D and 3D.

scientific article

Evidence for transcript networks composed of chimeric RNAs in human cells

scientific article

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

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

scientific article

From cells to chromatin: Capturing snapshots of genome organization with 5C technology ⬇️

scientific article published on November 5, 2012

Genomics tools for unraveling chromosome architecture ⬇️

scientific article published on October 1, 2010

Hi-C: a comprehensive technique to capture the conformation of genomes

scientific article published on 29 May 2012

Hi-C: a method to study the three-dimensional architecture of genomes

scientific article

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

scientific article

HiTC: exploration of high-throughput 'C' experiments

scientific article published on 24 August 2012

Highly structured homolog pairing reflects functional organization of the Drosophila genome

scientific article published on 03 October 2019

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture

scientific article published on 29 October 2021

Integrating one-dimensional and three-dimensional maps of genomes

scientific article

Integrative detection and analysis of structural variation in cancer genomes

scientific article published on 10 September 2018

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

scientific article

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

scientific article

Large domains of heterochromatin direct the formation of short mitotic chromosome loops

scientific article published on 11 September 2020

Long-Range Chromatin Interactions

scientific article published on October 2015

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

scientific article published on 25 June 2015

Mapping networks of physical interactions between genomic elements using 5C technology

scientific article

Mediator and cohesin connect gene expression and chromatin architecture

scientific article

Multi-contact 3C reveals that the human genome during interphase is largely not entangled

scientific article published on 14 September 2020

My5C: web tools for chromosome conformation capture studies

scientific article

Organization of the mitotic chromosome

scientific article

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

scientific article published on May 2014

Quantitative analysis of chromosome conformation capture assays (3C-qPCR).

scientific article

RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.

scientific article published on 8 August 2016

Randomized ligation control for chromosome conformation capture

scientific article published on June 2015

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

scientific article published on 19 July 2016

SMC complexes differentially compact mitotic chromosomes according to genomic context

scientific article published on 21 August 2017

SPEN integrates transcriptional and epigenetic control of X-inactivation

scientific article published on 05 February 2020

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

scientific article published on 05 July 2013

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

scientific article published on 29 October 2018

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations

scientific article published on 16 February 2012

Spatial organization of transcribed eukaryotic genes

scientific article published in 2022

Structural and functional diversity of Topologically Associating Domains

scientific article

Structural organization of the inactive X chromosome in the mouse.

scientific article

Systematic evaluation of chromosome conformation capture assays

scientific article published on 03 September 2021

The accessible chromatin landscape of the human genome

scientific article

The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications

scholarly article

The context of gene expression regulation

scientific article published on 2 April 2012

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos ⬇️

scientific article published on 03 October 2019

The long-range interaction landscape of gene promoters

scientific article (publication date: 6 September 2012)

The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome

scientific article published in Nature Communications

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

scientific article

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

scientific article (publication date: 2014)

Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.

scientific article published on 30 October 2011

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