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Dekker, Job
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Rotation Projects ?

Rotation Projects

Multiple rotation projects are available in several areas related to long-range gene regulation and higher order chromosome organization.  Projects include thorough analyses of the biochemical mechanisms of long-range gene regulation of specific disease-related genes, as well as large-scale analyses of chromosome organization using high-throughput genomics technologies (5C and Hi-C).  The lab employs a wide range of experimental approaches, including cell culture, protein biochemistry, microscopy, genomics as well computational approaches such as bioinformatics and modeling.  Specific rotation projects are determined dependent on the interest of the student.
One or more keywords matched the following items that are connected to Dekker, Job
Item TypeName
Academic Article Two regions within the DNA binding domain of nuclear factor I interact with DNA and stimulate adenovirus DNA replication independently.
Academic Article A closer look at long-range chromosomal interactions.
Academic Article The three 'C' s of chromosome conformation capture: controls, controls, controls.
Academic Article The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications.
Academic Article Mapping networks of physical interactions between genomic elements using 5C technology.
Academic Article GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p.
Academic Article Quantitative analysis of chromosome conformation capture assays (3C-qPCR).
Academic Article Gene regulation in the third dimension.
Academic Article Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction.
Academic Article Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization.
Academic Article Capturing chromosome conformation.
Academic Article Integrating one-dimensional and three-dimensional maps of genomes.
Academic Article The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.
Academic Article Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.
Academic Article Genome architecture and expression.
Academic Article Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Academic Article MORC family ATPases required for heterochromatin condensation and gene silencing.
Academic Article CTCF and cohesin help neurons raise their self-awareness.
Academic Article An integrated encyclopedia of DNA elements in the human genome.
Academic Article The long-range interaction landscape of gene promoters.
Academic Article From cells to chromatin: capturing snapshots of genome organization with 5C technology.
Academic Article Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
Academic Article A mechanical basis for chromosome function.
Academic Article Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.
Academic Article Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Academic Article Mapping chromatin interactions by chromosome conformation capture.
Academic Article A mechanism for Ikaros regulation of human globin gene switching.
Academic Article Long-range chromosomal interactions and gene regulation.
Academic Article Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C).
Academic Article Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery.
Academic Article Determining spatial chromatin organization of large genomic regions using 5C technology.
Academic Article Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Academic Article Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
Academic Article Mediator and cohesin connect gene expression and chromatin architecture.
Academic Article The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules.
Academic Article A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.
Academic Article Chromatin globules: a common motif of higher order chromosome structure?
Academic Article A user's guide to the encyclopedia of DNA elements (ENCODE).
Academic Article The structure and function of chromatin and chromosomes.
Academic Article The context of gene expression regulation.
Academic Article Hi-C: a comprehensive technique to capture the conformation of genomes.
Academic Article Analysis of long-range chromatin interactions using Chromosome Conformation Capture.
Academic Article Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Academic Article The accessible chromatin landscape of the human genome.
Academic Article Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.
Academic Article The hierarchy of the 3D genome.
Academic Article Nuclear biology: what's been most surprising?
Academic Article Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Academic Article Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?
Academic Article Organization of the mitotic chromosome.
Academic Article Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny.
Concept Gene Expression Regulation, Fungal
Concept Chromatin Immunoprecipitation
Concept Up-Regulation
Concept Chromatin
Concept Gene Expression Regulation, Leukemic
Concept Gene Expression Regulation, Developmental
Concept Gene Expression Regulation
Concept Gene Expression Regulation, Viral
Concept Gene Expression Regulation, Neoplastic
Concept Chromatin Assembly and Disassembly
Academic Article Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.
Academic Article Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Academic Article The Hitchhiker's guide to Hi-C analysis: practical guidelines.
Academic Article Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture.
Academic Article Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Academic Article Chromosome Conformation Capture (3C) in Budding Yeast.
Academic Article Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast.
Academic Article Genomics tools for unraveling chromosome architecture.
Academic Article Measuring Chromatin Structure in Budding Yeast.
Academic Article Hi-C in Budding Yeast.
Academic Article Condensin-driven remodelling of X chromosome topology during dosage compensation.
Academic Article Genome-wide maps of nuclear lamina interactions in single human cells.
Academic Article Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.
Academic Article Long-Range Chromatin Interactions.
Academic Article High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.
Academic Article Structural and functional diversity of Topologically Associating Domains.
Academic Article The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.
Academic Article Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.
Academic Article Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire.
Academic Article Activation of proto-oncogenes by disruption of chromosome neighborhoods.
Academic Article TAD disruption as oncogenic driver.
Academic Article Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.
Academic Article Structural organization of the inactive X chromosome in the mouse.
Academic Article SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.
Academic Article RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.
Academic Article Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.
Academic Article CTCF-mediated topological boundaries during development foster appropriate gene regulation.
Academic Article Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.
Academic Article Epigenetic characteristics of the mitotic chromosome in 1D and 3D.
Academic Article Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Academic Article C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.
Academic Article CBF?-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.
Academic Article ChIP-seq.
Academic Article Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions.
Academic Article Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis.
Academic Article 4C Analysis of 3C, ChIP-Loop, and Control Libraries.
Academic Article 5C Analysis of 3C, ChIP-Loop, and Control Libraries.
Academic Article 3C-Based Chromatin Interaction Analyses.
Academic Article Formaldehyde Cross-Linking.
Academic Article SMC complexes differentially compact mitotic chromosomes according to genomic context.
Academic Article Corrigendum: CTCF-mediated topological boundaries during development foster appropriate gene regulation.
Academic Article ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR).
Academic Article ChIP-chip.
Academic Article Generation of ChIP-Loop Libraries.
Academic Article Preparation of Cross-Linked Chromatin for ChIP.
Academic Article CBF?-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.
Academic Article Generation of Control Ligation Product Libraries for 3C Analyses.
Academic Article The 4D nucleome project.
Academic Article CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.
Academic Article Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
Academic Article Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.
Academic Article Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.
Academic Article Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
Academic Article Highly structured homolog pairing reflects functional organization of the Drosophila genome.
Academic Article The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.
Academic Article A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.
Academic Article SPEN integrates transcriptional and epigenetic control of X-inactivation.
Academic Article Ultrastructural Details of Mammalian Chromosome Architecture.
Academic Article Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain.
Academic Article Multi-contact 3C reveals that the human genome during interphase is largely not entangled.
Academic Article Detecting chromatin interactions between and along sister chromatids with SisterC.
Academic Article Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML.
Academic Article Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
Academic Article Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture.
Academic Article Systematic evaluation of chromosome conformation capture assays.
Academic Article Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.
Academic Article Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.
Academic Article Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.
Academic Article Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.
Academic Article Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Academic Article Cohesin-mediated loop anchors confine the locations of human replication origins.
Academic Article Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
Academic Article Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Academic Article CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.
Academic Article A cohesin traffic pattern genetically linked to gene regulation.
Academic Article Regulation of the mitotic chromosome folding machines.
Academic Article Capturing Chromosome Conformation Across Length Scales.
Academic Article Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq.
Academic Article Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis.
Academic Article Editorial overview: Multiscale regulation of genome folding in space, time, and across the tree of life.
Academic Article Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.
Academic Article Revisiting chromatin packaging in mouse sperm.
Academic Article RNA-mediated symmetry breaking enables singular olfactory receptor choice.
Academic Article Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.
Academic Article Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.
Academic Article Rules of engagement for condensins and cohesins guide mitotic chromosome formation.
Search Criteria
  • Chromatin
  • Regulation