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Dekker, Job

One or more keywords matched the following properties of Dekker, Job

Property	Value
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.

Property

Value

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 Type	Name
Academic Article	A closer look at long-range chromosomal interactions.
Academic Article	Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p.
Academic Article	The three 'C' s of chromosome conformation capture: controls, controls, controls.
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	Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex.
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	Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions.
Academic Article	My5C: web tools for chromosome conformation capture studies.
Academic Article	Capturing chromosome conformation.
Academic Article	Integrating one-dimensional and three-dimensional maps of genomes.
Academic Article	Sister cohesion and structural axis components mediate homolog bias of meiotic recombination.
Academic Article	The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.
Academic Article	Spatial partitioning of the regulatory landscape of the X-inactivation centre.
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	3C-based technologies to study the shape of the genome.
Academic Article	Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
Academic Article	Biological techniques: Chromosomes captured one by one.
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	Mapping chromatin interactions by chromosome conformation capture.
Academic Article	Chromosome conformation capture carbon copy technology.
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	Hi-C: a method to study the three-dimensional architecture of genomes.
Academic Article	The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules.
Academic Article	Chromatin globules: a common motif of higher order chromosome structure?
Academic Article	The structure and function of chromatin and chromosomes.
Academic Article	Evidence for transcript networks composed of chimeric RNAs in human cells.
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	HiTC: exploration of high-throughput 'C' experiments.
Academic Article	Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Academic Article	The hierarchy of the 3D genome.
Academic Article	Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?
Academic Article	Organization of the mitotic chromosome.
Concept	Chromosomes, Human, Pair 16
Concept	Chromosome Positioning
Concept	Chromosomes, Bacterial
Concept	Chromosomes
Concept	Chromosomes, Human
Concept	Chromosome Structures
Concept	Chromosome Inversion
Concept	Chromosome Pairing
Concept	Chromosomes, Artificial, Bacterial
Concept	Chromosomes, Fungal
Concept	Chromosomes, Mammalian
Concept	X Chromosome Inactivation
Concept	Chromosomes, Human, Pair 14
Concept	Chromosomes, Human, Pair 1
Concept	Chromosome Segregation
Concept	Chromosomes, Human, Pair 21
Concept	Chromosome Mapping
Concept	Chromosome Aberrations
Concept	X Chromosome
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	Chromosome Conformation Capture (3C) in Budding Yeast.
Academic Article	Randomized ligation control for chromosome conformation capture.
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	Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.
Academic Article	Condensin-driven remodelling of X chromosome topology during dosage compensation.
Academic Article	Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis.
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	The yeast genome undergoes significant topological reorganization in quiescence.
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	HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Academic Article	The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.
Academic Article	Activation of proto-oncogenes by disruption of chromosome neighborhoods.
Academic Article	The 3D Genome as Moderator of Chromosomal Communication.
Academic Article	Structural organization of the inactive X chromosome in the mouse.
Academic Article	A Guide to Packing Your DNA.
Academic Article	Mapping the 3D genome: Aiming for consilience.
Academic Article	Epigenetic characteristics of the mitotic chromosome in 1D and 3D.
Academic Article	Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.
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	Integrative detection and analysis of structural variation in cancer genomes.
Academic Article	A pathway for mitotic chromosome formation.
Academic Article	SMC complexes differentially compact mitotic chromosomes according to genomic context.
Academic Article	Generation of Control Ligation Product Libraries for 3C Analyses.
Academic Article	The 4D nucleome project.
Academic Article	The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome.
Academic Article	Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
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	Mechanisms and Functions of Chromosome Compartmentalization.
Academic Article	Large domains of heterochromatin direct the formation of short mitotic chromosome loops.
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	Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
Academic Article	Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.
Academic Article	Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.
Academic Article	Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture.
Academic Article	Erratum to: Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.
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.
Concept	Chromosomes, Insect
Academic Article	Spatial organization of transcribed eukaryotic genes.
Academic Article	Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.
Academic Article	Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.
Academic Article	Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Academic Article	Regulation of the mitotic chromosome folding machines.
Academic Article	Capturing Chromosome Conformation Across Length Scales.
Academic Article	Author Correction: Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Academic Article	Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus.
Academic Article	Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns.
Academic Article	Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis.
Academic Article	Rules of engagement for condensins and cohesins guide mitotic chromosome formation.
Academic Article	Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm.
Academic Article	The chromosome folding problem and how cells solve it.
Academic Article	Rules of engagement for condensins and cohesins guide mitotic chromosome formation.
Academic Article	Mitotic chromosomes harbor cell type- and species-specific structural features within a universal loop array conformation.

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X Chromosome