Job Dekker

发表

The Structure and Function of Chromatin and Chromosomes

William Stafford Noble, Yi Mao, C. Anthony Blau, 2011, Pacific Symposium on Biocomputing.

HiTC - Exploration of High Throughput ’C’ experiments

Emmanuel Barillot, Nicolas Servant, Elphège P. Nora, 2013 .

Organization of the Mitotic Chromosome

Job Dekker, Geoffrey Fudenberg, Maxim Imakaev, 2013, Science.

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

Rachel Patton McCord, Job Dekker, Janet L Stein, 2016, Biochimica et biophysica acta.

Gene Regulation in the Third Dimension

Job Dekker, J. Dekker, 2008, Science.

Regulation of gene expression through chromatin interaction networks

Job Dekker, 2007 .

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

Job Dekker, J. Dekker, N. Naumova, 2012, Methods.

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

Rachel Patton McCord, Zhaohui S. Qin, David M. Gilbert, 2019, Stem cell reports.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.

Marc A Marti-Renom, Imen Lassadi, Isabelle Goiffon, 2015, Cell reports.

Yeast Silent Mating Type Loci Form Heterochromatic Clusters through Silencer Protein-Dependent Long-Range Interactions

Job Dekker, A. Miele, J. Dekker, 2009, PLoS genetics.

An Integrative Framework for Detecting Structural Variations in Cancer Genomes

William Stafford Noble, Feng Yue, Jesse R. Dixon, 2017, bioRxiv.

The yeast genome undergoes significant topological reorganization in quiescence

Job Dekker, James R Broach, J. Broach, 2015, Nucleic acids research.

The context of gene expression regulation

Job Dekker, J. Dekker, J. Gibcus, 2012, F1000 biology reports.

The 4 D nucleome project

Job Dekker, Victor O. Leshyk, J. Shendure, 2017 .

Corrigendum: CTCF-mediated topological boundaries during development foster appropriate gene regulation.

Danny Reinberg, Job Dekker, Varun Narendra, 2017, Genes & development.

Ultrastructural details of mammalian chromosome architecture

Leonid A. Mirny, Oliver J. Rando, Job Dekker, 2019, bioRxiv.

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis

Job Dekker, Bryan R Lajoie, Michael T Laub, 2015, Genes & development.

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

Job Dekker, J. Dekker, N. V. van Berkum, 2009, Methods in molecular biology.

Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C).

Job Dekker, A. Miele, J. Dekker, 2009, Methods in molecular biology.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Eric S. Lander, Leonid A. Mirny, Job Dekker, 2010, Journal of visualized experiments : JoVE.

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

John A. Stamatoyannopoulos, Ian Dunham, Job Dekker, 2010, Nucleic acids research.

The three 'C' s of chromosome conformation capture: controls, controls, controls

Job Dekker, J. Dekker, 2005, Nature Methods.

Mapping the 3D genome: Aiming for consilience

Job Dekker, J. Dekker, 2016, Nature Reviews Molecular Cell Biology.

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

Wouter de Laat, Erik Splinter, Job Dekker, 2007, Nature Protocols.

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

Job Dekker, Bryan R Lajoie, Gaurav Jain, 2016, American journal of human genetics.

Measuring the reproducibility and quality of Hi-C data

Mark Gerstein, William Stafford Noble, Anshul Kundaje, 2017, Genome Biology.

High-throughput genome scaffolding from in-vivo DNA interaction frequency

Noam Kaplan, Job Dekker, J. Dekker, 2013, Nature Biotechnology.

The Three-dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Marc A Marti-Renom, George M Church, Job Dekker, 2022 .

Rachel Patton McCord, Haoyue Zhang, Francis S Collins, 2013, Genome research.

SMC complexes differentially compact mitotic chromosomes according to genomic context

Jonathan Baxter, Job Dekker, Geoffrey Fudenberg, 2017, Nature Cell Biology.

Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation

Houda Belaghzal, Job Dekker, J. Dekker, 2016, bioRxiv.

A pathway for mitotic chromosome formation

J. R. Paulson, Leonid A. Mirny, Johannes Nuebler, 2018, Science.

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

Edith Heard, Job Dekker, J. Dekker, 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR).

Job Dekker, J. Dekker, Tae Hoon Kim, 2018, Cold Spring Harbor protocols.

Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction*

Job Dekker, J. Dekker, 2008, Journal of Biological Chemistry.

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

Job Dekker, Janet L Stein, Gary S Stein, 2016, Genome research.

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

Job Dekker, J. Dekker, Jon-Matthew Belton, 2015, Cold Spring Harbor protocols.

CTCF-mediated topological boundaries during development foster appropriate gene regulation

Danny Reinberg, Job Dekker, D. Reinberg, 2016, Genes & development.

TAD disruption as oncogenic driver.

Job Dekker, J. Dekker, Anne-Laure Valton, 2016, Current opinion in genetics & development.

GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p

Job Dekker, J. Dekker, 2007, Genome Biology.

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

Wouter de Laat, Job Dekker, J. Dekker, 2012, Methods.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Fei Ji, Job Dekker, Gaurav Jain, 2017, Molecular cell.

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

Thomas G. Gilgenast, Jennifer E. Phillips-Cremins, Job Dekker, 2016, Cell stem cell.

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

Job Dekker, J. Dekker, 2014, Epigenetics & Chromatin.

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

David E Hill, Rachel Patton McCord, Heng Zhu, 2011, Nature Methods.

My5C: web tools for chromosome conformation capture studies

Job Dekker, Bryan R Lajoie, J. Dekker, 2009, Nature Methods.

Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex

Chiara Lanzuolo, Valerio Orlando, Job Dekker, 2007, Nature Cell Biology.

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

Boris Lenhard, Paul Flicek, Rachel Patton McCord, 2013, Genome research.

Long-range chromosomal interactions and gene regulation.

Job Dekker, A. Miele, J. Dekker, 2008, Molecular bioSystems.

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

Anders S Hansen, Job Dekker, Xavier Darzacq, 2018, bioRxiv.

Molecular Cell Review The Hierarchy of the 3 D Genome

Job Dekker, J. Dekker, J. Gibcus, 2013 .

Ultrastructural Details of Mammalian Chromosome Architecture.

Job Dekker, Nezar Abdennur, Leonid A Mirny, 2020, Molecular cell.

Integrating one-dimensional and three-dimensional maps of genomes

Job Dekker, J. Dekker, N. Naumova, 2010, Journal of Cell Science.

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

Simona Bianco, Mario Nicodemi, Damien J Downes, 2018, Nature Genetics.

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Noam Kaplan, Job Dekker, Bryan R Lajoie, 2015, Methods.

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

Nir Friedman, Bryan Lajoie, Oliver J. Rando, 2015, Cell.

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Philip Cayting, Katrina Learned, Daniel Blankenberg, 2012, Genome Biology.

Enhanced yeast one-hybrid (eY1H) assays for high-throughput gene-centered regulatory network mapping

Bryan Lajoie, Chad L Myers, Job Dekker, 2011, Nature Methods.

From cells to chromatin: capturing snapshots of genome organization with 5C technology.

Josée Dostie, Job Dekker, J. Dekker, 2012, Methods.

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

Job Dekker, Geoffrey Fudenberg, Leonid Mirny, 2014, Nature.

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

Stylianos E. Antonarakis, Filip Pattyn, Frank Speleman, 2009, PLoS genetics.

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.

Ho-Ryun Chung, Fidel Ramírez, Thomas Manke, 2015, Molecular cell.

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

Boris Lenhard, Paul Flicek, Thomas Carroll, 2015 .

A mechanical basis for chromosome function.

Nancy Kleckner, Job Dekker, Ruth Padmore, 2004, Proceedings of the National Academy of Sciences of the United States of America.