Publications by authors named "Job Dekker"

100Publications

Is Involved in Corneal Stroma Development by Regulating Neural Crest Migration.

Int J Mol Sci 2020 Oct 21;21(20). Epub 2020 Oct 21.

Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.3390/ijms21207807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7594026PMC
October 2020

Detecting chromatin interactions between and along sister chromatids with SisterC.

Nat Methods 2020 10 23;17(10):1002-1009. Epub 2020 Sep 23.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.

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http://dx.doi.org/10.1038/s41592-020-0930-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541687PMC
October 2020

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

Nat Struct Mol Biol 2020 Dec 14;27(12):1105-1114. Epub 2020 Sep 14.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.

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http://dx.doi.org/10.1038/s41594-020-0506-5DOI Listing
December 2020

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

Elife 2020 09 11;9. Epub 2020 Sep 11.

Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.7554/eLife.57212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7515631PMC
September 2020

Mechanisms and Functions of Chromosome Compartmentalization.

Trends Biochem Sci 2020 May 18;45(5):385-396. Epub 2020 Feb 18.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tibs.2020.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275117PMC
May 2020

Ultrastructural Details of Mammalian Chromosome Architecture.

Mol Cell 2020 05 25;78(3):554-565.e7. Epub 2020 Mar 25.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2020.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222625PMC
May 2020

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.

Mol Cell 2020 01 5;77(2):324-337.e8. Epub 2019 Nov 5.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980774PMC
January 2020

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

Nat Cell Biol 2019 11 4;21(11):1393-1402. Epub 2019 Nov 4.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.

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http://dx.doi.org/10.1038/s41556-019-0406-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858582PMC
November 2019

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

Cell Stem Cell 2019 11 5;25(5):682-696.e8. Epub 2019 Sep 5.

Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909193033
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http://dx.doi.org/10.1016/j.stem.2019.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842438PMC
November 2019

Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Nature 2019 Aug;572(7771):E22

Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-019-1454-2DOI Listing
August 2019

Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Nature 2019 06 5;570(7761):395-399. Epub 2019 Jun 5.

Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-019-1275-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206897PMC
June 2019

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

Genome Res 2019 02 17;29(2):236-249. Epub 2019 Jan 17.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.241547.118
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http://dx.doi.org/10.1101/gr.241547.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360813PMC
February 2019

Higher-Order Organization Principles of Pre-translational mRNPs.

Mol Cell 2018 11 8;72(4):715-726.e3. Epub 2018 Nov 8.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6239896PMC
November 2018

3C-Based Chromatin Interaction Analyses.

Cold Spring Harb Protoc 2018 09 4;2018(9). Epub 2018 Sep 4.

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http://dx.doi.org/10.1101/pdb.top097832DOI Listing
September 2018

5C Analysis of 3C, ChIP-Loop, and Control Libraries.

Cold Spring Harb Protoc 2018 09 4;2018(9). Epub 2018 Sep 4.

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http://dx.doi.org/10.1101/pdb.prot097899DOI Listing
September 2018

4C Analysis of 3C, ChIP-Loop, and Control Libraries.

Cold Spring Harb Protoc 2018 09 4;2018(9). Epub 2018 Sep 4.

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http://dx.doi.org/10.1101/pdb.prot097881DOI Listing
September 2018

Generation of Control Ligation Product Libraries for 3C Analyses.

Cold Spring Harb Protoc 2018 08 1;2018(8). Epub 2018 Aug 1.

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http://dx.doi.org/10.1101/pdb.prot097865DOI Listing
August 2018

Generation of ChIP-Loop Libraries.

Cold Spring Harb Protoc 2018 08 1;2018(8). Epub 2018 Aug 1.

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http://dx.doi.org/10.1101/pdb.prot097857DOI Listing
August 2018

Generation of 3C Libraries from Cross-Linked Cells.

Cold Spring Harb Protoc 2018 08 1;2018(8). Epub 2018 Aug 1.

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http://dx.doi.org/10.1101/pdb.prot097840DOI Listing
August 2018

C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.

Nat Methods 2018 06 7;15(6):433-436. Epub 2018 May 7.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.

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http://dx.doi.org/10.1038/s41592-018-0006-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6202229PMC
June 2018

Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions.

Cold Spring Harb Protoc 2018 05 1;2018(5). Epub 2018 May 1.

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http://dx.doi.org/10.1101/pdb.top082586DOI Listing
May 2018

ChIP-seq.

Cold Spring Harb Protoc 2018 05 1;2018(5). Epub 2018 May 1.

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http://dx.doi.org/10.1101/pdb.prot082644DOI Listing
May 2018

ChIP-chip.

Cold Spring Harb Protoc 2018 05 1;2018(5). Epub 2018 May 1.

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http://dx.doi.org/10.1101/pdb.prot082636DOI Listing
May 2018

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

Cold Spring Harb Protoc 2018 05 1;2018(5). Epub 2018 May 1.

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http://dx.doi.org/10.1101/pdb.prot082628DOI Listing
May 2018

ChIP.

Cold Spring Harb Protoc 2018 04 2;2018(4). Epub 2018 Apr 2.

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http://dx.doi.org/10.1101/pdb.prot082610DOI Listing
April 2018

Preparation of Cross-Linked Chromatin for ChIP.

Cold Spring Harb Protoc 2018 04 2;2018(4). Epub 2018 Apr 2.

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http://dx.doi.org/10.1101/pdb.prot082602DOI Listing
April 2018

Formaldehyde Cross-Linking.

Cold Spring Harb Protoc 2018 04 2;2018(4). Epub 2018 Apr 2.

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http://dx.doi.org/10.1101/pdb.prot082594DOI Listing
April 2018

A pathway for mitotic chromosome formation.

Science 2018 02 18;359(6376). Epub 2018 Jan 18.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1126/science.aao6135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924687PMC
February 2018

The 4D nucleome project.

Nature 2017 09;549(7671):219-226

Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature23884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617335PMC
September 2017

SMC complexes differentially compact mitotic chromosomes according to genomic context.

Nat Cell Biol 2017 Sep 21;19(9):1071-1080. Epub 2017 Aug 21.

Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK.

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http://dx.doi.org/10.1038/ncb3594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640152PMC
September 2017

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

Cell 2017 May;169(5):930-944.e22

Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674173053
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http://dx.doi.org/10.1016/j.cell.2017.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538188PMC
May 2017

Shelterin components mediate genome reorganization in response to replication stress.

Proc Natl Acad Sci U S A 2017 05 10;114(21):5479-5484. Epub 2017 May 10.

Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892;

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http://dx.doi.org/10.1073/pnas.1705527114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5448194PMC
May 2017

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

Methods 2017 07 18;123:56-65. Epub 2017 Apr 18.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10462023163046
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http://dx.doi.org/10.1016/j.ymeth.2017.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522765PMC
July 2017

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

Crit Rev Biochem Mol Biol 2017 Apr 15;52(2):185-204. Epub 2017 Feb 15.

b Howard Hughes Medical Institute Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA.

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http://dx.doi.org/10.1080/10409238.2017.1287160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5456460PMC
April 2017

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

Mol Cell 2017 Feb;65(3):432-446.e5

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765173003
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http://dx.doi.org/10.1016/j.molcel.2017.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5421375PMC
February 2017

Mapping the 3D genome: Aiming for consilience.

Authors:
Job Dekker

Nat Rev Mol Cell Biol 2016 Nov;17(12):741-742

Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, Massachusetts 01605-0103, USA.

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http://dx.doi.org/10.1038/nrm.2016.151DOI Listing
November 2016

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.

Proc Natl Acad Sci U S A 2016 10 10;113(43):E6572-E6581. Epub 2016 Oct 10.

Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10021; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454;

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http://dx.doi.org/10.1073/pnas.1613914113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087062PMC
October 2016

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

Biochim Biophys Acta 2016 11 9;1859(11):1389-1397. Epub 2016 Aug 9.

Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5071180PMC
http://dx.doi.org/10.1016/j.bbagrm.2016.08.003DOI Listing
November 2016

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

Genome Res 2016 09 19;26(9):1188-201. Epub 2016 Jul 19.

Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA;

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http://dx.doi.org/10.1101/gr.201624.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052043PMC
September 2016

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

Cell Stem Cell 2016 05;18(5):611-24

Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859942PMC
May 2016

TAD disruption as oncogenic driver.

Curr Opin Genet Dev 2016 02 22;36:34-40. Epub 2016 Apr 22.

Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0959437X163001
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http://dx.doi.org/10.1016/j.gde.2016.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880504PMC
February 2016

A Guide to Packing Your DNA.

Cell 2016 Apr;165(2):259-61

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http://dx.doi.org/10.1016/j.cell.2016.03.039DOI Listing
April 2016

The 3D Genome as Moderator of Chromosomal Communication.

Cell 2016 Mar;164(6):1110-1121

Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, E25-526C, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788811PMC
March 2016

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

Am J Hum Genet 2016 Jan;98(1):185-201

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA; Howard Hughes Medical Institute. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716690PMC
January 2016

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

Cell Rep 2015 Dec 19;13(9):1855-67. Epub 2015 Nov 19.

Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.10.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681004PMC
December 2015

Long-Range Chromatin Interactions.

Cold Spring Harb Perspect Biol 2015 Oct 1;7(10):a019356. Epub 2015 Oct 1.

National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.

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http://dx.doi.org/10.1101/cshperspect.a019356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588061PMC
October 2015

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

Genome Biol 2015 Sep 28;16:214. Epub 2015 Sep 28.

Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA.

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http://dx.doi.org/10.1186/s13059-015-0768-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587679PMC
September 2015

Structural and functional diversity of Topologically Associating Domains.

FEBS Lett 2015 Oct 5;589(20 Pt A):2877-84. Epub 2015 Sep 5.

Institut Curie, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 75248 Paris Cedex 05, France. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2015.08.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598308PMC
October 2015

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

Genes Dev 2015 Aug;29(15):1661-75

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA;

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http://dx.doi.org/10.1101/gad.265876.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536313PMC
August 2015

The yeast genome undergoes significant topological reorganization in quiescence.

Nucleic Acids Res 2015 Sep 21;43(17):8299-313. Epub 2015 Jul 21.

Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA

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http://nar.oxfordjournals.org/content/43/17/8299.full.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv723
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http://dx.doi.org/10.1093/nar/gkv723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787801PMC
September 2015

Measuring Chromatin Structure in Budding Yeast.

Cold Spring Harb Protoc 2015 Jul 1;2015(7):614-8. Epub 2015 Jul 1.

Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

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http://dx.doi.org/10.1101/pdb.top077552DOI Listing
July 2015

Hi-C in Budding Yeast.

Cold Spring Harb Protoc 2015 Jul 1;2015(7):649-61. Epub 2015 Jul 1.

Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

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http://dx.doi.org/10.1101/pdb.prot085209DOI Listing
July 2015

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.

Cell 2015 Jul 25;162(1):108-19. Epub 2015 Jun 25.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674150063
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http://dx.doi.org/10.1016/j.cell.2015.05.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509605PMC
July 2015

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

Cold Spring Harb Protoc 2015 Jun 1;2015(6):593-8. Epub 2015 Jun 1.

Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

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http://dx.doi.org/10.1101/pdb.prot085191DOI Listing
June 2015

Randomized ligation control for chromosome conformation capture.

Cold Spring Harb Protoc 2015 Jun 1;2015(6):587-92. Epub 2015 Jun 1.

Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

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http://dx.doi.org/10.1101/pdb.prot085183DOI Listing
June 2015

Chromosome Conformation Capture (3C) in Budding Yeast.

Cold Spring Harb Protoc 2015 Jun 1;2015(6):580-6. Epub 2015 Jun 1.

Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

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http://dx.doi.org/10.1101/pdb.prot085175DOI Listing
June 2015

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

Nature 2015 Jul 1;523(7559):240-4. Epub 2015 Jun 1.

Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720-3204, USA.

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http://dx.doi.org/10.1038/nature14450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498965PMC
July 2015

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

Genome Res 2015 Apr 12;25(4):504-13. Epub 2015 Feb 12.

Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom;

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http://dx.doi.org/10.1101/gr.184986.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381522PMC
April 2015

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

Methods 2015 Jan 6;72:65-75. Epub 2014 Nov 6.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.10.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4347522PMC
January 2015

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

Authors:
Job Dekker

Epigenetics Chromatin 2014 25;7(1):25. Epub 2014 Nov 25.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103 USA.

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http://dx.doi.org/10.1186/1756-8935-7-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247682PMC
December 2014

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

Nature 2014 Dec 12;516(7531):432-435. Epub 2014 Oct 12.

Laboratory of Biochemistry and Molecular Biology National Cancer Institute, National Institutes of Health Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1038/nature13833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465753PMC
December 2014

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.

Cell 2014 May;157(4):950-63

Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France; Collège de France, 11 place Marcelin-Berthelot, Paris 75005, France. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427251PMC
May 2014

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

Nat Biotechnol 2013 Dec 24;31(12):1143-7. Epub 2013 Nov 24.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880131PMC
December 2013

Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny.

Genes Dev 2013 Nov;27(22):2439-44

Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois 60612, USA;

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http://dx.doi.org/10.1101/gad.227165.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841733PMC
November 2013

Organization of the mitotic chromosome.

Science 2013 Nov 7;342(6161):948-53. Epub 2013 Nov 7.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School (UMMS), 368 Plantation Street, Worcester, MA 01605-0103, USA.

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http://dx.doi.org/10.1126/science.1236083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040465PMC
November 2013

Biological techniques: Chromosomes captured one by one.

Nature 2013 Oct 25;502(7469):45-6. Epub 2013 Sep 25.

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http://dx.doi.org/10.1038/nature12691DOI Listing
October 2013

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

Nat Rev Genet 2013 Jun 9;14(6):390-403. Epub 2013 May 9.

Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-2324, USA.

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http://dx.doi.org/10.1038/nrg3454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874835PMC
June 2013

Nuclear biology: what's been most surprising?

Cell 2013 Mar;152(6):1207-8

University of Massachusetts Medical School, USA.

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http://dx.doi.org/10.1016/j.cell.2013.02.041DOI Listing
March 2013

The hierarchy of the 3D genome.

Mol Cell 2013 Mar;49(5):773-82

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3741673PMC
March 2013