Job Dekker

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

Cell Stem Cell 2019 Nov 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

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

Nat Cell Biol 2019 Nov 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

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

Mol Cell 2019 Oct 22. Epub 2019 Oct 22.

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
October 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 Jun 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
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

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

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

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

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

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 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

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

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-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-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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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://mirnylab.mit.edu/publications/pdf/Naumova_2013_Scienc
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http://www.sciencemag.org/cgi/doi/10.1126/science.1236083
Publisher Site
http://dx.doi.org/10.1126/science.1236083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040465PMC
November 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

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

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

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149748PMC
http://dx.doi.org/10.1016/j.cell.2013.02.041DOI Listing
March 2013

Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.

Genome Res 2013 Feb 14;23(2):260-9. Epub 2012 Nov 14.

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

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http://genome.cshlp.org/cgi/doi/10.1101/gr.138032.112
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http://dx.doi.org/10.1101/gr.138032.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561867PMC
February 2013

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

Methods 2012 Nov 15;58(3):192-203. Epub 2012 Aug 15.

Programs in Systems Biology and Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10462023120017
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http://dx.doi.org/10.1016/j.ymeth.2012.07.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874837PMC
November 2012

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

Methods 2012 Nov 5;58(3):255-67. Epub 2012 Nov 5.

Department of Biochemistry and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Room 815A, Montréal, Québec, Canada H3G1Y6.

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http://dx.doi.org/10.1016/j.ymeth.2012.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874844PMC
November 2012

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

Nat Methods 2012 Oct 2;9(10):999-1003. Epub 2012 Sep 2.

Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.2148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816492PMC
October 2012

The long-range interaction landscape of gene promoters.

Nature 2012 Sep;489(7414):109-13

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

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http://dx.doi.org/10.1038/nature11279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3555147PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012