Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub.

Autor: Bascom GD; Department of Chemistry, New York University, New York, NY 10003., Myers CG; Department of Chemistry, New York University, New York, NY 10003., Schlick T; Department of Chemistry, New York University, New York, NY 10003; schlick@nyu.edu.; Courant Institute of Mathematical Sciences, New York University, New York, NY 10012.; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, 200122 Shanghai, China.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2019 Mar 12; Vol. 116 (11), pp. 4955-4962. Date of Electronic Publication: 2019 Feb 04.

Cohesin Loss Eliminates All Loop Domains.

Autor: Rao SSP; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA., Huang SC; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Glenn St Hilaire B; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA., Engreitz JM; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Perez EM; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Kieffer-Kwon KR; Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA., Sanborn AL; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA., Johnstone SE; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA., Bascom GD; Department of Chemistry, New York University, New York, NY 10003, USA., Bochkov ID; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Huang X; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA., Shamim MS; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA., Shin J; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA., Turner D; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Ye Z; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA., Omer AD; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Robinson JT; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Schlick T; Department of Chemistry, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China., Bernstein BE; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA., Casellas R; Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA., Lander ES; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA., Aiden EL; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA. Electronic address: erez@erez.com.

Publikováno v: Cell [Cell] 2017 Oct 05; Vol. 171 (2), pp. 305-320.e24.

Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements.

Autor: Bascom GD; Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States., Sanbonmatsu KY; Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory , Bikini Atoll Road, SM 30, Los Alamos, New Mexico 87545, United States., Schlick T; Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States.; Courant Institute of Mathematical Sciences, New York University , 251 Mercer Street, New York, New York 10012, United States.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2016 Aug 25; Vol. 120 (33), pp. 8642-53. Date of Electronic Publication: 2016 Jun 16.

Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.

Autor: Nikolova EN; Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA., Bascom GD, Andricioaei I, Al-Hashimi HM

Publikováno v: Biochemistry [Biochemistry] 2012 Oct 30; Vol. 51 (43), pp. 8654-64. Date of Electronic Publication: 2012 Oct 18.