Local volume concentration, packing domains, and scaling properties of chromatin.

Autor: Carignano MA; Department of Biomedical Engineering, Northwestern University, Evanston, United States., Kroeger M; Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH Zurich, Zurich, Switzerland., Almassalha LM; Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Evanston, United States., Agrawal V; Department of Biomedical Engineering, Northwestern University, Evanston, United States., Li WS; Applied Physics Program, Northwestern University, Chicago, United States., Pujadas-Liwag EM; Department of Biomedical Engineering, Northwestern University, Evanston, United States., Nap RJ; Department of Biomedical Engineering, Northwestern University, Evanston, United States., Backman V; Department of Biomedical Engineering, Northwestern University, Evanston, United States., Szleifer I; Department of Biomedical Engineering, Northwestern University, Evanston, United States.; Department of Chemistry, Northwestern University, Evanston, United States.

Publikováno v: ELife [Elife] 2024 Sep 27; Vol. 13. Date of Electronic Publication: 2024 Sep 27.

Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure.

Autor: Shim AR; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Frederick J; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Pujadas EM; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Kuo T; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Ye IC; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Pritchard JA; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Dunton CL; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Gonzalez PC; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Acosta N; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Jain S; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Anthony NM; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America., Almassalha LM; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America.; Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, United States of America., Szleifer I; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Department of Chemistry, Northwestern University, Evanston, Illinois, United States of America., Backman V; Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America.; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America.

Publikováno v: PloS one [PLoS One] 2024 May 28; Vol. 19 (5), pp. e0301000. Date of Electronic Publication: 2024 May 28 (Print Publication: 2024).

Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism.

Autor: Pujadas Liwag EM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA., Wei X; Department of Surgery, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA., Acosta N; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA., Carter LM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA., Yang J; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA., Almassalha LM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA.; Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA., Jain S; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA., Daneshkhah A; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA., Rao SSP; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.; School of Medicine, Stanford University, Stanford, CA, 94305, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA., Seker-Polat F; Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL, 60611, USA., MacQuarrie KL; Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Pediatrics, Northwestern University, Chicago, IL, 60611, USA.; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA., Ibarra J; Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Pediatrics, Northwestern University, Chicago, IL, 60611, USA.; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA., Agrawal V; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA., Aiden EL; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.; 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.; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX, 77030, USA., Kanemaki MT; Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.; Department of Biological Science, The University of Tokyo, Tokyo, 113-0033, Japan., Backman V; Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA. v-backman@northwestern.edu.; Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA. v-backman@northwestern.edu., Adli M; Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL, 60611, USA. adli@northwestern.edu.

Publikováno v: Genome biology [Genome Biol] 2024 Mar 22; Vol. 25 (1), pp. 77. Date of Electronic Publication: 2024 Mar 22.

Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function.

Autor: Li Y; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Eshein A; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Virk RKA; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Eid A; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Wu W; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Frederick J; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., VanDerway D; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Gladstein S; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Huang K; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China., Shim AR; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Anthony NM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Bauer GM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Zhou X; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Agrawal V; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Pujadas EM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Jain S; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Esteve G; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Chandler JE; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Nguyen TQ; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Bleher R; Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA., de Pablo JJ; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA., Szleifer I; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Dravid VP; Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA., Almassalha LM; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA., Backman V; Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA. v-backman@northwestern.edu.

Publikováno v: Science advances [Sci Adv] 2021 Jan 01; Vol. 7 (1). Date of Electronic Publication: 2021 Jan 01 (Print Publication: 2021).

Physical and data structure of 3D genome.

Autor: Huang K; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA., Li Y; Applied Physics Program, Northwestern University, Evanston, IL 60208, USA., Shim AR; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA., Virk RKA; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA., Agrawal V; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA., Eshein A; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA., Nap RJ; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA., Almassalha LM; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.; Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA., Backman V; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA., Szleifer I; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.

Publikováno v: Science advances [Sci Adv] 2020 Jan 10; Vol. 6 (2), pp. eaay4055. Date of Electronic Publication: 2020 Jan 10 (Print Publication: 2020).