Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.

Autor: Iurlaro M; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland., Masoni F; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Faculty of Science, University of Basel, Basel, Switzerland., Flyamer IM; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland., Wirbelauer C; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland., Iskar M; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland., Burger L; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Swiss Institute of Bioinformatics, Basel, Switzerland., Giorgetti L; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland., Schübeler D; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. dirk@fmi.ch.; Faculty of Science, University of Basel, Basel, Switzerland. dirk@fmi.ch.

Publikováno v: Nature genetics [Nat Genet] 2024 Jun; Vol. 56 (6), pp. 1203-1212. Date of Electronic Publication: 2024 May 30.

Cooltools: Enabling high-resolution Hi-C analysis in Python.

Autor: Abdennur N; Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America.; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America., Abraham S; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America., Fudenberg G; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America., Flyamer IM; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland., Galitsyna AA; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America., Goloborodko A; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria., Imakaev M; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America., Oksuz BA; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America., Venev SV; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America., Xiao Y; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2024 May 06; Vol. 20 (5), pp. e1012067. Date of Electronic Publication: 2024 May 06 (Print Publication: 2024).

Trisomies Reorganize Human 3D Genome.

Autor: Zhegalova IV; Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia.; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia., Vasiluev PA; Research Centre for Medical Genetics, 115522 Moscow, Russia., Flyamer IM; Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland., Shtompel AS; Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.; Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia., Glazyrina E; Medical Genetic Center LLC Progen, 117630 Moscow, Russia., Shilova N; Research Centre for Medical Genetics, 115522 Moscow, Russia., Minzhenkova M; Research Centre for Medical Genetics, 115522 Moscow, Russia., Markova Z; Research Centre for Medical Genetics, 115522 Moscow, Russia., Petrova NV; Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia., Dashinimaev EB; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia., Razin SV; Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.; Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia., Ulianov SV; Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.; Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.

Publikováno v: International journal of molecular sciences [Int J Mol Sci] 2023 Nov 07; Vol. 24 (22). Date of Electronic Publication: 2023 Nov 07.

Pairtools: from sequencing data to chromosome contacts.

Autor: Abdennur N; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, MA.; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA., Fudenberg G; Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, CA, USA., Flyamer IM; Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland., Galitsyna AA; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria., Goloborodko A; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria., Imakaev M; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA., Venev SV; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Feb 15. Date of Electronic Publication: 2023 Feb 15.

MCM complexes are barriers that restrict cohesin-mediated loop extrusion.

Autor: Dequeker BJH; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria., Scherr MJ; Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany., Brandão HB; Harvard Program in Biophysics, Harvard University, Cambridge, MA, USA.; Illumina Inc., San Diego, CA, USA., Gassler J; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.; Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany., Powell S; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria., Gaspar I; Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany., Flyamer IM; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, UK., Lalic A; Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany., Tang W; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria., Stocsits R; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria., Davidson IF; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria., Peters JM; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria., Duderstadt KE; Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany. duderstadt@biochem.mpg.de.; Department of Physics, Technical University of Munich, Garching, Germany. duderstadt@biochem.mpg.de., Mirny LA; Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. leonid@mit.edu., Tachibana K; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria. tachibana@biochem.mpg.de.; Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany. tachibana@biochem.mpg.de.

Publikováno v: Nature [Nature] 2022 Jun; Vol. 606 (7912), pp. 197-203. Date of Electronic Publication: 2022 May 18.