Concepedia

Loop Extrusion Simulation

Loop Extrusion Simulation is a computational modeling framework that, as a member of the class of molecular dynamics simulation methods, specifically represents the mechanistic process of chromatin loop extrusion mediated by cohesin and CTCF proteins through stochastic or deterministic algorithms to reproduce and predict three-dimensional genome organization.

18

Publications

1.1K

Citations

79

Authors

49

Institutions

Publications per year

2017–2026

17

Parents

Publications

18

Chromosome Compaction by Active Loop Extrusion

Anton Goloborodko, John F. Marko, Leonid A. Mirny · Biophysical Journal · 2016 · 345 citations · Full text

, , +17

Chromosome organization by one-sided and two-sided loop extrusion

Edward J. Banigan, Aafke A. van den Berg, Hugo B. Brandão et al. · eLife · 2020 · 163 citations · Full text

, , +17

Principles of meiotic chromosome assembly revealed in S. cerevisiae

Stephanie A. Schalbetter, Geoffrey Fudenberg, Jonathan Baxter et al. · Nature Communications · 2019 · 139 citations · Full text

, , +17

A Brownian ratchet model for DNA loop extrusion by the cohesin complex

Torahiko L. Higashi, Georgii Pobegalov, Minzhe Tang et al. · eLife · 2021 · 107 citations · Full text

, , +17

DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

Stefanos K. Nomidis, Enrico Carlon, Stephan Gruber et al. · Nucleic Acids Research · 2022 · 56 citations · Full text

, , +16

1–5 of 18

Authors

79

  1. JF
    John F. Marko

    Northwestern University, United States

    3 publications · 564 citations

    3

    h-index

  2. FU
    Frank Uhlmann

    The Francis Crick Institute, United Kingdom

    2 publications · 158 citations

    2

    h-index

  3. KS
    Katherine S. Pollard

    Gladstone Institutes, United States

    2 publications · 154 citations

    2

    h-index

  4. HB
    Hugo B. Brandão

    Massachusetts Institute of Technology, United States

    2 publications · 197 citations

    2

    h-index

  5. LA
    Leonid A. Mirny

    Massachusetts Institute of Technology, United States

    2 publications · 508 citations

    2

    h-index

1–5 of 79

Institutions

49

  1. Northwestern University

    Evanston, United States

    4 h-index

    8 publications

    714 citations

  2. Massachusetts Institute of Technology

    Cambridge, United States

    3 h-index

    8 publications

    1.3K citations

  3. Japan Science and Technology Agency

    Tokyo, Japan

    2 h-index

    2 publications

    37 citations

  4. Chan Zuckerberg Initiative (United States)

    Redwood City, United States

    2 h-index

    2 publications

    154 citations

  5. QB3

    San Francisco, United States

    2 h-index

    2 publications

    154 citations

  6. University of Sussex

    Brighton, United Kingdom

    2 h-index

    6 publications

    462 citations

  7. The Francis Crick Institute

    London, United Kingdom

    2 h-index

    12 publications

    892 citations

  8. Gladstone Institutes

    San Francisco, United States

    2 h-index

    4 publications

    308 citations

1–8 of 49

Venues

  1. Nature Communications

    3 publications · 203 citations

    3

    h-index

  2. Nucleic Acids Research

    3 publications · 124 citations

    3

    h-index

  3. bioRxiv (Cold Spring Harbor Laboratory)

    Repository · 2 publications · 26 citations

    2

    h-index

  4. eLife

    2 publications · 270 citations

    2

    h-index

  5. Biophysical Journal

    1 publications · 345 citations

    1

    h-index

1–5