Search details
1.
Cohesin Loss Eliminates All Loop Domains.
Cell
; 171(2): 305-320.e24, 2017 Oct 05.
Article
in English
| MEDLINE | ID: mdl-28985562
2.
Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture.
Nature
; 589(7841): 299-305, 2021 01.
Article
in English
| MEDLINE | ID: mdl-33299181
3.
Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.
Nucleic Acids Res
; 52(2): 583-599, 2024 Jan 25.
Article
in English
| MEDLINE | ID: mdl-38015443
4.
Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability.
Proc Natl Acad Sci U S A
; 120(20): e2221324120, 2023 05 16.
Article
in English
| MEDLINE | ID: mdl-37155888
5.
Chromatin transitions triggered by LH density as epigenetic regulators of the genome.
Nucleic Acids Res
; 50(18): 10328-10342, 2022 10 14.
Article
in English
| MEDLINE | ID: mdl-36130289
6.
Brownian dynamics simulations of mesoscale chromatin fibers.
Biophys J
; 122(14): 2884-2897, 2023 07 25.
Article
in English
| MEDLINE | ID: mdl-36116007
7.
Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry.
Proc Natl Acad Sci U S A
; 117(13): 7216-7224, 2020 03 31.
Article
in English
| MEDLINE | ID: mdl-32165536
8.
Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations.
Int J Mol Sci
; 24(7)2023 Mar 29.
Article
in English
| MEDLINE | ID: mdl-37047368
9.
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub.
Proc Natl Acad Sci U S A
; 116(11): 4955-4962, 2019 03 12.
Article
in English
| MEDLINE | ID: mdl-30718394
10.
RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.
Int J Mol Sci
; 23(16)2022 Aug 17.
Article
in English
| MEDLINE | ID: mdl-36012512
11.
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.
Biophys J
; 120(6): 1040-1053, 2021 03 16.
Article
in English
| MEDLINE | ID: mdl-33096082
12.
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element.
J Am Chem Soc
; 143(30): 11404-11422, 2021 08 04.
Article
in English
| MEDLINE | ID: mdl-34283611
13.
RAG-Web: RNA structure prediction/design using RNA-As-Graphs.
Bioinformatics
; 36(2): 647-648, 2020 01 15.
Article
in English
| MEDLINE | ID: mdl-31373604
14.
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nature
; 517(7536): 635-9, 2015 Jan 29.
Article
in English
| MEDLINE | ID: mdl-25409153
15.
Sensitive effect of linker histone binding mode and subtype on chromatin condensation.
Nucleic Acids Res
; 47(10): 4948-4957, 2019 06 04.
Article
in English
| MEDLINE | ID: mdl-30968131
16.
Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes.
Biophys J
; 118(9): 2066-2076, 2020 05 05.
Article
in English
| MEDLINE | ID: mdl-31668748
17.
Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.
J Struct Biol
; 209(3): 107438, 2020 03 01.
Article
in English
| MEDLINE | ID: mdl-31874236
18.
An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.
Methods
; 162-163: 74-84, 2019 06 01.
Article
in English
| MEDLINE | ID: mdl-30928508
19.
A pipeline for computational design of novel RNA-like topologies.
Nucleic Acids Res
; 46(14): 7040-7051, 2018 08 21.
Article
in English
| MEDLINE | ID: mdl-30137633
20.
Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.
J Comput Chem
; 40(21): 1919-1930, 2019 08 05.
Article
in English
| MEDLINE | ID: mdl-30994934