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Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding

Molecules (Basel, Switzerland), 2023-06, Vol.28 (12), p.4833

2023

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ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures

Molecules (Basel, Switzerland), 2024-03, Vol.29 (6), p.1244

2024

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Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010501-e1010501

2022

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Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

PLoS computational biology, 2018-06, Vol.14 (6), p.e1006222-e1006222

2018

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A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect

The Journal of chemical physics, 2014-09, Vol.141 (10), p.105102-105102

2014

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3D structure stability of the HIV-1 TAR RNA in ion solutions: A coarse-grained model study

The Journal of chemical physics, 2019-10, Vol.151 (16), p.165101-165101

2019

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SS-RNN: A Strengthened Skip Algorithm for Data Classification Based on Recurrent Neural Networks

Frontiers in genetics, 2021-10, Vol.12, p.746181-746181

2021

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Imputation Methods for scRNA Sequencing Data

Applied sciences, 2022-10, Vol.12 (20), p.10684

2022

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Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

Frontiers in molecular biosciences, 2021-04, Vol.8, p.666369-666369

2021

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RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures

Frontiers in bioinformatics, 2022-01, Vol.1, p.809082-809082

2022

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Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling

Biophysical journal, 2017-03, Vol.112 (6), p.1094-1104

2017

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rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation

Biophysical journal, 2022-01, Vol.121 (1), p.142-156

2022

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RNA structure prediction： Progress and perspective

Chinese physics B, 2014-07, Vol.23 (7), p.88-97

2014

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Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions

Biophysical journal, 2023-04, Vol.122 (8), p.1503-1516

2023

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Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions

Biophysical journal, 2018-10, Vol.115 (8), p.1403-1416

2018

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Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

RNA (Cambridge), 2019-11, Vol.25 (11), p.1532-1548

2019

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Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

Biophysical journal, 2015-12, Vol.109 (12), p.2654-2665

2015

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What is the best reference state for building statistical potentials in RNA 3D structure evaluation?

RNA (Cambridge), 2019-07, Vol.25 (7), p.793-812

2019

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Heel bone mineral density and various oral diseases: a bidirectional Mendelian randomization

Journal of bone and mineral metabolism, 2023-09, Vol.41 (5), p.673-681

2023

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MLBKFD: Probabilistic Model Methods to Infer Pseudo Trajectories from Single-cell Data

Journal of computational biophysics and chemistry, 2024-08, Vol.23 (6), p.723-739

2024

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Cortex Fraxini (Qingpi) Protects Rat Pheochromocytoma Cells against 6-Hydroxydopamine-Induced Apoptosis

Parkinson's disease, 2015-01, Vol.2015 (2015), p.393-403

2015

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Potential of mean force between like-charged nanoparticles: Many-body effect

Scientific reports, 2016-03, Vol.6 (1), p.23434-23434, Article 23434

2016

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A novel knowledge-based potential for RNA 3D structure evaluation

Chinese physics B, 2018-03, Vol.27 (3), p.38701

2018

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Proliferative marker Ki-67 in gallbladder carcinomas: high expression level predicts early recurrence after surgical resection

Cancer letters, 2002-02, Vol.176 (2), p.191-198

2002

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3D structure stability of RNA hairpin controlled by loop size

2017 29th Chinese Control And Decision Conference (CCDC), 2017, p.6821-6825

2017

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Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding

ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures

Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect

3D structure stability of the HIV-1 TAR RNA in ion solutions: A coarse-grained model study

SS-RNN: A Strengthened Skip Algorithm for Data Classification Based on Recurrent Neural Networks

Imputation Methods for scRNA Sequencing Data

Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures

Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling

rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation

RNA structure prediction： Progress and perspective

Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions

Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions

Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

What is the best reference state for building statistical potentials in RNA 3D structure evaluation?

Heel bone mineral density and various oral diseases: a bidirectional Mendelian randomization

MLBKFD: Probabilistic Model Methods to Infer Pseudo Trajectories from Single-cell Data

Cortex Fraxini (Qingpi) Protects Rat Pheochromocytoma Cells against 6-Hydroxydopamine-Induced Apoptosis

Potential of mean force between like-charged nanoparticles: Many-body effect

A novel knowledge-based potential for RNA 3D structure evaluation

Proliferative marker Ki-67 in gallbladder carcinomas: high expression level predicts early recurrence after surgical resection

3D structure stability of RNA hairpin controlled by loop size

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