Author details

Full Name

Yi Xiao

Affiliation

ORCID

Career Start Year

1995

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37032165	[Antimicrobial resistance and plasmid-mediated colistin resistance mechanism of diarrheagenic recovered from foods in parts of China in 2020].		2023
36227564	Exploring the Binding Process of Cognate Ligand to Add Adenine Riboswitch Aptamer by Using Explicit Solvent Molecular Dynamics (MD) Simulation.	Methods in Molecular Biology	2023
35164295	Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction.	Molecules	2022
35400173	Antitumor Activities of tRNA-Derived Fragments and tRNA Halves from Non-pathogenic Escherichia coli Strains on Colorectal Cancer and Their Structure-Activity Relationship.	mSystems	2022
34361572	Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search.	Molecules	2021
34300045	Modeling of the Long-Term Epidemic Dynamics of COVID-19 in the United States.	Int J Environ Res Public Health	2021
33005304	3dRNA: Building RNA 3D structure with improved template library.	Computational and Structural Biotechnology Journal	2020
32023436	Electrostatics of Prokaryotic Ribosome and Its Biological Implication.	Biophysical Journal	2020
32371455	RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.	RNA	2020
32290077	Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2.	Viruses	2020
32522558	Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ RNA Riboswitches.	Journal of Molecular Biology	2020
32688556	Using the generalized Born surface area model to fold proteins yields more effective sampling while qualitatively preserving the folding landscape.	Physical Review E	2020
33076020	Molecular dynamics study of ways of RNA base-pair formation.	Physical Review E	2020
32575289	Pathway regulation mechanism revealed by cotranslational folding of villin headpiece subdomain HP35.	Physical Review E	2020
30780336	Dynamics of metal ions around an RNA molecule.	Physical Review E	2019
31574664	Molecular dynamics simulation of the binding process of ligands to the add adenine riboswitch aptamer.	Physical Review E	2019
31450739	3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction.	International Journal of Molecular Sciences	2019
31389931	A novel folding pathway of the villin headpiece subdomain HP35.	Physical Chemistry Chemical Physics	2019
31114906	HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.	Nucleic Acids Res	2019
29459676	Genomic Variants in NEURL, GJA1 and CUX2 Significantly Increase Genetic Susceptibility to Atrial Fibrillation.	Scientific Reports	2018
28682144	Structural modeling of human cardiac sodium channel pore domain.	Journal of Biomolecular Structure and Dynamics	2018
29186336	3dRPC: a web server for 3D RNA-protein structure prediction.		2018
29641288	Angiotensin II increases angiogenesis by NF-ÎºB-mediated transcriptional activation of angiogenic factor AGGF1.	FASEB Journal	2018
28138060	RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.	RNA	2017
28463400	Using 3dRNA for RNA 3-D Structure Prediction and Evaluation.	Current Protocols in Bioinformatics	2017
28482022	Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis.	Nucleic Acids Research	2017
28358834	A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.	PLoS ONE	2017
27841650	Types and concentrations of metal ions affect local structure and dynamics of RNA.	Physical Review E	2016
28317012	Using 3dRPC for RNA-protein complex structure prediction.		2016
26486723	Computational evidence that fast translation speed can increase the probability of cotranslational protein folding.	Scientific Reports	2015
25712091	3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures.	Nucleic Acids Research	2015
25883046	RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.	RNA	2015
25542231	Electrolyte disorders assessment in solid tumor patients treated with anti-EGFR monoclonal antibodies: a pooled analysis of 25 randomized clinical trials.	Tumor Biology	2015
26764725	Computational study of stability of an H-H-type pseudoknot motif.		2015
26066200	Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.		2015
25055914	Computational methods to predict long noncoding RNA functions based on co-expression network.	Methods in Molecular Biology	2014
25338883	A fast tomographic method for searching the minimum free energy path.	Journal of Chemical Physics	2014
25489078	Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.	Proceedings of the National Academy of Sciences of the United States of America	2014
24663240	Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations.	PLoS ONE	2014
23496542	Simulation study of the role of the ribosomal exit tunnel on protein folding.		2013
22830440	Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.	Journal of Biomolecular Structure and Dynamics	2013
22908909	Preorientation of protein and RNA just before contacting.	Journal of Biomolecular Structure and Dynamics	2013
24124522	How to use not-always-reliable binding site information in protein-protein docking prediction.	PLoS ONE	2013
23848713	Binding free-energy calculation of an ion-peptide complex by constrained dynamics.		2013
23843247	Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.	Proteins	2013
24091687	Large-scale study of long non-coding RNA functions based on structure and expression features.	Science China Life Sciences	2013
23677788	Lytic infection of Kaposi's sarcoma-associated herpesvirus induces DNA double-strand breaks and impairs non-homologous end joining.	Journal of General Virology	2013
23635126	Efficiently finding the minimum free energy path from steepest descent path.	Journal of Chemical Physics	2013
23712416	A novel protocol for three-dimensional structure prediction of RNA-protein complexes.	Scientific Reports	2013
23071898	Automated and fast building of three-dimensional RNA structures.	Scientific Reports	2012