Author details

Full Name

Yaoqi Zhou

Affiliation

ORCID

Career Start Year

1996

Papers

199

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
35120933	High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing.	International Journal of Biological Macromolecules	2022
36369947	High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage.	RNA Biology	2022
35751593	Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.		2022
35696081	Computational Prediction of N- and O-Linked Glycosylation Sites for Human and Mouse Proteins.	Methods in Molecular Biology	2022
35670973	Long Non-Coding RNAs Profiling Using Microarray in Papillary Thyroid Carcinoma.	Methods in Molecular Biology	2022
35670972	Liposomal siRNA Delivery in Papillary Thyroid Carcinoma Cells.	Methods in Molecular Biology	2022
35534620	Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment.	Scientific Reports	2022
34633841	Self-Inhibitory Peptides Targeting the Neisseria gonorrhoeae MtrCDE Efflux Pump Increase Antibiotic Susceptibility.	Antimicrobial Agents and Chemotherapy	2022
35104320	SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.		2022
35348613	Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.	Briefings in Bioinformatics	2022
34364941	Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease.	International Journal of Biological Macromolecules	2021
33704363	Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.		2021
34117606	Argonaute proteins: structures and their endonuclease activity.	Molecular Biology Reports	2021
34163498	From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs.	Frontiers in Plant Science	2021
33986288	Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement.	Nature Communications	2021
34037398	RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks.	Journal of Chemical Information and Modeling	2021
33983382	SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning.		2021
34021744	RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.		2021
33119734	DescribePROT: database of amino acid-level protein structure and function predictions.	Nucleic Acids Res	2021
33221906	EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments.	Nucleic Acids Research	2021
33106872	Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network.		2021
34406339	De novo protein design by an energy function based on series expansion in distance and orientation dependence.		2021
34498061	Structure-aware protein-protein interaction site prediction using deep graph convolutional network.		2021
31390220	Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning.	Journal of Computational Biology	2020
31914596	DNA sequence repeats identify numerous Type I restriction-modification systems that are potential epigenetic regulators controlling phase-variable regulons; phasevarions.	FASEB Journal	2020
32369579	GM-DockZn: a geometry matching-based docking algorithm for zinc proteins.		2020
31845383	SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map.	Journal of Computational Chemistry	2020
31638408	All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State.	Journal of Computational Biology	2020
31874386	Recent advances in glycoinformatic platforms for glycomics and glycoproteomics.	Current Opinion in Structural Biology	2020
31872260	Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity.	Nucleic Acids Research	2020
31870849	DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server.	Journal of Molecular Biology	2020
32681638	Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search.	Database : the journal of biological databases and curation	2020
32569587	Interplay of hydrophobic and hydrophilic interactions in sequence-dependent cell penetration of spontaneous membrane-translocating peptides revealed by bias-exchange metadynamics simulations.	Biochimica et Biophysica Acta - Biomembranes	2020
32723795	Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct Specificity Genes That Can Switch System Specificity by Recombination.	mSystems	2020
32555615	Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease.	PLoS ONE	2020
31504193	Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning.		2020
31392430	DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state.	Journal of Cheminformatics	2019
32173600	SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.		2019
31779641	RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants.	Genome Biol	2019
31776342	RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.	Nature Communications	2019
30449682	Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells.	Cell Metab	2019
30260702	Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides.	FASEB Journal	2019
30535134	Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.		2019
30823753	Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations.	Journal of Chemical Physics	2019
31184403	Assessment of methods for predicting the effects of PTEN and TPMT protein variants.	Hum Mutat	2019
30698427	SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites.	Journal of Chemical Information and Modeling	2019
30903686	SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties.		2019
31209948	Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge.	Hum Mutat	2019
30945202	Experimentally Validated Plant lncRNAs in EVLncRNAs Database.	Methods in Molecular Biology	2019
31345106	Predicting functional long non-coding RNAs validated by low throughput experiments.	RNA Biology	2019