DeepACP: A Novel Computational Approach for Accurate Identification of Anticancer Peptides by Deep Learning Algorithm

Lezheng Yu, Runyu Jing, Fengjuan Liu, +2

Molecular Therapy — Nucleic Acids

Artificial IntelligenceConvolutional Neural NetworkEngineeringMachine LearningAutoencoders +22

The applications of deep learning algorithms on in silico druggable proteins identification

Lezheng Yu, Xue Li, Fengjuan Liu, +3

Journal of Advanced Research

Comparative Analysis of Oncogenes Identified by Microarray and RNA-Sequencing as Biomarkers for Clinical Prognosis

Yuan Liu, Runyu Jing, Junmei Xu, +4

Biomarkers in Medicine

autoBioSeqpy: A Deep Learning Tool for the Classification of Biological Sequences

Runyu Jing, Yizhou Li, Xue Li, +3

Journal of Chemical Information and Modeling

EngineeringMachine LearningMachine Learning ToolAutoencodersMolecular Biology +21

Combination use of protein–protein interaction network topological features improves the predictive scores of deleterious non-synonymous single-nucleotide polymorphisms

Yiming Wu, Runyu Jing, Jiang Lin, +6

Amino Acids

Genome-wide Association StudyFunctional GenomicsGenotype-phenotype AssociationInteractomicsGenetics +8

DeepT3 2.0: improving type III secreted effector predictions by an integrative deep learning framework

Runyu Jing, Tingke Wen, Chengxiang Liao, +4

NAR Genomics and Bioinformatics

DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors

Lezheng Yu, Fengjuan Liu, Yizhou Li, +2

Frontiers in Microbiology

layerUMAP: A tool for visualizing and understanding deep learning models in biological sequence classification using UMAP

Runyu Jing, Li C. Xue, Menglong Li, +2

iScience

EngineeringMachine LearningMachine Learning ToolAutoencodersDeep Learning Models +17

Classification of multi-family enzymes by multi-label machine learning and sequence-based descriptors

Yuelong Wang, Runyu Jing, Yongpan Hua, +4

Analytical Methods

Multiple Instance LearningMolecular BiologyPathologyGenomicsMulti-label Machine Learning +22

Narrowing the Gap Between In Vitro and In Vivo Genetic Profiles by Deconvoluting Toxicogenomic Data In Silico

Yuan Liu, Runyu Jing, Zhining Wen, +1

Frontiers in Pharmacology