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List of works by Yudong Cai

A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes

article

A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana

scientific article

A committee of NNA classifiers for the prediction of the binding between miRNAs and the target genes using a novel coding method

article

A comparison of computational methods for identifying virulence factors

scientific article

A computational method for the identification of candidate drugs for non-small cell lung cancer.

scientific article

A computational method for the identification of new candidate carcinogenic and non-carcinogenic chemicals

scientific article published on 21 July 2015

A hybrid computational method for the discovery of novel reproduction-related genes

scientific article

A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes.

scientific article published on 04 February 2014

A knowledge-based method to predict the cooperative relationship between transcription factors.

scientific article

A method to distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis.

scientific article published on 23 January 2015

A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology ⬇️

scientific article published on November 21, 2003

A novel approach to predict active sites of enzyme molecules

scientific article published in April 2004

A novel computational approach to predict transcription factor DNA binding preference

scientific article published in February 2009

A novel computational method to predict transcription factor DNA binding preference.

scientific article published on August 2006

A novel method of predicting protein disordered regions based on sequence features.

scientific article published on 22 April 2013

A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach.

scientific article

A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomas

scientific article

Alternative Polyadenylation Modification Patterns Reveal Essential Posttranscription Regulatory Mechanisms of Tumorigenesis in Multiple Tumor Types

scientific article published on 15 June 2020

An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization

scientific article published on 10 July 2007

An ensemble prognostic model for colorectal cancer

scientific article

An information-theoretic machine learning approach to expression QTL analysis

scientific article

An integrated method for the identification of novel genes related to oral cancer

scientific article

Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm.

scientific article published on 3 February 2016

Analysis and prediction of drug-drug interaction by minimum redundancy maximum relevance and incremental feature selection.

scientific article published on 11 January 2016

Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks

scientific article

Analysis and prediction of translation rate based on sequence and functional features of the mRNA.

scientific article

Analysis of Expression Pattern of snoRNAs in Different Cancer Types with Machine Learning Algorithms ⬇️

scientific article published on 02 May 2019

Analysis of Gene Expression Profiles in the Human Brain Stem, Cerebellum and Cerebral Cortex

scientific article

Analysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic Cancer

scientific article

Analysis of Lymphoma-Related Genes with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Enrichment

scientific article published in 2022

Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway

scientific article published on 18 July 2019

Analysis of protein pathway networks using hybrid properties.

article

Analysis of the preferences for splice codes across tissues

scientific article published on 27 October 2015

Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway

scientific article

Application of SVM to predict membrane protein types

scientific article published in February 2004

Application of systems biology and bioinformatics methods in biochemistry and biomedicine

scientific article published on 31 December 2013

Application of systems biology and bioinformatics methods in biochemistry and biomedicine 2014.

scientific article published on 19 April 2015

Applications of Bioinformatics and Systems Biology in Precision Medicine and Immunooncology

scientific article

Artificial neural network method for discriminating coding regions of eukaryotic genes

article

Artificial neural network method for predicting protein secondary structure content

scientific article published in June 2002

Artificial neural network method for predicting the specificity of GalNAc-transferase

scientific article published in October 1997

Artificial neural network model for predicting alpha-turn types

scientific article published in March 1999

Artificial neural network model for predicting membrane protein types

scientific article published in February 2001

Artificial neural network model for predicting protein subcellular location

scientific article published in January 2002

Artificial neural network model for predicting the specificity of GalNAc-transferase

scientific article published in December 1996

Automatic transcription factor classifier based on functional domain composition

scientific article published on 21 June 2006

Boosting classifier for predicting protein domain structural class

scientific article published in August 2005

Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma.

scientific article

Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property

scientific article

Classification of non-small cell lung cancer based on copy number alterations

scientific article

Classification of transcription factors using protein primary structure

scientific article published in July 2010

Classifying ten types of major cancers based on reverse phase protein array profiles

scientific article published on 30 March 2015

Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network

scientific article

Computational methods for protein-protein interaction and their application

scientific article

Computational prediction and analysis of protein γ-carboxylation sites based on a random forest method.

scientific article published on 23 August 2012

Computational proteomics, systems biology and clinical implications

Computational systems biology methods in molecular biology, chemistry biology, molecular biomedicine, and biopharmacy

scientific article

Computationally identifying virulence factors based on KEGG pathways

scientific article

Cooperativity among short amyloid stretches in long amyloidogenic sequences

scientific article

Crosstissue coexpression network of aging

scientific article published on 13 July 2011

Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective.

scientific article published on 18 December 2017

Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches.

scientific article published on 8 January 2012

Demonstration of two novel methods for predicting functional siRNA efficiency

scientific article

Discovery of new candidate genes related to brain development using protein interaction information

scientific article published on 30 January 2015

Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties.

scientific article published on 24 September 2014

Discriminating between lysine sumoylation and lysine acetylation using mRMR feature selection and analysis

scientific article

Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection

scientific article published on 14 September 2017

Dysfunctions associated with methylation, microRNA expression and gene expression in lung cancer

scientific article

Exploring Mouse Protein Function via Multiple Approaches

scientific article

Finding candidate drugs for hepatitis C based on chemical-chemical and chemical-protein interactions

scientific article

Functional association between influenza A (H1N1) virus and human

scientific article published on 28 August 2009

GalNAc-transferase specificity prediction based on feature selection method.

scientific article

Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System

scientific article

Gene expression profiling gut microbiota in different races of humans

scientific article

Gene ontology and KEGG enrichment analyses of genes related to age-related macular degeneration

scientific article

Genetic differences among ethnic groups.

scientific article published on 21 December 2015

HIV-1 protease cleavage site prediction based on amino acid property

scientific article published in January 2009

Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma

scientific article

Homology-based gene prediction using neural nets

scientific article published in December 1998

Identification and analysis of the cleavage site in a signal peptide using SMOTE, dagging, and feature selection methods

scientific article published on 01 February 2018

Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network

scientific article published on 08 July 2020

Identification of Candidate Genes Related to Inflammatory Bowel Disease Using Minimum Redundancy Maximum Relevance, Incremental Feature Selection, and the Shortest-Path Approach.

scientific article published on 14 February 2017

Identification of Differentially Expressed Genes between Original Breast Cancer and Xenograft Using Machine Learning Algorithms.

scientific article published on 12 March 2018

Identification of Genes Associated with Breast Cancer Metastasis to Bone on a Protein-Protein Interaction Network with a Shortest Path Algorithm

scientific article published on 11 January 2017

Identification of Influenza A/H7N9 virus infection-related human genes based on shortest paths in a virus-human protein interaction network

scientific article

Identification of New Candidate Genes and Chemicals Related to Esophageal Cancer Using a Hybrid Interaction Network of Chemicals and Proteins

scientific article

Identification of age-related macular degeneration related genes by applying shortest path algorithm in protein-protein interaction network

scientific article published on 18 December 2013

Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network

scientific article

Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds.

scientific article

Identification of leukemia stem cell expression signatures through Monte Carlo feature selection strategy and support vector machine

scientific article published on 29 May 2019

Identification of lung-cancer-related genes with the shortest path approach in a protein-protein interaction network.

scientific article published on 22 May 2013

Identification of novel candidate drivers connecting different dysfunctional levels for lung adenocarcinoma using protein-protein interactions and a shortest path approach

scientific article published on 14 July 2016

Identification of retinoblastoma related genes with shortest path in a protein-protein interaction network

scientific article published on 22 May 2012

Identification of the Gene Expression Rules That Define the Subtypes in Glioma

article

Identification of the copy number variant biomarkers for breast cancer subtypes

scientific article published on 10 September 2018

Identify catalytic triads of serine hydrolases by support vector machines

scientific article

Identifying Methylation Pattern and Genes Associated with Breast Cancer Subtypes ⬇️

scientific article published on 31 August 2019

Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach

scientific article

Identifying Novel Candidate Genes Related to Apoptosis from a Protein-Protein Interaction Network

scientific article

Identifying Patients with Atrioventricular Septal Defect in Down Syndrome Populations by Using Self-Normalizing Neural Networks and Feature Selection.

scientific article published on 12 April 2018

Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network

scientific article (publication date: 2013)

Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities.

scientific article published on 4 January 2016

Identifying protein complexes using hybrid properties

scientific article published in November 2009

Inferring novel genes related to oral cancer with a network embedding method and one-class learning algorithms

scientific article published on 27 August 2019

Information-theoretic analysis of protein sequences shows that amino acids self-cluster

scientific article published on 01 October 2002

Investigating gene methylation signatures for fetal intolerance prediction

scientific article published in 2021

Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm.

scientific article published on 18 May 2016

Is it a paradox or misinterpretation?

scientific article published in May 2001

Multiple classifier integration for the prediction of protein structural classes.

scientific article

Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition

scientific article

Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma.

scientific article

Novel computational methods and tools in biomedicine and biopharmacy

scientific article

OPMSP: A Computational Method Integrating Protein Interaction and Sequence Information for the Identification of Novel Putative Oncogenes

scientific article

Operon prediction based on SVM

scientific article published on 23 May 2006

Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches

scientific article published on 11 December 2011

Predicting 22 protein localizations in budding yeast

scientific article published in October 2004

Predicting A-to-I RNA editing by feature selection and random forest.

scientific article

Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities

scientific article

Predicting DNA-binding sites of proteins based on sequential and 3D structural information

scientific article published on 22 January 2014

Predicting N-terminal acetylation based on feature selection method

scientific article published on 3 June 2008

Predicting O-glycosylation sites in mammalian proteins by using SVMs

scientific article published in June 2006

Predicting biological functions of compounds based on chemical-chemical interactions

scientific article

Predicting chemical toxicity effects based on chemical-chemical interactions

scientific article

Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions

scientific article published on 04 September 2013

Predicting enzyme family class in a hybridization space.

scientific article

Predicting enzyme subclass by functional domain composition and pseudo amino acid composition

scientific article published in May 2005

Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties

scientific article

Predicting membrane protein types with bragging learner

scientific article published in January 2008

Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins

scientific article

Predicting miRNA's target from primary structure by the nearest neighbor algorithm

scientific article

Predicting protease types by hybridizing gene ontology and pseudo amino acid composition

scientific article

Predicting protein oxidation sites with feature selection and analysis approach

scientific article published in January 2012

Predicting protein phenotypes based on protein-protein interaction network

scientific article

Predicting protein quaternary structure by pseudo amino acid composition

scientific article

Predicting protein structural class by functional domain composition

scientific article

Predicting protein structural class with AdaBoost Learner

scientific article published in January 2006

Predicting protein subcellular locations with feature selection and analysis

scientific article published on April 2010

Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines.

scientific article

Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition.

scientific article

Predicting subcellular localization with AdaBoost Learner

scientific article published in January 2008

Predicting subcellular location of proteins using integrated-algorithm method

scientific article published on 7 August 2009

Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition ⬇️

scientific article

Predicting the protein SUMO modification sites based on Properties Sequential Forward Selection (PSFS).

scientific article published on 23 April 2007

Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties

scientific article

Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins

scientific article

Prediction and analysis of cell-penetrating peptides using pseudo-amino acid composition and random forest models

scientific article

Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.

scientific article published on 5 September 2017

Prediction and analysis of protein hydroxyproline and hydroxylysine

scientific article

Prediction and analysis of protein methylarginine and methyllysine based on Multisequence features

scientific article published on 4 May 2011

Prediction and analysis of protein palmitoylation sites

scientific article published on 12 November 2010

Prediction of RNA-binding proteins by voting systems

scientific article

Prediction of S-nitrosylation modification sites based on kernel sparse representation classification and mRMR algorithm.

scientific article

Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition.

scientific article

Prediction of active sites of enzymes by maximum relevance minimum redundancy (mRMR) feature selection

scientific article published on 2 November 2012

Prediction of antimicrobial peptides based on sequence alignment and feature selection methods

scientific article

Prediction of aptamer-target interacting pairs with pseudo-amino acid composition.

scientific article published on 22 January 2014

Prediction of beta-turns

scientific article published on 01 May 1998

Prediction of beta-turns with learning machines

scientific article published in May 2003

Prediction of body fluids where proteins are secreted into based on protein interaction network

scientific article

Prediction of cancer drugs by chemical-chemical interactions

scientific article (publication date: 2014)

Prediction of carbamylated lysine sites based on the one-class k-nearest neighbor method

scientific article published in November 2013

Prediction of compounds' biological function (metabolic pathways) based on functional group composition

scientific article

Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties

scientific article

Prediction of drug indications based on chemical interactions and chemical similarities

scientific article

Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways

scientific article published on 05 September 2013

Prediction of gene phenotypes based on GO and KEGG pathway enrichment scores

scientific article

Prediction of interaction between small molecule and enzyme using AdaBoost

scientific article published on 14 February 2009

Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity

scientific article published on June 2010

Prediction of interactiveness of proteins and nucleic acids based on feature selections

scientific article published on 9 October 2009

Prediction of lysine ubiquitination with mRMR feature selection and analysis

scientific article published on 26 January 2011

Prediction of membrane protein types by incorporating amphipathic effects

scientific article published in March 2005

Prediction of membrane protein types in a hybrid space

scientific article published on 9 February 2008

Prediction of mucin-type O-glycosylation sites by a two-staged strategy

scientific article published on 22 July 2010

Prediction of multi-type membrane proteins in human by an integrated approach.

scientific article

Prediction of nucleosome positioning based on transcription factor binding sites

scientific article

Prediction of peptidase category based on functional domain composition

scientific article published on 03 September 2008

Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles

scientific article

Prediction of protease types in a hybridization space

scientific article published on 9 November 2005

Prediction of protein amidation sites by feature selection and analysis.

scientific article published on 21 June 2013

Prediction of protein cleavage site with feature selection by random forest

scientific article

Prediction of protein domain with mRMR feature selection and analysis

scientific article

Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis

scientific article

Prediction of protein secondary structure content by artificial neural network

scientific article

Prediction of protein structural classes by neural network

scientific article published in August 2000

Prediction of protein structural classes by support vector machines.

scientific article

Prediction of protein structural classes using hybrid properties

scientific article published in August 2008

Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFS

scientific article

Prediction of protein-protein interactions based on PseAA composition and hybrid feature selection

scientific article published on 24 January 2009

Prediction of small molecules' metabolic pathways based on functional group composition

scientific article

Prediction of subcellular protein localization based on functional domain composition.

scientific article

Prediction of tyrosine sulfation with mRMR feature selection and analysis

scientific article published on 11 November 2010

Protein sumoylation sites prediction based on two-stage feature selection.

scientific article

Recognition of Immune Cell Markers of COVID-19 Severity with Machine Learning Methods

scientific article published on 28 April 2022

Signal propagation in protein interaction network during colorectal cancer progression

scientific article published on 20 March 2013

Support Vector Machines for predicting HIV protease cleavage sites in protein

scientific article published in January 2002

Support vector machine for SAR/QSAR of phenethyl-amines

scientific article published in July 2007

Support vector machine for predicting alpha-turn types.

scientific article

Support vector machines for predicting protein structural class

scientific article

Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence.

scientific article

Support vector machines for predicting the specificity of GalNAc-transferase

scientific article published in January 2002

Support vector machines for prediction of protein domain structural class

scientific article

Support vector machines for prediction of protein signal sequences and their cleavage sites

scientific article published in January 2003

Support vector machines for prediction of protein subcellular location

scientific article published in October 2000

Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect

scientific article published in January 2002

Support vector machines for the classification and prediction of ?-turn types

scientific article published on 01 July 2002

Systems genetics - deciphering the complex disease with a systems approach

scientific article published on 31 July 2016

The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

scientific article

The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life

scientific article

The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases

scientific article published on 08 May 2016

Tissue Expression Difference between mRNAs and lncRNAs

scientific article published on 31 October 2018

Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins

scientific article

Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location

scientific article published in Journal of Biological Chemistry

Using GO-PseAA predictor to predict enzyme sub-class.

scientific article

Using LogitBoost classifier to predict protein structural classes

scientific article published on 25 July 2005

Using compound similarity and functional domain composition for prediction of drug-target interaction networks

scientific article published in November 2010

Using functional domain composition to predict enzyme family classes

scientific article published in January 2005

Using neural networks for prediction of domain structural classes

scientific article published in January 2000

Using neural networks for prediction of subcellular location of prokaryotic and eukaryotic proteins

scientific article published in September 2000

Weighted passive nearest neighbor algorithm: A newly-developed supervised classifier

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