Yixue Li

发表

Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing

Lei Liu, Hong Li, Tiancheng Liu, 2015, Comput. Math. Methods Medicine.

Global and threshold-free Transcriptional Regulatory Networks reconstruction through integrating ChIP-Chip and expression data.

Yi Yang, Zili Zhang, Yixue Li, 2011, Current protein & peptide science.

Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance

Hui Yu, Yixue Li, Yuan-Yuan Li, 2006, PLoS Comput. Biol..

SchistoDB: an updated genome resource for the three key schistosomes of humans

Yixue Li, Jessica C. Kissinger, David S. Roos, 2012, Nucleic Acids Res..

SysZNF: the C2H2 zinc finger gene database

Yixue Li, Michael Kreutzer, Peter Lorenz, 2008, Nucleic Acids Res..

The self-organization model reveals systematic characteristics of aging

Xianzheng Sha, Yin Wang, Yixue Li, 2020, Theoretical Biology and Medical Modelling.

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

Yixue Li, Yu-Dong Cai, Xiao-Jun Liu, 2007, Bioinform..

Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

Hui Yu, Yixue Li, Yuan-Yuan Li, 2011, BMC Bioinformatics.

Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study

Yixue Li, Shan Cong, Xiao-Tu Ma, 2013, J. Chem. Inf. Model..

PAnnBuilder: an R package for assembling proteomic annotation data

Hong Li, Yixue Li, Guohui Ding, 2009, Bioinform..

Sorting out inherent features of head-to-head gene pairs by evolutionary conservation

Hui Yu, Yixue Li, Yuan-Yuan Li, 2010, BMC Bioinformatics.

DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels

Xiang Shen, Hui Yu, Yixue Li, 2009, Database J. Biol. Databases Curation.

Active and Passive Nearest Neighbor Algorithm: A Newly-Developed Supervised Classifier

Lei Liu, Yixue Li, Kairui Feng, 2011, ICIC.

On the estimation of false positives in peptide identifications using decoy search strategy

Quanhu Sheng, Yixue Li, Haixu Tang, 2009, Proteomics.

The 3DGD: a database of genome 3D structure

Chuan Wang, Chao Li, Yixue Li, 2014, Bioinform..

Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation

Lei Liu, Yixue Li, Bin Kang, 2008, PLoS Comput. Biol..

SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry

Yong-Hwan Lee, Yixue Li, Guohui Ding, 2008, Nucleic Acids Res..

Sys-BodyFluid: a systematical database for human body fluid proteome research

Rong Zeng, Chuan Wang, Hong Li, 2008, Nucleic Acids Res..

AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology

Guang Li, Peng Li, Feng Xu, 2007, Nucleic Acids Res..

Combinatorial network of transcriptional regulation and microRNA regulation in human cancer

Hui Yu, Yixue Li, Yuan-Yuan Li, 2012, BMC Systems Biology.

Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity

Juan Cui, Yixue Li, Yuzong Chen, 2006, Proteomics.

Big Biological Data: Challenges and Opportunities

Yixue Li, Luonan Chen, Yixue Li, 2014, Genom. Proteom. Bioinform..

Review Process File

Yixue Li, Ying He, Tao Xu, 2012 .

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction

Yao Yu, Yun Li, Yixue Li, 2009, BMC Bioinformatics.

Exploration of gene–gene interaction effects using entropy-based methods

Yi Wang, Wei Huang, Yixue Li, 2008, European Journal of Human Genetics.

Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution

Yixue Li, Yuan-Yuan Li, Yixiang Shi, 2010, BMC Bioinformatics.

Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data

Hui Yu, Feng Wang, Yixue Li, 2007, BMC Bioinformatics.

cGRNexp: a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets

Chaochun Wei, Hui Yu, Yixue Li, 2012, 2012 IEEE 6th International Conference on Systems Biology (ISB).

Demonstration of two novel methods for predicting functional siRNA efficiency

Peilin Jia, Yixue Li, Yudong Cai, 2006, BMC Bioinformatics.

ITFP: an integrated platform of mammalian transcription factors

Qing Yang, Chaochun Wei, Yangyong Zhu, 2008, Bioinform..

Virtualisation of gene knockout experiments based on kinetic modelling: Escherichia coli as an algorithmic case

Yixue Li, Guohui Ding, Ru-Dong Li, 2017, Int. J. Comput. Biol. Drug Des..

A new technique for selecting features from protein sequences

Xing-Ming Zhao, Yixue Li, Yunping Zhu, 2006, Int. J. Pattern Recognit. Artif. Intell..

A cross-species analysis method to analyze animal models' similarity to human's disease state

Xuan Li, Yun Li, Yixue Li, 2012, BMC Systems Biology.

Differential networking meta-analysis of gastric cancer across Asian and American racial groups

Yixue Li, Yuan-Yuan Li, Wentao Dai, 2018, BMC Syst. Biol..

A HMM-based method to predict the transmembrane regions of \beta-barrel membrane proteins

Qi Liu, Yixue Li, Baohua Wang, 2003, Comput. Biol. Chem..

Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis

Chuanli Wang, Zhuo Wang, Yixue Li, 2012, BMC Systems Biology.

HIT: linking herbal active ingredients to targets

Hao Ye, Qi Liu, Ruixin Zhu, 2010, Nucleic Acids Res..

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information

Tao Huang, Lei Liu, Qi Liu, 2010, BMC Bioinformatics.

Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome

Xuan Li, Yajun Wang, Yao Yu, 2012, BMC Systems Biology.

IAOseq: inferring abundance of overlapping genes using RNA-seq data

Hong Sun, Yixue Li, Shuang Yang, 2015, BMC Bioinformatics.

A new strategy for better genome assembly from very short reads

Yixue Li, Yan Ji, Guohui Ding, 2011, BMC Bioinformatics.

Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling

Ying Wang, Xiaolin Wu, Yixue Li, 2012, J. Chem. Inf. Model..

Computational prediction and functional analysis of arsenic-binding proteins in human cells

Yixue Li, Shichao Pang, Junchen Yang, 2019, Quantitative Biology.

Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure

Qi Liu, Yixue Li, Baohua Wang, 2003, Comput. Biol. Chem..

Strategic planning for national biomedical big data infrastructure in China

Yixue Li, Zhen Wang, Zefeng Wang, 2017, Quantitative Biology.

Dr.VIS: a database of human disease-related viral integration sites

Xin Zhao, Qi Liu, Yixue Li, 2011, Nucleic Acids Res..

Identifying novel associations between small molecules and miRNAs based on integrated molecular networks

Jing Wang, Lei Yang, Xia Li, 2015, Bioinform..

Anti-clustering of circadian gene expression in mouse liver genome

Yixue Li, Bin Kang, Yuan-Yuan Li, 2012, 2012 IEEE 6th International Conference on Systems Biology (ISB).

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

Quanhu Sheng, Predrag Radivojac, Yixue Li, 2008, RECOMB.

A novel network-based method for measuring the functional relationship between gene sets

Xiang Li, Jie Sun, Xia Li, 2011, Bioinform..

Personalized anti-cancer drug combination prediction by an Integrated Multi-level Network

Hong Li, Yixue Li, Guohui Ding, 2020, bioRxiv.

Operon prediction based on SVM

Yixue Li, Zhi-Wei Cao, Yu-Dong Cai, 2006, Comput. Biol. Chem..

Predicting O-glycosylation sites in mammalian proteins by using SVMs

Rong Zeng, Yixue Li, Sujun Li, 2006, Comput. Biol. Chem..

SysPTM 2.0: an updated systematic resource for post-translational modification

Wei Li, Jing Li, Ling Li, 2014, Database J. Biol. Databases Curation.

In silico discovery of human natural antisense transcripts

Lei Liu, Hao Xu, Yixue Li, 2006, BMC Bioinformatics.

KDE Bioscience: Platform for bioinformatics analysis workflows

Vasa Curcin, Yike Guo, Yixue Li, 2005, Journal of Biomedical Informatics.

RabGTD: a comprehensive database of rabbit genome and transcriptome

Zhen Wang, Yixue Li, Qingyu Xiao, 2018, Database J. Biol. Databases Curation.

ECS: An automatic enzyme classifier based on functional domain composition

Yixue Li, Yu-Dong Cai, Ziliang Qian, 2007, Comput. Biol. Chem..

iGepros: an integrated gene and protein annotation server for biological nature exploration

Haibo Wang, Chaochun Wei, Yixue Li, 2011, BMC Bioinformatics.

ASD: a comprehensive database of allosteric proteins and modulators

Geng Wu, Qi Wang, Haifeng Chen, 2010, Nucleic Acids Res..

The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma

Tao Huang, Lei Liu, Qi Liu, 2011, Int. J. Comput. Biol. Drug Des..

Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma

Tao Huang, Lei Liu, Qi Liu, 2010, BCB '10.

Nonsynonymous Single-Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases

Bo Sun, Hong Li, Yixue Li, 2015, Comput. Math. Methods Medicine.

MPSS: an integrated database system for surveying a set of proteins

Chuan Wang, Yang Zhong, Yixue Li, 2005, Bioinform..

dbDEPC 2.0: updated database of differentially expressed proteins in human cancers

Jing Li, Hong Li, Yixue Li, 2011, Nucleic Acids Res..

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics

Rong Zeng, James P. Reilly, Quanhu Sheng, 2008, Bioinform..

GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations

Yixue Li, Qiang Lu, Qingwei Xu, 2008, BMC Bioinformatics.

Predicting protein-protein interactions based on protein-domain relationships

Yixue Li, Yunping Zhu, Bing Wang, 2005, Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005..

Supplementary Table S16

Tao Xu, Thomas Meitinger, Xu Lin, 2012 .

Improving protein secondary structure prediction by using the residue conformational classes

De-Shuang Huang, Yixue Li, Yunping Zhu, 2005, Pattern Recognit. Lett..

On Loan-to-Value Ratios of Inventory Financing with Doubly Stochastic Poisson Default Processes

Yu Xu, Yixue Li, Wenqiang Dai, 2006, 2006 IEEE Asia-Pacific Conference on Services Computing (APSCC'06).

Scoring hidden Markov models to discriminate -barrel membrane proteins

Yong Deng, Qi Liu, Yixue Li, 2004, Comput. Biol. Chem..

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

Haipeng Li, Yixue Li, Yu-Dong Cai, 2010, Molecular Diversity.

An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis

Lei Liu, Yixue Li, Yuan-Yuan Li, 2011, BMC Systems Biology.

Classification of protein quaternary structure by functional domain composition

Chuan Wang, Yixue Li, Xiaojing Yu, 2006, BMC Bioinformatics.

cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data

Yixue Li, Zhen Wang, Hong Li, 2016, Bioinform..

A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes

Jing Yang, Yixue Li, Yuan-Yuan Li, 2016, BMC Systems Biology.

CHSMiner: a GUI tool to identify chromosomal homologous segments

Zhen Wang, Lei Liu, Yixue Li, 2009, Algorithms for Molecular Biology.

An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification

Hong Sun, Yin Wang, Yan Zhu, 2012, BMC Systems Biology.

Prediction of contact map integrated PNN with conformational energy

Yixue Li, Yunping Zhu, Bing Wang, 2005, Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005..

Hierarchical modularity of nested bow-ties in metabolic networks

Jing Zhao, Hong Yu, Yixue Li, 2006, BMC Bioinformatics.

Identification of Hepatocellular Carcinoma-Related Genes with a Machine Learning and Network Analysis

Zhen Wang, Yixue Li, Xiao Dong, 2015, J. Comput. Biol..

Corrigendum: Prioritizing functional phosphorylation sites based on multiple feature integration

Zhen Wang, Yixue Li, Qingyu Xiao, 2016, Scientific Reports.

Biological data integration and high-performance computing

Yixue Li, 2007, China HPC.

dbDEPC: a database of Differentially Expressed Proteins in human Cancers

Chuan Wang, Hong Li, Yixue Li, 2009, Nucleic Acids Res..

MPSQ: a web tool for protein-state searching

Lei Liu, Chuan Wang, Yao Yu, 2008, Bioinform..

Tumor classification based on independent component analysis

Yan Chen, Yixue Li, Yunping Zhu, 2006, Int. J. Pattern Recognit. Artif. Intell..

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies

Di Wu, Xiaojing Wang, Jing Sun, 2008, BMC Bioinformatics.

Knowledge guided analysis of microarray data

Lei Liu, Jiong Yang, Yixue Li, 2006, J. Biomed. Informatics.

Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families

Qi Liu, Yixue Li, Guohui Ding, 2006, PLoS Comput. Biol..

Protein coding gene CRNKL1 as a potential prognostic biomarker in esophageal adenocarcinoma

Zhen Wang, Zhen Li, Yixue Li, 2017, Artif. Intell. Medicine.

Discrimination of approved drugs from experimental drugs by learning methods

Ruixin Zhu, Yixue Li, Zhi-Wei Cao, 2011, BMC Bioinformatics.

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

Yinglin Wang, Yixue Li, Lin Lu, 2007, Biochemical and biophysical research communications.

Analysis and application of large-scale protein-protein interaction data sets

Yixue Li, Jingchun Sun, Jinlin Xu, 2005 .

Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds

Xuan Li, Yun Li, Yixue Li, 2011, J. Bioinform. Comput. Biol..

Whole genome sequencing of disease animal models

Yixue Li, 2016, BIBM.

The combination approach of SVM and ECOC for powerful identification and classification of transcription factor

Qing Yang, Chaochun Wei, Yangyong Zhu, 2008, BMC Bioinformatics.

Human gene expression sensitivity according to large scale meta-analysis

Christian Gieger, Yang Zhong, Yixue Li, 2009, BMC Bioinformatics.

Comparison of Modularization Methods in Application to Different Biological Networks

Lei Liu, Zhuo Wang, Yazhu Chen, 2006, VDMB.

Short communication Support Vector Machine for predicting -turn types

Kuo-Chen Chou, Yixue Li, Yu-Dong Cai, 2003 .

Modular co-evolution of metabolic networks

Jing Zhao, Hong Yu, Yixue Li, 2007, BMC Bioinformatics.

cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets

Chaochun Wei, Hui Yu, Yixue Li, 2013, BMC Systems Biology.

Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis

Yixue Li, Junyi Li, Quanxue Li, 2017, Artif. Intell. Medicine.

Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin

Wu Wei, Xiaojing Wang, Yixue Li, 2007, International Conference on Computational Science.

Refined phylogenetic profiles method for predicting protein-protein interactions

Zhen Liu, Qi Liu, Yixue Li, 2005, Bioinform..

DNetDB: The human disease network database based on dysfunctional regulation mechanism

Jing Yang, Yixue Li, Yuan-Yuan Li, 2016, BMC Systems Biology.

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

Quanhu Sheng, Predrag Radivojac, Yixue Li, 2008, RECOMB.

An efficient method for statistical significance calculation of transcription factor binding sites

Yixue Li, Ziliang Qian, Lingyi Lu, 2007, Bioinformation.

A Brief Review of Computational Gene Prediction Methods

Yazhu Chen, Yixue Li, Zhuo Wang, 2004, Genomics, proteomics & bioinformatics.

A novel index of protein-protein interface propensity improves interface residue recognition

Yixue Li, Yuan-Yuan Li, Aiping Wu, 2016, BMC Systems Biology.

Prediction of membrane protein types in a hybrid space.

Yixue Li, Wencong Lu, Ziliang Qian, 2008, Journal of proteome research.

The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease

Xianzheng Sha, Yin Wang, Yixue Li, 2020, BioData Mining.

Applying software product line engineering in building web portals for supercomputing services

Yixue Li, David E. Hudak, Rajiv Ramnath, 2013, SAC '13.

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

Chuan Wang, Qi Liu, Zhongming Zhao, 2007, BMC Bioinformatics.

Bioinformatics Applications Note Gene Expression Dcgl: an R Package for Identifying Differentially Coexpressed Genes and Links from Gene Expression Microarray Data

Hui Yu, Yixue Li, Yuan-Yuan Li, 2022 .