Yixue Li

According to our database1, Yixue Li authored at least 97 papers between 2003 and 2018.

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Bibliography

2018
Differential networking meta-analysis of gastric cancer across Asian and American racial groups.
BMC Systems Biology, 2018

RabGTD: a comprehensive database of rabbit genome and transcriptome.
Database, 2018

2017
Virtualisation of gene knockout experiments based on kinetic modelling: Escherichia coli as an algorithmic case.
I. J. Computational Biology and Drug Design, 2017

Protein coding gene CRNKL1 as a potential prognostic biomarker in esophageal adenocarcinoma.
Artificial Intelligence in Medicine, 2017

Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis.
Artificial Intelligence in Medicine, 2017

2016
DNetDB: The human disease network database based on dysfunctional regulation mechanism.
BMC Systems Biology, 2016

A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes.
BMC Systems Biology, 2016

A novel index of protein-protein interface propensity improves interface residue recognition.
BMC Systems Biology, 2016

cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data.
Bioinformatics, 2016

Whole genome sequencing of disease animal models.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
Identification of Hepatocellular Carcinoma-Related Genes with a Machine Learning and Network Analysis.
Journal of Computational Biology, 2015

Nonsynonymous Single-Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases.
Comp. Math. Methods in Medicine, 2015

Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing.
Comp. Math. Methods in Medicine, 2015

IAOseq: inferring abundance of overlapping genes using RNA-seq data.
BMC Bioinformatics, 2015

DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism.
Bioinformatics, 2015

Identifying novel associations between small molecules and miRNAs based on integrated molecular networks.
Bioinformatics, 2015

2014
Big Biological Data: Challenges and Opportunities.
Genomics, Proteomics & Bioinformatics, 2014

The 3DGD: a database of genome 3D structure.
Bioinformatics, 2014

SysPTM 2.0: an updated systematic resource for post-translational modification.
Database, 2014

2013
SchistoDB: an updated genome resource for the three key schistosomes of humans.
Nucleic Acids Research, 2013

Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study.
Journal of Chemical Information and Modeling, 2013

cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.
BMC Systems Biology, 2013

Applying software product line engineering in building web portals for supercomputing services.
Proceedings of the 28th Annual ACM Symposium on Applied Computing, 2013

2012
Dr.VIS: a database of human disease-related viral integration sites.
Nucleic Acids Research, 2012

dbDEPC 2.0: updated database of differentially expressed proteins in human cancers.
Nucleic Acids Research, 2012

Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling.
Journal of Chemical Information and Modeling, 2012

A cross-species analysis method to analyze animal models' similarity to human's disease state.
BMC Systems Biology, 2012

Combinatorial network of transcriptional regulation and microRNA regulation in human cancer.
BMC Systems Biology, 2012

An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification.
BMC Systems Biology, 2012

Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome.
BMC Systems Biology, 2012

Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis.
BMC Systems Biology, 2012

cGRNexp: a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

Anti-clustering of circadian gene expression in mouse liver genome.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

2011
HIT: linking herbal active ingredients to targets.
Nucleic Acids Research, 2011

ASD: a comprehensive database of allosteric proteins and modulators.
Nucleic Acids Research, 2011

A Negative Cooperativity Mechanism of Human CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations.
Journal of Chemical Information and Modeling, 2011

Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds.
J. Bioinformatics and Computational Biology, 2011

The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma.
I. J. Computational Biology and Drug Design, 2011

An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis.
BMC Systems Biology, 2011

iGepros: an integrated gene and protein annotation server for biological nature exploration.
BMC Bioinformatics, 2011

Link-based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs.
BMC Bioinformatics, 2011

Discrimination of Approved Drugs from Experimental Drugs by Learning Methods.
BMC Bioinformatics, 2011

A new strategy for better genome assembly from very short reads.
BMC Bioinformatics, 2011

A novel network-based method for measuring the functional relationship between gene sets.
Bioinformatics, 2011

Active and Passive Nearest Neighbor Algorithm: A Newly-Developed Supervised Classifier.
Proceedings of the Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 2011

2010
dbDEPC: a database of Differentially Expressed Proteins in human Cancers.
Nucleic Acids Research, 2010

Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution.
BMC Bioinformatics, 2010

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information.
BMC Bioinformatics, 2010

Sorting out inherent features of head-to-head gene pairs by evolutionary conservation.
BMC Bioinformatics, 2010

DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data.
Bioinformatics, 2010

Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.
Nucleic Acids Research, 2009

Sys-BodyFluid: a systematical database for human body fluid proteome research.
Nucleic Acids Research, 2009

SysZNF: the C2H2 zinc finger gene database.
Nucleic Acids Research, 2009

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.
BMC Bioinformatics, 2009

Human gene expression sensitivity according to large scale meta-analysis.
BMC Bioinformatics, 2009

PAnnBuilder: an R package for assembling proteomic annotation data.
Bioinformatics, 2009

DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels.
Database, 2009

CHSMiner: a GUI tool to identify chromosomal homologous segments.
Algorithms for Molecular Biology, 2009

2008
Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation.
PLoS Computational Biology, 2008

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.
Nucleic Acids Research, 2008

AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology.
Nucleic Acids Research, 2008

The combination approach of SVM and ECOC for powerful identification and classification of transcription factor.
BMC Bioinformatics, 2008

GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations.
BMC Bioinformatics, 2008

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies.
BMC Bioinformatics, 2008

ITFP: an integrated platform of mammalian transcription factors.
Bioinformatics, 2008

MPSQ: a web tool for protein-state searching.
Bioinformatics, 2008

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics.
Bioinformatics, 2008

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics.
Proceedings of the Research in Computational Molecular Biology, 2008

2007
ECS: An automatic enzyme classifier based on functional domain composition.
Computational Biology and Chemistry, 2007

Modular co-evolution of metabolic networks.
BMC Bioinformatics, 2007

Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data.
BMC Bioinformatics, 2007

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.
BMC Bioinformatics, 2007

An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization.
Bioinformatics, 2007

Biological data integration and high-performance computing.
Proceedings of the CHINA HPC 2007, 2007

Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin.
Proceedings of the Computational Science - ICCS 2007, 7th International Conference, Beijing, China, May 27, 2007

2006
Correction: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance.
PLoS Computational Biology, 2006

Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance.
PLoS Computational Biology, 2006

Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families.
PLoS Computational Biology, 2006

KDE Bioscience: Platform for bioinformatics analysis workflows.
, 2006

Knowledge guided analysis of microarray data.
, 2006

Tumor classification based on independent component analysis.
IJPRAI, 2006

A new technique for selecting features from protein sequences.
IJPRAI, 2006

Operon prediction based on SVM.
Computational Biology and Chemistry, 2006

Predicting O-glycosylation sites in mammalian proteins by using SVMs.
Computational Biology and Chemistry, 2006

Hierarchical modularity of nested bow-ties in metabolic networks.
BMC Bioinformatics, 2006

Classification of protein quaternary structure by functional domain composition.
BMC Bioinformatics, 2006

In silico discovery of human natural antisense transcripts.
BMC Bioinformatics, 2006

Demonstration of two novel methods for predicting functional siRNA efficiency.
BMC Bioinformatics, 2006

Comparison of Modularization Methods in Application to Different Biological Networks.
Proceedings of the Data Mining and Bioinformatics, First International Workshop, 2006

On Loan-to-Value Ratios of Inventory Financing with Doubly Stochastic Poisson Default Processes.
Proceedings of The 1st IEEE Asia-Pacific Services Computing Conference, 2006

2005
Improving protein secondary structure prediction by using the residue conformational classes.
Pattern Recognition Letters, 2005

Refined phylogenetic profiles method for predicting protein-protein interactions.
Bioinformatics, 2005

MPSS: an integrated database system for surveying a set of proteins.
Bioinformatics, 2005

2004
Scoring hidden Markov models to discriminate -barrel membrane proteins.
Computational Biology and Chemistry, 2004

2003
Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure.
Computational Biology and Chemistry, 2003

A HMM-based method to predict the transmembrane regions of \beta-barrel membrane proteins.
Computational Biology and Chemistry, 2003


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