Yixue Li

According to our database1, Yixue Li authored at least 100 papers between 2003 and 2020.

Collaborative distances:



In proceedings 
PhD thesis 


On csauthors.net:


A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.
BMC Bioinform., 2020

Computational prediction and functional analysis of arsenic-binding proteins in human cells.
Quant. Biol., 2019

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

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

Strategic planning for national biomedical big data infrastructure in China.
Quant. Biol., 2017

Virtualisation of gene knockout experiments based on kinetic modelling: Escherichia coli as an algorithmic case.
Int. J. Comput. Biol. Drug Des., 2017

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

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

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

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

A novel index of protein-protein interface propensity improves interface residue recognition.
BMC Syst. Biol., 2016

cisASE: a likelihood-based method for detecting putative <i>cis</i>-regulated allele-specific expression in RNA sequencing data.
Bioinform., 2016

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

Identification of Hepatocellular Carcinoma-Related Genes with a Machine Learning and Network Analysis.
J. Comput. Biol., 2015

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

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

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

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

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

Big Biological Data: Challenges and Opportunities.
Genom. Proteom. Bioinform., 2014

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

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

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

Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study.
J. Chem. Inf. Model., 2013

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

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

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

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

Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling.
J. Chem. Inf. Model., 2012

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

Combinatorial network of transcriptional regulation and microRNA regulation in human cancer.
BMC Syst. Biol., 2012

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

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

Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis.
BMC Syst. Biol., 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

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

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

A Negative Cooperativity Mechanism of Human CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations.
J. Chem. Inf. Model., 2011

Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds.
J. Bioinform. Comput. Biol., 2011

The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma.
Int. J. Comput. Biol. Drug Des., 2011

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

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

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

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

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

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

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

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

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

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

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

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

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

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

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics.
J. Comput. Biol., 2009

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

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

PAnnBuilder: an R package for assembling proteomic annotation data.
Bioinform., 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 Mol. Biol., 2009

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 Res., 2008

AtPID: <i>Arabidopsis thaliana</i> protein interactome database - an integrative platform for plant systems biology.
Nucleic Acids Res., 2008

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

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

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

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

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

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

ECS: An automatic enzyme classifier based on functional domain composition.
Comput. Biol. Chem., 2007

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

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

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

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

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.
Int. J. Pattern Recognit. Artif. Intell., 2006

A new technique for selecting features from protein sequences.
Int. J. Pattern Recognit. Artif. Intell., 2006

Operon prediction based on SVM.
Comput. Biol. Chem., 2006

Predicting <i>O</i>-glycosylation sites in mammalian proteins by using SVMs.
Comput. Biol. Chem., 2006

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

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

<i>In silico </i>discovery of human natural antisense transcripts.
BMC Bioinform., 2006

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

Improving protein secondary structure prediction by using the residue conformational classes.
Pattern Recognit. Lett., 2005

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

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

Scoring hidden Markov models to discriminate -barrel membrane proteins.
Comput. Biol. Chem., 2004

Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure.
Comput. Biol. Chem., 2003

A HMM-based method to predict the transmembrane regions of \beta-barrel membrane proteins.
Comput. Biol. Chem., 2003