Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer.

[BibT_eX]

[DOI]

Feng Li

Jingwen Wang

Briefings Bioinform., 2024

2023

Tumor biology, immune infiltration and liver function define seven hepatocellular carcinoma subtypes linked to distinct drivers, survival and drug response.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, December, 2023

Open a new epoch of arsenic trioxide investigation: ATOdb.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, October, 2023

CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data.

[BibT_eX]

[DOI]

Nucleic Acids Res., January, 2023

CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories.

[BibT_eX]

[DOI]

Nucleic Acids Res., January, 2023

IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions.

[BibT_eX]

[DOI]

Nucleic Acids Res., January, 2023

2022

AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species.

[BibT_eX]

[DOI]

Briefings Bioinform., November, 2022

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.

[BibT_eX]

[DOI]

Andrew E. Teschendorff

Nucleic Acids Res., 2022

LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2022

TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2022

HCDT: an integrated highly confident drug-target resource.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2022

Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

PRES: a webserver for decoding the functional perturbations of RNA editing sites.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Identifying and characterizing drug sensitivity-related lncRNA-TF-gene regulatory triplets.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

2021

Research on Restoration Algorithm of Tomb Murals Based on Sequential Similarity Detection.

[BibT_eX]

[DOI]

Wang Liu

Xia Li

Fengjiao Wu

Sci. Program., 2021

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2021

LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2021

Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2021

LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2021

A Novel Multi-Ensemble Method for Identifying Essential Proteins.

[BibT_eX]

[DOI]

J. Comput. Biol., 2021

SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

CeRNASeek: an R package for identification and analysis of ceRNA regulation.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

2020

LncTarD: a manually-curated database of experimentally-supported functional lncRNA?target regulations in human diseases.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2020

LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2020

Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer.

[BibT_eX]

[DOI]

Briefings Bioinform., 2020

A comprehensive overview of oncogenic pathways in human cancer.

[BibT_eX]

[DOI]

Briefings Bioinform., 2020

RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data.

[BibT_eX]

[DOI]

Briefings Bioinform., 2020

Highly Precise Birefringence Demodulation to Overcome the Sensing Limitation From the Free Spectral Range on the Fiber Lyot Filter.

[BibT_eX]

[DOI]

IEEE Access, 2020

Construct the Students' Consumption Portrait Based on Large-scale Campus Data.

[BibT_eX]

[DOI]

Proceedings of the ICMLC 2020: 2020 12th International Conference on Machine Learning and Computing, 2020

2019

CellMarker: a manually curated resource of cell markers in human and mouse.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2019

CancerSEA: a cancer single-cell state atlas.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2019

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2019

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2019

Breast cancer prognosis signature: linking risk stratification to disease subtypes.

[BibT_eX]

[DOI]

Briefings Bioinform., 2019

Survey of miRNA-miRNA cooperative regulation principles across cancer types.

[BibT_eX]

[DOI]

Briefings Bioinform., 2019

Systematic review regulatory principles of non-coding RNAs in cardiovascular diseases.

[BibT_eX]

[DOI]

Briefings Bioinform., 2019

Landscape of the long non-coding RNA transcriptome in human heart.

[BibT_eX]

[DOI]

Briefings Bioinform., 2019

Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability.

[BibT_eX]

[DOI]

Briefings Bioinform., 2019

Improving Identification of Essential Proteins by a Novel Ensemble Method.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

An Effective Method to Improve the Accuracy of Precise Funding in Campus.

[BibT_eX]

[DOI]

Proceedings of the 3rd International Conference on Computer Science and Application Engineering, 2019

2018

Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2018

DiseaseEnhancer: a resource of human disease-associated enhancer catalog.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2018

SEECancer: a resource for somatic events in evolution of cancer genome.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2018

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2018

LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2018

Combinatorial epigenetic regulation of non-coding RNAs has profound effects on oncogenic pathways in breast cancer subtypes.

[BibT_eX]

[DOI]

Briefings Bioinform., 2018

2017

LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2017

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2017

miRNA-miRNA crosstalk: from genomics to phenomics.

[BibT_eX]

[DOI]

Briefings Bioinform., 2017

A comprehensive overview of lncRNA annotation resources.

[BibT_eX]

[DOI]

Briefings Bioinform., 2017

2016

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2016

2015

ViRBase: a resource for virus-host ncRNA-associated interactions.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2015

Prediction of potential disease-associated microRNAs based on random walk.

[BibT_eX]

[DOI]

Bioinform., 2015

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

[BibT_eX]

[DOI]

Bioinform., 2015

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2015

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2015

2014

The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2014

LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2014

2013

Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2013

SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression.

[BibT_eX]

[DOI]

Bioinform., 2013

Topologically inferring risk-active pathways toward precise cancer classification by directed random walk.

[BibT_eX]

[DOI]

Bioinform., 2013

Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease.

[BibT_eX]

[DOI]

Bioinform., 2013

2012

Screening for cancer associated MiRNAs through co-gene, co-function and co-pathway analysis.

[BibT_eX]

[DOI]

Comput. Biol. Medicine, 2012

Dissection of human MiRNA regulatory influence to subpathway.

[BibT_eX]

[DOI]

Briefings Bioinform., 2012

2011

DOSim: An R package for similarity between diseases based on Disease Ontology.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

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

[BibT_eX]

[DOI]

Bioinform., 2011

A sub-pathway-based approach for identifying drug response principal network.

[BibT_eX]

[DOI]

Bioinform., 2011

A robust approach based on Weibull distribution for clustering gene expression data.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2011

2010

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2010

2009

Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways.

[BibT_eX]

[DOI]

Bioinform., 2009

A Novel Method to Select High-risk Disease-Related Regions after a Genome Wide Haplotype-Based Association Study: An Application to Alcoholism.

[BibT_eX]

[DOI]

Proceedings of the Sixth International Conference on Fuzzy Systems and Knowledge Discovery, 2009

Clinical Information Driven Ensemble Clustering for Inferring Robust Tumor Subtypes.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009

Global Similarity and Local Variance in Human Gene Coexpression Networks.

[BibT_eX]

[DOI]

Proceedings of the Artificial Intelligence and Computational Intelligence, 2009

2008

Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2008

Apparently low reproducibility of true differential expression discoveries in microarray studies.

[BibT_eX]

[DOI]

Bioinform., 2008

Towards patterns tree of gene coexpression in eukaryotic species.

[BibT_eX]

[DOI]

Bioinform., 2008

A Systematic Method Based on Haplotype Analysis: Application to Risk Alleles and Genes Mining for RA.

[BibT_eX]

[DOI]

Proceedings of the Fourth International Conference on Natural Computation, 2008

A SNP and KEGG Based Approach to Mine Risk Pathways Associated with Bipolar Disorder.

[BibT_eX]

[DOI]

Proceedings of the Fourth International Conference on Natural Computation, 2008

2007

A Heuristic Approach for Target SNP Mining Based on Genome-Wide IBD Profile.

[BibT_eX]

[DOI]

Fan Zhang

Xia Li

Ivan Viktorovich Krivosheev

Binsheng Gong

Lei Du

Chunquan Li

Proceedings of the Third International Conference on Natural Computation, 2007

The Research on the Relationship Between Adrenergic Receptor Subtypes.

[BibT_eX]

[DOI]

Proceedings of the Third International Conference on Natural Computation, 2007

2006

Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling.

[BibT_eX]

[DOI]

BMC Bioinform., 2006

Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules.

[BibT_eX]

[DOI]

Bioinform., 2006

An Analysis of Gene Expression Relationships Between Periodically Expressed Genes in the Hela Cells.

[BibT_eX]

[DOI]

Proceedings of the Computational Intelligence and Bioinformatics, 2006

Association Research on Potassium Channel Subtypes and Functional Sites.

[BibT_eX]

[DOI]

Proceedings of the Computational Intelligence and Bioinformatics, 2006

Analysis of Sib-Pair IBD Profiles Using Ensemble Decision Tree Approach: Application to Alcoholism.

[BibT_eX]

[DOI]

Proceedings of the Computational Intelligence and Bioinformatics, 2006

A Novel Method for Expanding Current Annotations in Gene Ontology.

[BibT_eX]

[DOI]

Proceedings of the Computational Intelligence and Bioinformatics, 2006

2005

Towards precise classification of cancers based on robust gene functional expression profiles.

[BibT_eX]

[DOI]

BMC Bioinform., 2005

G Protein Binding Sites Analysis.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

A Novel Ensemble Decision Tree Approach for Mining Genes Coding Ion Channels for Cardiopathy Subtype.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

A Novel Feature Ensemble Technology to Improve Prediction Performance of Multiple Heterogeneous Phenotypes Based on Microarray Data.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

A New Method for Gene Functional Prediction Based on Homologous Expression Profile.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

A Novel Visualization Classifier and Its Applications.

[BibT_eX]

[DOI]

Jie Li

Xianglong Tang

Xia Li

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

Large-Scale Ensemble Decision Analysis of Sib-Pair IBD Profiles for Identification of the Relevant Molecular Signatures for Alcoholism.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

Analysis of Sib-Pair IBD Profiles and Genomic Context for Identification of the Relevant Molecular Signatures for Alcoholism.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

Application of a Genetic Algorithm - Support Vector Machine Hybrid for Prediction of Clinical Phenotypes Based on Genome-Wide SNP Profiles of Sib Pairs.

[BibT_eX]

[DOI]

Proceedings of the Fuzzy Systems and Knowledge Discovery, Second International Conference, 2005

2004

Reverse Engineering of Multiple Time-delayed Gene Regulatory Networks.