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Transitive functional annotation by shortest-path analysis of gene expression data
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Context-dependent clustering for dynamic cellular state modeling of microarray gene expression
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm520openalex-snapshot
An efficient strategy for extensive integration of diverse biological data for protein function prediction
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn574openalex-snapshot
Shortest path analysis using partial correlations for classifying gene functions from gene expression data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp311openalex-snapshot
Complex discovery from weighted PPI networks
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp661openalex-snapshot
PathGen: a transitive gene pathway generator
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq508openalex-snapshot
Using coalitional games on biological networks to measure centrality and power of genes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr002openalex-snapshot
Recovering key biological constituents through sparse representation of gene expression
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr288openalex-snapshot
The role of indirect connections in gene networks in predicting function
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt685openalex-snapshot
Genes related to differentiation are correlated with the gene regulatory network structure
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx706openalex-snapshot
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
inferred← citeshttps://doi.org/10.1093/biostatistics/kxp018openalex-snapshot
Variable selection and dependency networks for genomewide data
inferred← citeshttps://doi.org/10.1093/database/bau014openalex-snapshot
YTRP: a repository for yeast transcriptional regulatory pathways
inferred← citeshttps://doi.org/10.1093/hmg/ddl051openalex-snapshot
Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes
inferred← citeshttps://doi.org/10.1093/molbev/msaa267openalex-snapshot
Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data
inferred← citeshttps://doi.org/10.1093/molbev/msx230openalex-snapshot
Natural Selection Drives Rapid Functional Evolution of Young Drosophila Duplicate Genes
inferred← citeshttps://doi.org/10.1093/nar/gkg838openalex-snapshot
Functional modules by relating protein interaction networks and gene expression
inferred← citeshttps://doi.org/10.1093/nar/gkh557openalex-snapshot
Transcription factor binding element detection using functional clustering of mutant expression data
inferred← citeshttps://doi.org/10.1093/nar/gkl225openalex-snapshot
VIRGO: computational prediction of gene functions
inferred← citeshttps://doi.org/10.1093/nar/gkm408openalex-snapshot
Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease
inferred← citeshttps://doi.org/10.1093/nar/gkn972openalex-snapshot
Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1093/nar/gkp406openalex-snapshot
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
inferred← citeshttps://doi.org/10.1093/nar/gks904openalex-snapshot
Reverse engineering and analysis of large genome-scale gene networks
inferred← citeshttps://doi.org/10.1093/nar/gkz662openalex-snapshot
Malaria.tools—comparative genomic and transcriptomic database for Plasmodium species
inferred← citeshttps://doi.org/10.1097/00054725-200405000-00020openalex-snapshot
New Approaches to Gene Hunting in IBD
inferred← citeshttps://doi.org/10.1097/mib.0000000000000893openalex-snapshot
Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohnʼs Disease
inferred← citeshttps://doi.org/10.1101/2024.01.25.577142openalex-snapshot
Comparative transcriptome database for Camellia sinensis reveals genes important for flavonoid synthesis in tea plants
inferred← citeshttps://doi.org/10.1101/639179openalex-snapshot
www.Malaria.tools - comparative genomic and transcriptomic database for Plasmodium species
inferred← citeshttps://doi.org/10.1101/gr.1397903openalex-snapshot
Toward a Functional Annotation of the Human Genome Using Artificial Transcription Factors
inferred← citeshttps://doi.org/10.1103/physreve.81.046118openalex-snapshot
Random matrix analysis of localization properties of gene coexpression network
inferred← citeshttps://doi.org/10.1104/pp.104.045179openalex-snapshot
Identification of Genes Required for Embryo Development in Arabidopsis
inferred← citeshttps://doi.org/10.1105/tpc.113.111039openalex-snapshot
Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales
inferred← citeshttps://doi.org/10.1109/access.2018.2806478openalex-snapshot
Protein Function Prediction Using Function Associations in Protein–Protein Interaction Network
inferred← citeshttps://doi.org/10.1109/access.2019.2909946openalex-snapshot
MiMod: A New Algorithm for Mining Biological Network Modules
inferred← citeshttps://doi.org/10.1109/bibe.2003.1188925openalex-snapshot
Towards automated derivation of biological pathways using high-throughput biological data
inferred← citeshttps://doi.org/10.1109/bibe.2006.253342openalex-snapshot
Prediction of Protein Function Using Common-Neighbors in Protein-Protein Interaction Networks
inferred← citeshttps://doi.org/10.1109/bibm.2008.82openalex-snapshot
Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles
inferred← citeshttps://doi.org/10.1109/bibm.2009.46openalex-snapshot
High Functional Coherence in k-Partite Protein Cliques of Protein Interaction Networks
inferred← citeshttps://doi.org/10.1109/bibm49941.2020.9313242openalex-snapshot
Stage-Specific Co-expression Network Analysis for Cancer Biomarker Discovery
inferred← citeshttps://doi.org/10.1109/bmei.2008.157openalex-snapshot
Detection of Changes in Transitive Associations by Shortest-path Analysis of Protein Interaction Networks Integrated with Gene Expression Profiles
inferred← citeshttps://doi.org/10.1109/cbms.2006.76openalex-snapshot
Discovering Gene Clusters via Integrated Analysis on Time-Series and Group-Comparative Microarray Datasets
inferred← citeshttps://doi.org/10.1109/cso.2011.105openalex-snapshot
Community Detection by Affinity Propagation with Various Similarity Measures
inferred← citeshttps://doi.org/10.1109/fccm.2006.48openalex-snapshot
Hardware/Software Integration for FPGA-based All-Pairs Shortest-Paths
inferred← citeshttps://doi.org/10.1109/grc.2009.5255161openalex-snapshot
Predicting gene function with positive and unlabeled examples
inferred← citeshttps://doi.org/10.1109/icassp.2005.1416416openalex-snapshot
Network constrained clustering for gene microarray data
inferred← citeshttps://doi.org/10.1109/icde.2007.367900openalex-snapshot
Labeling network motifs in protein interactomes for protein function prediction
inferred← citeshttps://doi.org/10.1109/icmlc.2010.5581099openalex-snapshot
Genetic regulatory networks established by shortest path algorithm and conditional probabilities for ovarian carcinoma microarray data
inferred← citeshttps://doi.org/10.1109/iihmsp.2010.8openalex-snapshot
Possible Disease-Link Genetic Pathways Constructed by Hierarchical Clustering and Conditional Probabilities of Ovarian Carcinoma Microarray Data
inferred← citeshttps://doi.org/10.1109/ipdps.2006.1639347openalex-snapshot
Parallel FPGA-based all-pairs shortest-paths in a directed graph
inferred← citeshttps://doi.org/10.1109/isbi.2004.1398755openalex-snapshot
Wavelet analysis of gene expression (WAGE)
inferred← citeshttps://doi.org/10.1109/jbhi.2020.2991763openalex-snapshot
Matrix Factorization-based Technique for Drug Repurposing Predictions
inferred← citeshttps://doi.org/10.1109/ssdbm.2007.35openalex-snapshot
Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways
inferred← citeshttps://doi.org/10.1111/biom.12508openalex-snapshot
CCor: A Whole Genome Network-Based Similarity Measure Between Two Genes
inferred← citeshttps://doi.org/10.1111/imcb.12793openalex-snapshot
Transcriptional network analysis of peripheral blood leukocyte subsets in multiple sclerosis identifies a pathogenic role for a cytotoxicity‐associated gene network in myeloid cells
inferred← citeshttps://doi.org/10.1111/j.1742-4658.2005.04946.xopenalex-snapshot
Utilizing logical relationships in genomic data to decipher cellular processes
inferred← citeshttps://doi.org/10.1111/ppl.14474openalex-snapshot
Comparative transcriptome database for Camellia sinensis reveals genes related to the cold sensitivity and albino mechanism of ‘Anji Baicha’
inferred← citeshttps://doi.org/10.11234/gi1990.14.675openalex-snapshot
GOODIES: GO Based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological Entities
inferred← citeshttps://doi.org/10.1128/msystems.01178-22openalex-snapshot
Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method
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