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Biotech Software & Internet ReportVol. 2, No. 3 Views from the WebBioCartaDarryl NishimuraDarryl NishimuraSearch for more papers by this authorPublished Online:5 Jul 2004https://doi.org/10.1089/152791601750294344AboutSectionsPDF/EPUB ToolsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetailsCited ByInterCellar enables interactive analysis and exploration of cell−cell communication in single-cell transcriptomic data11 January 2022 | Communications Biology, Vol. 5, No. 1Increased trunk fat is associated with altered gene expression in breast tissue of normal weight women27 January 2022 | npj Breast Cancer, Vol. 8, No. 1Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury9 September 2022 | Genome Medicine, Vol. 14, No. 1Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture5 September 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sequencing profiles and diagnostic signatures linked with response to ramucirumab in gastric cancer14 February 2020 | Molecular Case StudiesMutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer22 January 2020 | Cancers, Vol. 12, No. 2Intratumoral Heterogeneity and Longitudinal Changes in Gene Expression Predict Differential Drug Sensitivity in Newly Diagnosed and Recurrent Glioblastoma24 February 2020 | Cancers, Vol. 12, No. 2A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases6 February 2020 | International Journal of Environmental Research and Public Health, Vol. 17, No. 3Network‑based identification of signature genes KLF6 and SPOCK1 associated with oral submucous fibrosis30 January 2020 | Molecular and Clinical OncologyPathBank: a comprehensive pathway database for model organisms11 October 2019 | Nucleic Acids Research, Vol. 48, No. D1Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs31 October 2019Oncobox Method for Scoring Efficiencies of Anticancer Drugs Based on Gene Expression Data31 October 2019Proinflammatory status-stratified blood transcriptome profiling of civilian women with PTSDPsychoneuroendocrinology, Vol. 111Increased cardiovascular and atherosclerosis markers in blood of older patients with atopic dermatitisAnnals of Allergy, Asthma & Immunology, Vol. 124, No. 1Genetic architecture study of rheumatoid arthritis and juvenile idiopathic arthritis15 January 2020 | PeerJ, Vol. 8Comorbidity Network Analyses of Global Rheumatoid Arthritis and Type 2 Diabetes Reveal IL2 & IL6 as Common Role Players30 April 2020GA-PPI-Net: A Genetic Algorithm for Community Detection in Protein-Protein Interaction Networks22 July 2020Signaling Pathway Analysis Combined With the Strength Variations of Interactions Between Genes Under Different ConditionsIEEE Access, Vol. 8Identifying disease-associated signaling pathways through a novel effector gene analysis14 August 2020 | PeerJ, Vol. 8Pathway Activity Score Learning for Dimensionality Reduction of Gene Expression Data15 October 2020HisCoM-PAGE: software for hierarchical structural component models for pathway analysis of gene expression dataGenomics & Informatics, Vol. 17, No. 4ADGRL4/ELTD1 Silencing in Endothelial Cells Induces ACLY and SLC25A1 and Alters the Cellular Metabolic Profile25 November 2019 | Metabolites, Vol. 9, No. 12The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens3 January 2019 | Genome Biology, Vol. 20, No. 1Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays15 February 2019 | BMC Bioinformatics, Vol. 20, No. 1Efficient proximal gradient algorithm for inference of differential gene networks2 May 2019 | BMC Bioinformatics, Vol. 20, No. 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Raftery, and Ka Yee Yeung7 October 2019 | Journal of Computational Biology, Vol. 26, No. 10Gene set analysis and reduction for a continuous phenotype: Identifying markers of birth weight variation based on embryonic stem cells and immunologic signaturesComputers in Biology and Medicine, Vol. 113The metaRbolomics Toolbox in Bioconductor and beyond23 September 2019 | Metabolites, Vol. 9, No. 10Measuring consistency among gene set analysis methods: A systematic study20 December 2019 | Journal of Bioinformatics and Computational Biology, Vol. 17, No. 05Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway26 September 2019 | Toxicologic Pathology, Vol. 47, No. 7Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources3 June 2019 | Briefings in Bioinformatics, Vol. 20, No. 5pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks25 September 2019 | Frontiers in Genetics, Vol. 10H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks5 September 2019 | Cells, Vol. 8, No. 9A Pathway-Based Kernel Boosting Method for Sample Classification Using Genomic Data31 August 2019 | Genes, Vol. 10, No. 9Network as a Biomarker: A Novel Network-Based Sparse Bayesian Machine for Pathway-Driven Drug Response Prediction9 August 2019 | Genes, Vol. 10, No. 8CAG Repeat Not Polyglutamine Length Determines Timing of Huntington’s Disease OnsetCell, Vol. 178, No. 4Exploring the cross-phenotype network region of disease modules reveals concordant and discordant pathways between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis1 April 2019 | Human Molecular Genetics, Vol. 28, No. 14Identification and Functional Inference for Tumor-Associated Long Non-Coding RNAIEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 16, No. 4Gene expression and DNA methylation as mechanisms of disturbed metabolism in offspring after exposure to a prenatal HF dietJournal of Lipid Research, Vol. 60, No. 7Genetic Predisposition for Immune System, Hormone, and Metabolic Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Pilot Study24 May 2019 | Frontiers in Pediatrics, Vol. 7Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle22 May 2019 | Frontiers in Cellular and Infection Microbiology, Vol. 9GWAS of smoking behaviour in 165,436 Japanese people reveals seven new loci and shared genetic architecture25 March 2019 | Nature Human Behaviour, Vol. 3, No. 5Analysis of Hypoxiamir-Gene Regulatory Network Identifies Critical MiRNAs Influencing Cell-Cycle Regulation Under Hypoxic ConditionsMicroRNA, Vol. 8, No. 3Prediction of Acquired Taxane Resistance Using a Personalized Pathway-Based Machine Learning MethodCancer Research and Treatment, Vol. 51, No. 2Insights into Inflammatory Priming of Adipose-Derived Mesenchymal Stem Cells: Validation of Extracellular Vesicles-Embedded miRNA Reference Genes as A Crucial Step for Donor Selection23 April 2019 | Cells, Vol. 8, No. 4Hypersensitive IFN Responses in Lupus Keratinocytes Reveal Key Mechanistic Determinants in Cutaneous Lupus11 February 2019 | The Journal of Immunology, Vol. 202, No. 7MR4Cancer: a web server prioritizing master regulators for cancer23 July 2018 | Bioinformatics, Vol. 35, No. 4Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs23 January 2019 | Frontiers in Pharmacology, Vol. 10HumanNet v2: human gene networks for disease research10 November 2018 | Nucleic Acids Research, Vol. 47, No. D1Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers4 January 2019 | Frontiers in Oncology, Vol. 8Circulating miRs-183-5p, 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