All Stories

  1. A formalization of one of the main claims of “Overlap of vitamin A and vitamin D target genes with CAKUT-related processes” by Ozisik et al. 20211
  2. CyTargetLinker app update: A flexible solution for network extension in Cytoscape
  3. A bioinformatics workflow to decipher transcriptomic data from vitamin D studies
  4. History of rare diseases and their genetic causes - a data driven approach
  5. Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes
  6. Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials
  7. Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus–A Co-expression Network Based Analysis
  8. Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression
  9. Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform
  10. Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.
  11. Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases
  12. CyTargetLinker app update: A flexible solution for network extension in Cytoscape
  13. Review and gap analysis: molecular pathways leading to fetal alcohol spectrum disorders
  14. MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases
  15. Diabetes: looking beyond the genes for better understanding
  16. Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disorders
  17. Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes
  18. Advancing food, nutrition, and health research in Europe by connecting and building research infrastructures in a DISH-RI: Results of the EuroDISH project
  19. Explicit interactions between drug targets and disease-related proteins facilitates drug discovery.
  20. Role of 1α,25-Dihydroxyvitamin D3 in Adipogenesis of SGBS Cells: New Insights into Human Preadipocyte Proliferation
  21. Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations
  22. Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D
  23. A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions
  24. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research
  25. A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants
  26. Adverse outcome pathways: opportunities, limitations and open questions
  27. Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures
  28. Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways
  29. Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
  30. Myocardial and Serum Galectin-3 Expression Dynamics Marks Post-Myocardial Infarction Cardiac Remodelling
  31. Open Source cheminformatics library in Java
  32. Maternal folate depletion during early development and high fat feeding from weaning elicit similar changes in gene expression, but not in DNA methylation, in adult offspring
  33. Rett syndrome – biological pathways leading from MECP2 to disorder phenotypes
  34. Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia
  35. Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3
  36. Organ-Specific Gene Expression Changes in the Fetal Liver and Placenta in Response to Maternal Folate Depletion
  37. XMetDB: an open access database for xenobiotic metabolism
  38. New insights in Rett syndrome using pathway analysis for transcriptomics data
  39. Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes
  40. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources
  41. Gene promoter DNA methylation patterns have a limited role in orchestrating transcriptional changes in the fetal liver in response to maternal folate depletion during pregnancy
  42. Reactome from a WikiPathways Perspective
  43. The systems biology format converter
  44. The FAIR Guiding Principles for scientific data management and stewardship
  45. Inferring causal molecular networks: empirical assessment through a community-based effort
  46. The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands
  47. A community-created database of biological knowledge, freely available and easy to reuse
  48. Current systems biology approaches in hazard assessment of nanoparticles
  49. PathVisio 3: An Extendable Pathway Analysis Toolbox
  50. The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands
  51. The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research
  52. Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism
  53. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization
  54. Easily import and use WikiPathways biological pathways in the common network biology tool Cytoscape
  55. A network biology workflow to study transcriptomics data of the diabetic liver
  56. Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life
  57. CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis
  58. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org
  59. A pathway approach to investigate the function and regulation of SREBPs
  60. Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets
  61. An outline of what Open PHACTS is
  62. Marginal selenium deficiency down-regulates inflammation-related genes in splenic leukocytes of the mouse
  63. GO-Elite: a flexible solution for pathway and ontology over-representation
  64. Effect of supplementation with an 80:20cis9,trans11 conjugated linoleic acid blend on the human platelet proteome
  65. Toward interoperable bioscience data
  66. An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
  67. Exposing WikiPathways as Linked Open Data
  68. WikiPathways: building research communities on biological pathways
  69. Measuring impact in online resources with the CI­number (the CitedIn Number for online impact)
  70. Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention
  71. 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting
  72. Using a data triangle to understand molecular nutrition
  73. Exploring pathway interactions in insulin resistant mouse liver
  74. The nutritional phenotype database*. A real data structure for systems biology
  75. Answering biological questions: querying a systems biology database for nutrigenomics
  76. The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research
  77. Connecting the Human Variome Project to nutrigenomics
  78. From Nanotechnology to Nanomedicine: Applications to Cancer Research
  79. Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes
  80. Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets
  81. A Combined Transcriptomics and Lipidomics Analysis of Subcutaneous, Epididymal and Mesenteric Adipose Tissue Reveals Marked Functional Differences
  82. Nature Europe site should highlight most productive countries
  83. Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies
  84. Time-Resolved and Tissue-Specific Systems Analysis of the Pathogenesis of Insulin Resistance
  85. Identification of novel ER-α target genes in breast cancer cells: Gene- and cell-selective co-regulator recruitment at target promoters determines the response to 17β-estradiol and tamoxifen
  86. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
  87. Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon
  88. Pathway Enrichment Based on Text Mining and Its Validation on Carotenoid and Vitamin A Metabolism
  89. Mining Biological Pathways Using WikiPathways Web Services
  90. Reduction of colonic inflammation in HLA-B27 transgenic rats by feeding Marie Ménard apples, rich in polyphenols
  91. Community curation on WikiPathways: How we assist knowledge collection
  92. An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions
  93. Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation
  94. Bioinformatics for the NuGO proof of principle study: analysis of gene expression in muscle of ApoE3*Leiden mice on a high-fat diet using PathVisio
  95. The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation
  96. The role of bioinformatics in pathway curation
  97. Validating nutrient-related gene expression changes from microarrays using RT2 PCR-arrays
  98. The public road to high-quality curated biological pathways
  99. WikiPathways: Pathway Editing for the People
  100. Presenting and exploring biological pathways with PathVisio
  101. Differential valine metabolism in adipose tissue of low and high fat-oxidizing obese subjects
  102. Impact of supervised gene signatures of early hypoxia on patient survival
  103. Genetic variation in thioredoxin interacting protein (TXNIP) is associated with hypertriglyceridaemia and blood pressure in diabetes mellitus
  104. Fasting induces a biphasic adaptive metabolic response in murine small intestine
  105. Linking microarray reporters with protein functions
  106. Gene profiling of cathepsin K deficiency in atherogenesis: profibrotic but lipogenic
  107. Microarray profiling of human white adipose tissue after exogenous leptin injection
  108. Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress
  109. Up-regulation of CD36/FAT in preadipocytes in familial combined hyperlipidemia
  110. Gene Profiling in Atherosclerosis Reveals a Key Role for Small Inducible Cytokines: Validation Using a Novel Monocyte Chemoattractant Protein Monoclonal Antibody
  111. A systematic review of large scale and heterogeneous gene array data in heart failure
  112. Protein profiling of 3T3-L1 adipocyte differentiation and (tumor necrosis factor ?-mediated) starvation
  113. Erythrocyte antioxidant defense response against cigarette smoking in humans—the glutathione S-transferase vulnerability
  114. Thrombospondin-2 Is Essential for Myocardial Matrix Integrity: Increased Expression Identifies Failure-Prone Cardiac Hypertrophy
  115. Role of the Rhoa/Rho Kinase System in Flow-Related Remodeling of Rat Mesenteric Small Arteries in Vivo
  116. Inhibition of various glutathione S-transferase isoenzymes by RRR-α-tocopherol
  117. Tocotrienols Inhibit Human Glutathione S-Transferase P1-1
  118. Hypochlorous acid is a potent inhibitor of GST P1-1
  119. Inhibition of human glutathione S-transferase P1-1 by tocopherols and α-tocopherol derivatives
  120. No reduction of α-tocopherol quinone by glutathione in rat liver microsomes
  121. α-Tocopherol Inhibits Human Glutathione S-Transferase π
  122. A Study on the Interaction between Hydroxylamine Analogues and Oxyhemoglobin in Intact Erythrocytes
  123. Erythrocyte glutathione S transferase as a marker of oxidative stress at birth
  124. Changes in levels of catalase and glutathione in erythrocytes of patients with stable asthma, treated with beclomethasone dipropionate
  125. Changes in levels of catalase and glutathione in erythrocytes of patients with stable asthma, treated with beclomethasone dipropionate
  126. Only the glutathione dependent antioxidant enzymes are inhibited by haematotoxic hydroxylamines
  127. Two Mechanisms for Toxic Effects of Hydroxylamines in Human Erythrocytes: Involvement of Free Radicals and Risk of Potentiation
  128. Oxidative effects in human erythrocytes caused by some oximes and hydroxylamine
  129. Hydroxylamine Treatment Increases Glutathione-Protein and Protein-Protein Binding in Human Erythrocytes
  130. In vitro haematotoxic effects of three methylated hydroxylamines
  131. Glutathione depletion in human erythrocytes as an indicator for microsomal activation of cyclophosphamide and 3-hydroxyacetanilide
  132. Physiologically based toxicokinetic modeling of 1,3-butadiene lung metabolism in mice becomes more important at low doses
  133. Development of a software package for computer simulations: The use of a sorted event list for reduction of calculation times
  134. Influence of oxygen supply on liver condition and elimination of dimethylacetamide in the isolated perfused rat liver
  135. Changes in blood glutathione concentrations, and in erythrocyte glutathione reductase and glutathione S-transferase activity after running training and after participation in contests
  136. Genetic deficiency of human class mu glutathione S-transferase isoenzymes in relation to the urinary excretion of the mercapturic acids of Z- and E-1,3-dichloropropene
  137. Influence of glutathione on the formation of cysteine alkylation products in human hemoglobin
  138. Separation of human haemoglobin alkylated at β93 cysteine from its native form by fast protein liquid chromatography
  139. Urinary cyclophosphamide assay as a method for biological monitoring of occupational exposure to cyclophosphamide
  140. Kinetics of the formation and secretion of the aniline metabolite 4-aminophenol and its conjugates by isolated rat hepatocytes