All Stories

  1. ELIXIR and Toxicology: a community in development

    Article • F1000Research, October 2023, Faculty of 1000, Ltd.

    Dr Antony John Williams, Dr John M Hancock, Prof. Iseult Lynch, Professor Nikolaos S. Thomaidis, Professor Chris Evelo

  2. Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington’s disease

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  3. A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability

    Article • NanoImpact, July 2023, Elsevier

    Professor Chris Evelo

  4. The FAIR Cookbook - the essential resource for and by FAIR doers

    Article • Scientific Data, May 2023, Springer Science + Business Media

    Robert T. Giessmann, Professor Chris Evelo

  5. Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations

    Article • Orphanet Journal of Rare Diseases, April 2023, Springer Science + Business Media

    Professor Chris Evelo

  6. PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity

    Article • Journal of Cheminformatics, March 2023, Springer Science + Business Media

    Professor Chris Evelo

  7. Molecular Adverse Outcome Pathways: towards the implementation of transcriptomics data in risk assessments

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  8. Different B cell activation patterns in asymptomatic and symptomatic COVID-19 patients

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  9. Systems Biology in ELIXIR: modelling in the spotlight

    Article • F1000Research, November 2022, Faculty of 1000, Ltd.

    Dr John M Hancock, Professor Chris Evelo

  10. Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients

    Article • Frontiers in Immunology, September 2022, Frontiers

    Professor Chris Evelo

  11. The future of food and nutrition in ELIXIR

    Article • F1000Research, August 2022, Faculty of 1000, Ltd.

    Matúš Kalaš, Dr John M Hancock, Professor Chris Evelo

  12. A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma

    Article • Frontiers in Oncology, April 2022, Frontiers

    Professor Chris Evelo

  13. Overlap of vitamin A and vitamin D target genes with CAKUT-related processes

    Article • F1000Research, April 2022, Faculty of 1000, Ltd.

    Professor Chris Evelo

  14. Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

    Article • PLOS One, April 2022, PLOS

    Professor Chris Evelo

  15. 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

    Article • Data Science, March 2022, IOS Press

    Professor Chris Evelo

  16. An approach to the proposal of drug combination for cancer therapy using a pathway data connectivity approach

    Article • March 2022, American Chemical Society (ACS)

    Professor Chris Evelo

  17. A systematically derived overview of the non-ubiquitous pathways and genes that define the molecular and genetic signature of the healthy trabecular meshwork

    Article • Genomics, March 2022, Elsevier

    Professor Chris Evelo

  18. PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

    Article • Journal of Cheminformatics, February 2022, Springer Science + Business Media

    Professor Chris Evelo

  19. Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

    Article • Applied In Vitro Toxicology, February 2022, Mary Ann Liebert Inc

    Professor Chris Evelo

  20. The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework

    Article • Frontiers in Toxicology, February 2022, Frontiers

    Professor Chris Evelo

  21. Converging pathways found in copy number variation syndromes with high schizophrenia risk

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  22. A Systems Biology Workflow to Support the Diagnosis of Pyrimidine and Urea Cycle Disorders

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  23. A Simple Standard for Sharing Ontological Mappings (SSSOM)

    Article • Database, January 2022, Oxford University Press (OUP)

    Professor Chris Evelo

  24. Impact of In Utero Folate Exposure on DNA Methylation and Its Potential Relevance for Later‐Life Health—Evidence from Mouse Models Translated to Human Cohorts

    Article • Molecular Nutrition & Food Research, December 2021, Wiley

    Professor Chris Evelo

  25. An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

    Article • Genes & Nutrition, December 2021, Springer Science + Business Media

    Professor Chris Evelo

  26. Comparison of metabolic states using genome-scale metabolic models

    Article • PLoS Computational Biology, November 2021, PLOS

    Professor Chris Evelo

  27. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

    Article • Molecular Systems Biology, October 2021, EMBO

    Jun.-Prof. Dr. Andreas Dräger, Professor Chris Evelo

  28. Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts

    Article • International Journal of Molecular Sciences, August 2021, MDPI AG

    Professor Chris Evelo

  29. Ten simple rules for creating reusable pathway models for computational analysis and visualization

    Article • PLoS Computational Biology, August 2021, PLOS

    Professor Chris Evelo

  30. Tolerogenic effects of 1,25-dihydroxyvitamin D on dendritic cells involve induction of fatty acid synthesis

    Article • The Journal of Steroid Biochemistry and Molecular Biology, July 2021, Elsevier

    Professor Chris Evelo

  31. Integrative multiomics analysis of human atherosclerosis reveals a serum response factor‐driven network associated with intraplaque hemorrhage

    Article • Clinical and Translational Medicine, June 2021, Wiley

    Professor Chris Evelo

  32. Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue

    Article • Frontiers in Nutrition, May 2021, Frontiers

    Professor Chris Evelo

  33. Ten simple rules to make your publication look better

    Article • PLoS Computational Biology, May 2021, PLOS

    Professor Chris Evelo

  34. Overlap of vitamin A and vitamin D target genes with CAKUT-related processes

    Article • F1000Research, May 2021, Faculty of 1000, Ltd.

    Professor Chris Evelo

  35. The need for standardisation in life science research - an approach to excellence and trust.

    Article • F1000Research, May 2021, Faculty of 1000, Ltd.

    Professor Chris Evelo

  36. A resource to explore the discovery of rare diseases and their causative genes

    Article • Scientific Data, May 2021, Springer Science + Business Media

    Professor Chris Evelo

  37. Investigating the molecular processes behind the cell-specific toxicity response to titanium dioxide nanobelts

    Article • March 2021, Springer Science + Business Media

    Professor Chris Evelo

  38. Blunted nutrient-response pathways in adipose tissue following high fat meals in men with metabolic syndrome: A randomized postprandial transcriptomic study

    Article • Clinical Nutrition, March 2021, Elsevier

    Professor Chris Evelo

  39. ELIXIR‐EXCELERATE: establishing Europe's data infrastructure for the life science research of the future

    Article • The EMBO Journal, February 2021, EMBO

    Dr John M Hancock, Professor Chris Evelo

  40. A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

    Article • Scientific Data, January 2021, Springer Science + Business Media

    Professor Chris Evelo

  41. Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content

    Article • January 2021, American Chemical Society (ACS)

    Professor Chris Evelo

  42. Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content

    Article • January 2021, American Chemical Society (ACS)

    Professor Chris Evelo

  43. The need for standardisation in life science research - an approach to excellence and trust.

    Article • F1000Research, December 2020, Faculty of 1000, Ltd.

    Professor Chris Evelo

  44. WikiPathways: connecting communities

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Professor Chris Evelo

  45. Ten simple rules on how to write a standard operating procedure

    Article • PLoS Computational Biology, September 2020, PLOS

    Professor Chris Evelo

  46. SBML Level 3: an extensible format for the exchange and reuse of biological models

    Article • Molecular Systems Biology, August 2020, EMBO

    Jun.-Prof. Dr. Andreas Dräger, Brett G Olivier, Professor Chris Evelo

  47. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

    Article • Scientific Data, July 2020, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger, Professor Chris Evelo

  48. We want to collaborate on exchanging what we know on how the new coronavirus works

    Article • Scientific Data, May 2020, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger, Professor Chris Evelo

  49. The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension

    Article • Investigative Ophthalmology & Visual Science, April 2020, Association for Research in Vision and Ophthalmology (ARVO)

    Professor Chris Evelo

  50. Standards make the world go round

    Article • EMBnet journal, March 2020, EMBnet Stichting

    Professor Chris Evelo

  51. EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic Models

    Article • Metabolites, February 2020, MDPI AG

    Professor Chris Evelo

  52. Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle Breeding

    Article • Frontiers in Genetics, February 2020, Frontiers

    Tomasz Sadkowski, Professor Chris Evelo

  53. Stratifying cellular metabolism during weight loss: an interplay of metabolism, metabolic flexibility and inflammation

    Article • Scientific Reports, February 2020, Springer Science + Business Media

    Professor Chris Evelo

  54. FAIR Principles: Interpretations and Implementation Considerations

    Article • Data Intelligence, January 2020, The MIT Press

    Dr Simon J Coles, Professor Chris Evelo

  55. Network Analysis of Genome-Wide Association Studies for Chronic Obstructive Pulmonary Disease in the Context of Biological Pathways

    Article • American Review of Respiratory Disease, December 2019, American Thoracic Society

    Harry Gosker, Kelly Stewart, Professor Chris Evelo

  56. Logical modelling reveals the PDC-PDK interaction as the regulatory switch driving metabolic flexibility at the cellular level

    Article • Genes & Nutrition, September 2019, Springer Science + Business Media

    Professor Chris Evelo

  57. Subcutaneous Adipose Tissue and Systemic Inflammation Are Associated With Peripheral but Not Hepatic Insulin Resistance in Humans

    Article • Diabetes, September 2019, American Diabetes Association

    Professor Chris Evelo

  58. CyTargetLinker app update: A flexible solution for network extension in Cytoscape

    Article • F1000Research, August 2019, Faculty of 1000, Ltd.

    Professor Chris Evelo

  59. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

    Article • Nature Communications, June 2019, Springer Science + Business Media

    Dr Olexandr Isayev, Dr Mahmoud M ElHefnawi, Professor Chris Evelo

  60. Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open‐angle glaucoma

    Article • Acta Ophthalmologica, June 2019, Wiley

    Professor Chris Evelo

  61. A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

    Article • The Journal of Steroid Biochemistry and Molecular Biology, May 2019, Elsevier

    Professor Chris Evelo

  62. History of rare diseases and their genetic causes - a data driven approach

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  63. Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes

    Article • The World Journal of Biological Psychiatry, March 2019, Taylor & Francis

    Professor Chris Evelo

  64. Addendum: The FAIR Guiding Principles for scientific data management and stewardship

    Article • Scientific Data, March 2019, Springer Science + Business Media

    Professor Chris Evelo

  65. Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

    Article • Frontiers in Genetics, February 2019, Frontiers

    Professor Chris Evelo

  66. Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

    Article • Frontiers in Genetics, December 2018, Frontiers

    Professor Chris Evelo, Dr Lyle Burgoon

  67. Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus–A Co-expression Network Based Analysis

    Article • Frontiers in Physiology, December 2018, Frontiers

    Professor Chris Evelo

  68. Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression

    Article • Genes, October 2018, MDPI AG

    Professor Chris Evelo

  69. Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

    Article • F1000Research, October 2018, Faculty of 1000, Ltd.

    Professor Chris Evelo

  70. Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

    Article • October 2018, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Chris Evelo

  71. Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.

    Article • F1000Research, September 2018, Faculty of 1000, Ltd.

    Professor Chris Evelo

  72. Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases

    Article • Journal of Proteomics, September 2018, Elsevier

    Professor Chris Evelo

  73. Exploring the cellular network of metabolic flexibility in the adipose tissue

    Article • Genes & Nutrition, July 2018, Springer Science + Business Media

    Professor Chris Evelo

  74. CyTargetLinker app update: A flexible solution for network extension in Cytoscape

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Professor Chris Evelo

  75. Review and gap analysis: molecular pathways leading to fetal alcohol spectrum disorders

    Article • Molecular Psychiatry, June 2018, Springer Science + Business Media

    Professor Chris Evelo

  76. MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases

    Article • Human Mutation, May 2018, Wiley

    Professor Chris Evelo

  77. Diabetes: looking beyond the genes for better understanding

    Article • PLOS One, April 2018, PLOS

    Elisa Cirillo, Professor Chris Evelo

  78. Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disorders

    Article • The World Journal of Biological Psychiatry, March 2018, Taylor & Francis

    Professor Chris Evelo

  79. Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  80. Advancing food, nutrition, and health research in Europe by connecting and building research infrastructures in a DISH-RI: Results of the EuroDISH project

    Article • Trends in Food Science & Technology, March 2018, Elsevier

    Professor Chris Evelo

  81. Explicit interactions between drug targets and disease-related proteins facilitates drug discovery.

    Article • F1000Research, January 2018, Faculty of 1000, Ltd.

    Professor Chris Evelo

  82. Role of 1α,25-Dihydroxyvitamin D3 in Adipogenesis of SGBS Cells: New Insights into Human Preadipocyte Proliferation

    Article • Cellular Physiology and Biochemistry, January 2018, Karger Publishers

    Ingrid Felicidade, Professor Chris Evelo

  83. Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

    Article • NanoImpact, January 2018, Elsevier

    Professor Chris Evelo

  84. Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D

    Article • Journal of Molecular Endocrinology, December 2017, Bioscientifica

    Professor Chris Evelo

  85. A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions

    Article • Toxicological Sciences, November 2017, Oxford University Press (OUP)

    Professor Chris Evelo

  86. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

    Article • Nucleic Acids Research, November 2017, Oxford University Press (OUP)

    Professor Chris Evelo

  87. A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

    Article • Frontiers in Genetics, November 2017, Frontiers

    Professor Chris Evelo

  88. Adverse outcome pathways: opportunities, limitations and open questions

    Article • Archives of Toxicology, October 2017, Springer Science + Business Media

    Professor Chris Evelo

  89. Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

    Article • Journal of Proteome Research, October 2017, American Chemical Society (ACS)

    Professor Chris Evelo

  90. Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways

    Article • Genomics, October 2017, Elsevier

    Professor Chris Evelo

  91. Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

    Article • Journal of Cheminformatics, September 2017, Springer Science + Business Media

    Dr Miquel Rojas Cherto, Professor Chris Evelo

  92. Myocardial and Serum Galectin-3 Expression Dynamics Marks Post-Myocardial Infarction Cardiac Remodelling

    Article • Heart Lung and Circulation, July 2017, Elsevier

    Professor Chris Evelo

  93. Open Source cheminformatics library in Java

    Article • Journal of Cheminformatics, June 2017, Springer Science + Business Media

    Dr Miquel Rojas Cherto, Professor Chris Evelo

  94. 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

    Article • Molecular Nutrition & Food Research, February 2017, Wiley

    Professor Chris Evelo

  95. Reliable Granular References to Changing Linked Data

    Article • January 2017, Springer Science + Business Media

    Professor Chris Evelo

  96. Rett syndrome – biological pathways leading from MECP2 to disorder phenotypes

    Article • Orphanet Journal of Rare Diseases, November 2016, Springer Science + Business Media

    Professor Chris Evelo

  97. Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

    Article • Epigenetics & Chromatin, November 2016, Springer Science + Business Media

    Professor Chris Evelo

  98. Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

    Article • Epigenetics & Chromatin, October 2016, Springer Science + Business Media

    Professor Chris Evelo

  99. Organ-Specific Gene Expression Changes in the Fetal Liver and Placenta in Response to Maternal Folate Depletion

    Article • Nutrients, October 2016, MDPI AG

    Professor Chris Evelo

  100. XMetDB: an open access database for xenobiotic metabolism

    Article • Journal of Cheminformatics, September 2016, Springer Science + Business Media

    Professor Chris Evelo

  101. New insights in Rett syndrome using pathway analysis for transcriptomics data

    Article • Wiener Medizinische Wochenschrift, August 2016, Springer Science + Business Media

    Professor Chris Evelo

  102. Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes

    Article • July 2016, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  103. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

    Article • PLoS Computational Biology, June 2016, PLOS

    Professor Chris Evelo, Dr Alexander Pico

  104. 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

    Article • Molecular Nutrition & Food Research, June 2016, Wiley

    Professor Chris Evelo

  105. Reactome from a WikiPathways Perspective

    Article • PLoS Computational Biology, May 2016, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  106. The systems biology format converter

    Article • BMC Bioinformatics, April 2016, Springer Science + Business Media

    Professor Chris Evelo

  107. The FAIR Guiding Principles for scientific data management and stewardship

    Article • Scientific Data, March 2016, Springer Science + Business Media

    Dr Niklas U Blomberg, Gaby Appleton, Luiz Olavo Bonino da Silva Santos, Professor Chris Evelo

  108. Inferring causal molecular networks: empirical assessment through a community-based effort

    Article • Nature Chemical Biology, February 2016, Nature

    Professor Julio Saez-Rodriguez, Professor Chris Evelo

  109. The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands

    Article • F1000Research, January 2016, Faculty of 1000, Ltd.

    Prof Barend Mons, Professor Chris Evelo

  110. Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

    Article • MedChemComm, January 2016, Royal Society of Chemistry

    Professor Chris Evelo

  111. A community-created database of biological knowledge, freely available and easy to reuse

    Article • Nucleic Acids Research, October 2015, Oxford University Press (OUP)

    Dr Alexander Pico, Professor Chris Evelo

  112. Current systems biology approaches in hazard assessment of nanoparticles

    Article • October 2015, Cold Spring Harbor Laboratory Press

    Professor Chris Evelo

  113. Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

    Article • BMC Bioinformatics, August 2015, Springer Science + Business Media

    Professor Chris Evelo

  114. Integrative network-based analysis of mRNA and microRNA expression in 1,25-dihydroxyvitamin D3-treated cancer cells

    Article • Genes & Nutrition, August 2015, Springer Science + Business Media

    Professor Chris Evelo

  115. A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

    Article • BMC Genomics, June 2015, Springer Science + Business Media

    Professor Chris Evelo

  116. PathVisio 3: An Extendable Pathway Analysis Toolbox

    Article • PLoS Computational Biology, February 2015, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  117. The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands

    Article • F1000Research, February 2015, Faculty of 1000, Ltd.

    Rob Hooft, Professor Chris Evelo, Prof Barend Mons

  118. Puzzling with the pathways of life

    Article • January 2015, University of Maastricht

    Professor Chris Evelo

  119. The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

    Article • PLOS One, December 2014, PLOS

    Professor Chris Evelo

  120. 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

    Article • Genes & Nutrition, September 2014, Springer Science + Business Media

    Professor Chris Evelo

  121. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

    Article • F1000Research, September 2014, Faculty of 1000, Ltd.

    Professor Chris Evelo, Dr Alexander Pico

  122. Easily import and use WikiPathways biological pathways in the common network biology tool Cytoscape

    Article • F1000Research, July 2014, Faculty of 1000, Ltd.

    Dr Alexander Pico, Professor Chris Evelo

  123. Solution for expression when biological objects are the same

    Article • January 2014, Springer Science + Business Media

    Dr Antony John Williams, Professor Chris Evelo

  124. A network biology workflow to study transcriptomics data of the diabetic liver

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Professor Chris Evelo

  125. Applying linked data approaches to pharmacology: Architectural decisions and implementation

    Article • Semantic Web – Interoperability Usability Applicability, January 2014, IOS Press

    Dr Antony John Williams, Professor Chris Evelo

  126. Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

    Article • Genes & Nutrition, December 2013, Springer Science + Business Media

    Professor Chris Evelo

  127. CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis

    Article • PLOS One, December 2013, PLOS

    Professor Chris Evelo

  128. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org

    Article • Nucleic Acids Research, April 2013, Oxford University Press (OUP)

    Professor Chris Evelo

  129. A pathway approach to investigate the function and regulation of SREBPs

    Article • Genes & Nutrition, March 2013, Springer Science + Business Media

    Professor Chris Evelo

  130. Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets

    Article • PLOS One, November 2012, PLOS

    Professor Chris Evelo

  131. An outline of what Open PHACTS is

    Article • Drug Discovery Today, November 2012, Elsevier

    Dr Antony John Williams, Dr Niklas U Blomberg, Professor Chris Evelo

  132. Marginal selenium deficiency down-regulates inflammation-related genes in splenic leukocytes of the mouse

    Article • The Journal of Nutritional Biochemistry, September 2012, Elsevier

    Professor Chris Evelo

  133. GO-Elite: a flexible solution for pathway and ontology over-representation

    Article • Bioinformatics, June 2012, Oxford University Press (OUP)

    Professor Chris Evelo, Dr Alexander Pico

  134. Effect of supplementation with an 80:20cis9,trans11 conjugated linoleic acid blend on the human platelet proteome

    Article • May 2012, Wiley

    Professor Chris Evelo

  135. Toward interoperable bioscience data

    Article • Nature Genetics, February 2012, Springer Science + Business Media

    Professor Chris Evelo

  136. An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

    Article • BMC Genomics, January 2012, Springer Science + Business Media

    Professor Chris Evelo

  137. Exposing WikiPathways as Linked Open Data

    Article • Nature Precedings, December 2011, Springer Science + Business Media

    Professor Chris Evelo

  138. WikiPathways: building research communities on biological pathways

    Article • Nucleic Acids Research, November 2011, Oxford University Press (OUP)

    Dr Alexander Pico, Professor Chris Evelo

  139. Measuring impact in online resources with the CI­number (the CitedIn Number for online impact)

    Article • Nature Precedings, June 2011, Springer Science + Business Media

    Professor Chris Evelo

  140. Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention

    Article • Physiological Genomics, April 2011, American Physiological Society

    Professor Chris Evelo

  141. 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

    Article • BMC Medical Genomics, March 2011, Springer Science + Business Media

    Professor Chris Evelo

  142. Using a data triangle to understand molecular nutrition

    Article • Nature Reports Climate Change, February 2011, Nature

    Professor Chris Evelo

  143. Exploring pathway interactions in insulin resistant mouse liver

    Article • BMC Systems Biology, January 2011, Springer Science + Business Media

    Professor Chris Evelo

  144. The nutritional phenotype database*. A real data structure for systems biology

    Article • Nature Reports Climate Change, November 2010, Nature

    Professor Chris Evelo

  145. Answering biological questions: querying a systems biology database for nutrigenomics

    Article • Genes & Nutrition, October 2010, Springer Science + Business Media

    Professor Chris Evelo

  146. The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

    Article • Genes & Nutrition, October 2010, Springer Science + Business Media

    Professor Chris Evelo

  147. Connecting the Human Variome Project to nutrigenomics

    Article • Genes & Nutrition, October 2010, Springer Science + Business Media

    Professor Chris Evelo

  148. From Nanotechnology to Nanomedicine: Applications to Cancer Research

    Article • Current Molecular Medicine, October 2010, Bentham Science Publishers

    Professor Chris Evelo

  149. Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

    Article • Drug Discovery Today, October 2010, Elsevier

    Professor Chris Evelo

  150. Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets

    Article • PLoS Biology, August 2010, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  151. A Combined Transcriptomics and Lipidomics Analysis of Subcutaneous, Epididymal and Mesenteric Adipose Tissue Reveals Marked Functional Differences

    Article • PLOS One, July 2010, PLOS

    Professor Chris Evelo

  152. Nature Europe site should highlight most productive countries

    Article • Nature, June 2010, Springer Science + Business Media

    Professor Chris Evelo

  153. Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

    Article • Genes & Nutrition, February 2010, Springer Science + Business Media

    Professor Chris Evelo

  154. Time-Resolved and Tissue-Specific Systems Analysis of the Pathogenesis of Insulin Resistance

    Article • PLOS One, January 2010, PLOS

    Professor Chris Evelo

  155. 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

    Article • Molecular and Cellular Endocrinology, January 2010, Elsevier

    Professor Chris Evelo

  156. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Professor Chris Evelo, Dr Alexander Pico

  157. Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon

    Article • Molecular Nutrition & Food Research, December 2009, Wiley

    Professor Chris Evelo, Professor Lutz Schomburg

  158. Pathway Enrichment Based on Text Mining and Its Validation on Carotenoid and Vitamin A Metabolism

    Article • OMICS A Journal of Integrative Biology, October 2009, Mary Ann Liebert Inc

    Professor Chris Evelo

  159. Mining Biological Pathways Using WikiPathways Web Services

    Article • PLOS One, July 2009, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  160. Reduction of colonic inflammation in HLA-B27 transgenic rats by feeding Marie Ménard apples, rich in polyphenols

    Article • British Journal Of Nutrition, July 2009, Cambridge University Press

    Professor Chris Evelo

  161. Community curation on WikiPathways: How we assist knowledge collection

    Article • Nature Precedings, April 2009, Springer Science + Business Media

    Professor Chris Evelo

  162. An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions

    Article • Genes & Nutrition, March 2009, Springer Science + Business Media

    Professor Chris Evelo

  163. Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation

    Article • Genes & Nutrition, November 2008, Springer Science + Business Media

    Professor Chris Evelo

  164. 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

    Article • Genes & Nutrition, November 2008, Springer Science + Business Media

    Professor Chris Evelo

  165. The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation

    Article • Genes & Nutrition, November 2008, Springer Science + Business Media

    Professor Chris Evelo

  166. The role of bioinformatics in pathway curation

    Article • Genes & Nutrition, November 2008, Springer Science + Business Media

    Professor Chris Evelo

  167. Validating nutrient-related gene expression changes from microarrays using RT2 PCR-arrays

    Article • Genes & Nutrition, November 2008, Springer Science + Business Media

    Professor Chris Evelo

  168. The public road to high-quality curated biological pathways

    Article • Drug Discovery Today, October 2008, Elsevier

    Professor Chris Evelo, Dr Alexander Pico

  169. WikiPathways: Pathway Editing for the People

    Article • PLoS Biology, July 2008, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  170. Presenting and exploring biological pathways with PathVisio

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Dr Alexander Pico, Professor Chris Evelo

  171. Differential valine metabolism in adipose tissue of low and high fat-oxidizing obese subjects

    Article • PROTEOMICS - CLINICAL APPLICATIONS, October 2007, Wiley

    Professor Chris Evelo

  172. Impact of supervised gene signatures of early hypoxia on patient survival

    Article • Radiotherapy and Oncology, June 2007, Elsevier

    Professor Chris Evelo

  173. Genetic variation in thioredoxin interacting protein (TXNIP) is associated with hypertriglyceridaemia and blood pressure in diabetes mellitus

    Article • Diabetic Medicine, May 2007, Wiley

    Professor Chris Evelo

  174. Fasting induces a biphasic adaptive metabolic response in murine small intestine

    Article • BMC Genomics, January 2007, Springer Science + Business Media

    Professor Chris Evelo

  175. Linking microarray reporters with protein functions

    Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

    Professor Chris Evelo

  176. Gene profiling of cathepsin K deficiency in atherogenesis: profibrotic but lipogenic

    Article • The Journal of Pathology, November 2006, Wiley

    Professor Chris Evelo

  177. Microarray profiling of human white adipose tissue after exogenous leptin injection

    Article • European Journal of Clinical Investigation, March 2006, Wiley

    Professor Chris Evelo

  178. Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress

    Article • Physiological Genomics, February 2006, American Physiological Society

    Professor Guido R Haenen, Professor Chris Evelo

  179. Article • BMC Bioinformatics, January 2006, Springer Science + Business Media

    Professor Chris Evelo

  180. Up-regulation of CD36/FAT in preadipocytes in familial combined hyperlipidemia

    Article • The FASEB Journal, October 2005, Federation of American Societies For Experimental Biology (FASEB)

    Professor Chris Evelo

  181. Gene Profiling in Atherosclerosis Reveals a Key Role for Small Inducible Cytokines: Validation Using a Novel Monocyte Chemoattractant Protein Monoclonal Antibody

    Article • Circulation, June 2005, Wolters Kluwer Health

    Professor Chris Evelo

  182. A systematic review of large scale and heterogeneous gene array data in heart failure

    Article • March 2005, Elsevier

    Professor Chris Evelo

  183. Protein profiling of 3T3-L1 adipocyte differentiation and (tumor necrosis factor ?-mediated) starvation

    Article • Cellular and Molecular Life Sciences, February 2005, Springer Science + Business Media

    Professor Chris Evelo

  184. Erythrocyte antioxidant defense response against cigarette smoking in humans—the glutathione S-transferase vulnerability

    Article • Journal of Biochemical and Molecular Toxicology, January 2005, Wiley

    Professor Chris Evelo, Professor Hilmi Orhan

  185. Thrombospondin-2 Is Essential for Myocardial Matrix Integrity: Increased Expression Identifies Failure-Prone Cardiac Hypertrophy

    Article • Circulation Research, September 2004, Wolters Kluwer Health

    Professor Chris Evelo

  186. Role of the Rhoa/Rho Kinase System in Flow-Related Remodeling of Rat Mesenteric Small Arteries in Vivo

    Article • Journal of Vascular Research, January 2004, Karger Publishers

    Professor Chris Evelo

  187. Inhibition of various glutathione S-transferase isoenzymes by RRR-α-tocopherol

    Article • Toxicology in Vitro, June 2003, Elsevier

    Professor Guido R Haenen, Professor Chris Evelo

  188. Tocotrienols Inhibit Human Glutathione S-Transferase P1-1

    Article • IUBMB Life, August 2002, Wiley

    Professor Guido R Haenen, Professor Chris Evelo

  189. Hypochlorous acid is a potent inhibitor of GST P1-1

    Article • Chemico-Biological Interactions, October 2001, Elsevier

    Professor Guido R Haenen, Professor Chris Evelo

  190. Inhibition of human glutathione S-transferase P1-1 by tocopherols and α-tocopherol derivatives

    Article • Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, July 2001, Elsevier

    Professor Guido R Haenen, Professor Chris Evelo

  191. No reduction of α-tocopherol quinone by glutathione in rat liver microsomes

    Article • Biochemical Pharmacology, March 2001, Elsevier

    Professor Guido R Haenen, Professor Chris Evelo

  192. α-Tocopherol Inhibits Human Glutathione S-Transferase π

    Article • Biochemical and Biophysical Research Communications, January 2001, Elsevier

    Professor Guido R Haenen, Professor Chris Evelo

  193. A Study on the Interaction between Hydroxylamine Analogues and Oxyhemoglobin in Intact Erythrocytes

    Article • August 2000, Elsevier

    Professor Chris Evelo

  194. Erythrocyte glutathione S transferase as a marker of oxidative stress at birth

    Article • Archives of Disease in Childhood Fetal & Neonatal, September 1999, BMJ

    Professor Chris Evelo

  195. Changes in levels of catalase and glutathione in erythrocytes of patients with stable asthma, treated with beclomethasone dipropionate

    Article • June 1999, European Respiratory Society (ERS)

    Professor Chris Evelo

  196. Changes in levels of catalase and glutathione in erythrocytes of patients with stable asthma, treated with beclomethasone dipropionate

    Article • European Respiratory Journal, June 1999, European Respiratory Society (ERS)

    Professor Chris Evelo

  197. Only the glutathione dependent antioxidant enzymes are inhibited by haematotoxic hydroxylamines

    Article • Human & Experimental Toxicology, October 1998, SAGE Publications

    Professor Chris Evelo

  198. Only the glutathione dependent antioxidant enzymes are inhibited by haematotoxic hydroxylamines

    Article • Human & Experimental Toxicology, October 1998, SAGE Publications

    Professor Chris Evelo

  199. Two Mechanisms for Toxic Effects of Hydroxylamines in Human Erythrocytes: Involvement of Free Radicals and Risk of Potentiation

    Article • September 1998, Elsevier

    Professor Chris Evelo

  200. Oxidative effects in human erythrocytes caused by some oximes and hydroxylamine

    Article • Archives of Toxicology, April 1998, Springer Science + Business Media

    Professor Chris Evelo

  201. Hydroxylamine Treatment Increases Glutathione-Protein and Protein-Protein Binding in Human Erythrocytes

    Article • December 1997, Elsevier

    Professor Chris Evelo

  202. In vitro haematotoxic effects of three methylated hydroxylamines

    Article • Archives of Toxicology, April 1997, Springer Science + Business Media

    Professor Chris Evelo

  203. Glutathione depletion in human erythrocytes and rat liver: a study on the interplay between bioactivation and inactivation functions of liver and blood

    Article • Toxicology in Vitro, June 1996, Elsevier

    Professor Chris Evelo

  204. Glutathione depletion in human erythrocytes as an indicator for microsomal activation of cyclophosphamide and 3-hydroxyacetanilide

    Article • Toxicology, November 1993, Elsevier

    Professor Chris Evelo

  205. Physiologically based toxicokinetic modeling of 1,3-butadiene lung metabolism in mice becomes more important at low doses

    Article • November 1993, Environmental Health Perspectives

    Professor Chris Evelo

  206. Development of a software package for computer simulations: The use of a sorted event list for reduction of calculation times

    Article • Computers in Biology and Medicine, July 1993, Elsevier

    Professor Chris Evelo

  207. Influence of oxygen supply on liver condition and elimination of dimethylacetamide in the isolated perfused rat liver

    Article • Toxicology in Vitro, July 1992, Elsevier

    Professor Chris Evelo

  208. Changes in blood glutathione concentrations, and in erythrocyte glutathione reductase and glutathione S-transferase activity after running training and after participation in contests

    Article • European Journal of Applied Physiology and Occupational Physiology, January 1992, Springer Science + Business Media

    Professor Chris Evelo

  209. 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

    Article • Archives of Toxicology, February 1991, Springer Science + Business Media

    Professor Chris Evelo

  210. Influence of glutathione on the formation of cysteine alkylation products in human hemoglobin

    Article • Toxicology, November 1988, Elsevier

    Professor Chris Evelo

  211. Separation of human haemoglobin alkylated at β93 cysteine from its native form by fast protein liquid chromatography

    Article • Journal of Chromatography B Biomedical Sciences and Applications, January 1988, Elsevier

    Professor Chris Evelo

  212. Urinary cyclophosphamide assay as a method for biological monitoring of occupational exposure to cyclophosphamide

    Article • International Archives of Occupational and Environmental Health, June 1986, Springer Science + Business Media

    Professor Chris Evelo

  213. Kinetics of the formation and secretion of the aniline metabolite 4-aminophenol and its conjugates by isolated rat hepatocytes

    Article • Xenobiotica, January 1984, Taylor & Francis

    Professor Chris Evelo

  214. Toxicological stress indicators in human red blood cells : changes in glutathione and glutathione S-transferase as biological markers for electrophilic and oxidative stress

    Article • University of Maastricht

    Professor Chris Evelo