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GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
Cell type heterogeneity in gene co-expression networks: implications for toxicological research2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Imke B. Bruns, Yingxue Li, James L. Stevens, Bob van de Water, Giulia Callegaro
3citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment2024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
5citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl22024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl72024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl32024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl12024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl82024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl62024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment_Suppl52024 ALTEX article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Steven J. Kunnen, Emma Arnesdotter, Christian Tobias Willenbockel, Mathieu Vinken, Bob van de Water
0citations -
Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation2025 iScience article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Steven J. Kunnen, Giulia Callegaro, Jeffrey J. Sutherland, Panuwat Trairatphisan, Hugo W van Kessel, Lukas S. Wijaya, +11 more
4citations -
P22-09: Application of Weighted Gene Co-expression Network Analysis as Mode of Action Screening Method for Suspected Non-Genotoxic Carcinogens Inducing Oxidative Stress2023 Toxicology Letters article Biochemistry, Genetics and Molecular Biology Carcinogens and Genotoxicity Assessment
Christina H. J. Veltman, Jeroen L. A. Pennings, Marije Niemeijer, B. Islam, Emiel Rorije, Marco J. Zeilmaker, +4 more
0citations -
The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment2021 Archives of Toxicology article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Giulia Callegaro, Steven J. Kunnen, Panuwat Trairatphisan, Solène Grosdidier, Marije Niemeijer, Wouter den Hollander, +9 more
43citations -
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data2023 Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Ping‐Han Hsieh, Camila M. Lopes‐Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
12citations -
NetTDP: permutation-based true discovery proportions for differential co-expression network analysis2022 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Menglan Cai, Anna Vesely, Xu Chen, Limin Li, Jelle J. Goeman
1citations -
Co-expression patterns of microglia markers Iba1, TMEM119 and P2RY12 in Alzheimer's disease2022 Neurobiology of Disease article Neuroscience Neuroinflammation and Neurodegeneration Mechanisms Open access
Boyd Kenkhuis, Antonios Somarakis, Lynn R.T. Kleindouwel, Willeke van Roon‐Mom, Thomas Höllt, Louise van der Weerd
190citations -
Recommendations for the analysis of gene expression data to identify intrinsic differences between similar tissues2020 Genomics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Tooba Abbassi‐Daloii, Hermien E. Kan, Vered Raz, Peter A.C. ’t Hoen
16citations -
KidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease2023 European Journal of Human Genetics article Biochemistry, Genetics and Molecular Biology Genomics and Rare Diseases Open access
Floranne Boulogne, Laura R. Claus, Henry H. Wiersma, Roy Oelen, Floor Schukking, Niek de Klein, +15 more
15citations