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GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint 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 -
Utilizing gene co-expression networks with the rat kidney TXG-MAPr tool to enhance safety assessment, biomarker identification and human translation2023 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
1citations -
Genetic modulation of immune gene co-expression in the aged mouse hippocampus by the Apbb1ip locus2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neuroinflammation and Neurodegeneration Mechanisms Open access
James E. Tomkins, Aditi Methi, Gerard A. Bouland, Birte Doludda, Kitty B. Murphy, Jeremy A. Miller, +2 more
0citations -
Systematic comparison of temporal transcriptional responses to hepatotoxicants in primary human hepatocytes and HepaRG cells using concentration-response modelling of gene co-expression networks2023 bioRxiv (Cold Spring Harbor Laboratory) preprint 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 -
KidneyNetwork: Using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease2022 Research Square preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Floranne Boulogne, Laura R. Claus, Henry H. Wiersma, Roy Oelen, Floor Schukking, Niek de Klein, +15 more
2citations -
A Network-based Transcriptomic Landscape of HepG2 cells to Uncover Causal Gene Cytotoxicity Interactions Underlying Drug-Induced Liver Injury2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Lukas S. Wijaya, Attila Gábor, Iris Pot, Luca van de Have, Julio Sáez-Rodríguez, James L. Stevens, +3 more
1citations -
The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Agricultural and Biological Sciences Chromosomal and Genetic Variations Open access
Alexandre Hild Aono, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, +13 more
0citations -
Temporal transcriptome analysis of the endothelial response to tumour necrosis factor2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology interferon and immune responses Open access
EC Struck, Tatiana Belova, Ping‐Han Hsieh, Jacob Odeberg, Marieke L. Kuijjer, Philip Dusart, +1 more
0citations -
Understanding functional consequences of type 2 diabetes risk loci using the universal data integration and visualization R package CONQUER2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Gerard A. Bouland, Joline W. J. Beulens, Joey Nap, Arno R. van der Slik, Arnaud Zaldumbide, Leen M. ‘t Hart, +1 more
1citations -
WWP2 osteoarthritis risk allele rs1052429-A confers risk by affecting cartilage matrix deposition via hypoxia associated genes2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Osteoarthritis Treatment and Mechanisms Open access
Margo Tuerlings, George M. C. Janssen, Ilja Boone, Marcella van Hoolwerff, Alejandro Rodríguez Ruiz, Evelyn Houtman, +7 more
1citations -
The human hepatocyte TXG-MAPr: WGCNA transcriptomic modules to support mechanism-based risk assessment2021 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
1citations -
Long Non-Coding RNAs in Response to Ebola Virus Vaccine-Induced Immunity2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer-related molecular mechanisms research Open access
Izabela Mamede, Thomaz Lüscher Dias, Isabelle Franco Moscardini, Barbara Marinho, Fernando Marcon, Thiago Dominguez Crespo Hirata, +11 more
0citations -
Elucidating another level of epigenetic regulation in osteoarthritis by identifying functional cis -acting long non-coding RNAs and their targets in articular cartilage2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Osteoarthritis Treatment and Mechanisms Open access
Marcella van Hoolwerff, Paula I. Metselaar, Margo Tuerlings, H. Eka D. Suchiman, Nico Lakenberg, Y.F. Ramos, +6 more
0citations -
NAC Transcription Factors ATAF1 and ANAC055 Negatively Regulate Thermomemory in Arabidopsis2021 Research Square preprint Agricultural and Biological Sciences Plant Stress Responses and Tolerance Open access
Nouf Owdah Alshareef, Yong Woo, Tobias de Werk, Iman Kamranfar, Bernd Mueller‐Roeber, Mark A. Tester, +2 more
1citations -
Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Agricultural and Biological Sciences Powdery Mildew Fungal Diseases Open access
Jiangzhao Qian, Heba M. M. Ibrahim, Myriam Erz, Florian Kümmel, Ralph Panstruga, Stefan Kusch
2citations -
Prediction of gene cluster function based on transcriptional regulatory networks uncovers a novel locus required for desferrioxamine B biosynthesis2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Microbial Natural Products and Biosynthesis Open access
Hannah E. Augustijn, Zachary L. Reitz, Le Zhang, Jeanine A. Boot, Somayah S. Elsayed, Gregory L. Challis, +2 more
6citations -
Deletion of RFX6, a Diabetes-Associated Gene, Impairs iPSC-Derived Islet Organoid Development and Survival, With No Impact on the Generation of PDX1+/NKX6.1+ Progenitors2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Pancreatic function and diabetes Open access
Noura Aldous, Ahmed Kamel Elsayed, Bushra Memon, Sadaf Ijaz, Sikander Hayat, Essam Mohamed Abdelalim
0citations -
Loss-of-function variants in the KCNQ5 gene are associated with genetic generalized epilepsies2021 medRxiv preprint Biochemistry, Genetics and Molecular Biology Ion channel regulation and function Open access
Johanna Krüger, Julian Schubert, Josua Kegele, Audrey Labalme, Miaomiao Mao, Jacqueline Heighway, +15 more
3citations -
Transcriptional response to host chemical cues underpins expansion of host range in a fungal plant pathogen lineage2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Agricultural and Biological Sciences Plant pathogens and resistance mechanisms Open access
Stefan Kusch, Justine Larrouy, Heba M. M. Ibrahim, Noémie Gasset, Olivier Navaud, Malick Mbengué, +4 more
1citations -
Systematic prioritization of candidate genes in disease loci identifies TRAFD1 as a master regulator of IFNγ signalling in celiac disease2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Celiac Disease Research and Management Open access
Adriaan van der Graaf, Maria Magdalena Zorro, Annique Claringbould, Urmo Võsa, Raúl Aguirre‐Gamboa, Chan Li, +13 more
6citations -
Spatio-temporal transcriptomic analysis reveals distinct nephrotoxicity, DNA damage and regeneration response after cisplatin2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Chemotherapy-induced organ toxicity mitigation Open access
Lukas S. Wijaya, Steven J. Kunnen, Panuwat Trairatphisan, Ciaran P. Fisher, Meredith E. Crosby, Kai Schaefer, +11 more
0citations
25 results