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The Network Zoo: a multilingual package for the inference and analysis of biological networks2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Marouen Ben Guebila, Tian Wang, Camila M. Lopes‐Ramos, Viola Fanfani, Deborah A. Weighill, Rebekka Burkholz, +17 more
1citations -
On the flexibility of the cellular amination network in E. coli2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Helena Schulz-Mirbach, Alexandra Müller, Tong Wu, Pascal Pfister, Lennart Schada von Borzyskowski, Tobias J. Erb, +2 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 -
Modeling neuron-astrocyte interactions in neural networks using distributed simulation2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neural dynamics and brain function Open access
Han-Jia Jiang, Jugoslava Aćimović, Tiina Manninen, Iiro Ahokainen, Jonas Stapmanns, Mikko Lehtimäki, +4 more
4citations -
Invasive cancer cells soften collagen networks and disrupt stress-stiffening via volume exclusion, contractility and adhesion2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Irène Nagle, Margherita Tavasso, Ankur Bordoloi, Iain Muntz, Gijsje Hendrika Koenderink, Pouyan E. Boukany
1citations -
CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
James Shiniti Nagai, Nils B. Leimkühler, Michael T. Schaub, Rebekka K. Schneider, Ivan G. Costa
9citations -
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Daniel Osorio, Anna Capasso, S. Gail Eckhardt, Uma P. Giri, Alexander J. Somma, Todd M. Pitts, +8 more
2citations -
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Marouen Ben Guebila, Daniel C. Morgan, Kimberly Glass, Marieke L. Kuijjer, Dawn Lisa DeMeo, John Quackenbush
2citations -
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 -
Quantitative Mapping of Keratin Networks in 3D2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Skin and Cellular Biology Research Open access
Reinhard Windoffer, Nicole Schwarz, Sungjun Yoon, Teodora Piskova, Michael Scholkemper, Johannes Stegmaier, +3 more
2citations -
Modelling the mechanical cross-talk between cells and fibrous extracellular matrix using hybrid cellular Potts and molecular dynamics methods2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Erika Tsingos, Bente Hilde Bakker, Koen A.E. Keijzer, Hermen Jan Hupkes, Roeland M. H. Merks
1citations -
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 -
scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
0citations -
Intermediate filament network perturbation in the C. elegans intestine causes systemic toxicity2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Skin and Cellular Biology Research Open access
Florian Geisler, Sanne Remmelzwaal, Mike Boxem, Rudolf E. Leube
0citations -
Long-term human organotypic brain slice cultures: a detailed protocol to provide a comprehensive framework for single-neuron and neuronal network investigations2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neuroscience and Neuropharmacology Research Open access
Aniella Bak, Henner Koch, Karen M. J. van Loo, Katharina Schmied, Birgit Gittel, Yvonne G. Weber, +4 more
1citations