Systems Biology

Circulating miRNA-Protein Signatures Predict Outcomes in Pediatric Dilated Cardiomyopathy Vicentino, A. R., Karimpour-Fard, A., Hamza, T. H., Stauffer, B. L., Lavine, K. J., Miyamoto, S. D., Lipschultz, S., Sucharov, C. C. biorxiv.org/content/10.648…

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models Wang, C., Karimzadeh, M., Ravindra, N. G., Bounds, L. R., Alerasool, N., Huang, A. C., Ma, S., Gulbranson, D. R., Cui, H., Lee, Y., ... biorxiv.org/content/10.648…

New perspectives in assessing environmental risks for birds: a simple TKTD framework to link growth and reproduction energy budget to chemical stress Baudrot, V., Kaag, M., Charles, S. biorxiv.org/content/10.648…

Interpretable machine learning meets systems biology to decode genotype-phenotype maps Reguna Madhan, R. L., Balaji, R., Sinha, H., Bhatt, N. biorxiv.org/content/10.648…

A Multiscale Computational Architecture to Study Signaling Dynamics at Cell-Cell Interfaces Wu, Y. biorxiv.org/content/10.648…

Canonical Analysis of Fluorescent Timer-Anchored Transcriptomes Resolves Joint Temporal and Developmental Progression Irie, N., Reda, O., Satou, Y., Ono, M. biorxiv.org/content/10.648…

A Unified Dynamical-Systems and Control-Theoretic Model for Single-Cell Fate Dynamics Redd, D. M., Green, S. G., Terooatea, T. W. biorxiv.org/content/10.648…

Dissecting the Network Architecture of a Plant Circadian Clock Model: Identifying Key Regulatory Mechanisms and Essential Interactions Singh, S. K., Srivastava, A. biorxiv.org/content/10.648…

GeNETop: Context-Specific Genome-Scale Constrained Models Using Network Topology, Flux Variability, and Transcriptomics Troitino-Jordedo, D., Mansouri, A., Minebois, R., Querol, A., Remondini, D., Balsa-Canto, E. biorxiv.org/content/10.648…

MICA: Model-Informed Change-point Analysis Lotfi, M., Kaderali, L. biorxiv.org/content/10.648…

TRAILBLAZER: generative multicellular perturbation model of biology Grzybowski, A. T., Nener, J., Selvamani, P., Badarinarayan, S. S., Chandramohan, N. biorxiv.org/content/10.648…

BoolDog: integrated Boolean and semi-quantitative network modelling in Python Bleker, C., Zagorscak, M., Blejec, A., Gruden, K., Zupanic, A. biorxiv.org/content/10.648…

Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome Nde, J., Majila, K., Zimmermann, R., Kempf, C., Zhang, Y., Cesare, J., Thornton, J., Workman, J., Florens, L., Viswanath, S., Washburn, M. biorxiv.org/content/10.648…

Informing agent-based models with spatial data using convolutional autoencoders Wang, B.-r., Liao, C.-y. A., Danen, E., Neubert, E., Eduati, F. biorxiv.org/content/10.648…

A stress-function tradeoff organizes epithelial heterogeneity across spatial scales in the human thyroid Korem Kohanim, Y., Barkai, T., Novoselsky, R., Shir, S., Bahar Halpern, K., Reich-Zeliger, S., Elkahal, J., Tessler, I., Shivatzki, S., ... biorxiv.org/content/10.648…

The Female Biomarker Challenge: Sex-Specific Network Robustness Constrains Biological Age Estimation and Geroscience Trial Design Harding, A. S., Coward, J., Tian, T. biorxiv.org/content/10.648…

Alveolar-Basal Intermediates Drive Pulmonary Fibrosis via Coordination of a Pro-Fibrotic Signaling Niche in Silicosis Zhao, B., Warheit-Niemi, H. I., Cook, K. C. S., Pitstick, L., Toth, A., Elitz, A., McCormack, F. X., Zacharias, A. L., Zacharias, W. J. biorxiv.org/content/10.648…

A high-throughput cost-efficient in vitro platform for the screening of immune senomodulators Carraro, C., Zajac, T., Lindenberg, S., Leidner, J., Ragogna, A., Hussein, B., Mueller, S., van Uelft, M., Theis, H., De Domenico, E., Beyer, M., ... biorxiv.org/content/10.648…

1100 Synthetic Benchmark Problems for Dynamic Modeling of Cellular Processes Neubrand, N., Rachel, T., Litwin, T., Timmer, J., Kreutz, C., Hess, M. biorxiv.org/content/10.648…

A Network-Based Approach for Prioritizing Candidate Genes in Alzheimer's Disease Malhotra, N., Samanta, S., Deshpande, A. biorxiv.org/content/10.648…