121 papers
Systems biology moves beyond studying individual genes or proteins to understand how they work together as a complex, living network. Instead of looking at isolated parts, this field examines the intricate conversations between molecules that drive life, revealing how cellular systems respond to changes and maintain balance. It is a holistic approach that turns vast amounts of data into a coherent story of how organisms function as a whole.
At Gist.Science, we ensure these breakthroughs remain accessible to everyone by processing every new preprint in this category directly from bioRxiv. Our team generates both plain-language explanations for the curious mind and detailed technical summaries for researchers, bridging the gap between rapid scientific discovery and clear understanding.
Below are the latest preprints in systems biology, freshly curated and summarized to help you navigate the cutting edge of network science.
This paper presents a versatile photolithographic method using commercially available reagents to pattern sealed microfluidic devices with diverse biomolecules, enabling in situ surface modification and demonstrating distinct advantages of covalent versus noncovalent DNA binding for target capture and gene expression, respectively.
This paper presents an enhanced cell-tracking algorithm that utilizes open multi-agent systems and an Extended Kalman Filter to model, parameterize, and predict the complex dynamics, interactions, and lineage of heterogeneous cell populations, such as osteosarcoma and mesenchymal stromal cells, in co-culture microscopy videos.
By integrating spatial and single-cell transcriptomics, this study reveals that celiac disease disrupts the normal crypt-villus organization through shortened distances between BMP- and WNT-producing mesenchymal cells, causing enterocytes to acquire a novel, aberrant identity characterized by overlapping zonal programs and gastric metaplasia.
This paper presents a NetLogo-based agent-based model that successfully replicates the key phases of actin polymerization, including global treadmilling and the competition between nucleation and elongation, demonstrating its utility as a tool for simulating complex molecular mechanisms through parameter manipulation.
The authors developed a computational deconvolution method combined with a population model to overcome the limitations of bulk proteomics and imperfect cell synchronization, successfully resolving cell cycle-dependent protein dynamics for 563 proteins in budding yeast and revealing significant metabolic variations across cell cycle phases.
This paper introduces Signal Hierarchical Petri Nets, a novel computational formalism that achieves emergent threshold dynamics and spontaneous homeostasis by bidirectionally coupling metabolic state (ATP levels) with regulatory control, enabling the in silico recapitulation of adaptive cellular behaviors like pathway switching and tissue-specific drug accumulation without explicit programming.
This paper introduces a topology-based coherence matrix to demonstrate that hierarchical organization, specifically a dense feedback-rich middle layer, enables sparse gene regulatory networks to achieve robust global regulatory coordination by maintaining structural coherence across varying sparsity levels.
This study demonstrates that the aqueous extract of *Tamarindus indica* fruit pulp effectively stimulates hematopoiesis and significantly ameliorates phenylhydrazine-induced hemolytic anemia in male Wistar rats by reversing hematopathological changes, including RBC morphological distortions, elevated serum LDH, and bone marrow degeneration.
FLARE is a novel contrastive learning framework that enhances metabolite annotation by leveraging bidirectional peak-node alignment to capture fine-grained spectral-structural relationships, achieving state-of-the-art performance and demonstrating significant translational potential in cancer research.
This paper analyzes a simple epidemiological model coupling environmental and direct transmission mechanisms, revealing that their interaction induces complex dynamics such as multistability, backward bifurcations, and sensitivity to initial conditions governed by distinct environmental and combined threshold quantities.