139 papers
The paper introduces CELLSWARM, a novel framework that replaces traditional hand-coded rules with LLM-driven autonomous cell agents to accurately recapitulate tumor microenvironment dynamics while uniquely enabling cross-cancer generalization, clinical treatment response prediction, and the detection of indirect genetic perturbations.
This study reveals that inflammatory signals activate NF-κB to transcriptionally upregulate p53, shifting its dynamics from oscillatory to sustained accumulation, which paradoxically impairs DNA repair and demonstrates a counterintuitive functional antagonism between these two key stress-response pathways.
This paper introduces the Web of Microbes Agent, an autonomous system integrating a Bayesian Personalized Ranking model, a growth model, and a Large Language Model to accurately predict and orchestrate bacterial substrate preferences for applications in microbiome engineering and cultivation.
By integrating transcriptomic and lipidomic data, this study reveals that a specific phosphatidylinositol profile driven by arachidonic acid metabolism is essential for healthy colonocyte differentiation, while its disruption and the resulting shift toward monounsaturated fatty acid species in tumors highlight a critical mechanism underlying colon cancer malignization.
This study demonstrates that the distinct infection sites of two xylem-colonizing pathogens, *Xanthomonas campestris* and *Ralstonia solanacearum*, expose them to different xylem sap flow constraints, driving the evolution of opposite regulatory programs that optimize trade-offs between multiplication and dissemination to ensure successful host colonization.
This study establishes a rigorous statistical framework for a two-phase ageing model using longitudinal data from Drosophila and mice, revealing that the transition to the frail "Smurf" state is governed by an exponentially increasing hazard rate followed by a distinct period of high early mortality and a subtle negative dependence on prior non-Smurf lifespan.
By integrating multi-omics approaches on human kidney biopsies, this study elucidates how complement-mediated dysregulation in podocytes and parietal epithelial cells drives glomerular injury and fibrosis in focal segmental glomerulosclerosis, revealing potential targets for stage-specific interventions.
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.
Using parallel sequential fluorescence in situ hybridization (par-seqFISH) to profile individual bacteriophage lambda transcripts within infected *E. coli*, this study reveals that while lysogenic fate requires consensus activity among all coinfecting phages, lytic cells can harbor individual phages exhibiting lysogenic activity, thereby demonstrating how whole-cell fate decisions emerge from the stochastic and heterogeneous behavior of distinct viral genomes.
This study demonstrates that microgravity accelerates aging and impairs neuromuscular function in *C. elegans* by suppressing mechanoreceptor gene expression, but these detrimental effects can be mitigated by restoring tactile stimulation through physical contact with beads in the culture medium.
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.
This study analyzes a decade of longitudinal proteomic data from middle-aged adults to demonstrate that organ-specific aging clocks are stable, dynamic indicators that track subclinical risk factors, reveal the central role of immune and adipose systems, and reflect the profound impact of menopause and medication on multi-organ aging trajectories.
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 demonstrates that evolutionary dynamics on degenerate fitness landscapes are not neutral, as stochastic mutation-selection processes induce a directional drift toward flatter, more robust regions driven by the interaction between population variability and landscape curvature.
Through a five-layer integrative systems analysis, this study reveals that *Leishmania* stage differentiation is governed primarily by post-transcriptional mechanisms, specifically highlighting the essential role of differential protein degradation and translation regulation in driving parasite development despite constitutive gene transcription.
By developing spatially resolved models of the yeast galactose switch that integrate experimentally derived intracellular architectures, this study demonstrates that accounting for 3D cellular organization and local reaction rules—particularly ER-associated translation—significantly alters regulatory predictions compared to traditional well-mixed assumptions.
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 paper introduces NEWT, a multimodal deep learning framework that integrates diverse biological data sources into a unified representation to improve drug-target prediction accuracy and reconstruct developmental lineage hierarchies, thereby bridging pharmacogenomic and single-cell transcriptomic analyses.
This study presents an AI-driven, multi-omic framework that integrates large-scale datasets and causal genetic analyses to identify 29 high-confidence and 16 novel therapeutic targets shared between aging and 12 age-related diseases, highlighting convergent inflammatory pathways and specific genes like IL6R as promising candidates for drug repurposing.