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Every paper Pith has read. Search by title, abstract, or pith.
52 papers in q-bio.CB · page 1
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Limit cycles sweep through rare Turing pattern regimes
How nature discovers rare Turing islands: exploration by common limit cycles
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Nutrient depletion separates sibling bacterial colonies
Kin-ematic Exclusion in Active Matter: Modelling Mutual Inhibition in \textit{Pseudomonas aeruginosa} Sibling Colonies
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3D model checks if cell division rules build plant symmetry
3D mechano-geometric multicellular model of apical stem cell-driven plant morphogenesis
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Mobile nuclei shuttle signals like pigeon post in slime mold
Coexistence of trapped and flow-transported nuclei enables fast pigeon post communication across multinucleated cell
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Extrinsic noise required to explain E
Essential Role of Extrinsic Noise in Models of E. coli Division Control
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Slowing cyclin B synthesis lengthens early fly cell cycles
Mathematical Modeling of Early Embryonic Cell Cycles of Drosophila melanogaster
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Multimodal LLM reasons with omics numbers and language together
OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning
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Benchmark sets standards for TCR-peptide sequence generation
TCRTransBench: A Comprehensive Benchmark for Bidirectional TCR-Peptide Sequence Generation
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Virtual cell models lose accuracy on unseen cells and perturbations
Benchmarking virtual cell models for in-the-wild perturbation response
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Neural net maps microtubule curvatures directly from noisy images
MTCurv: Deep learning for direct microtubule curvature mapping in noisy fluorescence microscopy images
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Invasive cells coagulate three times faster in melanoma clusters
Quantifying the effect of phenotype on clustering behaviour in melanoma: from monoculture to co-culture
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Hydrodynamics make uniform micro-collectives look heterogeneous
Hydrodynamic interactions mask the true heterogeneity of a microscopic collective
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Single-cell patterning creates ordered bacterial films with optical effects
Shaping nematic order in bacterial films with single-cell resolution patterning
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Multi-stage cell cycles improve models of cell proliferation and invasion
Multi-stage volume exclusion models for cell proliferation
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Low molecule counts mask weak contacts in cell collisions
Intrinsic stochasticity in cell polarity and contact inhibition of locomotion
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Intermediate-uptake T cells gain from dendritic cell clusters
Spatial dynamic modelling to understand how dendritic cell clustering affects T cell activation
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Coherence metric flags stress beyond perturbation size
Geometric coherence of single-cell CRISPR perturbations reveals regulatory architecture and predicts cellular stress
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Coherence metric links CRISPR size to stress and regulator type
Geometric coherence of single-cell CRISPR perturbations reveals regulatory architecture and predicts cellular stress
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Thermodynamic bound sets minimum cost to hold cell ion gradients
Unity and Diversity of Intracellular pH Maintenance Mechanisms
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Minimal adhesion model limits follower streams to short cohorts
Cell-cell adhesion cannot sustain extended follower streams in a minimal non-local model of leader-follower migration
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Marangoni flows cluster Piezo1 near focal adhesions
Marangoni-Driven Redistribution and Activity of Piezo1 Molecules in Epithelial and Cancer Cells
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Coherence of cell responses reveals stable gene-edit outcomes
From Syntax to Semantics: Geometric Stability as the Missing Axis of Perturbation Biology
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Varicosities form serotonin reservoirs via diffusive coupling
Compartmental-reaction diffusion framework for microscale dynamics of extracellular serotonin in brain tissue
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Graph conditions enable enumeration of autocatalytic subnetworks in large CRNs
Enumeration of Autocatalytic Subsystems in Large Chemical Reaction Networks
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Geometric structures partition cell survival regions
Matters of Life and Death in Computational Cell Biology
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Bacterial transitions lack single rate outside small-noise limit
Cell State Transitions Beyond the Small-Noise Limit
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Fine-tuned LLMs beat frontier models on cell perturbation prediction
SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction
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Cells keep receptors half-occupied to adapt chemotaxis across wide concentrations
Perfect adaptation in eukaryotic gradient sensing using cooperative allosteric binding
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Framework models multi-phase microbial growth with explicit rates and lags
Mono- and Polyauxic Growth Kinetics: A Semi-Mechanistic Framework for Complex Biological Dynamics
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Maximum entropy yields axon growth correlation exponent -1/2
Maximum-Entropy Model of Colored Noise in Superdiffusive Axonal Growth
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Simplified models preserve pembrolizumab therapy dynamics in CRC
Sensitivity analysis-guided model reduction of a mathematical model of pembrolizumab therapy for de novo metastatic MSI-H/dMMR colorectal cancer
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Graph topology decides when local interactions can produce order
Topological constraints on self-organisation in locally interacting systems
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Waddington vector field adds gene noise and cell signals to tissue models
Incorporating stochastic gene expression, signaling-mediated intercellular interactions, and regulated cell proliferation in models of coordinated tissue development
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Single pembrolizumab dose eradicates advanced MSI-H colorectal tumors
Optimisation of neoadjuvant pembrolizumab therapy for locally advanced MSI-H/dMMR colorectal cancer using data-driven delay integro-differential equations
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Domain length selects bistability of wave-pinning and travelling waves
Bistability of travelling waves and wave-pinning states in a mass-conserved reaction-diffusion system: From bifurcations to implications for actin waves
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Stiffness triggers hierarchical actin phase transitions
Hierarchical phase transitions as mechanical checkpoints of intracellular organization
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Fungi-cyanobacteria pairs consolidate regolith simulant without added nutrients
Weaving Life into Regolith: Engineered Autotrophic-Heterotrophic Consortia for Autonomous Biofabrication from Granular Feedstocks
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π-graphs distinguish endothelial connectivity beyond standard graphs
A Mathematical Reconstruction of Endothelial Cell Networks
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Two dimensions explain most ion channel variability in neurons
Dimensionality reduction of neuronal degeneracy reveals two interfering physiological mechanisms
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FP-IRL recovers rewards and transitions from trajectories without sampling
FP-IRL: Fokker--Planck Inverse Reinforcement Learning -- A Physics-Constrained Approach to Markov Decision Processes
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Method recovers underdamped dynamics from noisy discrete trajectories
Inferring the dynamics of underdamped stochastic systems
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ALE finite-element scheme keeps mass exactly conserved on moving domains
A Conservative Finite Element ALE Scheme for Mass-Conserving Reaction-Diffusion Equations on Evolving Two-Dimensional Domains
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Mean approximate probability enables feasible probabilistic logic
Probabilistic Approximate Logic and its Implementation in the Logical Imagination Engine
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Models map EMT tipping points and path symmetry
Mathematical Modeling of Plasticity and Heterogeneity in EMT
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Brightness analysis measures GPCR clusters despite uneven membranes
Molecular Brightness analysis of GPCR oligomerization in the presence of spatial heterogeneity
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Basolateral fluids shape tissues by controlling hydration
Stay hydrated: Basolateral fluids shaping tissues
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CTC stiffness flips adhesion site in large versus small vessels
Unraveling the vascular fate of deformable circulating tumor cells via a hierarchical computational model
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Light-altering methods target single nerve cells
Single-cell micro- and nano-photonic technologies
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Focal adhesion growth explains why cells spread on stiff substrates
Cell Shape and Durotaxis Follow from Mechanical Cell-Substrate Reciprocity and Focal Adhesion Dynamics: A Unifying Mathematical Model