Clay weekly context brief for the Quantitative Biology category (ISO week 2026-W35). Clay tracks publications from the Quantitative Biology feed list. Below are recent items from this category, each with its source and a short description of what the publication covers when one is available in the source feed. Recent publications: 1. Stochastic mutation as a mechanism for the emergence of SARS-CoV-2 new variants -- A Scientific Conjecture on Artificial Intelligence Paradigm Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2502.10471 The article summaries authors' researches on spreading dynamics of COVID 19 by use of the method of continuously asking and answering questions. 2. Ten simple rules for non-visual, reproducible and accessible bioinformatics Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2608.14400 Bioinformatics workflows rely heavily on visual representations. 3. Bringing analytic rigor to agentic AI for science: The Brain Researcher platform for neuroimaging data analysis Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2608.19902 AI agents can execute scientific analyses, but an analytic output becomes a defensible claim only after alternatives are weighed and the claim is limited to what the evidence supports. 4. Correlations at criticality in ecological communities Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2608.20086 Ecological communities are continually reshaped by invasion, exclusion, and diversification, processes that naturally drive them toward the boundary of dynamical stability. 5. Automatic bioinformatic software named entity recognition from literature Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2608.19201 Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale. 6. Monroe: A Molecular Foundation Model for In-Context Probabilistic Inference Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2608.18982 Bioassay activity prediction is often data-limited because drug-discovery datasets rely on time-consuming and expensive wet-lab experiments for data generation and evaluation. 7. Positive equilibria in mass action networks: geometry and bounds Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2409.06877 Any mass action network gives rise to a parameterised family of polynomial equations whose positive solutions are the positive equilibria of the network. 8. Continuum modeling of fluidic and elastic flow during growth-driven wound closure in partial-EMT cell monolayers Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/2607.05820 Large-scale circular gap closure occurs over a time scale on which cell growth and proliferation become important. 9. COLD-CI: A large-scale very high-resolution label polygon dataset for cocoa and non-cocoa classification in Cote d'Ivoire Source: q-bio.OT (Other Quantitative Biology) Link: https://arxiv.org/abs/2606.20767 Spatially explicit information on cocoa cultivation is essential for land-use planning, deforestation monitoring, environmental assessment, and supply-chain analysis. 10. A quantitative model for the emergent population dynamics of the melanoma MITF rheostat Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2607.11820 Cancer progression is driven by the ability of cells with identical driver mutations to adopt biologically distinct adaptive phenotypes. 11. Quantifying Memorization and Privacy Risks in Genomic Language Models Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2603.08913 Genomic language models (GLMs) have emerged as powerful tools for learning representations of DNA sequences, enabling advances in variant prediction, regulatory element identification, and cross-task transfer learning. 12. Decoding silent reading from non-invasive EEG Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2608.20186 Non-invasive decoding of inner speech faces a fundamental data problem: a corpus pairing brain activity with a person's spontaneous inner monologue cannot be collected, and the available proxy paradigms (cued repetitive and retrospectively reported generative inner speech) are slow to acquire, poorly time-locked, and subject compliance is unverifiable. 13. Novel models of trait evolution via an expansion of Lande's fitness function: The Ornstein-Uhlenbeck process meets the Little Prince's boa Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2608.20232 Adaptive topographies form the foundation for much of our understanding of evolutionary change. 14. Quantum Kernel Estimation for the Discovery of Early Lung Cancer Detection Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2608.19304 Lung cancer screening with low-dose chest computed tomography reduces mortality, but its impact is limited by uptake, adherence, and management challenges. 15. EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2302.12177 Predicting the binding sites of target proteins plays a fundamental role in drug discovery. 16. On the Convergence Rate Lower Bound of Biochemical Computational Modules Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2608.12109 Biochemical reaction networks have become a central theoretical framework for implementing molecular computation. 17. TRAECR: A Tool for Preprocessing Positron Emission Tomography Imaging for Statistical Modeling Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/2511.04458 Positron emission tomography (PET) imaging is widely used in a number of clinical applications, including cancer and Alzheimer's disease (AD) diagnosis, monitoring of disease development, and treatment effect evaluation. 18. Current validation practice undermines surgical AI development Source: q-bio.OT (Other Quantitative Biology) Link: https://arxiv.org/abs/2511.03769 Surgical data science (SDS) is rapidly advancing, yet clinical adoption of artificial intelligence (AI) in surgery remains limited, with inadequate validation as an important contributing factor. 19. Smart membrane: high content in situ monitoring barrier on chip with artificial neuronal network Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2608.01239 Conventional transepithelial electrical resistance (TEER) technique provides only a low-content analysis of cell-layer conditions, necessitating repeated microscopic assessments of morphology and cell-cell contacts outside the incubator for barrier-on-chip systems. 20. scVGAE: A ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2403.08959 Single-cell RNA sequencing (scRNA-seq) provides high-resolution measurements of cellular heterogeneity, but sparsity and technical zeros can obscure biological structure and complicate downstream analysis. 21. The Thousand Brains Theory 2.0: An Extension for the Long-Range Connections of the Neocortical Heterarchy Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2507.05888 Vernon Mountcastle hypothesized that the basis for intelligence in mammals is the replication of a general computational unit, the cortical column. 22. Trilobite tridents: A model of lift, drag and stability for queue formation Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2506.15922 The trident like cephalic projections of Walliserops trifurcatus have been interpreted as sexually selected weapons for intraspecific combat. 23. Longitudinal Bayesian Learning of Continuous Disease Position across the Alzheimer's Disease Continuum Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2608.19436 Alzheimer's disease (AD) progresses as a continuous biological process, whereas most existing neuroimaging-based artificial intelligence methods remain limited to discrete diagnosis or clinical score prediction from cross-sectional imaging. 24. Geometric-Chemical Distance Between Protein Surfaces Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2603.09860 Proteins recognize, bind, and catalyze through molecular surfaces, where geometry and chemical patterning determine interaction. 25. A General Theory for Phenotypic Association in Biological Systems Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2608.08571 Biological recognition rarely rests on one strong bond. 26. From Raw Segmentations to Simulation-Ready Cardiac Meshes: An Automated Framework for Anatomical Reconstruction and Virtual Cohort Generation Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/2607.02564 Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. 27. BODIESReg: An Open-Source Pipeline for Registering 3D Body Scans Using Pose-Aligned Initialization Source: q-bio.OT (Other Quantitative Biology) Link: https://arxiv.org/abs/2607.15463 Biomechanical models are used to quantify and optimize human movement in clinical rehabilitation, sports science, and occupational health. 28. Necessary and sufficient condition for hysteresis in the mathematical model of the cell type regulation of \textit{Bacillus subtilis} Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2009.06524 The key to a robust life system is to ensure that each cell population is maintained in an appropriate state. 29. OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2606.12838 Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. 30. The Role of Grid Cells in Reducing Spatial Aliasing in Hippocampal Place Representations Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2608.18569 Spatial aliasing occurs when two or more distinct locations produce highly similar place-cell representations, primarily due to environmental symmetry or repetitive structures. 31. Mathematical modelling of immune persistence and relapse pathways in CAR T-cell therapy for B-ALL Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2608.17955 Chimeric antigen receptor (CAR) T-cell therapy has transformed the treatment of B-cell acute lymphoblastic leukaemia (B-ALL). 32. Flow Matching Meets 3D Curvilinear Structure Segmentation in Medical Imaging Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2608.19965 Segmentation of curvilinear anatomical structures in 3D medical images remains challenging due to complex topology, severe class imbalance, weak contrast, and large variations in structure morphology. 33. Task- and dataset-specific information in protein language models Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2608.12090 Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology. 34. muxvizpy: a Python library for the analysis of multilayer biological networks Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2608.07344 Biological systems are inherently multilayered: the same entities---genes, cells, or bacterial species---participate simultaneously in qualitatively distinct types of interactions, each carrying complementary information that no single relational view can capture. Sources in this brief: q-bio.BM (Biomolecules); q-bio.CB (Cell Behavior); q-bio.GN (Genomics); q-bio.MN (Molecular Networks); q-bio.NC (Neurons and Cognition); q-bio.OT (Other Quantitative Biology); q-bio.PE (Populations and Evolution); q-bio.QM (Quantitative Methods); q-bio.TO (Tissues and Organs). Selected 34 of 486 available items for this weekly brief.