Model Board
Each subheading shows the most recent computational models published in each journal or preprint server. As journals publish, this page is autonomously updated and clicking the links will send you to the article.
- Genomic Next-Token Predictors are In-Context Learners
- Moonshine.jl: a Julia package for genome-scale model-based ancestral recombination graph inference
- CMADiff: Cross-Modal Aligned Diffusion for Controllable Protein Generation
- An optimal control approach to nonlinear wave speed selection in reaction-diffusion equations
- Modeling flexible behavior with remapping-based hippocampal sequence learning
- Binary Latent Protein Fitness Landscapes for Quantum Annealing Optimization
- SCALE:Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction
- Integrative modelling of protein-glycan interactions with HADDOCK3
- Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
- Sympatric speciation by symmetry-breaking: The three-clade case
- TRAILBLAZER: generative multicellular perturbation model of biology
- Expanding TheCellMap.org to visualize a genome-scale genetic interaction network for a human cell line
- A Unified Dynamical-Systems and Control-Theoretic Model for Single-Cell Fate Dynamics
- Canonical Analysis of Fluorescent Timer-Anchored Transcriptomes Resolves Joint Temporal and Developmental Progression
- Dissecting the Network Architecture of a Plant Circadian Clock Model: Identifying Key Regulatory Mechanisms and Essential Interactions
- GeNETop: Context-Specific Genome-Scale Constrained Models Using Network Topology, Flux Variability, and Transcriptomics
- MICA: Model-Informed Change-point Analysis
- Interpretable machine learning meets systems biology to decode genotype-phenotype maps
- A Multiscale Computational Architecture to Study Signaling Dynamics at Cell-Cell Interfaces
- BoolDog: integrated Boolean and semi-quantitative network modelling in Python
- Automated bioinformatic pipeline for unbiased detection of tuberculosis transmission clusters: Real-time impact and retrospective insights
- EVOLVE-HBV: A retrospective cross-sectional study to quantify and characterise HBV infection, exposure, immunity and susceptibility in a rural population in KwaZulu-Natal, South Africa
- Recent measles virus infection increased the severity of infectious disease in WWI with the exception of pandemic influenza
- Advantages of a Two-Stage Randomized Trial Design to Evaluate Antimicrobial Treatment Strategies: a Simulation Study
- Game Over for the Baseline: Anomalous Burden and Structural Seasonal Shifts in Post-Pandemic U.S. Influenza Hospitalization, 2009 to 2025
- Environmental reservoirs of high-risk ESBL- and carbapenemase-producing E. coli and Klebsiella in maternity wards in Yaounde (Cameroon): Whole-genome sequencing and antimicrobial susceptibility studies
- Genomic epidemiology of ESBL-producing Escherichia coli and Klebsiella pneumoniae across the human-animal-environment interface in peri-urban pig farms in Yaounde, Cameroon
- Socioeconomic risk factors and human immunosuppressive conditions are major drivers of human leishmaniasis in southern Europe
- Evolution and impact of the strategy to eliminate gambiense human African trypanosomiasis in Guinea
- Identifying Plasma Proteins Associated with Risk of Solid Cancers: A 25-Year Prospective Analysis of 4,712 Circulating Proteins in the ARIC Study
- Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling
- Illuminating cell states by a comprehensive and interpretable single cell foundation model
- FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis
- Author Correction: Generalizable and scalable protein stability prediction with rewired protein generative models
- EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles
- Antithetic integral feedback control redesigned for improved dynamics and lower noise
- Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes
- Fast, long-range intercellular signal propagation through growth-assisted positive feedback
- Competition and compromise between exogenous probiotics and native microbiota
- Dynamics of genetic circuits in Pseudomonas protegens
- On the optimal integration of intelligent agents into network systems to steer cooperation
- Stretch and flow at the gliovascular interface: High-fidelity modeling of astrocyte endfeet
- Mechanical compliance enhances the impulsive energy absorption of glassy polymer films
- Operator-level quantum acceleration of non-logconcave sampling
- Strategy evolution on temporal hypergraphs
- Global metabolic coherence as a derived property of microbial communities: A discrete hodge framework
- Optimal control of Alzheimer’s disease model via multi-target combination therapy
- The evolution of cooperation in the division of labor on generalized networks with a single output
- Tumor Mutational Burden Shapes Success and Resistance in Cancer Immunotherapy
- An extensive study of two-node McCulloch-pitts networks
- Persistence for a class of nonautonomous systems of differential equations with unbounded delays
- A stochastic reaction-diffusion HIV/AIDS model with implications for long-Acting ART
- Combining model-based and data-driven models: An application to synthetic biology resource competition
- Dynamical analysis of a spatially heterogeneous disease model with degenerate structure
- The impact of migration-mediated multi-threshold control strategies on disease spread of a Filippov patch epidemic model
- PHA synthase variant design using a conditional variational autoencoder
- Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure
- Mechanism of Hsp70 activation: How J-domain proteins push for ATP hydrolysis
- Direct causality measures unravel complex networks of cardiovascular dynamics and their modifications with postural stress
- Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries
- Identifies Tipping Points of cell Fate Transitions by Network Relative Entropy
- Mono- and Polyauxic Growth Kinetics: A Semi-Mechanistic Framework for Complex Biological Dynamics
- Transient and Asymptotic Dynamics of a Bioeconomic Fishery Model with Market Price Fluctuation and Effort Capacity Constraints
- Vector Encoding of Phylogenetic Trees by Ordered Leaf Attachment
- Counting Spinal Phylogenetic Networks
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- Understanding the temperature response of biological systems: Part II - Network-level mechanisms and emergent dynamics
- Understanding the temperature response of biological systems: Part I - Phenomenological descriptions and microscopic models
- Primer: Drug discovery and patient-derived organoids: Primer: Innovative approaches for drug discovery
- Regime Shifts in Lakes: Observations, Models and Experiments
- Bridging Mechanism and Data: Hybrid Modeling Approaches for Cancer and Aging Research
- Derivations of animal movement models with accumulated memory
- Rate-induced tipping in a lake eutrophication model coupled with human activities
- Order-Dependent dissimilarity measures on phylogenetic trees
- Extending a 1D Multi-Scale Plant Growth Model to Include Branching under Environmental and Soil Nutrient Dynamics
- Evolutionarily stable strategy in advective patchy environments