https://modelome.curieus.net/new/ New bio AI models found by a daily sweep of papers and code hosts, grouped by day. en https://modelome.curieus.net/entry/effiedes-8d7d8e6c6b/ https://modelome.curieus.net/entry/effiedes-8d7d8e6c6b/ Thu, 29 Oct 2026 00:00:00 GMT Protein sequence design https://modelome.curieus.net/entry/scpyviewer-a-python-native-interactive-v-72236be0ac/ https://modelome.curieus.net/entry/scpyviewer-a-python-native-interactive-v-72236be0ac/ Thu, 29 Oct 2026 00:00:00 GMT scPyviewer: a Python-native interactive viewer from AnnData single-cell data https://modelome.curieus.net/entry/didynet-a-robust-framework-for-different-8c90953aae/ https://modelome.curieus.net/entry/didynet-a-robust-framework-for-different-8c90953aae/ Thu, 29 Oct 2026 00:00:00 GMT DiDyNet: a robust framework for differential dynamic network inference from longitudinal multi-omics data. https://modelome.curieus.net/entry/mlheatmap-an-interactive-application-for-85b1f4734c/ https://modelome.curieus.net/entry/mlheatmap-an-interactive-application-for-85b1f4734c/ Thu, 29 Oct 2026 00:00:00 GMT MLHeatmap: an interactive application for transcriptomic marker-panel discovery. https://modelome.curieus.net/entry/an-embedding-based-framework-enables-sta-2200ab0d09/ https://modelome.curieus.net/entry/an-embedding-based-framework-enables-sta-2200ab0d09/ Thu, 29 Oct 2026 00:00:00 GMT An embedding-based framework enables statistical testing of gene-set function hypotheses inferred by large language models. https://modelome.curieus.net/entry/crispr-escape-dilution-f1b1190dac/ https://modelome.curieus.net/entry/crispr-escape-dilution-f1b1190dac/ Wed, 28 Oct 2026 00:00:00 GMT CRISPR Escape Dilution: a Nucleic acids models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/radagent-automating-radseq-pipelines-wit-1cf12cffa9/ https://modelome.curieus.net/entry/radagent-automating-radseq-pipelines-wit-1cf12cffa9/ Wed, 28 Oct 2026 00:00:00 GMT RADAgent: Automating RADseq Pipelines with Private Open-Source LLMs https://modelome.curieus.net/entry/cohort-effects-not-treatment-response-do-3567fe7b4a/ https://modelome.curieus.net/entry/cohort-effects-not-treatment-response-do-3567fe7b4a/ Wed, 28 Oct 2026 00:00:00 GMT Cohort Effects, Not Treatment Response, Dominate Public Immunotherapy Cohorts: Evidence from Microbiome and Tumor Genomic Data https://modelome.curieus.net/entry/predicting-enzyme-turnover-numbers-and-e-beab1d826d/ https://modelome.curieus.net/entry/predicting-enzyme-turnover-numbers-and-e-beab1d826d/ Wed, 28 Oct 2026 00:00:00 GMT Predicting Enzyme Turnover Numbers and Enabling Rational Enzyme Evolution. https://modelome.curieus.net/entry/dfn-kcr-a-dual-branch-deep-learning-mode-3a49e2c1b8/ https://modelome.curieus.net/entry/dfn-kcr-a-dual-branch-deep-learning-mode-3a49e2c1b8/ Wed, 28 Oct 2026 00:00:00 GMT DFN-kcr: a dual-branch deep learning model with attention-guided fusion for predicting lysine crotonylation sites in human non-histone proteins. https://modelome.curieus.net/entry/a-leakage-aware-genomic-prediction-pipel-b88c67400f/ https://modelome.curieus.net/entry/a-leakage-aware-genomic-prediction-pipel-b88c67400f/ Wed, 28 Oct 2026 00:00:00 GMT A leakage-aware genomic prediction pipeline for meropenem resistance in Klebsiella pneumoniae using transformer-based resistome representation learning. https://modelome.curieus.net/entry/uncovering-smooth-structures-in-single-c-c00fd5628d/ https://modelome.curieus.net/entry/uncovering-smooth-structures-in-single-c-c00fd5628d/ Wed, 28 Oct 2026 00:00:00 GMT Uncovering smooth structures in single-cell data with neighbor embeddings guided by predictability-computability-stability. https://modelome.curieus.net/entry/gmx-mmpbsa-01ce092b7b/ https://modelome.curieus.net/entry/gmx-mmpbsa-01ce092b7b/ Sun, 25 Oct 2026 00:00:00 GMT Free energy calculation for GROMACS https://modelome.curieus.net/entry/virtual-st-uncertainty-9c50a59827/ https://modelome.curieus.net/entry/virtual-st-uncertainty-9c50a59827/ Sat, 24 Oct 2026 00:00:00 GMT Virtual-ST Uncertainty: a Cells · omics models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/panagram-reveals-pangenome-architectures-5f1b7ece86/ https://modelome.curieus.net/entry/panagram-reveals-pangenome-architectures-5f1b7ece86/ Fri, 23 Oct 2026 00:00:00 GMT Panagram reveals pangenome architectures underlying trait variation in plants and animals https://modelome.curieus.net/entry/nufold-rna-structure-database-large-scal-2fbb7f8670/ https://modelome.curieus.net/entry/nufold-rna-structure-database-large-scal-2fbb7f8670/ Fri, 23 Oct 2026 00:00:00 GMT NuFold RNA Structure Database: Large-Scale RNA Tertiary Structure Prediction with Confidence Metrics https://modelome.curieus.net/entry/fragment-level-graph-encoding-for-interp-6fdc469456/ https://modelome.curieus.net/entry/fragment-level-graph-encoding-for-interp-6fdc469456/ Fri, 23 Oct 2026 00:00:00 GMT Fragment-Level Graph Encoding for Interpretable Molecular Property Prediction https://modelome.curieus.net/entry/gpugem-gpu-based-linear-optimisation-of--962bab18be/ https://modelome.curieus.net/entry/gpugem-gpu-based-linear-optimisation-of--962bab18be/ Thu, 22 Oct 2026 00:00:00 GMT gpuGEM: GPU-based linear optimisation of genome-scale metabolic models https://modelome.curieus.net/entry/on-the-selectivity-of-generative-models--207679e773/ https://modelome.curieus.net/entry/on-the-selectivity-of-generative-models--207679e773/ Thu, 22 Oct 2026 00:00:00 GMT On the Selectivity of Generative Models in Structure-Based Drug Design https://modelome.curieus.net/entry/protglycandock-towards-accurate-protein--602cc20fff/ https://modelome.curieus.net/entry/protglycandock-towards-accurate-protein--602cc20fff/ Thu, 22 Oct 2026 00:00:00 GMT ProtGlycanDock: Towards Accurate Protein-Glycan Docking with Tailored Dataset, Benchmark and Model https://modelome.curieus.net/entry/cellnet-74b0885217/ https://modelome.curieus.net/entry/cellnet-74b0885217/ Sat, 17 Oct 2026 00:00:00 GMT CellNet: a Cells · omics datasets. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/stamp-v1-9fe5c19a98/ https://modelome.curieus.net/entry/stamp-v1-9fe5c19a98/ Thu, 15 Oct 2026 00:00:00 GMT STAMP-V1: a Small molecules models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/perturbenergy-432fed449b/ https://modelome.curieus.net/entry/perturbenergy-432fed449b/ Thu, 15 Oct 2026 00:00:00 GMT PerturbEnergy: a Cells · omics models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/dummest-a-simpler-and-faster-model-for-f-24dab23481/ https://modelome.curieus.net/entry/dummest-a-simpler-and-faster-model-for-f-24dab23481/ Thu, 15 Oct 2026 00:00:00 GMT DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family https://modelome.curieus.net/entry/schfbimamba-a-bidirectional-mamba-autoen-5220cf2b71/ https://modelome.curieus.net/entry/schfbimamba-a-bidirectional-mamba-autoen-5220cf2b71/ Thu, 15 Oct 2026 00:00:00 GMT scHFBiMamba: a bidirectional Mamba autoencoder for cardiac disease-state classification from single-nucleus RNA-seq data https://modelome.curieus.net/entry/dc-flow-target-conditioned-cyclic-peptid-c8795569d3/ https://modelome.curieus.net/entry/dc-flow-target-conditioned-cyclic-peptid-c8795569d3/ Thu, 15 Oct 2026 00:00:00 GMT DC-Flow: Target-Conditioned Cyclic Peptide Design via Delayed-Coupling Flow Matching https://modelome.curieus.net/entry/octmole-multiscale-3d-molecular-generati-adc8c19ba8/ https://modelome.curieus.net/entry/octmole-multiscale-3d-molecular-generati-adc8c19ba8/ Thu, 15 Oct 2026 00:00:00 GMT OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows https://modelome.curieus.net/entry/computational-design-of-protein-conforma-06cf9ea73a/ https://modelome.curieus.net/entry/computational-design-of-protein-conforma-06cf9ea73a/ Wed, 14 Oct 2026 00:00:00 GMT Computational design of protein conformational landscapes for metamorphic behavior https://modelome.curieus.net/entry/molp2sbench-do-llms-really-reason-from-m-97e18ddb6b/ https://modelome.curieus.net/entry/molp2sbench-do-llms-really-reason-from-m-97e18ddb6b/ Tue, 13 Oct 2026 00:00:00 GMT MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure? https://modelome.curieus.net/entry/masked-diffusion-language-agents-for-too-f10ce125e8/ https://modelome.curieus.net/entry/masked-diffusion-language-agents-for-too-f10ce125e8/ Tue, 13 Oct 2026 00:00:00 GMT Masked Diffusion Language Agents for Tool-Integrated Chemical Reasoning https://modelome.curieus.net/entry/mast-motif-augmented-diffusion-with-sear-055ec8dfdf/ https://modelome.curieus.net/entry/mast-motif-augmented-diffusion-with-sear-055ec8dfdf/ Sat, 10 Oct 2026 00:00:00 GMT MAST: Motif-Augmented Diffusion with Search Tree for Spectroscopic Molecular Structure Elucidation https://modelome.curieus.net/entry/ragenome-scaling-retrieval-based-genomic-0979f55319/ https://modelome.curieus.net/entry/ragenome-scaling-retrieval-based-genomic-0979f55319/ Sat, 10 Oct 2026 00:00:00 GMT RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts https://modelome.curieus.net/entry/hrpv2-an-automated-and-enhanced-method-f-7deabaa62c/ https://modelome.curieus.net/entry/hrpv2-an-automated-and-enhanced-method-f-7deabaa62c/ Thu, 08 Oct 2026 00:00:00 GMT HRPv2: an automated and enhanced method for full-length homology-based R-gene prediction https://modelome.curieus.net/entry/atom-jepa-joint-embedding-predictive-arc-64523b22a0/ https://modelome.curieus.net/entry/atom-jepa-joint-embedding-predictive-arc-64523b22a0/ Thu, 08 Oct 2026 00:00:00 GMT Atom-JEPA: Joint-Embedding Predictive Architecture for 3D Atomistic Systems https://modelome.curieus.net/entry/causalbind-causal-modeling-and-learning--b3a2c2a3dd/ https://modelome.curieus.net/entry/causalbind-causal-modeling-and-learning--b3a2c2a3dd/ Thu, 08 Oct 2026 00:00:00 GMT CausalBind: Causal Modeling and Learning for Protein-Molecule Virtual Screening https://modelome.curieus.net/entry/coldddi-evaluating-knowledge-utilization-c44f4a09eb/ https://modelome.curieus.net/entry/coldddi-evaluating-knowledge-utilization-c44f4a09eb/ Wed, 07 Oct 2026 00:00:00 GMT ColdDDI: Evaluating Knowledge Utilization in Cold-Start Drug-Drug Interaction Prediction https://modelome.curieus.net/entry/idiom-2c69e50391/ https://modelome.curieus.net/entry/idiom-2c69e50391/ Sat, 03 Oct 2026 00:00:00 GMT Disordered protein region language model https://modelome.curieus.net/entry/rippleplm-structural-and-property-decoup-fb43b7d84f/ https://modelome.curieus.net/entry/rippleplm-structural-and-property-decoup-fb43b7d84f/ Sat, 03 Oct 2026 00:00:00 GMT RipplePLM: Structural and Property Decoupling for Protein Mutation Effect Generation https://modelome.curieus.net/entry/mirror-score-calibrated-inference-only-s-bdc08a8b20/ https://modelome.curieus.net/entry/mirror-score-calibrated-inference-only-s-bdc08a8b20/ Thu, 01 Oct 2026 00:00:00 GMT Mirror-Score: Calibrated, Inference-only Scoring Exposes the Limits of Sequence-compatibility Ranking in D-peptide Design https://modelome.curieus.net/entry/ambimodbench-009ff7ba8d/ https://modelome.curieus.net/entry/ambimodbench-009ff7ba8d/ Wed, 30 Sep 2026 00:00:00 GMT AmbiModBench: a Cells · omics datasets. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/flow-matching-based-protein-structure-to-dab6a57cf6/ https://modelome.curieus.net/entry/flow-matching-based-protein-structure-to-dab6a57cf6/ Wed, 30 Sep 2026 00:00:00 GMT Flow-Matching-Based Protein Structure Tokenizer Made Efficient and Easy https://modelome.curieus.net/entry/mospr-histology-to-gene-expression-predi-f8df160e15/ https://modelome.curieus.net/entry/mospr-histology-to-gene-expression-predi-f8df160e15/ Wed, 30 Sep 2026 00:00:00 GMT MoSPR: Histology-to-Gene Expression Prediction with Morpho-Spatial Macrostates and Low-Rank Molecular Programs https://modelome.curieus.net/entry/gyronovo-error-guided-fragment-imputatio-011fba6562/ https://modelome.curieus.net/entry/gyronovo-error-guided-fragment-imputatio-011fba6562/ Tue, 29 Sep 2026 00:00:00 GMT GyroNovo: Error-Guided Fragment Imputation with Mass-Aware Attention for \textit{De Novo} Peptide Sequencing https://modelome.curieus.net/entry/enm-bd-56b9d6f73e/ https://modelome.curieus.net/entry/enm-bd-56b9d6f73e/ Sun, 27 Sep 2026 00:00:00 GMT ENM-BD: a Proteins models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/topoflow-41227a02fd/ https://modelome.curieus.net/entry/topoflow-41227a02fd/ Sun, 27 Sep 2026 00:00:00 GMT TopoFlow: a Proteins models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/sherlock-63603b299a/ https://modelome.curieus.net/entry/sherlock-63603b299a/ Sun, 27 Sep 2026 00:00:00 GMT SHERLOCK: a Cells · omics models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/pop-corn-31bebe4b4d/ https://modelome.curieus.net/entry/pop-corn-31bebe4b4d/ Sun, 27 Sep 2026 00:00:00 GMT Pop-Corn: a Cells · omics models. Code and paper links, licence, inputs and outputs. https://modelome.curieus.net/entry/predicting-single-mutation-effects-on-bi-783579e71f/ https://modelome.curieus.net/entry/predicting-single-mutation-effects-on-bi-783579e71f/ Sun, 27 Sep 2026 00:00:00 GMT Predicting single mutation effects on binding affinity at protein-protein interfaces based on MMPBSA calculations https://modelome.curieus.net/entry/srnamap-a-lightweight-browser-based-web--1d461c7e82/ https://modelome.curieus.net/entry/srnamap-a-lightweight-browser-based-web--1d461c7e82/ Sun, 27 Sep 2026 00:00:00 GMT sRNAMap: a lightweight, browser-based web application for small RNA mapping, analysis and visualisation https://modelome.curieus.net/entry/a-first-order-approximation-of-a-joint-p-1645979a49/ https://modelome.curieus.net/entry/a-first-order-approximation-of-a-joint-p-1645979a49/ Sun, 27 Sep 2026 00:00:00 GMT A first order approximation of a joint Potts and phylogenetic model