AI x Bio Discovery
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aixbiobot.bsky.social
AI x Bio Discovery
@aixbiobot.bsky.social
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Automated discovery of AI x Bio preprint papers.
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aixbiobot.bsky.social
ONCOchannelome: A computational framework to investigate altered ion channels across tumor types [new]
Identifies diff. expressed ion channels/networks via transcriptomics, understanding tumor behavior.
Figure 1 Figure 2 Figure 3 Table 1
November 30, 2025 at 3:00 AM
aixbiobot.bsky.social
PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA [new]
PatchDNA: Flexible, vocab-free DNA patching via evolution guides better LMs.
Figure 1 Figure 2 Table 2 Table 1
November 30, 2025 at 2:38 AM
aixbiobot.bsky.social
Can We Extract Physics-like Energies from Generative Protein Diffusion Models? [new]
Examines diffusion models to relate learned functions to thermodynamics for protein folding, testing the ability to capture learned energies.
Figure 2 Figure 3 Figure 4 Figure 6
November 30, 2025 at 1:56 AM
aixbiobot.bsky.social
Genetic diversity, predictive protein structures, and interaction networks of Cysteine-Rich Receptor-Like Kinases in Arabidopsis thaliana [new]
Figure 1 Figure 2 Figure 3 Figure 4
November 30, 2025 at 1:54 AM
aixbiobot.bsky.social
RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions [new]
RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions Figure 1 Figure 2 Figure 3
November 30, 2025 at 1:32 AM
aixbiobot.bsky.social
ClsDiff-AMP30: Generating Antimicrobial Peptides by a Classifier Guidance Noise Predictor [new]
Generates short antimicrobial peptides using a classifier-guided diffusion model, optimizing for antimicrobial activity and low toxicity.
ClsDiff-AMP30: Generating Antimicrobial Peptides by a Classifier Guidance Noise Predictor Figure 2 Figure 3 Figure 4
November 29, 2025 at 7:08 PM
aixbiobot.bsky.social
Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement [new]
Single-cell & spatial omics via disentangled learning; cross-modal prediction & spatial mapping.
Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement Figure 1 Figure 2 Figure 3
November 29, 2025 at 6:45 PM
aixbiobot.bsky.social
SIRP: A Self-Supervised Fluorescence Denoising method with Implicit Representation Priors [new]
Denoises fluoro-microscopy via implicit nets & neighbor-sample; preserves detail @ low SNR.
SIRP: A Self-Supervised Fluorescence Denoising method with Implicit Representation Priors Figure 1 Figure 2 Figure 3
November 29, 2025 at 6:43 PM
aixbiobot.bsky.social
A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics [new]
DNA methylation models: Accuracy/efficiency trade-offs in 3 CpG methylation dynamics methods.
A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics Figure 1 Figure 2 Figure 3
November 29, 2025 at 4:58 PM
aixbiobot.bsky.social
Ovo, an Open-Source Ecosystem for De Novo Protein Design [new]
Ecosystem consolidates protein design models, workflows, data, and visualization into a scalable, open-source platform for experts and non-experts.
Ovo, an Open-Source Ecosystem for De Novo Protein Design Figure 1 Figure 2 Figure 3
November 29, 2025 at 10:52 AM
aixbiobot.bsky.social
LARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics [new]
Cell-type specific spatial ligand-receptor analysis reveals signaling mechanisms.
LARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics Figure 1 Figure 2 Figure 3
November 29, 2025 at 9:06 AM
aixbiobot.bsky.social
NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing [new]
NanoporeDB: Structural database of multimeric protein nanopore models for functional interpretation and application advancement.
Figure 2 Figure 3
November 29, 2025 at 3:52 AM
aixbiobot.bsky.social
Deep-learning model guided discovery and characterization of bacterial unspecific peroxygenases [new]
Deep learning found bacterial UPOs, bypassing eukaryotic issues & boosting use.
Deep-learning model guided discovery and characterization of bacterial unspecific peroxygenases Figure 1 Figure 2 Figure 3
November 29, 2025 at 3:50 AM
aixbiobot.bsky.social
Composite biomaterials of polyelectrolyte complex micelle nanoparticles in hyaluronic acid gels enable local, targeted miR-92a inhibition and enhanced angiogenesis in diabetic wound repair [new]
Composite biomaterials of polyelectrolyte complex micelle nanoparticles in hyaluronic acid gels enable local, targeted miR-92a inhibition and enhanced angiogenesis in diabetic wound repair Figure 1 Figure 3 Figure 4
November 29, 2025 at 3:48 AM
aixbiobot.bsky.social
Rewriting protein alphabets with language models [new]
Leverages language models to create a new 20-letter protein alphabet. This enables fast, sensitive homology searches without structural data.
Rewriting protein alphabets with language models Figure 2 Figure 3 Figure 4
November 29, 2025 at 3:06 AM
aixbiobot.bsky.social
Fine-Tuning Protein Language Models Enhances the Identification and Interpretation of the Transcription Factors [new]
Fine-tuning ProtLMs aids TF ID & DNA binding. Attn weights/motifs boost interpretability.
Figure 1 Figure 2 Figure 3 Figure 4
November 29, 2025 at 3:04 AM
aixbiobot.bsky.social
RNA degradation modulates unique aging-related gene expression in naked mole-rats [new]
NMR cells show increased RNA turnover, particularly in aging-related pathways, suggesting RNA degradation modulates gene expression during aging.
Figure 1 Figure 2 Figure 3 Figure 4
November 29, 2025 at 1:20 AM
aixbiobot.bsky.social
CPIExtract: A software package to collect and harmonize small molecule and protein interactions [updated]
Gathers/unifies compound-protein data, filters, harmonizes IDs, computes binding values.
CPIExtract: A software package to collect and harmonize small molecule and protein interactions Figure 1
November 28, 2025 at 9:56 PM
aixbiobot.bsky.social
mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain. [new]
Multivariate & functional regression for fine-mapping traits across cells.
Figure 1 Figure 2 Figure 3 Figure 4
November 28, 2025 at 8:34 PM
aixbiobot.bsky.social
Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress [new]
Antibiotic stress & bacterial survival: Morphology links survival under 168 antibiotics; ID'ing action modes via neural net.
Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress Figure 1 Figure 2 Figure 3
November 28, 2025 at 7:51 PM
aixbiobot.bsky.social
Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors [new]
FGT spatial atlas: mol. features linked to TME. IDs HPV/TGFβ, oncogene phenotypes, & novel PCD niche for prognosis.
Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors Figure 1 Figure 2 Figure 3
November 28, 2025 at 6:47 PM
aixbiobot.bsky.social
MARRVEL-MCP enables natural language variant interpretation through autonomous workflow construction [new]
LLMs interpret rare disease variants via nat. lang. & autonomous genomic DB workflows.
MARRVEL-MCP enables natural language variant interpretation through autonomous workflow construction Figure 1 Figure 2 Figure 4
November 28, 2025 at 6:04 PM
aixbiobot.bsky.social
GRNITE: Gene Regulatory Network Inference with Text Embeddings [new]
Infers gene networks by creating a prior interaction graph using text embeddings optimized with a graph neural network and scRNA-seq data.
GRNITE: Gene Regulatory Network Inference with Text Embeddings Figure 1 Figure 2 Figure 4
November 28, 2025 at 10:56 AM
aixbiobot.bsky.social
k-spaces: Mixtures of Gaussian latent variable models [new]
Combines dimension reduction & clustering via Gaussian latent variable models, applicable to genomics data like gene expression and scRNA-seq.
k-spaces: Mixtures of Gaussian latent variable models Figure 1 Figure 2 Figure 3
November 28, 2025 at 10:54 AM
aixbiobot.bsky.social
Slab-PTM: A Coarse-Grained Force Field Parameter Patch for Modeling Post-Translational Modification Effects on Biomolecular Condensates [new]
Slab-PTM: A Coarse-Grained Force Field Parameter Patch for Modeling Post-Translational Modification Effects on Biomolecular Condensates Figure 1 Figure 2 Figure 3
November 28, 2025 at 3:07 AM