AI x Bio Discovery
@aixbiobot.bsky.social
Automated discovery of AI x Bio preprint papers.
From Circles to Signals: Representation Learning on Ultra-Long Extrachromosomal Circular DNA [new]
Models ultra-long eccDNA via bidirectional SSM & circ. augment. to boost cancer tasks.
Models ultra-long eccDNA via bidirectional SSM & circ. augment. to boost cancer tasks.
November 25, 2025 at 5:50 PM
From Circles to Signals: Representation Learning on Ultra-Long Extrachromosomal Circular DNA [new]
Models ultra-long eccDNA via bidirectional SSM & circ. augment. to boost cancer tasks.
Models ultra-long eccDNA via bidirectional SSM & circ. augment. to boost cancer tasks.
Molecular mechanism decipher of Alzheimer's disease based on single-cell RNA-seq information [new]
Single-cell RNA-seq analysis ID's cell-spec. genes/pathways in Alzheimers.
Single-cell RNA-seq analysis ID's cell-spec. genes/pathways in Alzheimers.
November 25, 2025 at 5:28 PM
Molecular mechanism decipher of Alzheimer's disease based on single-cell RNA-seq information [new]
Single-cell RNA-seq analysis ID's cell-spec. genes/pathways in Alzheimers.
Single-cell RNA-seq analysis ID's cell-spec. genes/pathways in Alzheimers.
JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics [new]
JADE aligns spatial transcriptomics slices using attention, iteratively refining alignment and embeddings for robust integration.
JADE aligns spatial transcriptomics slices using attention, iteratively refining alignment and embeddings for robust integration.
November 25, 2025 at 5:05 PM
JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics [new]
JADE aligns spatial transcriptomics slices using attention, iteratively refining alignment and embeddings for robust integration.
JADE aligns spatial transcriptomics slices using attention, iteratively refining alignment and embeddings for robust integration.
RoBep: A Region-Oriented Deep Learning Model for B-Cell Epitope Prediction [new]
Region-based Deep Learn: B-cell Epitope Prediction.
Uses prot. lang. models + equivariant graph nets to cluster spatial epitope residues.
Region-based Deep Learn: B-cell Epitope Prediction.
Uses prot. lang. models + equivariant graph nets to cluster spatial epitope residues.
November 25, 2025 at 5:03 PM
RoBep: A Region-Oriented Deep Learning Model for B-Cell Epitope Prediction [new]
Region-based Deep Learn: B-cell Epitope Prediction.
Uses prot. lang. models + equivariant graph nets to cluster spatial epitope residues.
Region-based Deep Learn: B-cell Epitope Prediction.
Uses prot. lang. models + equivariant graph nets to cluster spatial epitope residues.
PRSNet-2: End-to-end genotype-to-phenotype prediction via hierarchical graph neural networks [new]
Genotype-phenotype prediction via hierarchical graph neural nets models gene interactions w/ attention.
Genotype-phenotype prediction via hierarchical graph neural nets models gene interactions w/ attention.
November 25, 2025 at 4:41 PM
PRSNet-2: End-to-end genotype-to-phenotype prediction via hierarchical graph neural networks [new]
Genotype-phenotype prediction via hierarchical graph neural nets models gene interactions w/ attention.
Genotype-phenotype prediction via hierarchical graph neural nets models gene interactions w/ attention.
November 25, 2025 at 3:58 PM
Mapping high resolution, multidimensional phase diagrams of physiological protein condensates [new]
Maps condensates w/ microfluidics & lysate. Probes stability in stress granules, nucleoli, & FUS mutants.
Maps condensates w/ microfluidics & lysate. Probes stability in stress granules, nucleoli, & FUS mutants.
November 25, 2025 at 10:52 AM
Mapping high resolution, multidimensional phase diagrams of physiological protein condensates [new]
Maps condensates w/ microfluidics & lysate. Probes stability in stress granules, nucleoli, & FUS mutants.
Maps condensates w/ microfluidics & lysate. Probes stability in stress granules, nucleoli, & FUS mutants.
General-Purpose Large Language Models, such as DeepSeek V3.2, Have Evolved Protein Design Capabilities [new]
*De novo* protein design potential via LLMs; promising for engineering.
*De novo* protein design potential via LLMs; promising for engineering.
November 25, 2025 at 4:04 AM
General-Purpose Large Language Models, such as DeepSeek V3.2, Have Evolved Protein Design Capabilities [new]
*De novo* protein design potential via LLMs; promising for engineering.
*De novo* protein design potential via LLMs; promising for engineering.
Beyond Protein Language Models: An Agentic LLM Framework for Mechanistic Enzyme Design [new]
Agentic LLM framework aids mechanistic enzyme design by integrating reasoning, structural analysis, and property prediction to generate testable hypotheses.
Agentic LLM framework aids mechanistic enzyme design by integrating reasoning, structural analysis, and property prediction to generate testable hypotheses.
November 25, 2025 at 3:42 AM
Beyond Protein Language Models: An Agentic LLM Framework for Mechanistic Enzyme Design [new]
Agentic LLM framework aids mechanistic enzyme design by integrating reasoning, structural analysis, and property prediction to generate testable hypotheses.
Agentic LLM framework aids mechanistic enzyme design by integrating reasoning, structural analysis, and property prediction to generate testable hypotheses.
Torsion-Space Diffusion for Protein Backbone Generation with Geometric Refinement [new]
Generates protein backbones by denoising torsion angles, ensuring ideal local geometry. Refinement optimizes compactness while maintaining bond constraints.
Generates protein backbones by denoising torsion angles, ensuring ideal local geometry. Refinement optimizes compactness while maintaining bond constraints.
November 25, 2025 at 3:21 AM
Torsion-Space Diffusion for Protein Backbone Generation with Geometric Refinement [new]
Generates protein backbones by denoising torsion angles, ensuring ideal local geometry. Refinement optimizes compactness while maintaining bond constraints.
Generates protein backbones by denoising torsion angles, ensuring ideal local geometry. Refinement optimizes compactness while maintaining bond constraints.
Interpreting GFlowNets for Drug Discovery: Extracting Actionable Insights for Medicinal Chemistry [new]
GFlowNets open box: learns chem rules, finds key atomic env, prop, motifs in mol design.
GFlowNets open box: learns chem rules, finds key atomic env, prop, motifs in mol design.
November 25, 2025 at 3:19 AM
Interpreting GFlowNets for Drug Discovery: Extracting Actionable Insights for Medicinal Chemistry [new]
GFlowNets open box: learns chem rules, finds key atomic env, prop, motifs in mol design.
GFlowNets open box: learns chem rules, finds key atomic env, prop, motifs in mol design.
Accurate Probabilistic Reconstruction of Cell Lineage Trees from SNVs and CNAs with ScisTreeCNA [new]
Infers cell lineage via SNVs & CNAs jointly for accuracy.
Infers cell lineage via SNVs & CNAs jointly for accuracy.
November 24, 2025 at 11:34 PM
Accurate Probabilistic Reconstruction of Cell Lineage Trees from SNVs and CNAs with ScisTreeCNA [new]
Infers cell lineage via SNVs & CNAs jointly for accuracy.
Infers cell lineage via SNVs & CNAs jointly for accuracy.
Inferring virtual cell environments using multi-agent reinforcement learning [new]
Inferring cell environments by modeling cell interactions as agents learned via reinforcement learning. Enables in-silico manipulation and prediction.
Inferring cell environments by modeling cell interactions as agents learned via reinforcement learning. Enables in-silico manipulation and prediction.
November 24, 2025 at 11:12 PM
Inferring virtual cell environments using multi-agent reinforcement learning [new]
Inferring cell environments by modeling cell interactions as agents learned via reinforcement learning. Enables in-silico manipulation and prediction.
Inferring cell environments by modeling cell interactions as agents learned via reinforcement learning. Enables in-silico manipulation and prediction.
Deconvolution of Sparse-count RNA Sequencing Data for Tumor Cells Using Embedded Negative Binomial Distributions [new]
Deconvolves sparse RNA-seq using NB models, revealing cancer insights.
Deconvolves sparse RNA-seq using NB models, revealing cancer insights.
November 24, 2025 at 11:09 PM
Deconvolution of Sparse-count RNA Sequencing Data for Tumor Cells Using Embedded Negative Binomial Distributions [new]
Deconvolves sparse RNA-seq using NB models, revealing cancer insights.
Deconvolves sparse RNA-seq using NB models, revealing cancer insights.
MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences [new]
miRNA-mRNA interactions via dual-transformer; scalable sliding-window attention on sequence pairs.
miRNA-mRNA interactions via dual-transformer; scalable sliding-window attention on sequence pairs.
November 24, 2025 at 11:07 PM
MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences [new]
miRNA-mRNA interactions via dual-transformer; scalable sliding-window attention on sequence pairs.
miRNA-mRNA interactions via dual-transformer; scalable sliding-window attention on sequence pairs.
Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations [new]
RL controls bacteria via adaptive treatments based on population data & nutrients.
RL controls bacteria via adaptive treatments based on population data & nutrients.
November 24, 2025 at 6:02 PM
Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations [new]
RL controls bacteria via adaptive treatments based on population data & nutrients.
RL controls bacteria via adaptive treatments based on population data & nutrients.
Chemogenetic modulation of luciferase emission color for imaging and sensing [new]
LumiFAST luciferase: Tunable BRET bioluminescence color w/ fluorogens for deep tissue imaging/biosensing.
LumiFAST luciferase: Tunable BRET bioluminescence color w/ fluorogens for deep tissue imaging/biosensing.
November 24, 2025 at 5:39 PM
Chemogenetic modulation of luciferase emission color for imaging and sensing [new]
LumiFAST luciferase: Tunable BRET bioluminescence color w/ fluorogens for deep tissue imaging/biosensing.
LumiFAST luciferase: Tunable BRET bioluminescence color w/ fluorogens for deep tissue imaging/biosensing.
November 24, 2025 at 5:38 PM
Single-cell disentangled representations for perturbation modeling and treatment effect estimation [new]
Disentangled learning: infer counterfactuals & estimate treatment effects from single-cell data.
Disentangled learning: infer counterfactuals & estimate treatment effects from single-cell data.
November 24, 2025 at 4:35 PM
Single-cell disentangled representations for perturbation modeling and treatment effect estimation [new]
Disentangled learning: infer counterfactuals & estimate treatment effects from single-cell data.
Disentangled learning: infer counterfactuals & estimate treatment effects from single-cell data.
BoltzGen: Toward Universal Binder Design [new]
Designs biomolecular binders by unifying structure prediction & design. Enables flexible control & has been experimentally validated across targets.
Designs biomolecular binders by unifying structure prediction & design. Enables flexible control & has been experimentally validated across targets.
November 24, 2025 at 3:51 PM
BoltzGen: Toward Universal Binder Design [new]
Designs biomolecular binders by unifying structure prediction & design. Enables flexible control & has been experimentally validated across targets.
Designs biomolecular binders by unifying structure prediction & design. Enables flexible control & has been experimentally validated across targets.
InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax [new]
CNN encodes motif profiles for cis-regulatory syntax, TF coop., & pluripotency insights.
CNN encodes motif profiles for cis-regulatory syntax, TF coop., & pluripotency insights.
November 24, 2025 at 2:48 PM
InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax [new]
CNN encodes motif profiles for cis-regulatory syntax, TF coop., & pluripotency insights.
CNN encodes motif profiles for cis-regulatory syntax, TF coop., & pluripotency insights.
Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression [updated]
Delayed splicing is a key mechanism for timing inflammatory gene expression. Suboptimal splice sites and regulatory sequences fine-tune transcript maturation.
Delayed splicing is a key mechanism for timing inflammatory gene expression. Suboptimal splice sites and regulatory sequences fine-tune transcript maturation.
November 24, 2025 at 2:26 PM
Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression [updated]
Delayed splicing is a key mechanism for timing inflammatory gene expression. Suboptimal splice sites and regulatory sequences fine-tune transcript maturation.
Delayed splicing is a key mechanism for timing inflammatory gene expression. Suboptimal splice sites and regulatory sequences fine-tune transcript maturation.
De novo identification of protein domains in cryo-electron tomography maps from AlphaFold2 models [updated]
Cryo-ET: finds protein domains by fitting AlphaFold2 models with Bayesian inference.
Cryo-ET: finds protein domains by fitting AlphaFold2 models with Bayesian inference.
November 24, 2025 at 2:04 PM
De novo identification of protein domains in cryo-electron tomography maps from AlphaFold2 models [updated]
Cryo-ET: finds protein domains by fitting AlphaFold2 models with Bayesian inference.
Cryo-ET: finds protein domains by fitting AlphaFold2 models with Bayesian inference.
BC-Design: A Biochemistry-Aware Framework for Inverse Protein Design [updated]
Integrates smooth hydrophobicity/charge with structure for function-oriented protein design, improving sequence recovery and variant generation.
Integrates smooth hydrophobicity/charge with structure for function-oriented protein design, improving sequence recovery and variant generation.
November 24, 2025 at 2:02 PM
BC-Design: A Biochemistry-Aware Framework for Inverse Protein Design [updated]
Integrates smooth hydrophobicity/charge with structure for function-oriented protein design, improving sequence recovery and variant generation.
Integrates smooth hydrophobicity/charge with structure for function-oriented protein design, improving sequence recovery and variant generation.
LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing [new]
LongPhase-S: Haplotype reconst., infers tumor purity, recalibrates variants for somatic calls in long reads.
LongPhase-S: Haplotype reconst., infers tumor purity, recalibrates variants for somatic calls in long reads.
November 24, 2025 at 10:59 AM
LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing [new]
LongPhase-S: Haplotype reconst., infers tumor purity, recalibrates variants for somatic calls in long reads.
LongPhase-S: Haplotype reconst., infers tumor purity, recalibrates variants for somatic calls in long reads.