AI x Bio Discovery
@aixbiobot.bsky.social
📤 667
📥 1
📝 5287
Automated discovery of AI x Bio preprint papers.
Fitness Landscape for Antibodies 2: Benchmarking Reveals That Protein AI Models Cannot Yet Consistently Predict Developability Properties
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about 4 hours ago
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CRISPR-HAWK: Haplotype- and Variant-aware guide design toolkit for CRISPR-Cas
[new] Incorporates genetic variation for improved gRNA design. Population diversity analysis reveals variants affecting on-target activity.
about 5 hours ago
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Automated Image-Based Cell Sorting by Targeted Photopolymerization
[new] Enables high-throughput cell sorting using image analysis and targeted photopolymerization to selectively remove unwanted cells.
about 9 hours ago
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Iterative Epitope Expansion Enables Structure-Guided de novoDesign of IgE-Binding Miniproteins Targeting the FcεRI Interface
][new] Epitope Expansion: de novo mini-proteins target IgE-FcεRI via sequential binding.
about 10 hours ago
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BCR repertoire analysis and cloning of antibody candidates targeting native and Asp7-isomerized beta-amyloid
[new] Identified anti-amyloid antibody candidates (esp. Asp7-isomerized) via BCR-seq and B cell lineage analysis.
about 10 hours ago
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DEEPGEOSEARCH: LLM-POWERED SCHEMALESS RETRIEVALFOR BIOMEDICAL DATA DISCOVERY
[new] LLM extracts study attributes from dataset text, harmonizes terminology, and ranks datasets by contextual alignment with queries.
about 11 hours ago
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Moving from Association to Causation: Instrumental factor models for causal inference in high-dimensional multi-omics data
[new] Causal effects in hi-dim omics: supervised IV & low-dim instrumental factors.
about 12 hours ago
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SuperFocus enables whole-slide cell-level spatial omics from spot-based measurements and histology across modalities
[new] AI-powered single-cell spatial omics imputes whole-slide features via spot data/histology.
about 13 hours ago
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Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images
[new] Cryo-EM optimization via Sliced Wasserstein: wider basins, robust gradients.
about 15 hours ago
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Ensemble-DeepSets: an interpretable deep learning framework for single-cell resolution profiling of immunological aging
[new] Immune age pred. fr. cell data; reveals aging, links to SLE.
1 day ago
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OMNI: Optimized Multi-view Network Integration with Heterogeneous Graph Attention for Biomedical Interaction Prediction
[new] OMNI: Predicts biomedical relationships in networks using a novel graph attention network.
1 day ago
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Deep learning analyses of DNA sequences resolve the retention of the Duffy-null resistance to Plasmodium vivax malaria in Africa
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1 day ago
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CoPhaser: generic modeling of biological cycles in scRNA-seq with context-dependent periodic manifolds
[new] scRNA-seq models cycles, separates periodic/nonperiodic variation via VAE, revealing cycle dynamics.
1 day ago
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Fully computational design of PAM-relaxed Staphylococcus aureus Cas9 with expanded targeting capability
[new] New SaCas9 KRH variant broadens genome editing via relaxed PAM (NNNRRT).
1 day ago
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Variational Inference with Node Embeddings (VINE) for Scalable Bayesian Phylogenetics
[new] Fast Bayesian phylogenetics via VINE inference.
1 day ago
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Clearing the whey: Efficient inhibition and removal of chymosin from whey by de novo designed protein-based inhibitors
[new] New proteins inhibit/remove chymosin in whey, enabling sustainable food & protease control.
2 days ago
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To Predict is to Design: Unlocking Generative Capabilities in All-Atom Structure Predictors via Geometric Score Distillation
[new] Geom score distills all-atom prot design via frozen diffusion.
2 days ago
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SpaceTrooper: a quality control framework for imaging-basedspatial omics data
[new] Data-driven QC combines expression & morphology features to identify low-quality cells from spatial omics data, improving downstream analysis.
2 days ago
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FlashAffinity: Bridging the Accuracy-Speed Gap in Protein-Ligand Binding Affinity Prediction
[new] Fast, accurate virtual screening via lightweight docking & EGNN affinity predictor.
2 days ago
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Genome-Level Hierarchical Attention Transformer with Multi-Head Attention Weighted Sum for Broad-Spectrum Antimicrobial Resistance Prediction and Discovery of Resistance-Related Genomic Contexts
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2 days ago
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A Computational Pipeline for Glioblastoma Vaccine Development: Integrating Novel Omics-Driven OIP5 Target Discovery to Create a Deep Learning-Based Immunogenicity Framework for Personalized Immunother...
[new]
2 days ago
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Sampling Function-Related Metastable States of Proteins With DASH
[new] Uses deep learning & MD to sample protein's metastable states from native, revealing new conformations, allosteric sites, & activators.
2 days ago
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A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics
[new] Gen. model fixes spatial transcriptomics' defects via multimodal, joint opt.
2 days ago
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Self-Supervised Missing Wedge Correction in Soft X-Ray Tomography: Towards Accurate Cellular Morphology and Volume Quantification
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2 days ago
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Highly Efficient Multiplexed Genome Engineering and Clone Selection to Enable Next Generation Induced Pluripotent Stem Cell (iPSC)-based Cell Therapies
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2 days ago
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Biophysically Grounded Deep Learning Improves Protein-Protein ΔΔG Prediction
](new] SKEMPI2 has data leakage. Adding biophysical priors to residue representations improves mutation-induced binding affinity change prediction.
2 days ago
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TASC: A transcriptome-driven machine learning classifier to explore molecular heterogeneity and relapse-associated programs in T-cell Acute Lymphoblastic Leukemia
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2 days ago
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B-PPI: A Cross-Attention Model for Large-Scale Bacterial Protein-Protein Interaction Prediction
[new] Predicts bacterial PPIs using embeddings from a protein language model and cross-attention on a large, bacteria-specific dataset.
2 days ago
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A Hybridization-Based Novel DNA Storage Technology with Rapid Read Performance
[new] Hybridization-based DNA storage offers fast read speeds, high parallelism, and encryption, addressing limitations of synthesis/sequencing methods.
2 days ago
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Engineered translation release factor 1 suppresses disease-causing nonsense mutations and enables multi-site nonstandard amino acids incorporation
[new]
2 days ago
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How medically important antimicrobials bind to the 30S ribosomal subunit in a bacterial pathogen
[new] Predicts Borrelia ribosome-antimicrobial binding variability via computation, analyzing past structures.
2 days ago
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MAGNET: an all-in-one foundation model for cross-modal and cross-dimensional microscopic image restoration
[new] Univ. micro image restor w/ multi-task,& X modal/dim capab.
3 days ago
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A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction
[new] U-Net: Representation learning, prediction, & controllable seq. gen. using genomic data.
3 days ago
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CancerSTFormer enables multi-scale analysis of spot-resolution spatial transcriptomes and dissects the gene and immune regulatory responses of targeted therapies
[new]
3 days ago
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MOTLAB: A Weighted Multi-Omics Transfer Learning Approach to Mitigate Breast Cancer Racial Disparities
[new] MOTLAB: weighted multi-omics integ., data aug., boosts transfer learning; mitigates breast cancer racial disparities.
3 days ago
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FlashDeconv enables atlas-scale, multi-resolution spatial deconvolution via structure-preserving sketching
[new] Leverage-score sampling enables fast deconvolution, preserving rare cell signals and revealing spatial architecture.
3 days ago
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A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction
[updated] DL models eval RNA struct pred, acc, gen, incl complexes.
3 days ago
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Transcriptome-Conditioned Personalized De Novo Drug Generation for AML Using Metaheuristic Assembly and Target-Driven Filtering
[new] De novo drug design via RNA-seq IDs AML biomarkers, generates ligands targeting hotspots for personalized leads.
3 days ago
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Clever Hans in Chemistry: Chemist Style Signals Confound Activity Prediction on Public Benchmarks
[new] Chemist Style Signals Confound Activity Prediction Models trained on public data can predict bioactivity by inferring the submitting chemist's intent.
3 days ago
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How Much Does Protein Structure Really Help? A Case Study in Mutation-Induced Stability Prediction
[new] PLMs predict mut. stability, fold prior. Geom. needed 4 atypical variants.
4 days ago
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Integrating NMR restraints into coarse-grained simulations: toward accurate conformational ensembles of complex protein systems
[new] NN-enhanced CG sim. for accurate protein ensembles via NMR.
4 days ago
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Large generative mRNA language foundation model for efficient coding sequence generation and design with mRNA-GPT
[new] mRNA-GPT: LLM gen. mRNA seqs, trains on bact., euk., & archaeal data.
4 days ago
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Queryome: Orchestrating Retrieval, Reasoning, and Synthesis across Biomedical Literature
[new] Orchestrates LLM agents for iterative, evidence-based synthesis across biomedical literature, improving reasoning on complex queries.
4 days ago
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Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo
[new] DL models trained on chromatin data design synthetic enhancers active in mouse embryo tissues (heart, limb, CNS).
4 days ago
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Mechanistic Interpretability of Fine-Tuned Protein Language Models for Nanobody Thermostability Prediction
[new] Sparse autoencoders analyze fine-tuned PLMs, revealing nanobody thermostability principles & design guides.
4 days ago
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SurfDiff: protein surface profiling for selective or broadly reactive epitope prioritisation in binder and immunogen design
[new] Epitope prioritz.: structure/seq. for surface comparison & binder design.
4 days ago
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Drug-like antibodies with low immunogenicity in human panels designed with Latent-X2
[new] Generates developable, non-immunogenic antibodies de novo. It models bound complex, sequence, and structure, achieving high affinity & low immunogenicity.
4 days ago
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Deep Learning Classification of EEG Responses to Multi-Dimensional Transcranial Electrical Stimulation
[new] Classifies EEG responses to transcranial electrical stimulation with deep learning to objectively measure brain state, bypassing sensory input.
4 days ago
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SynCraft: Guiding Large Language Models to Predict Edit Sequences for Molecular Synthesizability Optimization
[new] LLM predicts atom edits to optimize molecular synthesizability, addressing generative AI limits.
4 days ago
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Molecular interactions underlying selective partitioning of clients into MED1 and FUS condensates
[new] Charge/aromaticity guides protein partitioning in MED1/FUS condensates, IDing binding sites.
4 days ago
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