AIMC Journal:
bioRxiv

Showing 881 to 890 of 4938 articles

Real-time mass defect-driven prediction of glycopeptide precursors enables enrichment-free serum glycoproteomics

bioRxiv Jul 5, 2026
Glycopeptide enrichment remains a cornerstone in glycoproteomics, but bias and reproducibility issues continue to hinder biological insight and clinical translation. Using curated glycoproteomics datasets and machine learning, we trained a glycopepti...
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Benchmarking large language models for ACMG/AMP variant interpretation and variant calling

bioRxiv Jul 5, 2026
Agentic large language models are increasingly used across the genomic workflow, from variant calling to clinical interpretation, yet they are evaluated by accuracy alone, a single figure that cannot say whether a system is safe or where in the workf...
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A High-Confidence Atlas of Protein Methylation Enables AI-Driven Detection of Methylated Peptides

bioRxiv Jul 4, 2026
Lysine and arginine methylation regulate chromatin dynamics, transcription, and cellular signaling, however confident mass spectrometry (MS)-based detection and localization of this modification remain challenging. We reanalyzed eight public human me...
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Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2

bioRxiv Jul 4, 2026
Inferring orthologs and annotating coding genes remain central challenges in genomics, evident by the growing gap between assembled and annotated genomes. TOGA (Tool to infer Orthologs from Genome Alignments) addresses this challenge by integrating g...
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Connectome-scale self-supervised representation learning reveals neuronal organization beyond canonical labels

bioRxiv Jul 4, 2026
Dense electron-microscopy connectomes provide synaptic-resolution maps of neuronal structure and wiring, but learning scalable representations that integrate structure and connectivity for connectome discovery with minimal human intervention remains ...
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TRIOPS: A deep learning framework for prediction of T cell receptor-MHC binding specificity

bioRxiv Jul 4, 2026
T cell receptor (TCR) recognition is MHC-restricted, yet accurately predicting a TCR's restricting HLA allele remains an open problem. We present TRIOPS, a dual-branch convolutional model with soft cross-attention that predicts TCR-MHC restriction fr...
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Programmable acoustic single cell manipulation with model-free machine learning

bioRxiv Jul 3, 2026
Precise, non-invasive manipulation of individual living cells remains a central challenge in biomedical science, with far-reaching implications for single-cell analysis, tissue engineering, and the study of cell-cell interactions. Here, we report the...
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Curiosity shapes brain-like architectures and functions

bioRxiv Jul 3, 2026
How does complex cognition emerge from simpler underlying processes? We show that two components are sufficient: infant-like curiosity and brain-like biophysical constraints jointly drive the emergence of complex neuronal architectures and cognitive ...
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Evo 2's Perception of Single Nucleotide Substitutions in the Genes of Two Plant Model Organisms

bioRxiv Jul 3, 2026
Although DNA Large Language Models (DNA-LLMs) offer a path to decoding genetic complexity, our ability to evaluate these models is constrained by our incomplete understanding of the very same genetic syntax and functional logic that these models are ...
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Artificial intelligence virtual cell immune recovery model for screening traditional Chinese medicine ingredients

bioRxiv Jul 3, 2026
Screening therapeutic candidates from single-cell transcriptomes requires a target that is closer to treatment response than disease-signature reversal. In immune diseases, post-treatment recovery may follow patient- and lineage-specific trajectories...
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