AIMC Journal:
bioRxiv

Showing 731 to 740 of 4938 articles

FENNEC: photon-level deep learning for classifying bursts in diffusion-based single-molecule FRET

bioRxiv Jul 16, 2026
Single-molecule Forster resonance energy transfer (smFRET) reports on biomolecular conformational dynamics by measuring distance changes between donor and acceptor fluorophores. In diffusion-based smFRET, however, the detection of genuine conformatio...
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Mapping the Transcriptional Landscape of Drug Responses in Primary Human Cells Using High-Throughput DRUG-seq

bioRxiv Jul 16, 2026
To advance our understanding of drug action in physiologically-relevant systems, we developed a high-throughput transcriptomic atlas of compound responses in primary human cell types. Leveraging the scalable and cost-effective Digital RNA with the pe...
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Biological Continued Pretraining Reshapes the Capability Profile of a Foundation Model Without Catastrophic Forgetting

bioRxiv Jul 16, 2026
It is widely assumed that continued pretraining (CPT) on a narrow, out-of-distribution corpus such as raw biological sequence must trade away a general-purpose model's broad competence --- the "alignment tax" or catastrophic-forgetting intuition. We ...
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Evaluating the use of non-linear models in data-driven rescoring of peptide-spectrum matches

bioRxiv Jul 16, 2026
In mass spectrometry (MS)-based proteomics, computational tools match acquired tandem MS spectra to peptides from a sequence database. Machine learning increasingly supports this task through peptide-spectrum match (PSM) rescoring, in which a classif...
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Spatio-temporal 3D Mapping of Mouse Cerebellar Vascularization during Embryonic Development

bioRxiv Jul 16, 2026
Despite major advances in the study of cerebellar neurogenesis, cerebellar angiogenesis during embryogenesis remains poorly described. Recent advances in tissue clearing, light-sheet microscopy, and artificial intelligence have increasingly enabled d...
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What Do Generative Models Learn About Adaptive Immune Receptor Repertoires? A Benchmark Study

bioRxiv Jul 16, 2026
Generative models are increasingly used to model adaptive immune receptor repertoire (AIRR) sequence distributions, promising to decode the sequence diversity shaping immune responses and accelerate the design of therapeutic antibodies and T-cell rec...
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Site-dependent transcriptomic signatures of endometriosis are conserved across hormonal states

bioRxiv Jul 16, 2026
Endometriosis, a chronic condition in which endometrial tissue grows at other sites in the body, produces lesions whose gene expression profiles vary by anatomical location and menstrual cycle stage. The extent to which these location-dependent trans...
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Genomic foundation model embeddings encode higher-order viral genome architecture beyond sequence composition: a benchmark of Evo 2

bioRxiv Jul 16, 2026
Genomic foundation models such as Evo 2 are increasingly applied to microbial genomics, yet how well their representations capture viral genome organisation, and how reliably they generate viral sequence, remain poorly characterised. We present a rep...
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{Sigma}0-EvoCell: An AI-Native Ontology that Unifies Evolutionary and Cell Biology in Latent Space

bioRxiv Jul 16, 2026
Foundation models for biology achieve impressive pattern recognition on molecular sequences and single-cell transcriptomics, yet they fail to outperform simple linear baselines for predicting genetic perturbation effects, exposing a gap between stati...
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MInt-HDX: Leveraging Hydrogen-Deuterium Exchange Mass Spectrometry and Machine-Learning to Improve Protein-Ligand Docking.

bioRxiv Jul 16, 2026
Understanding protein structural dynamics is central to elucidating biological function and guiding therapeutic discovery. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) typically offers peptide-level, and sometimes residue-level, time-depend...
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