bioRxiv

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Colon-Specific Epigenetic Clocks from Minimal Features Reveal Disease-Driven Aging

bioRxiv Jan 1, 2025
Epigenetic clocks estimate chronological and biological age from DNA methylation patterns, but conventional models typically train on hundreds of thousands of CpG sites and large training cohorts. We previously demonstrated that tissue-unique methyla...
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SpatialProp: tissue perturbation modeling with spatially resolved single-cell transcriptomics

bioRxiv Jan 1, 2025
Perturbational studies are the gold standard for identifying causal relationships between components of biological systems. Recent technological advances, including Perturb-seq and related assays, have enabled high-throughput screening of genetic per...
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AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level

bioRxiv Jan 1, 2025
Deep-learning methods have transformed our ability to predict the three-dimensional structures of folded proteins from sequence, and coarse-grained simulations have made it possible to study intrinsically disordered proteins at the proteome scale. Mo...
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Substrate-enhanced filamentation of 3-methylcrotonyl-CoA carboxylase in Legionella pneumophila

bioRxiv Jan 1, 2025
3-Methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent carboxylase that metabolizes the amino acid leucine. MCC is present in bacteria, fungi, plants, and animals. In humans, its overexpression is linked to cancer, and its deficiency is linked ...
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Deep learning analyses of DNA sequences resolve the retention of the Duffy-null resistance to Plasmodium vivax malaria in Africa

bioRxiv Jan 1, 2025
P. vivax, the most geographically widespread human malaria parasite with millions of clinical cases per year, is however quasi absent in sub-Saharan Africa. Positive selection targeting the rs2814778 protective mutation, also known as the Duffy-null ...
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Circuit specific specialization of human basal ganglia astrocytes

bioRxiv Jan 1, 2025
Astrocytes shape synapses and circuits, yet human basal ganglia astrocyte diversity is incompletely defined. We built a multimodal atlas by integrating single-nucleus RNA-sequencing and chromatin accessibility with DNA methylation, 3D chromatin confo...
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Muscle activation prediction in essential tremor through neuromusculoskeletal digital twinning and deep neural networks

bioRxiv Jan 1, 2025
Essential tremor (ET) is the most common movement disorder in adults, affecting up to 5% of the population over 65 years of age. Accurately predicting the dynamics of ET for each individual is crucial for optimizing therapies, such as sub-motor thres...
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Generative design and construction of functional plasmids with a DNA language model

bioRxiv Jan 1, 2025
DNA language models offer a new paradigm for sequence design, yet their ability to generate functional genomic sequences remains underexplored. Plasmids act as a good testbed for evaluating DNA language model generation potential due to their simplic...
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DeepDOX1: A Dual-Drive Framework Integrating Deep Learning and First-Principles Physics for Drug-Protein Affinity Prediction

bioRxiv Jan 1, 2025
In this work, we present DeepDOX1, a dual-drive drug-protein affinity (DPA) prediction tool features the tight integration of a concise AI architecture and a quantum mechanics based representation. The first-principle physics generated features incor...
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Machine learning applied to otolith microchemical data to discriminate stock of origin in salmon

bioRxiv Jan 1, 2025
A key challenge in ecosystem-based fisheries management is sustainably harvesting co-occurring species and populations that differ in their vulnerability to fishing. This challenge is exemplified in western Alaska Chinook salmon, where recent populat...
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