bioRxiv

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A Transformer based method for the Cap Analysis of Gene Expression and Gene Expression Tag associated 5’ cap site prediction in RNA

bioRxiv Jan 1, 2025
5’ RNA capping is one of the major post-transcriptional modifications for the mobility and stability of RNA molecules. Measuring 5’ caps of RNAs can help quantify expression levels of mRNAs and lncRNAs. One of the most successful RNAseq methods that ...
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Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells

bioRxiv Jan 1, 2025
Base editors create precise nucleotide changes in DNA, but their off-target activity remains challenging to quantify. Here, we develop and deploy a direct, in cellulo sequencing assay that simultaneously measures both Cas9-mediated unwinding and deam...
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AI methods and biologically informed data curation enable accurate RNA m5C prediction

bioRxiv Jan 1, 2025
5-methylcytosine (m5C) RNA modifications influence nearly every aspect of RNA metabolism, but their transcriptome wide detection is limited by costly, error-prone assays. To bridge this experimental gap, a wave of AI tools now predicts putative m5C s...
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Leveraging the largest harmonized epigenomic data collection for metadata prediction validated and augmented over 350,000 public epigenomic datasets

bioRxiv Jan 1, 2025
Epigenomic data found in public databases often suffer from issues of non-standardization and incompleteness in their associated metadata. There are currently no automated approaches to validate or correct missing or inaccurate information listed in ...
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Enhancing fMRI decoded neurofeedback with co-adaptive training: simulation and proof-of-principle evidence

bioRxiv Jan 1, 2025
A significant challenge for neurofeedback training research and related clinical applications, is participants’ difficulty in learning to induce specific brain patterns during training. Here, we address this issue in the context of fMRI-based decoded...
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STARNet enables spatially resolved inference of gene regulatory networks from spatial multi-omics data

bioRxiv Jan 1, 2025
Biological tissues are composed of distinct microenvironments that spatially orchestrate gene expression and cell identity. However, the regulatory principles governing domain-specific cellular functions remain poorly understood due to the lack of ef...
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SynGlue: AI-Driven Designer for Clinically Actionable Multi-Target Therapeutics

bioRxiv Jan 1, 2025
The rational design of multi-targeting compounds and targeted protein degraders, such as PROTACs, remains a significant challenge in drug discovery. Here, we introduce SynGlue, a modular generative AI platform that integrates fragment-based reasoning...
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PyCLM: programming-free, closed-loop microscopy for real-time measurement, segmentation, and optogenetic stimulation

bioRxiv Jan 1, 2025
In cell biology, optical techniques are increasingly used to measure cells’ internal states (biosensors) and to stimulate cellular responses (optogenetics). Yet the design of all-optical experiments is often manual: a pre-determined stimulus pattern ...
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Automating Candidate Gene Prioritization with Large Language Models: From Naive Scoring to Literature-Grounded Validation

bioRxiv Jan 1, 2025
Identifying promising therapeutic targets from thousands of genes in transcriptomic studies remains a major bottleneck in biomedical research. While large language models (LLMs) show potential for gene prioritization, they suffer from hallucination a...
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Variant-resolved prediction of context-specific isoform variation with a graph-based attention model

bioRxiv Jan 1, 2025
In eukaryotes, most genes produce multiple transcript isoforms that diversify the transcriptome and proteome, serving as a key mechanism of functional regulation. Genetic variation can disrupt the RNA processing signals that shape isoform structure a...
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