AIMC Journal:
bioRxiv

Showing 2211 to 2220 of 4956 articles

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome

bioRxiv Feb 28, 2026
The gut microbiome regulates many aspects of human biology, including immunity and inflammatory diseases, yet mechanistic discovery and translation remain constrained by fragmented workflows and manual hypothesis integration. Here, we present Eubiota...
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Deep genomic models of allele-specific measurements

bioRxiv Feb 27, 2026
Allele-specific quantification of sequencing data, such as gene expression, allows for a causal investigation of how DNA sequence variations influence cis gene regulation. Current methods for analyzing allele-specific measurements for causal analysis...
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A Data-Driven Image Extraction and Analysis Pipeline for Plant Phenotyping in Controlled Environments

bioRxiv Feb 27, 2026
Advances in automation, imaging, and artificial intelligence have enabled researchers to capture large volumes of high-quality plant data for understanding crop growth, stress, and genotype-by-environment interactions. While genomics has achieved rem...
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Uncertainty-aware synthetic lethality prediction with pretrained foundation models

bioRxiv Feb 27, 2026
Synthetic lethality (SL) offers a promising paradigm for targeted cancer therapy, yet experimental identification of SL gene pairs remains costly, context-dependent, and biased toward well-studied genes. Existing computational approaches often rely o...
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MAP: A Knowledge-driven Framework for Predicting Single-cell Responses for Unprofiled Drugs

bioRxiv Feb 27, 2026
Predicting how cells respond to chemical perturbations is one of the goals for building virtual cells, yet experimentally profiled compounds cover only a small fraction of this space. Existing models struggle to generalize to unprofiled compounds, as...
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AbiOmics: An End-to-End Pipeline to Train Machine Learning Models for Discrimination of Plant Abiotic Stresses Using Transcriptomic Profiling Data

bioRxiv Feb 27, 2026
Abiotic stresses are primary constraints on global crop productivity, reducing yields by up to 80%. While traditional phenotypic sensing detects stress only after physiological symptoms emerge and often fails to discriminate specific stressor types, ...
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PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery

bioRxiv Feb 27, 2026
The convergence of large language model-powered autonomous agent systems and single-cell biology promises a paradigm shift in biomedical discovery. However, existing biological agent systems, building upon single-agent architectures, are narrowly spe...
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Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution

bioRxiv Feb 27, 2026
The spatial organization of microbial communities is a critical determinant of host-microbe interactions, yet species-level mapping remains challenging due to high 16S rRNA sequence homology and spectral crosstalk in multiplexed fluorescence in situ ...
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Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites

bioRxiv Feb 27, 2026
Transcription factors recognise and bind specific DNA sequence patterns in promoters and enhancers thereby regulating gene expression. Variations in the DNA sequence of transcription factor binding sites (TFBSs) can alter gene regulation and may disr...
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A Framework for Autonomous AI-Driven Drug Discovery

bioRxiv Feb 26, 2026
The exponential increase in biomedical data offers unprecedented opportunities for drug discovery, yet overwhelms traditional data analysis methods, limiting the pace of new drug development. Here we introduce a framework for autonomous artificial in...
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