AIMC Journal:
bioRxiv

Showing 2101 to 2110 of 4956 articles

Relationship Between Gene Expression and Drug Response in Triple-Negative Breast Cancer: Leveraging Single-Cell RNA Sequencing and Machine Learning to Identify Biomarker Profiles

bioRxiv Mar 8, 2026
Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by limited therapeutic options and poor prognosis. To address these challenges, we combined single-cell RNA sequencing (scRNA-seq) data with advanced machine learning techniq...
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Popformer: Learning general signatures of positive selection with a self-supervised transformer

bioRxiv Mar 6, 2026
Understanding natural selection can help shed light on the genetics underpinning adaptive evolution. The widespread availability of large-scale human genetic variation data has led to the development of data-driven methods for detecting signatures of...
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Optimal spatial release strategies for confined gene drives and Wolbachia

bioRxiv Mar 6, 2026
Gene drives are genetic elements that can rapidly spread through populations, offering potential solutions for controlling disease vectors and pests. In some scenarios, it is necessary to utilize drives that can be confined to only target populations...
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Reliable prediction of short linear motifs in the human proteome

bioRxiv Mar 6, 2026
Short linear motifs (SLiMs) are small, often transient interaction modules within intrinsically disordered regions (IDRs) of proteins that interact with particular domains and thereby regulate numerous biological processes. The limited sequence infor...
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What Do Biological Foundation Models Compute? Sparse Autoencoders from Feature Recovery to Mechanistic Interpretability

bioRxiv Mar 6, 2026
Foundation models trained on protein and DNA sequences are increasingly deployed for variant interpretation, drug design, and gene regulation prediction, yet their internal representations remain opaque, limiting both biological insight and trust in ...
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AI-Driven Generation of Cortisol-Binding Peptides for Non-Invasive Stress Detection

bioRxiv Mar 6, 2026
Cortisol is a primary biomarker of stress, released in sweat at concentrations that directly correlate with physiological stress levels. Detecting cortisol non-invasively offers significant potential for real-time stress monitoring and healthcare app...
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PAVR: High-Resolution Cellular Imaging via a Physics-Aware Volumetric Reconstruction Framework

bioRxiv Mar 6, 2026
The rapid convergence of advanced microscopy and deep learning is transforming cell biology by enabling imaging systems in which optical encoding and computational inference are jointly optimized for volumetric information capture and interpretation....
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dAMN: a genome scale neural-mechanistic hybrid model to predict bacterial growth dynamics

bioRxiv Mar 6, 2026
This study presents dAMN, a hybrid neural-mechanistic model that integrates neural networks with genome-scale dynamic flux balance analysis (dFBA) to predict bacterial growth curves across diverse nutrient environments. dAMN uses neural networks to i...
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Phenotypic reversion and target prioritization for cellular inflammation via representation learning with foundation models

bioRxiv Mar 6, 2026
The identification of genetic perturbations that can reverse disease-associated cellular phenotypes toward a healthy state is a central challenge in early drug discovery. We present a proof-of-concept framework leveraging single-cell foundation model...
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Circular RNA identification using a genomic language model and a small number of authenticated examples

bioRxiv Mar 6, 2026
Genomic language models (gLMs) hold great promise for deciphering biological sequences, yet their effectiveness is hindered by the limited number of experimentally verified examples available for model training, a ubiquitous bottleneck for supervised...
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