bioRxiv

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Adapting CRISPR-associated transposons for rapid and high-throughput reverse genetics

bioRxiv Jan 1, 2025
CRISPR-associated transposons (CAST) use guide RNAs to direct their transposition and are being harnessed as tools for programmable genome engineering across diverse bacterial species. However, CAST systems have not been adapted for high-throughput g...
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Predicting strain-specific metabolic capabilities in the Genus Pseudomonas using a Flux-to-AI approach unravels hidden cell envelope properties

bioRxiv Jan 1, 2025
Bacteria from the Pseudomonas genus are omnipresent in air, soil, and water. They have been widely studied for their broad metabolic versatility and presence in the epidemiological chain, bioproduction, bioremediation, and disease processes. Each yea...
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Star-Motifs: Revealing Single-Cell Spatiotypes from Routine Histology Using Star-Convex Neighborhoods

bioRxiv Jan 1, 2025
The tumor microenvironment (TME) is a dynamic interplay among cancer, immune, and stromal cells that profoundly influences tumor growth, progression, and treatment response. Although recent spatial transcriptomics and multiplex imaging technologies o...
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Predicting the invasiveness of threshold-dependent gene drives

bioRxiv Jan 1, 2025
Gene drives hold great promise for controlling disease vectors or invasive species due to their capacity to rapidly spread through a population from a small initial release. This same property also raises serious concerns about unintended spillover i...
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PertAdapt: Unlocking Single-Cell Foundation Models for Genetic Perturbation Prediction via Condition-Sensitive Adaptation

bioRxiv Jan 1, 2025
Single-cell foundation models (FMs) pretrained on massive unlabeled scRNA-seq data show strong potential in predicting transcriptional responses to unseen genetic perturbations. However, existing approaches insufficiently transfer pretrained knowledg...
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MkAtt-SDN2GO: Multi-kernel Attentive-SDN2GO Network for Protein Function Prediction in Humans

bioRxiv Jan 1, 2025
Accurately annotating the functions of uncharacterised human proteins remains a major bottleneck in biology. We present MkAtt–SDN2GO, a neural architecture that extends SDN2GO by integrating adaptive multi-kernel convolution and attention mechanisms ...
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scDNAm-GPT Captures Genome-wide CpG Dependencies in Single-cell DNA methylomes to Revolutionize Epigenetic Analysis

bioRxiv Jan 1, 2025
Single-cell DNA methylomes are challenging to interpret because of sparse CpG coverage and the complexity of genome-wide sequences. We present scDNAm-GPT, a universal foundation model that uses context-aware CpG tokenization, a Mamba backbone, and cr...
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ProtAttn-QuadNet: An attention-based deep learning framework for protein–protein interaction prediction using ProtBERT embeddings

bioRxiv Jan 1, 2025
Protein–protein interactions (PPIs) form the backbone of most cellular processes, governing signal transduction, gene regulation, and metabolic control. However, experimental approaches to identifying PPIs remain expensive, laborious, and often incom...
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The hippocampus as an epistemic forager: When curiosity and reward jointly steer exploration and hippocampal replay

bioRxiv Jan 1, 2025
Hippocampal replay is a widely studied phenomenon wherein special neurons of the hippocampus encoding spacial locations – place cells – show a sequential reactivation during periods of immobility, often representing trajectories to or from reward loc...
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Fine-Tuning Protein Language Models Enhances the Identification and Interpretation of the Transcription Factors

bioRxiv Jan 1, 2025
Transcription factors (TFs) are pivotal regulators of gene expression and play essential roles in diverse cellular activities. The three-dimensional organization of the genome and transcriptional regulation are predominantly orchestrated by TFs. By r...
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