bioRxiv

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Discovery of molecular glues by modeling ternary complex conformational ensembles and thermodynamic stability

bioRxiv Jan 1, 2025
The rational design of molecular glue degraders is challenging because glue-mediated protein degradation depends on a complex interplay of molecular mechanisms: an effective molecular glue must simultaneously bring together two distinct proteins to f...
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RoBep: A Region-Oriented Deep Learning Model for B-Cell Epitope Prediction

bioRxiv Jan 1, 2025
Accurate in silico identification of B-cell epitope residues is crucial for antibody design and structure-guided vaccine development. Although recent protein language models and structure-aware methods can capture spatial information of tertiary stru...
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MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases

bioRxiv Jan 1, 2025
Terpene synthases (TPSs) are enzymes that catalyze some of the most complex reactions in nature – the cyclizations of terpenes, which form the carbon backbones to the largest group of natural products, the terpenoids. On average, more than half of th...
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Medial Temporal Default Mode Network Selectively Encodes Autobiographical Visual Imagery

bioRxiv Jan 1, 2025
The human brain’s capacity to imagine visual scenes from memory is thought to rely on the medial temporal subsystem of the default mode network (MT-DMN), yet the neural codes supporting this ability remain poorly understood. We combined functional ma...
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A deep learning framework for building INDEL mutation rate maps

bioRxiv Jan 1, 2025
Germline short insertions and deletions (INDELs) are pervasive genetic variants that shape genome evolution and contribute to human disease. However, accurately quantifying fine-scale INDEL mutation rates remains challenging due to data limitations a...
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From Circles to Signals: Representation Learning on Ultra-Long Extrachromosomal Circular DNA

bioRxiv Jan 1, 2025
Extrachromosomal circular DNA (eccDNA) is a covalently closed circular DNA molecule that plays an important role in cancer biology. Genomic foundation models have recently emerged as a powerful direction for DNA sequence modeling, enabling the direct...
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SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data

bioRxiv Jan 1, 2025
Cell–cell communication (CCC) drives the coordinated cellular dynamics underlying development, regeneration, and disease. Recent advances in spatiotemporal transcriptomics now enable measurement of gene expression within both spatial context and deve...
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Contrasting Biological Pathways Underlie Agronomic Traits in Two Coffea canephora Breeding Populations

bioRxiv Jan 1, 2025
This study reveals that distinct breeding populations of Coffea canephora can achieve agronomic success through fundamentally different biological strategies. To uncover this, we performed a comparative genomic analysis of two populations (‘Premature...
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CodonTranslator: a conditional codon language model for codon optimization across life domains

bioRxiv Jan 1, 2025
Codon optimization involves selecting synonymous codons to match host-specific preferences. It is critical for heterologous expression but remains challenging due to the combinatorial design space. Under long-term evolutionary selection, natural codi...
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Enhanced Tactile Coding in Rat Neocortex Under Darkness

bioRxiv Jan 1, 2025
Sensory systems are known for their adaptability, responding dynamically to changes in environmental conditions. A key example of this adaptability is the enhancement of tactile perception in the absence of visual input. Despite behavioral studies sh...
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