bioRxiv

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Interpretable gene network inference with nonlinear causality

bioRxiv Jan 1, 2025
Interactions among genes orchestrate the growth and survival of all living systems. Such interactions are mediated by vast networks of time-dependent couplings, yet existing strategies for inferring gene networks from omics data do not account for th...
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Language network functional connectivity in infancy predicts developmental language trajectories

bioRxiv Jan 1, 2025
Although developmental language delays affect approximately 10% of children in the general population, the neurodevelopmental mechanisms that support normative language acquisition, and atypicalities that may predict later language delay, across the ...
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GDEE: A Structure-Based Platform for Gene Discovery and Enzyme Engineering

bioRxiv Jan 1, 2025
Enzymes are extensively utilized for catalyzing the production of value-added compounds in diverse sectors with significant economic impact. However, challenges such as poor protein expression, low catalytic activity, substrate/co-factor limitations,...
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A Shared Neural Marker Predicts Creative Performance Across Distinct Problem-Solving Tasks

bioRxiv Jan 1, 2025
Creativity is essential for innovation, yet the brain mechanisms supporting its moment-to-moment variability remain unclear. We hypothesize that creativity depends on dynamic fluctuations in neural flexibility, which determine the potential to genera...
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Integrating Protein and DNA Embeddings for Improving Genome-Wide Transcription Factor Binding Site Prediction

bioRxiv Jan 1, 2025
Transcription factors (TFs) regulate gene expression by binding to specific DNA sites on genome, making accurate TF binding site prediction critical for understanding gene regulation and downstream phenotypes. Current deep learning methods use only D...
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Multimodal foundation model predicts zero-shot functional perturbations and cell fate dynamics

bioRxiv Jan 1, 2025
Deciphering cell type-specific perturbation effects on genes and cellular states demands considerable experimental resources. To overcome this challenge, we propose Perturbation Transformer (PertFormer), a foundation model to uncover functional and r...
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MENDELSEEK: An algorithm that predicts Mendelian Genes and elucidates what makes them special

bioRxiv Jan 1, 2025
Although individual Mendelian diseases—those caused by a single gene—are rare, their collective disease burden is substantial. Identifying the causal gene for each condition is essential for accurate diagnosis and effective treatment. Yet, despite de...
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AmyloDeep: pLM-based ensemble model for predicting amyloid propensity from the amino acid sequence

bioRxiv Jan 1, 2025
Amyloids are predominantly β-sheet-rich, stable protein structures that can maintain their presence in the human body for multiple years. Amyloid protein aggregates contribute to the development of multiple neurodegenerative diseases, such as Alzheim...
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FixGrower: An efficient and robust curriculum for shaping fixation behavior in rodents

bioRxiv Jan 1, 2025
Center-port fixation is a common prerequisite for many freely-moving rodent tasks in neuroscience and psychology. However, typical protocols for shaping this behavior are non-standardized and inefficient. Moreover, motor errors in fixation termed ‘vi...
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A histomorphological atlas of resected mesothelioma discovered by self-supervised learning from 3446 whole-slide images

bioRxiv Jan 1, 2025
Mesothelioma is a highly lethal and poorly biologically understood disease which presents diagnostic challenges due to its morphological complexity. This study uses self-supervised AI (Artificial Intelligence) to map the histomorphological landscape ...
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