AI Medical Compendium

Comparative cross-species transcriptomic analysis identifies new candidates of Pooideae nitrate response

bioRxiv Mar 20, 2026

Nitrogen fertilizers are essential for crop productivity but cause environmental harm, necessitating the development of cultivars that thrive under limited nitrogen. This study investigates the transcriptomic response to nitrate in Arabidopsis thalia... read more

plant biology

Mapping spatial cell-cell communication programs by tailoring chains of cells for transformer neural networks

bioRxiv Mar 20, 2026

Recent advances in spatial transcriptomics and computational modeling enable the study of cellular interactions in situ. However, existing methods quantify ligand-receptor activity pairwise or between predefined cell groups, yielding overlapping sign... read more

bioinformatics

HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism

bioRxiv Mar 20, 2026

Motivation: The emergence of novel viral pathogens poses critical threats to global health, yet current computational approaches for viral risk assessment are predominantly virus-specific and require extensive retraining for each new threat. Computat... read more

bioinformatics

Systematic assessment of machine learning-based variant annotation methods for rare variant association testing

bioRxiv Mar 20, 2026

Machine learning-based annotation methods are increasingly used to assess the pathogenicity of genetic variants, but their performance at prioritizing variants for gene-level association testing remains poorly characterized. Here, we systematically b... read more

bioinformatics

Evolutionary and Deep Learning Models Highlight Deleterious Mutations Behind the History of Sugar Beet Breeding

bioRxiv Mar 20, 2026

Sugar beet (Beta vulgaris ssp. vulgaris) is a major global source of sucrose. Domestication and a history of breeding have shaped the distribution of deleterious mutations across the genome. Accurately resolving these variants offers a compelling ave... read more

genomics

Causal differential expression analysis under unmeasured confounders with causarray

bioRxiv Mar 20, 2026

Advances in single-cell sequencing and CRISPR technologies have enabled detailed case-control comparisons and experimental perturbations at single-cell resolution. However, uncovering causal relationships in observational genomic data remains challen... read more

genomics

Behavioral characterization of dynamic facial expression perception in rhesus monkeys (Macaca mulatta) using naturalistic and synthetic stimuli

bioRxiv Mar 20, 2026

Facial displays are an important channel of communication for primates, yet it remains unclear based on which criteria monkeys evaluate facial expressions. We trained two rhesus macaques to categorize videos of four facial expression types (neutral, ... read more

animal behavior and cognition

Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA

bioRxiv Mar 20, 2026

mRNA coding sequence design is a critical component in the development of mRNA vaccines, nucleic acid therapeutics, and heterologous gene expression systems. While large language models have recently been successfully applied to protein design and RN... read more

bioinformatics

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

bioRxiv Mar 20, 2026

Causal models of cellular systems hold the promise to empower broad biological discovery, including the systematic identification of novel targets for drug discovery. Predicting how genetic and pathway perturbations reshape gene expression across div... read more

systems biology

Serotonergic axons signal reward, sensory stimulation, and prepare for movement in primary somatosensory cortex

bioRxiv Mar 20, 2026

Serotonin is one of the main neuromodulators in the brain, involved in regulating mood, complex behaviors and sensory input. Serotonin reaches primary somatosensory cortex (S1) via axons of neurons located in the dorsal raphe nucleus (DRN). DRN neuro... read more

neuroscience

Artificial Intelligence Medical Compendium

Comparative cross-species transcriptomic analysis identifies new candidates of Pooideae nitrate response

Mapping spatial cell-cell communication programs by tailoring chains of cells for transformer neural networks

HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism

Systematic assessment of machine learning-based variant annotation methods for rare variant association testing

Evolutionary and Deep Learning Models Highlight Deleterious Mutations Behind the History of Sugar Beet Breeding

Causal differential expression analysis under unmeasured confounders with causarray

Behavioral characterization of dynamic facial expression perception in rhesus monkeys (Macaca mulatta) using naturalistic and synthetic stimuli

Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

Serotonergic axons signal reward, sensory stimulation, and prepare for movement in primary somatosensory cortex

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