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Construction of a Multitissue Cell Atlas Reveals Cell‐Type‐Specific Regulation of Molecular and Complex Phenotypes in Pigs

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The evolution of gene regulation in mammalian cerebellum development

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Mapping Cell Atlases at the Single‐Cell Level

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Identification, characterization, and design of plant genome sequences using deep learning

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A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs

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Revealing the Transcriptional and Metabolic Characteristics of Sebocytes Based on the Donkey Cell Transcriptome Atlas

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CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data

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Single-cell atlas comparison across vertebrates reveals auditory cell evolution and mechanisms for hair cell regeneration

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Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina

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Comparative single-cell transcriptomic map reveals divergence in leaves between two cotton species at cell type resolution

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Robust integration and annotation of single-cell and spatial omics data using interpretable gene programs

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Cross-species comparative single-cell transcriptomics highlights the molecular evolution and genetic basis of male infertility

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Decoding maize meristems maintenance and differentiation: integrating single-cell and spatial omics

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Convergent differentiation of multiciliated cells

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Mouse-to-human modeling of microglia single-nuclei transcriptomics identifies immune signaling pathways and potential therapeutic candidates associated with Alzheimer’s diseasePreprint

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Omnireg-gpt: a high-efficiency foundation model for comprehensive genomic sequence understanding

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Single-cell RNA sequencing of zebrafish olfactory epithelium reveals cellular heterogeneity and responses to a conspecific alarm substance

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UNICORN: Towards universal cellular expression prediction with a multi-task learning framework

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The Transcriptomic Signature of Donkey Ovarian Tissue Revealed by Cross-Species Comparative Analysis at Single-Cell Resolution

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Refining sequence-to-expression modelling with chromatin accessibility

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iVAE: an interpretable representation learning framework enhances clustering performance for single-cell data

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Dissecting cross‐lineage tumourigenesis under p53 inactivation through single‐cell multi‐omics and spatial transcriptomics

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Single-cell analysis reveals cellular heterogeneity and molecular features during postnatal pig testis development

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Family single-cell atlases reveal pig pregnancy and fetal growth restriction critical cell types

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Sekwencjonowanie transkryptomu pojedynczych komórek: droga do odkrywania bioróżnorodności komórkowej

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ScGOclust: leveraging gene ontology to compare cell types across distant species using scRNA-seq dataPreprint

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XChrom: A Cross‐Cell Chromatin Accessibility Prediction Model Integrating Genomic Sequence and Cellular Context

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Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigsPreprint

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Alternative integrative systems in nerveless animals: Chemoconnectomics before synapses

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Evolutionary conservation and divergence of phagocytic and coagulation programs across bilaterian circulating immune cells

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DanioDecima: A DNA sequence-to-function model of zebrafish embryogenesisPreprint

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Single-cell and spatial transcriptomic insights into fibrotic mechanisms and therapeutic opportunities

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A Comprehensive Comparative Analysis of Sequence‐Based Deep Learning Models for Single‐Cell Genomics

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Microwell platform for single-cell applications and future integration with artificial intelligence (AI)

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Mapping a differentiation architecture for hard tissue mineralization with large-scale single-cell atlases

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Inferring predictive genetic models and regulatory elements by deep learning of cross-species single-cell gene expression landscapesPreprint

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Deciphering single-cell transcriptional programs across species

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Deep Learning Integration of Multi-Species Functional Genomics to Reveal Conserved Gene Regulatory Logic

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A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell ModelPreprint

Pearce, J. D., Simmonds, S. E., Mahmoudabadi, G., Krishnan, L., Palla, G., Istrate, A.-M., Tarashansky, A. J., Nelson, B., Valenzuela, O., Li, D., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.25.650731 · Cited by 31 · see citing works

Predicting the regulatory genome

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