Jose Maria Polo

This study compares viral replication and host responses in airway epithelial cells to distinguish pathogenic from seasonal coronaviruses, finding HCoV-229E induces severe epithelial injury despite limited replication.

This paper develops a genetically engineered trophoblast organoid model of preeclampsia that recapitulates molecular and functional features of the disease.

This study investigates the role of DUSP6 in ADHD by generating DUSP6 knockouts in iPSC-derived dopaminergic neurons, finding increased dopamine secretion and transcriptomic changes linked to neurodevelopment and psychiatric disorders.

hoodscanR identifies and analyzes cell neighborhoods in spatial transcriptomics data, revealing transcriptional differences in tumor cells across neighborhoods.

DOMINO identifies spatial domains in spatial transcriptomic data with improved accuracy and scalability, outperforming existing methods on large datasets.

The paper examines DNA methylation dynamics in marsupial embryos, finding global demethylation in the trophectoderm but not the embryonic lineage, suggesting 5mC erasure in extraembryonic tissue is ancestral in therian mammals.

This paper describes a method to simultaneously profile the transcriptome and proteome from single cells, showing moderate correlation between the two modalities.

cellNexus enhances Human Cell Atlas data by adding quality control, metadata, normalization, and analysis layers to enable multi-study analyses and large-scale biological discovery.

This study investigates how a maternal low protein diet affects kidney development in mice, revealing molecular and cellular changes that reduce nephron number.

This paper introduces Airy beam light sheet microscopy to image subcellular dynamics in large tissues with high spatial and temporal resolution across multiple organisms and biological processes.

GRASP uses a graph neural network to predict RNA subcellular localization by modeling RNA structure, outperforming existing methods across RNA types and transcript lengths.

This study identifies oxidative stress and TERRA loss as drivers of placental aging in late-onset preeclampsia, showing antioxidant treatment can mitigate these effects.

This study isolates and characterizes contemporary seasonal human coronaviruses, showing differences in cell tropism and growth compared to lab-adapted strains.

The paper identifies neurogenesis-related gene expression as a clone-specific hallmark of brain metastasis in breast cancer using a new optical barcoding tool.

STAMP enables low-cost, high-throughput single-cell analysis by integrating transcriptomics and proteomics imaging, supporting both single and multimodal profiling of diverse cell types.

This study uses live microscopy to show that Hippo signalling regulates transcription by controlling the DNA dwell times of YAP and TEAD proteins.

This study profiles transcriptomes of dopaminergic neurons from ADHD and neurotypical iPSCs, identifying DEGs overlapping with ADHD GWAS results and suggesting delayed neuronal maturation.

The paper refutes claims that Sendai virus expression undermines the TNT reprogramming method, showing no detectable Sendai virus gene expression in TNT iPS cells.

The paper shows that RNase A treatment during ChIP-seq falsely reduces PRC2 chromatin occupancy signals, revealing limitations in using this method to study RNA-dependent chromatin regulation.

This paper introduces a xeno-free single-cell cloning method for CRISPR-edited human iPSCs, achieving high clonal survival and editing efficiency for improved disease modeling.

The paper identifies retrotransposon insertions as the main source of mutations in mouse induced pluripotent stem cells, showing hypomethylation of LINE-1 elements and their impact on gene regulation.

The paper analyzes the transcriptomic response of microglia in an Alzheimer's disease mouse model treated with scanning ultrasound, identifying differentially expressed genes and pathways related to phagocytosis and cell cycle activation.

This study identifies Nr6a1 as a master regulator of trunk-specific axial development in mice, controlling elongation, segmentation, and lineage allocation through Hox gene regulation and gene regulatory networks.

This paper develops a 3D spatial transcriptomic atlas of the mouse heart and provides a web tool for analysis and visualization.

The paper analyzes transcriptomes of zebrafish atoh7 mutant embryos to identify Atoh7-dependent genetic networks linked to retinal development and human eye diseases.

This study identifies that amyloid plaque phagocytosis through Hif1α controls microglial phenotypes in Alzheimer’s disease in both mice and humans.

This paper creates a single-cell brain atlas of Alzheimer’s disease, identifying cell-type specific gene expression patterns and regulatory networks associated with disease.

The paper reports the generation of four iPSC lines from PBMCs of an ADHD patient and their healthy sibling, confirming pluripotency and differentiation potential.

This paper develops a modular dCas9-SunTag DNMT3A system to improve DNA methylation editing specificity and reduce off-target effects compared to direct fusion constructs.