Krzysztof Polański

STEER-seq enables pooled single-cell perturbation screening in hiPSCs by using defined genomic integration and barcode tracking to study transcription factor effects on cell identity.

The paper identifies a CYP26A1/CRYAA progenitor-glial domain in the human retina that marks the presumptive macula and links it to regional gliogenic maturation and specialized Muller glial populations.

This paper creates a detailed heart atlas using multimodal data to identify cell states and disease-associated genetic variants in specific heart regions.

This paper creates an integrated multimodal atlas of the female reproductive system across the lifespan, identifying cell types and linking them to gynaecological pathologies.

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

This study uses single-cell transcriptomics to compare in vitro and in vivo chondrocyte differentiation, identifies off-target differentiation, and improves in vitro protocols by inhibiting FOXO1.

CellDISECT improves cell type discovery and counterfactual predictions by disentangling covariates and using synthetic data for training.

The paper maps the spatial organization of the human thymus across developmental stages using a multimodal atlas and identifies key cellular and molecular features of T cell development.

The paper integrates single-cell RNA-seq datasets across the GI tract to identify epithelial metaplasia in inflammatory diseases, showing its role in inflammation through immune cell interactions.

Genes2Genes aligns single-cell trajectories using a Bayesian DP framework, revealing gene-level mismatches and highlighting differences in T cell differentiation between in vitro and in vivo states.

Bin2cell reconstructs cells from high-resolution Visium HD data by integrating morphology and gene expression, improving downstream analysis on mouse brain and human colorectal cancer data.

This study constructs a multiomic atlas of human early skeletal development using single-nuclei transcriptomics, epigenomics, and spatial transcriptomics to uncover regulatory mechanisms and cell states involved in bone and joint formation.

This study develops a multi-omic reference of human cardiac development and identifies disruptions in Trisomy 21 hearts.

The paper creates a high-resolution human developing heart atlas using single-cell and spatial transcriptomics, identifies new cell types, and benchmarks in vitro models.

This paper creates a human embryonic limb cell atlas using single-cell and spatial transcriptomics, identifying novel cell populations and developmental patterns.

This paper uses spatial transcriptomics and single-cell data to identify cellular niches in the human heart, revealing new insights into cardiac function and potential drug targets.

The paper develops GASPACHO to identify dynamic eQTLs in antiviral responses using single-cell RNA-seq, uncovering thousands of eQTLs and linking them to disease risk loci.

The paper constructs a human fetal lung cell atlas from 5-22 post conception weeks, identifying new cell states and regulators of epithelial fates.

The paper maps the multi-organ functions of the human yolk sac during early development, revealing its roles in hematopoiesis, nutrition, and oxygen regulation.

This study creates a single-cell and single-nucleus transcriptomic atlas of human skeletal muscle ageing, revealing mechanisms in muscle stem cells, myofibers, and the microenvironment.

This study maps the temporal and spatial dynamics of the human endometrium using single-cell and spatial reference maps, identifying key signaling pathways regulating cell fate in vivo and in vitro.

MultiMAP integrates multimodal data by reducing dimensionality and preserving structure, outperforming existing methods in various tasks.

The paper introduces an interactive scRNA-Seq analysis environment based on Galaxy, integrating ~70 functions for scalable and accessible single-cell data analysis.

The paper characterizes the cellular composition and gene expression of the adult human heart using single-cell transcriptomics, identifying distinct cell types and their functional roles.

This study evaluates the impact of cold storage on scRNAseq data quality for lung, spleen, and oesophagus tissues, finding minimal effects within 24 hours but increased stress markers at 72 hours.

BBKNN integrates multiple mouse single cell RNA-Seq datasets into a unified landscape by efficiently removing batch effects and revealing cell type and organ-specific markers.

The paper uses single-cell transcriptomics to map hematopoiesis in human fetal liver, identifying cell differentiation trajectories and shifts in hematopoietic composition during development.

The paper profiles single-cell transcriptomes from the human first trimester fetal-maternal interface, revealing cellular composition and interactions critical for placentation.

BraCeR reconstructs B-cell receptor sequences and infers clonality from scRNA-seq data without needing additional Rep-seq.