Krzysztof Polański

STEER-seq: a recombinase based platform for pooled multimodal single-cell perturbation screening

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.

An early CYP26A1/CRYAA progenitor-glial domain marks the presumptive macular region during human retinal development

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.

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

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

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

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

An integrated single cell and spatial omics atlas of human prenatal development

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.

Integrating multi-covariate disentanglement with counterfactual analysis on synthetic data enables cell type discovery and counterfactual predictions.

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

Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases

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.

Gene-level alignment of single cell trajectories

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

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.

A multiomic atlas of human early skeletal development

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.

Developmental Dynamics of Human Cardiogenesis: A multi-omic reference and its disruption in Trisomy 21

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

A human developing heart atlas reveals cardiovascular cell diversity for in vitro model benchmarking

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.

A human embryonic limb cell atlas resolved in space and time

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

Spatially resolved multiomics of human cardiac niches

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.

Mapping interindividual dynamics of innate immune response at single-cell resolution

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.

A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

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

Multi-organ functions of yolk sac during human early development

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

Human skeletal muscle ageing atlas

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.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

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: Dimensionality Reduction and Integration of Multimodal Data

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

User-friendly, scalable tools and workflows for single-cell analysis

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

Cells and gene expression programs in the adult human heart

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.

Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation

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.

Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape

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.

Decoding the development of the blood and immune systems during human fetal liver haematopoiesis

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

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics

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

BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing

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