Jan N. Hansen

Generative machine learning unlocks the first proteome-wide image of human cells

A conditional latent diffusion transformer predicts immunofluorescence images of 12,800 human proteins from nucleus, ER and microtubule stains, outperforming PUPS and CELL-Diff, including on an unseen drug-treated cell line.

A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS

The paper generates a CRISPRi perturbation cell atlas in human induced pluripotent stem cells, identifies novel regulators of pluripotency and metabolism, and proposes a machine learning framework for predicting perturbation recipes.

Cell shapes decode molecular phenotypes in image-basedspatial proteomics

The paper analyzes how cell shape correlates with proteomic features across multiple cell lines using image-based spatial proteomics data.

A high-resolution spatial map of cilia-associated proteins in the human fallopian tube

The paper creates a high-resolution spatial map of cilia-associated proteins in the human fallopian tube using integrated transcriptomics and proteomics.

A high-resolution subcellular map of proteins in cells with motile cilia

The paper develops a high-throughput workflow to map protein expression and subcellular localization in motile ciliated cells across five human tissues, identifying 180 proteins with varying functional evidence scores.

Spatial Dynamics of the Developing Human Heart

This study maps spatial dynamics in early human heart development using single-cell and spatial transcriptomics, identifying cell states and novel features like cardiac fibroblasts and chromaffin cells.

Intrinsic Heterogeneity of Primary Cilia Revealed Through Spatial Proteomics

The paper uses spatial proteomics to analyze primary cilia proteomes across cell lines, revealing cell-type specificity and single-cilia heterogeneity, and identifies novel cilia proteins and potential genetic variants.

Proximity proteomics of primary cilia in human hypothalamic neurons

The paper identifies ciliary proteins in human hypothalamic neurons and finds new therapeutic targets for obesity, including LPAR1, which mediates ciliary shortening.

SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology

SubCell is a deep learning model for fluorescence microscopy that captures cellular morphology and protein organization, outperforming existing methods and enabling a multimodal approach to gene function.

High-parametric protein maps reveal the spatial organization in early-developing human lung

This study maps the spatial organization of the developing human lung using high-parametric protein imaging, revealing cell type composition and temporal changes across five developmental timepoints.

AI-readiness criteria for biomedical data

The paper defines AI-readiness criteria for biomedical data, encompassing seven dimensions, and evaluates them across flagship datasets to ensure ethical and explainable AI practices.

Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines

The paper introduces the CM4AI project, which aims to create AI-ready datasets of human cell architecture using multimodal data from cell lines.

Cylicins are a structural component of the sperm calyx being indispensable for male fertility in mice and human

This study investigates the role of Cylicins in spermiogenesis and male fertility using gene-editing in mice and exome sequencing in humans, finding that Cylicin deficiency causes infertility and structural sperm abnormalities.

Diversity and Function of Motile Ciliated Cell Types within Ependymal Lineages of the Zebrafish Brain

The paper characterizes motile ciliated cells in zebrafish brain ventricles, showing their developmental origins, functional roles in CSF flow, and impact on ventricular morphology.

Nucleo-cytoplasmic shuttling of splicing factor SRSF1 is required for development and cilia function

This study shows that SRSF1 shuttling between nucleus and cytoplasm is essential for ciliogenesis and development, as demonstrated by phenotypic defects in a mouse model with nuclear-retained SRSF1.