Publications by Irina Khven | EPFL Graph Search

Fine-grained mapping of neural progenitors subtypes in the embryonic brain unveils context-dependent roles of signalling on cell fate decisions

The mammalian brain develops through precisely orchestrated events that transform a simple neural tube into a complex structure. While single-cell RNA sequencing has revealed remarkable cellular heterogeneity, the lack of spatial context limits our underst ...

EPFL2025

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression

Joachim Lingner, Suliana Manley, Gioele La Manno, Can Aztekin, Irina Khven, Eftychia Kyriacou, Albert Dominguez Mantes, Evangelia Skoufa, Martin Weigert, Georgios Tsissios

Identification of spot-like structures in large, noisy microscopy images is a crucial step for many life-science applications. Imaging-based spatial transcriptomics (iST), in particular, relies on the precise detection of millions of transcripts in low sig ...

2025

Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations

Felix Naef, Gioele La Manno, Alex Russell Lederer, Irina Khven, Antonio Herrera Camacho, Albert Dominguez Mantes, Colas Noé Droin, Lorenzo Talamanca

Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms can be ...

2024

Sphingolipids control dermal fibroblast heterogeneity

Giovanni D'Angelo, Gioele La Manno, Olivier Burri, Romain Guiet, Sylvia Ho, Alex Russell Lederer, Laura Capolupo, Irina Khven, Galina Glousker

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual cells of the same type. However, we are only starting to characterize the function of these cell-to-cell differences in lipid composition. Here, ...

American Association for the Advancement of Science2022

Self-organizing in vitro mouse neural tube organoids mimic embryonic development

Matthias Lütolf, Gioele La Manno, Jisoo Park, Irina Khven, Hao-An Hsiung

The embryonic neural tube is the origin of the entire adult nervous system, and disturbances in its development cause life-threatening birth defects. However, the study of mammalian neural tube development is limited by the lack of physiologically realisti ...

COMPANY BIOLOGISTS LTD2022

Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation

Gioele La Manno, Alex Russell Lederer, Irina Khven

Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, a detailed mapping of transient cellular states during in v ...

CELL PRESS2022

Molecular architecture of the developing mouse brain

Gioele La Manno, Alex Russell Lederer, Irina Khven

The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of ...

NATURE PORTFOLIO2021