This study examines the low adoption of computational gene-panel-selection tools in targeted spatial transcriptomics, finding that most researchers still use manual or vendor panels.

bioRxiv · Oct 13, 2026 · PreprintBioinformatics

SubCellSpace: Automated characterization of subcellular mRNA localization patterns in spatial transcriptomics

D. J. Wouters, Jose Ignacio Alvira Larizgoitia, Nynke Tilkema, Paulien Van Minsel, Ceyhun Alar, Nick Seeuws, Ilias Theodorus Koulalis, Minkyoung Lee, Niels Vandermeulen, Srivathsan Adivarahan, Sandrine Da Cruz, Katy Vandereyken, Andreas E. Moor, Bernard Thienpont, Thierry Voet, Alejandro Sifrim

SubCellSpace identifies and characterizes subcellular mRNA localization patterns in spatial transcriptomics data using a computational framework.

bioRxiv · Apr 30, 2026 · PreprintBioinformatics

Luminal nutrients activate distinct patterns in submucosal and myenteric neurons in the mouse small intestine

Candice Fung, Tom Venneman, Amy Marie Holland, Tobie Martens, Milvia Alata, Marlene M. Hao, Ceyhun Alar, Yuuki Obata, Jan F. Tack, Alejandro Sifrim, Vassilis Pachnis, Werend Boesmans, Pieter Vanden Berghe

The paper shows that different luminal nutrients activate distinct calcium responses in submucosal and myenteric neurons of the mouse small intestine.

Nature · Jul 9, 2025Peer-reviewedNeuroscience

Defining the role of fibroblasts in skin expansion

Caroline Aguilera Stewart, Ceyhun Alar, Leslie Bargsted, Ioanna Kaklamanou, Gaia Andrea Gozza, Maria Pia Polito, Elena Enzo, Alejandro Sifrim, Mariaceleste Aragona

This study investigates how fibroblasts respond to stretching during skin expansion and shows their role in coordinating epidermal stem cell self-renewal.

bioRxiv · Mar 18, 2025 · PreprintCell Biology