Ghent University Academic Bibliography

Journal Article
A1
open access

SpatialData : an open and universal data framework for spatial omics

Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Wouter-Michiel Vierdag, Marcella Toth, Sonja Stockhaus, Rahul B. Shrestha, et al.

(2025) NATURE METHODS. 22(1). p.58-62

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Journal Article
A1
open access

brainlife.io : a decentralized and open-source cloud platform to support neuroscience research

Soichi Hayashi, Bradley A. Caron, Anibal Sólon Heinsfeld, Sophia Vinci-Booher, Brent McPherson, Daniel N. Bullock, Giulia Bertò, Guiomar Niso, Sandra Hanekamp, Daniel Levitas, et al.

(2024) NATURE METHODS. 21(5). p.809-813

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Miscellaneous

Circular RNA detection pipelines yield divergent sets of circular RNAs

Marieke Vromman (UGent) and Jo Vandesompele (UGent)

(2023) NATURE METHODS. 20(8). p.1135-1136

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Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Marieke Vromman (UGent) , Jasper Anckaert (UGent) , Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Trees-Juen Chuang, Roozbeh Dehghannasiri, Christoph Dieterich, Xin Dong, et al.

(2023) NATURE METHODS. 20(8). p.1159-1169

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Journal Article
A1
open access

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Johannes Bues, Marjan Biocanin, Joern Pezoldt, Riccardo Dainese, Antonius Chrisnandy, Saba Rezakhani, Wouter Saelens (UGent) , Vincent Gardeux, Revant Gupta, Rita Sarkis, et al.

(2022) NATURE METHODS. 19(3). p.323-330

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Journal Article
A1
open access

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Robbin Bouwmeester (UGent) , Ralf Gabriels (UGent) , Niels Hulstaert (UGent) , Lennart Martens (UGent) and Sven Degroeve (UGent)

(2021) NATURE METHODS. 18(11). p.1363-+

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Journal Article
A1
open access

Universal Spectrum Identifier for mass spectra

Eric W. Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche (UGent) , Ralf Gabriels (UGent) , Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, et al.

(2021) NATURE METHODS. 18(7). p.768-770

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The power of imaging to understand extracellular vesicle biology in vivo

Frederik J. Verweij, Leonora Balaj, Chantal M. Boulanger, David R. F. Carter, Ewoud B. Compeer, Gisela D’Angelo, Samir El Andaloussi, Jacky G. Goetz, Julia Christina Gross, Vincent Hyenne, et al.

(2021) NATURE METHODS. 18(9). p.1013-1026

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Journal Article
A1
open access

MISpheroID : a knowledgebase and transparency tool for minimum information in spheroid identity

Arne Peirsman (UGent) , Eva Blondeel (UGent) , Tasdiq Ahmed, Jasper Anckaert (UGent) , Dominique Audenaert (UGent) , Tom Boterberg (UGent) , Krisztina Buzas, Neil Carragher, Gastone Castellani, Flávia Castro, et al.

(2021) NATURE METHODS. 18(11). p.1294-1303

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NicheNet : modeling intercellular communication by linking ligands to target genes

Robin Browaeys (UGent) , Wouter Saelens (UGent) and Yvan Saeys (UGent)

(2020) NATURE METHODS. 17(2). p.159-162

Academic Bibliography

SpatialData : an open and universal data framework for spatial omics

brainlife.io : a decentralized and open-source cloud platform to support neuroscience research

Circular RNA detection pipelines yield divergent sets of circular RNAs

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Universal Spectrum Identifier for mass spectra

The power of imaging to understand extracellular vesicle biology in vivo

MISpheroID : a knowledgebase and transparency tool for minimum information in spheroid identity

NicheNet : modeling intercellular communication by linking ligands to target genes

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