Academic Bibliography

Search 200 years of publications by Ghent University researchers.

prof. dr. Yvan Saeys

Faculty of Sciences > Department of Applied mathematics, computer science and statistics

ORCID iD: 0000-0002-0415-1506

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SCIP : a scalable, reproducible, and open-source pipeline for morphological profiling image cytometry and microscopy data

Maxim Lippeveld (UGent) , Daniel Peralta (UGent) , Andrew Filby and Yvan Saeys (UGent)

(2024) CYTOMETRY PART A. 105(11). p.816-828
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Identification and characterization of multiple Paneth cell types in the mouse small intestine

Steven Timmermans (UGent) , Charlotte Wallaeys (UGent) , Natalia Garcia Gonzalez (UGent) , Lotte Pollaris (UGent) , Yvan Saeys (UGent) and Claude Libert (UGent)

(2024) CELLS. 13(17).
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Incorporating topological priors into low-dimensional visualizations through topological regularization

Edith Heiter (UGent) , Robin Vandaele, Tijl De Bie (UGent) , Yvan Saeys (UGent) and Jefrey Lijffijt (UGent)

(2024) IEEE ACCESS. 12. p.129541-129573
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An innate immune signature induced by AS01-or AS03-adjuvanted vaccines predicts the antibody response magnitude and quality consistently over time

Setareh Tasdighian (UGent) , Viviane Bechtold, Ahmed Essaghir, Yvan Saeys (UGent) and Wivine Burny

(2024) FRONTIERS IN IMMUNOLOGY. 15.
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Pattern or artifact? Interactively exploring embedding quality with TRACE

Edith Heiter (UGent) , Liesbet Martens (UGent) , Ruth Seurinck (UGent) , Martin Guilliams (UGent) , Tijl De Bie (UGent) , Yvan Saeys (UGent) and Jefrey Lijffijt (UGent)

(2024) MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES-RESEARCH TRACK AND DEMO TRACK, PT VIII, ECML PKDD 2024. In Lecture Notes in Computer Science 14948. p.379-382
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Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

Chananchida Sang-aram (UGent) , Robin Browaeys (UGent) , Ruth Seurinck (UGent) and Yvan Saeys (UGent)

(2024) ELIFE. 12.
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Evaluating feature attribution methods in the image domain

Arne Gevaert (UGent) , Axel-Jan Rousseau, Thijs Becker, Dirk Valkenborg, Tijl De Bie (UGent) and Yvan Saeys (UGent)

(2024) MACHINE LEARNING. 113. p.6019-6064
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Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools

Artuur Couckuyt (UGent) , Benjamin Rombaut (UGent) , Yvan Saeys (UGent) and Sofie Van Gassen (UGent)

(2024) BIOINFORMATICS. 40(4).
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- Miscellaneous
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Defining and benchmarking open problems in single-cell analysis

Malte D. Luecken, Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt (UGent) , Daniel C. Strobl, Nikolay S. Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, et al.

(2024) NATURE PORTFOLIO.
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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.

(2024) NATURE METHODS.

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