prof. dr. Kathleen Marchal

Journal Article
A1
open access

Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing : a case study on fluoroquinolone resistance

Bram Bloemen (UGent) , Mathieu Gand, Moniek Ringenier (UGent) , Bert Bogaerts, Kevin Vanneste, Kathleen Marchal (UGent) , Nancy H. C. Roosens, Jeroen Dewulf (UGent) , Filip Boyen (UGent) and Sigrid C. J. De Keersmaecker

(2025) FRONTIERS IN MICROBIOLOGY. 16.

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Journal Article
A2
open access

Detection of Bacillus production strains and contaminants in food enzyme products

Alexander Van Uffelen (UGent) , Andres Posadas Yabar (UGent) , Marie-Alice Fraiture (UGent) , Nancy H. C. Roosens, Sigrid C. J. De Keersmaecker, Kathleen Marchal (UGent) and Kevin Vanneste (UGent)

(2025) FOOD CHEMISTRY: MOLECULAR SCIENCES. 11.

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Journal Article
A2
open access

smartSim : simulation of splice aware single cell smart-seq3 data

Marie Van Hecke (UGent) and Kathleen Marchal (UGent)

(2025) BIOINFORMATICS ADVANCES. 5(1).

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Journal Article
A1
open access

EPS inhibitor treatment of Salmonella impacts evolution without selecting for resistance to biofilm inhibition

Mathieu Joos, Sybren Van Ginneken, Xabier Villanueva, Marie Dijkmans, Guglielmo A. Coppola, Camilo Andrés Pérez Romero, Thijs Vackier, Erik Van der Eycken (UGent) , Kathleen Marchal (UGent) , Bram Lories, et al.

(2025) NPJ BIOFILMS AND MICROBIOMES. 11(1).

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Conference Paper
C1
open access

Prior knowledge injection into deep learning models predicting gene expression from whole slide images

Max Hallemeesch, Marija Pizurica (UGent) , Paloma Rabaey (UGent) , Olivier Gevaert, Thomas Demeester (UGent) and Kathleen Marchal (UGent)

(2025) Second Workshop on Imageomics (Imageomics-AAAI-25) : discovering biological knowledge from images using AI.

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Journal Article
A1
open access

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

Yari Van Laere (UGent) , Marie-Alice Fraiture, Andrea Gobbo, Sigrid C. J. De Keersmaecker, Kathleen Marchal (UGent) , Nancy H. C. Roosens and Kevin Vanneste

(2025) FRONTIERS IN MICROBIOLOGY. 16.

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Journal Article
A1
open access

ELLIPSIS : robust quantification of splicing in scRNA-seq

Marie Van Hecke (UGent) , Niko Beerenwinkel, Thibault Lootens (UGent) , Jan Fostier (UGent) , Robrecht Raedt (UGent) and Kathleen Marchal (UGent)

(2025) BIOINFORMATICS. 41(2).

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Miscellaneous

Synthetic multimodal data modelling for data imputation

Francisco Carrillo-Perez, Marija Pizurica (UGent) , Kathleen Marchal (UGent) and Olivier Gevaert

(2025) NATURE BIOMEDICAL ENGINEERING. 9(4). p.421-425

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Journal Article
A1
open access

Digital profiling of gene expression from histology images with linearized attention

Marija Pizurica (UGent) , Yuanning Zheng, Francisco Carrillo-Perez, Humaira Noor, Wei Yao, Christian Wohlfart, Antoaneta Vladimirova, Kathleen Marchal (UGent) and Olivier Gevaert

(2024) NATURE COMMUNICATIONS. 15(1).

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Journal Article
A1
open access

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Alexander Van Uffelen (UGent) , Andres Posadas Yabar (UGent) , Nancy H. C. Roosens, Kathleen Marchal (UGent) , Sigrid C. J. De Keersmaecker and Kevin Vanneste

(2024) SCIENTIFIC DATA. 11(1).

Academic Bibliography

prof. dr. Kathleen Marchal

Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing : a case study on fluoroquinolone resistance

Detection of Bacillus production strains and contaminants in food enzyme products

smartSim : simulation of splice aware single cell smart-seq3 data

EPS inhibitor treatment of Salmonella impacts evolution without selecting for resistance to biofilm inhibition

Prior knowledge injection into deep learning models predicting gene expression from whole slide images

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

ELLIPSIS : robust quantification of splicing in scRNA-seq

Synthetic multimodal data modelling for data imputation

Digital profiling of gene expression from histology images with linearized attention

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

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