Ghent University Academic Bibliography

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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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

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 (UGent) , 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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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

Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling

Florence Buytaers, Bavo Verhaegen (UGent) , Tom Van Nieuwenhuysen (UGent) , Nancy H. C. Roosens, Kevin Vanneste, Kathleen Marchal (UGent) and Sigrid C. J. De Keersmaecker

(2024) FRONTIERS IN MICROBIOLOGY. 15.

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Miscellaneous

Synthetic multimodal data modelling for data imputation

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

(2024) NATURE BIOMEDICAL ENGINEERING.

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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).

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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

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

Stéphanie Nouws (UGent) , Bavo Verhaegen (UGent) , Sarah Denayer, Florence Crombé (UGent) , Denis Piérard (UGent) , Bert Bogaerts, Kevin Vanneste (UGent) , Kathleen Marchal (UGent) , Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker

(2023) FRONTIERS IN MICROBIOLOGY. 14.

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Journal Article
A1
open access

Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii

Yue Zhang, Yves Van de Peer (UGent) , Bei Lu, Sisi Zhang, Jingru Che, Jinming Chen, Kathleen Marchal (UGent) and Xingyu Yang

(2023) BMC BIOLOGY. 21(1).

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Journal Article
A1
open access

Competitive interactions facilitate resistance development against antimicrobials

Luka Svet, Ilse Parijs, Simon Isphording, Bram Lories, Kathleen Marchal (UGent) and Hans P. Steenackers

(2023) APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 89(10).

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Journal Article
A1
open access

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Bram Bloemen (UGent) , Mathieu Gand, Kevin Vanneste (UGent) , Kathleen Marchal (UGent) , Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker

(2023) SCIENTIFIC REPORTS. 13(1).

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Miscellaneous
open access

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (vol 52, pg 331, 2020)

Isidro Cortes-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung, Lixing Yang, Dmitry Gordenin, Leszek J. Klimczak, Cheng-Zhong Zhang, David S. Pellman, et al.

(2023) NATURE GENETICS. 55.

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Journal Article
A1
open access

Whole slide imaging-based prediction of TP53 mutations identifies an aggressive disease phenotype in prostate cancer

Marija Pizurica (UGent) , Maarten Larmuseau (UGent) , Kim Van der Eecken, Louise de Schaetzen van Brienen (UGent) , Francisco Carrillo-Perez, Simon Isphording (UGent) , Nicolaas Lumen (UGent) , Jo Van Dorpe (UGent) , Piet Ost (UGent) , Sofie Verbeke (UGent) , et al.

(2023) CANCER RESEARCH. 83(17). p.2970-2984

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Journal Article
A1
open access

Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

Johannes Berbers (UGent) , Kevin Vanneste, Nancy H. C. J. Roosens, Kathleen Marchal (UGent) , Pieter-Jan Ceyssens and Sigrid C. J. De Keersmaecker

(2023) MICROBIAL GENOMICS. 9(1).

Academic Bibliography

ELLIPSIS : robust quantification of splicing in scRNA-seq

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

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

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

Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling

Synthetic multimodal data modelling for data imputation

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

Digital profiling of gene expression from histology images with linearized attention

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii

Competitive interactions facilitate resistance development against antimicrobials

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (vol 52, pg 331, 2020)

Whole slide imaging-based prediction of TP53 mutations identifies an aggressive disease phenotype in prostate cancer

Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

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