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).

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WSI based prediction of TP53 mutations identifies 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, Nicolaas Lumen (UGent) , Jo Van Dorpe (UGent) , Piet Ost (UGent) , Sofie Verbeke (UGent) , et al.

(2023) CANCER RESEARCH. In Cancer Research 83(8, Supplement S).

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Journal Article
A1
open access

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Arne Claeys (UGent) , Peter Merseburger (UGent) , Jasper Staut (UGent) , Kathleen Marchal (UGent) and Jimmy Van den Eynden (UGent)

(2023) BMC GENOMICS. 24.

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Journal Article
A1
open access

Antibiotic cycling affects resistance evolution independently of collateral sensitivity

Pauline Brepoels, Kenny Appermans, Camilo Andrés Pérez Romero (UGent) , Bram Lories, Kathleen Marchal (UGent) and Hans P. Steenackers

(2022) MOLECULAR BIOLOGY AND EVOLUTION. 39(12).

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Journal Article
A2
open access

Extracting functional insights from loss-of-function screens using deep link prediction

Pieter-Paul Strybol (UGent) , Maarten Larmuseau (UGent) , Louise de Schaetzen van Brienen (UGent) , Tim Van den Bulcke and Kathleen Marchal (UGent)

(2022) CELL REPORTS METHODS. 2(2).

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Journal Article
A1
open access

Metagenomics to detect and characterize viruses in food samples at genome level? Lessons learnt from a norovirus study

Florence Buytaers, Bavo Verhaegen (UGent) , Mathieu Gand, Jolien D'aes, Kevin Vanneste (UGent) , Nancy H. C. Roosens, Kathleen Marchal (UGent) , Sarah Denayer and Sigrid C. J. De Keersmaecker

(2022) FOODS. 11(21).

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Journal Article
A1
open access

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Yue Zhang, Xingyu Yang, Yves Van de Peer (UGent) , Jinming Chen, Kathleen Marchal (UGent) and Tao Shi

(2022) PLANT JOURNAL. 112(3). p.830-846

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Comparative transcriptome analysis of two maize genotypes with different tolerance to salt stress

Taher Mohasseli, Razgar Seyed Rahmani, Reza Darvishzadeh, Sara Dezhsetan and Kathleen Marchal (UGent)

(2022) CEREAL RESEARCH COMMUNICATIONS. 50. p.797-810

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OMEN : network-based driver gene identification using mutual exclusivity

Dries Van Daele, Bram Weytjens (UGent) , Luc De Raedt and Kathleen Marchal (UGent)

(2022) BIOINFORMATICS. 38(12). p.3245-3251

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Miscellaneous
open access

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Arne Claeys (UGent) , Jasper Staut (UGent) , Peter Merseburger (UGent) , Kathleen Marchal (UGent) and Jimmy Van den Eynden (UGent)

(2022)

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Journal Article
A1
open access

Halvade somatic : somatic variant calling with Apache Spark

Dries Decap (UGent) , Louise de Schaetzen van Brienen (UGent) , Maarten Larmuseau (UGent) , Pascal Costanza, Charlotte Herzeel, Roel Wuyts, Kathleen Marchal (UGent) and Jan Fostier (UGent)

(2022) GIGASCIENCE. 11.

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Journal Article
A1
open access

BLSSpeller to discover novel regulatory motifs in maize

Razgar Seyed Rahmani, Dries Decap (UGent) , Jan Fostier (UGent) and Kathleen Marchal (UGent)

(2022) DNA RESEARCH. 29(4).

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Journal Article
A1
open access

Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

Arne Claeys (UGent) , Tom Luijts (UGent) , Kathleen Marchal (UGent) and Jimmy Van den Eynden (UGent)

(2021) PLOS Genetics. 17(2).

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Journal Article
A1
open access

First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin

Carine Yehouenou, Bert Bogaerts, Kevin Vanneste, Nancy H. C. Roosens, Sigrid C. J. De Keersmaecker, Kathleen Marchal (UGent) , Dissou Affolabi, Reza Soleimani, Hector Rodriguez-Villalobos, Francoise Van Bambeke, et al.

(2021) ANNALS OF CLINICAL MICROBIOLOGY AND ANTIMICROBIALS. 20(1).

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Journal Article
A1
open access

Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods

Bert Bogaerts, Stéphanie Nouws (UGent) , Bavo Verhaegen, Sarah Denayer, Julien Van Braekel, Raf Winand, Qiang Fu, Florence Crombé, Denis Piérard, Kathleen Marchal (UGent) , et al.

(2021) MICROBIAL GENOMICS. 7(3).

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Journal Article
A1
open access

A bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approaches

Bert Bogaerts, Thomas Delcourt, Karine Soetaert, Samira Boarbi, Pieter-Jan Ceyssens, Raf Winand, Julien Van Braekel, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Kathleen Marchal (UGent) , et al.

(2021) JOURNAL OF CLINICAL MICROBIOLOGY. 59(6).

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Journal Article
A1
open access

Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes

Razgar Seyed Rahmani, Tao Shi, Dongzhi Zhang, Xiaoping Gou, Jing Yi, Giles Miclotte (UGent) , Kathleen Marchal (UGent) and Jia Li

(2021) BMC GENOMICS. 22(1).

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DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil

Harry Lerner, Basak Ozturk, Anja B. Dohrmann, Joice Thomas, Kathleen Marchal (UGent) , Rene De Mot, Wim Dehaen, Christoph C. Tebbe and Dirk Springael

(2021) FEMS MICROBIOLOGY ECOLOGY. 97(5).

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Journal Article
A1
open access

Dynamic partitioning of search patterns for approximate pattern matching using search schemes

Luca Renders (UGent) , Kathleen Marchal (UGent) and Jan Fostier (UGent)

(2021) ISCIENCE. 24(7).

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Journal Article
A1
open access

Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak

Florence Buytaers, Assia Saltykova, Wesley Mattheus, Valeska Laisnez, Bavo Verhaegen, Nancy H. C. Roosens, Kevin Vanneste (UGent) , Naiima Hammami, Brigitte Pochet, Vera Cantaert, et al.

(2021) MICROBIAL GENOMICS. 7(4).

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Journal Article
A1
open access

Network-based analysis to identify drivers of metastatic prostate cancer using GoNetic

Louise de Schaetzen van Brienen (UGent) , Giles Miclotte (UGent) , Maarten Larmuseau (UGent) , Jimmy Van den Eynden (UGent) and Kathleen Marchal (UGent)

(2021) CANCERS. 13(21).

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Journal Article
A1
open access

Towards real-time and affordable strain-level metagenomics-based foodborne outbreak investigations using Oxford nanopore sequencing technologies

Florence Buytaers, Assia Saltykova, Sarah Denayer, Bavo Verhaegen (UGent) , Kevin Vanneste (UGent) , Nancy H. C. Roosens, Denis Pierard, Kathleen Marchal (UGent) and Sigrid C. J. De Keersmaecker

(2021) FRONTIERS IN MICROBIOLOGY. 12.

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Whole genome sequencing provides an added value to the investigation of staphylococcal food poisoning outbreaks

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

(2021) FRONTIERS IN MICROBIOLOGY. 12.

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Conference Paper
C3
open access

Multifocality in prostate cancer : implications for PAM50 subtyping using an index lesion-only approach

Kim Van der Eecken, Maarten Larmuseau (UGent) , Jan Vanwelkenhuyzen (UGent) , Nicolaas Lumen (UGent) , Kathleen Marchal (UGent) , Jo Van Dorpe (UGent) , Piet Ost (UGent) , Bram De Laere (UGent) and Sofie Verbeke (UGent)

(2021) Global Congress on Prostate and Bladder Cancer 2021, Abstracts.

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Journal Article
A1
open access

Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations

Bert Bogaerts, Raf Winand, Julien Van Braekel, Stefan Hoffman, Nancy H. C. Roosens, Sigrid C. J. De Keersmaecker, Kathleen Marchal (UGent) and Kevin Vanneste (UGent)

(2021) MICROBIAL GENOMICS. 7(11).

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Journal Article
A1
open access

Phylogenomic investigation of increasing fluoroquinolone resistance among Belgian cases of shigellosis between 2013 and 2018 indicates both travel-related imports and domestic circulation

Bert Bogaerts, Raf Winand, Julien Van Braekel, Wesley Mattheus, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Kathleen Marchal (UGent) , Kevin Vanneste and Pieter-Jan Ceyssens

(2021) MICROORGANISMS. 9(4).

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Journal Article
A2
open access

A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products

Florence E. Buytaers, Marie-Alice Fraiture, Bas Berbers, Els Vandermassen, Stefan Hoffman, Nina Papazova, Kevin Vanneste, Kathleen Marchal (UGent) , Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker

(2021) FOOD CHEMISTRY: MOLECULAR SCIENCES. 2.

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Journal Article
A1
open access

Whole-genome sequencing-based antimicrobial resistance characterization and phylogenomic investigation of 19 multidrug-resistant and extended-spectrum beta-lactamase-positive escherichia coli strains collected from hospital patients in Benin in 2019

Carine Laurence Yehouenou, Bert Bogaerts, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Kathleen Marchal (UGent) , Edmond Tchiakpe, Dissou Affolabi, Anne Simon, Francis Moise Dossou, Kevin Vanneste (UGent) , et al.

(2021) FRONTIERS IN MICROBIOLOGY. 12.

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Journal Article
A1
open access

Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

Tao Shi, Razgar Seyed Rahmani, Paul F. Gugger, Muhua Wang, Hui Li, Yue Zhang, Zhizhong Li, Qingfeng Wang, Yves Van de Peer (UGent) , Kathleen Marchal (UGent) , et al.

(2020) MOLECULAR BIOLOGY AND EVOLUTION. 37(8). p.2394-2413

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Journal Article
A1
open access

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

Joana Carlevaro-Fita, Andres Lanzos, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, Rory Johnson, Federico Abascal, Samirkumar B. Amin, Gary D. Bader, et al.

(2020) COMMUNICATIONS BIOLOGY. 3(1).

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Journal Article
A1
open access

Image-based dynamic phenotyping reveals genetic determinants of filamentation-mediated beta-lactam tolerance

Taiyeb Zahir, Dorien Wilmaerts, Sabine Franke, Bram Weytjens (UGent) , Rafael Camacho, Kathleen Marchal (UGent) , Johan Hofkens, Maarten Fauvart and Jan Michielsen

(2020) FRONTIERS IN MICROBIOLOGY. 11.

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A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay

Mathieu Gand, Wesley Mattheus, Nancy HC Roosens, Katelijne Dierick, Kathleen Marchal (UGent) , Sigrid CJ De Keersmaecker and Sophie Bertrand

(2020) FOOD MICROBIOLOGY. 87.

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Journal Article
A1
open access

Pathway and network analysis of more than 2500 whole cancer genomes

Matthew A Reyna, David Haan, Marta Paczkowska, Lieven Verbeke (UGent) , Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, et al.

(2020) NATURE COMMUNICATIONS. 11(1).

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Journal Article
A1
open access

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M Hess, Randi Istrup Juul, Ziao Lin, et al.

(2020) NATURE. 578(7793). p.102-111

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Journal Article
A1
open access

Integrative pathway enrichment analysis of multivariate omics data

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala Abd-Rabbo, Miles W Mee, Paul C Boutros, Jüri Reimand, the PCAWG Drivers and Functional Interpretation Working Group, et al.

(2020) NATURE COMMUNICATIONS. 11(1).

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Journal Article
A1
open access

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Shimin Shuai, Steven Gallinger, Lincoln Stein, the PCAWG Drivers and Functional Interpretation Working Group, Kathleen Marchal (UGent) and Sergio Pulido-Tamayo

(2020) NATURE COMMUNICATIONS. 11(1).