Ghent University Academic Bibliography

Conference Paper
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) Imageomics-AAAI-25 , Discovering Biological Knowledge from Images using AI, part of AAAI 2025.

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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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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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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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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

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

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
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

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
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).

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Journal Article
A1
open access

Pan-cancer analysis of whole genomes

Peter J. Campbell, Gad Getz, Jan O. Korbel, Joshua M. Stuart, Jennifer L. Jennings, Lincoln D. Stein, Marc D. Perry, Hardeep K. Nahal-Bose, B. F. Francis Ouellette, Constance H. Li, et al.

(2020) NATURE. 578(7793). p.82-93

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Journal Article
A1
open access

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates

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

(2020) SCIENTIFIC REPORTS. 10(1).

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Journal Article
A1
open access

First detection of a plasmid located carbapenem resistant bla(VIM-1) gene in E. coli isolated from meat products at retail in Belgium in 2015

Cristina Garcia-Graells, Bas Berbers, Bavo Verhaegen, Kevin Vanneste (UGent) , Kathleen Marchal (UGent) , Nancy H. C. Roosens, Nadine Botteldoorn and Sigrid C. J. De Keersmaecker

(2020) INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY. 324.

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Journal Article
A1
open access

Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination

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

(2020) ANTIBIOTICS-BASEL. 9(8).

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Journal Article
A1
open access

Strain-level metagenomic data analysis of enriched in vitro and in silico spiked food samples : paving the way towards a culture-free foodborne outbreak investigation using STEC as a case study

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

(2020) INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 21(16).

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Journal Article
A1
open access

A practical method to implement strain-level metagenomics-based foodborne outbreak investigation and source tracking in routine

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

(2020) MICROORGANISMS. 8(8).

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Journal Article
A1
open access

The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a national reference laboratory in a smaller country

Stéphanie Nouws (UGent) , Bert Bogaerts, Bavo Verhaegen, Sarah Denayer, Florence Crombé, Klara De Rauw, Denis Piérard, Kathleen Marchal (UGent) , Kevin Vanneste, Nancy H. C. Roosens, et al.

(2020) FOODS. 9(8).

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Culture-independent analysis of linuron-mineralizing microbiota and functions in on-farm biopurification systems via DNA-stable isotope probing : comparison with enrichment culture

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

(2020) ENVIRONMENTAL SCIENCE & TECHNOLOGY. 54(15). p.9387-9397

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Journal Article
A1
open access

A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium

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

(2020) FOOD MICROBIOLOGY. 91.

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A1
open access

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus

Bas Berbers, Assia Saltykova, Cristina Garcia-Graells, Patrick Philipp, Fabrice Arella, Kathleen Marchal (UGent) , Raf Winand, Kevin Vanneste, Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker

(2020) SCIENTIFIC REPORTS. 10(1).

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Journal Article
A1
open access

Sex differences in oncogenic mutational processes

Constance H. Li, Stephenie D. Prokopec, Ren X. Sun, Fouad Yousif, Nathaniel Schmitz, Paul C. Boutros, Sergio Pulido Tamayo (UGent) , Kathleen Marchal (UGent) , Lieven Verbeke (UGent) , [missing] PCAWG Tumour Subtypes and Clinical Translation, et al.

(2020) NATURE COMMUNICATIONS. 11(1).

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Miscellaneous
open access

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (vol 11, 4748, 2020)

Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, et al.

(2020) NATURE COMMUNICATIONS. 11(1).

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A1
open access

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, et al.

(2020) NATURE COMMUNICATIONS. 11(1).

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Journal Article
A1
open access

Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples

Louise de Schaetzen van Brienen (UGent) , Maarten Larmuseau (UGent) , Kim Van der Eecken, Frederic De Ryck (UGent) , Pauline Robbe Vandewalle, Anna Schuh, Jan Fostier (UGent) , Piet Ost (UGent) and Kathleen Marchal (UGent)

(2020) BMC MEDICAL GENOMICS. 13(1).

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Journal Article
A1
open access

Associating expression and genomic data using co-occurrence measures

Maarten Larmuseau (UGent) , Lieven Verbeke (UGent) and Kathleen Marchal (UGent)

(2019) BIOLOGY DIRECT. 14.

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Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Mathieu Gand, Wesley Mattheus, Assia Saltykova, Nancy Roosens, Katelijne Dierick, Kathleen Marchal (UGent) , Sigrid C. J. De Keersmaecker and Sophie Bertrand

(2019) APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 103(12). p.4987-4996

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Journal Article
A1
open access

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, et al.

(2019) NATURE COMMUNICATIONS. 10.

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Journal Article
A1
open access

IAMBEE : a web-service for the identification of adaptive pathways from parallel evolved clonal populations

Camilo Andrés Pérez Romero (UGent) , Bram Weytjens (UGent) , Dries Decap (UGent) , Toon Swings, Jan Michiels, Dries De Maeyer (UGent) and Kathleen Marchal (UGent)

(2019) NUCLEIC ACIDS RESEARCH. 47(W1). p.W151-W157

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Journal Article
A1
open access

Organellar carbon metabolism is co-ordinated with distinct developmental phases of secondary xylem

Desré Pinard, Ana Carolina Elisa Fierro Gutierrez (UGent) , Kathleen Marchal (UGent) , Alexander A Myburg and Eshchar Mizrachi

(2019) NEW PHYTOLOGIST. 222(4). p.1832-1845

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Journal Article
A1
open access

Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept

Assia Saltykova, Wesley Mattheus, Sophie Bertrand, Nancy HC Roosens, Kathleen Marchal (UGent) and Sigrid CJ De Keersmaecker

(2019) FRONTIERS IN MICROBIOLOGY. 10.

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Journal Article
A1
open access

Managing evidence in food safety and nutrition

Ermanno Cavalli, Mary Gilsenan, Jane Van Doren, Danica Grahek-Ogden, Jane Richardson, Fabrizio Abbinante, Claudia Cascio, Paul Devalier, Nikolai Brun, Igor Linkov, et al.

(2019) EFSA JOURNAL. 17(suppl. 1).

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The Crabtree effect shapes the Saccharomyces cerevisiae lag phase during the switch between different carbon sources

Gemma Perez-Samper, Bram Cerulus, Abbas Jariani, Lieselotte Vermeersch, Nuria Barrajon Simancas, Markus MM Bisschops, Joost van den Brink, Daniel Solis-Escalante, Brigida Gallone, Dries De Maeyer, et al.

(2018) MBIO. 9(5).

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Identification of novel genes involved in acetic acid tolerance of Saccharomyces cerevisiae using pooled-segregant RNA sequencing

Miguel Fernández-Niño, Sergio Pulido Tamayo (UGent) , Despina Stefanoska, Camilo Andrés Pérez Romero (UGent) , Daniel González-Ramos, Antonius JA van Maris, Kathleen Marchal (UGent) , Elke Nevoigt and Steve Swinnen

(2018) FEMS YEAST RESEARCH. 18(8).

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Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics

Pieter Albers, Bram Weytjens (UGent) , René De Mot, Kathleen Marchal (UGent) and Dirk Springael

(2018) MICROBIOLOGYOPEN. 7(2).

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Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium : consequences for the interspecies consortium metabolic model

Pieter Albers, Cédric Lood, Basak Özturk, Benjamin Horemans, Rob Lavigne, Vera van Noort, René De Mot, Kathleen Marchal (UGent) , Aminael Sanchez-Rodriguez and Dirk Springael

(2018) ENVIRONMENTAL MICROBIOLOGY. 20(1). p.85-96

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1-((2,4-Dichlorophenethyl)amino)3-phenoxypropan-2-ol kills Pseudomonas aeruginosa through extensive membrane damage

Valerie Defraine, Veerle Liebens, Evelien Loos, Toon Swings, Bram Weytjens, Carolina Fierro, Kathleen Marchal (UGent) , Liam Sharkey, Alex J O'Neill, Romu Corbau, et al.

(2018) FRONTIERS IN MICROBIOLOGY. 9.

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Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-

Assia Saltykova, Véronique Wuyts, Wesley Mattheus, Sophie Bertrand, Nancy HC Roosens, Kathleen Marchal (UGent) and Sigrid De Keersmaecker

(2018) PLOS ONE. 13(2).

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Modeling multi-valued biological interaction networks using fuzzy answer set programming

Mushthofa Mushthofa (UGent) , Steven Schockaert, Ling-Hong Hung, Kathleen Marchal (UGent) and Martine De Cock (UGent)

(2018) FUZZY SETS AND SYSTEMS. 345. p.63-82

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Effect of genomic distance on coexpression of coregulated genes in E. coli

Lucia Pannier, Enrique Merino, Kathleen Marchal (UGent) and Julio Collado-Vides

(2017) PLOS ONE. 12(4).

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The evolutionary significance of polyploidy

Yves Van de Peer (UGent) , Eshchar Mizrachi and Kathleen Marchal (UGent)

(2017) NATURE REVIEWS GENETICS. 18(7). p.411-424

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Network-based identification of adaptive pathways in evolved ethanol-tolerant bacterial populations

Toon Swings, Bram Weytjens (UGent) , Thomas Schalck, Camille Bonte, Natalie Verstraeten, Jan Michiels and Kathleen Marchal (UGent)

(2017) MOLECULAR BIOLOGY AND EVOLUTION. 34(11). p.2927-2943

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Book Chapter

Molecular subtyping of Salmonella Typhimurium with multiplex oligonucleotide ligation-PCR (MOL-PCR)

Véronique Wuyts, Wesley Mattheus, Nancy HC Roosens, Kathleen Marchal (UGent) , Sophie Bertrand and Sigrid CJ De Keersmaecker

(2017) Diagnostic bacteriology : methods and protocols. In Methods in Molecular Biology 1616. p.39-69

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Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains

Sam Crauwels, Filip Van Opstaele, Barbara Jaskula-Goiris, Jan Steensels, Christel Verreth, Lien Bosmans, Caroline Paulussen, Beatriz Herrera-Malaver, Ronnie de Jonge (UGent) , Jessika De Clippeleer (UGent) , et al.

(2017) FEMS YEAST RESEARCH. 17(1).

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Early differences in islets from prediabetic NOD mice : combined microarray and proteomic analysis

Inne Crèvecoeur, Valborg Gudmundsdottir, Saurabh Vig, Fernanda Marques Câmara Sodré, Wannes D’Hertog, Ana Carolina Elisa Fierro Gutierrez (UGent) , Leentje Van Lommel, Conny Gysemans, Kathleen Marchal (UGent) , Etienne Waelkens, et al.

(2017) DIABETOLOGIA. 60(3). p.475-489

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Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Eshchar Mizrachi, Lieven Verbeke (UGent) , Nanette Christie, Ana Carolina Elisa Fierro Gutierrez (UGent) , Shawn D Mansfield, Mark F Davis, Erica Gjersing, Gerald A Tuskan, Marc Van Montagu (UGent) , Yves Van de Peer (UGent) , et al.

(2017) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 114(5). p.1195-1200

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Miscellaneous

Principles of systems biology, no. 14 : [...] Network analysis of woody biomass

Eshchar Mizrachi, Lieven Verbeke (UGent) , Yves Van de Peer (UGent) , Kathleen Marchal (UGent) and Alexander A Myburg

(2017) CELL SYSTEMS. 4(2). p.141-141

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Book Chapter

Adaptive self-organizing organisms using a bio-inspired gene regulatory network controller: for the aggregation of evolutionary robots under a changing environment

Yao Yao (UGent) , Kathleen Marchal (UGent) and Yves Van de Peer (UGent)

(2016) Handbook of research on design, control and modeling of swarm robotics. In Advances in Computational Intelligence and Robotics p.68-82

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Book Chapter

Optimized MOL-PCR for characterization of microbial pathogens

Véronique Wuyts (UGent) , Nancy HC Roosens, Sophie Bertrand, Kathleen Marchal (UGent) and Sigrid CJ De Keersmaecker

(2016) Current protocols in cytometry. suppl. 75. p.13.15.1-13.15.15

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Elucidation of the mode of action of a new antibacterial compound active against Staphylococcus aureus and Pseudomonas aeruginosa

Evelien Gerits, Eline Blommaert, Anna Lippell, Alex J O'Neill, Bram Weytjens, Dries De Maeyer, Ana Carolina Fierro, Kathleen Marchal (UGent) , Arnaud Marchand, Patrick Chaltin, et al.

(2016) PLOS ONE. 11(5).

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Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment

Yao Yao (UGent) , Veronique Storme (UGent) , Kathleen Marchal (UGent) and Yves Van de Peer (UGent)

(2016) PEERJ. 4.

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SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis

Sergio Pulido Tamayo (UGent) , Bram Weytjens (UGent) , Dries De Maeyer (UGent) and Kathleen Marchal (UGent)

(2016) SCIENTIFIC REPORTS. 6.

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Simultaneous discovery of cancer subtypes and subtype features by molecular data integration

Thanh Le Van, Matthijs van Leeuwen, Ana Carolina Elisa Fierro Gutierrez (UGent) , Dries De Maeyer (UGent) , Jimmy Van den Eynden (UGent) , Lieven Verbeke (UGent) , Luc De Raedt, Kathleen Marchal (UGent) and Siegfries Nijssen

(2016) BIOINFORMATICS. 32(17). p.i445-i454

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Network-based analysis of eQTL data to prioritize driver mutations

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

(2016) GENOME BIOLOGY AND EVOLUTION. 8(3). p.481-494

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FabR regulates Salmonella biofilm formation via its direct target FabB

Kim Hermans, Stefanie Roberfroid, Inge M Thijs, Gwendoline Kint, David De Coster, Kathleen Marchal (UGent) , Jos Vanderleyden, Sigrid CJ De Keersmaecker and Hans P Steenackers

(2016) BMC GENOMICS. 17.

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EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Sergio Pulido Tamayo (UGent) , Jorge Duitama and Kathleen Marchal (UGent)

(2016) NUCLEIC ACIDS RESEARCH. 44(W1). p.W142-W146

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Vitamin D3 induces tolerance in human dendritic cells by activation of intracellular metabolic pathways

Gabriela Bomfim Ferreira, An-Sofie Vanherwegen, Guy Eelen, Ana Carolina Fierro Gutíerrez, Leentje Van Lommel, Kathleen Marchal (UGent) , Lieve Verlinden, Annemieke Verstuyf, Tatiane Nogueira, Maria Georgiadou, et al.

(2015) CELL REPORTS. 10(5). p.711-725

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SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

Jimmy Van den Eynden (UGent) , Ana Carolina Elisa Fierro Gutierrez (UGent) , Lieven Verbeke (UGent) and Kathleen Marchal (UGent)

(2015) BMC BIOINFORMATICS. 16.

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Ultraviolet-B radiation stimulates downward leaf curling in Arabidopsis thaliana

Ana Carolina Elisa Fierro Gutierrez (UGent) , Olivier Leroux (UGent) , Barbara De Coninck, Bruno PA Cammue, Kathleen Marchal (UGent) , Els Prinsen, Dominique Van Der Straeten (UGent) and Filip Vandenbussche (UGent)

(2015) PLANT PHYSIOLOGY AND BIOCHEMISTRY. 93. p.9-17

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Whole genome sequence analysis of Salmonella Enteritidis PT4 outbreaks from a national reference laboratory’s viewpoint

Véronique Wuyts (UGent) , Sarah Denayer, Nancy HC Roosens, Wesley Mattheus, Sophie Bertrand, Kathleen Marchal (UGent) , Katelijne Dierick and Sigrid CJ De Keersmaecker

(2015) PLOS CURRENTS OUTBREAKS.

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Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

S Crauwels, A Van Assche, Ronnie de Jonge (UGent) , AR Borneman, C Verreth, P Troels, G De Samblanx, Kathleen Marchal (UGent) , Yves Van de Peer (UGent) , KA Willems, et al.

(2015) APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 99(21). p.9123-9134

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Conference Paper
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Pathway relevance ranking for tumor samples through network-based data integration (award for Outstanding Oral Poster Presentation )

Lieven Verbeke (UGent) , Jimmy Van den Eynden (UGent) , Piet Demeester (UGent) , Kathleen Marchal (UGent) and Jan Fostier (UGent)

(2015) 23e Annual International Conference on Intelligent Systems for Molecular Biology, Abstracts.