Ghent University Academic Bibliography

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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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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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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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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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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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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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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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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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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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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
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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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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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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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- C3
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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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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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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- A2
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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.
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Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

Sergio Pulido Tamayo (UGent) , Aminael Sanchez Rodriguez (UGent) , Toon Swings, Bram Van den Berghe, Akanksha Dubey, Hans Steenackers, Jan Michiels, Jan Fostier (UGent) and Kathleen Marchal (UGent)

(2015) NUCLEIC ACIDS RESEARCH. 43(16).
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Pathway relevance ranking for tumor samples through network-based data integration

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

(2015) PLOS ONE. 10(7).
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A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium

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

(2015) APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 99(19). p.8137-8149
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- Conference Paper
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Identifying prokaryotic consortia that live in close interactions with algae

Assia Saltykova, Sergio Pulido-Tamayo, Marie Pazoutova, Stefan A Rensing, Tomoaki Nishiyama, Yves Van de Peer (UGent) , Kathleen Marchal (UGent) and Stephane Rombauts (UGent)

(2015) EUROPEAN JOURNAL OF PHYCOLOGY. 50(suppl. 1). p.145-146
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Adaptation to high ethanol reveals complex evolutionary pathways

Karin Voordeckers, Jacek Kominek, Anupam Das, Adriana Espinosa-Cantu, Dries De Maeyer, Kathleen Marchal (UGent) , Alexander DeLuna, Rob Jelier and Kevin Verstrepen

(2015) YEAST. 32(suppl. 1). p.S272-S272
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Studying the relationship between drug resistance and genomic variations in Leishmania donovani using a network-based method

MR Ticlla Ccenhua, S Pulido-Tamayo, H Imamura, Lieven Verbeke (UGent) , J Cotton, J-C Dujardin and Kathleen Marchal (UGent)

(2015) TROPICAL MEDICINE & INTERNATIONAL HEALTH. 20(suppl. 1). p.165-165
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User‐friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks

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

(2015) Food Microbiology, 20th Conference, Abstracts.
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Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance

Natalie Verstraeten, Wouter Joris Knapen, Cyrielle Ines Kint, Veerle Liebens, Bram Van den Bergh, Liselot Dewachter, Joran Elie Michiels, Qiang Fu, Charlotte Claudia David, Ana Carolina Fierro, et al.

(2015) MOLECULAR CELL. 59(1). p.9-21
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Adaptation to high ethanol reveals complex evolutionary pathways

Karin Voordeckers, Jacek Kominek, Anupam Das, Adriana Espinosa-Cantú, Dries De Maeyer, Ahmed Arslan, Michiel Van Pee, Elisa van der Zande, Wim Meert, Yudi Yang, et al.

(2015) PLOS GENETICS. 11(11).
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PheNetic : network-based interpretation of molecular profiling data

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

(2015) NUCLEIC ACIDS RESEARCH. 43(W1). p.W244-W250
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Guidelines for optimisation of a multiplex oligonucleotide ligation-PCR for characterisation of microbial pathogens in a microsphere suspension array

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

(2015) BIOMED RESEARCH INTERNATIONAL.
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- Miscellaneous
The usefulness of whole genome sequencing for outbreak investigation of food pathogens, Salmonella Enteritidis as a case study

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

(2015) LABINFO. p.15-18
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- Conference Paper
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Small-scale fermentation assay reveals differences in sugar consumption and (off)flavour production across Brettanomyces bruxellensis strains

Sam Crauwels, Filip Van Opstaele, Barbara Jaskula-Goiris, Christel Verreth, Jessika De Clippeleer (UGent) , Kathleen Marchal (UGent) , Gorik De Samblanx, Kris Willems, Kevin Verstrepen, Guido Aerts, et al.

(2015) Belgian Brewing Conference 2015, Abstracts.
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- Book Chapter
Path finding in biological networks

Lore Cloots, Dries De Maeyer and Kathleen Marchal (UGent)

(2014) Springer handbook of bio-/neuroinformatics. p.289-309
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Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments

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

(2014) PLOS ONE. 9(3).
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Photoreceptor-mediated bending towards UV-B in Arabidopsis

Filip Vandenbussche (UGent) , Kimberley Tilbrook, Ana Carolina Fierro, Kathleen Marchal (UGent) , Dirk Poelman (UGent) , Dominique Van Der Straeten (UGent) and Roman Ulm

(2014) MOLECULAR PLANT. 7(6). p.1041-1052
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Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

Ivan Ishchukov, Yan Wu, Sandra Van Puyvelde, Jos Vanderleyden and Kathleen Marchal (UGent)

(2014) BMC MICROBIOLOGY. 14.
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COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia

Pieter Meysman, Paolo Sonego, Luca Bianco, Qiang Fu, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Veerle Liebens, Jan Michiels, Kris Laukens, Kathleen Marchal (UGent) , et al.

(2014) NUCLEIC ACIDS RESEARCH. 42(D1). p.D649-D653
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Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast

Jorge Duitama, Aminael Sánchez-Rodriguez, Annelies Goovaerts, Sergio Pulido Tamayo (UGent) , Georg Hubmann, Maria R Foulquié-Moreno, Johan M Thevelein, Kelvin J Verstrepen and Kathleen Marchal (UGent)

(2014) BMC GENOMICS. 15.
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MAGIC: access portal to a cross-platform gene expression compendium for maize

Qiang Fu, Ana Carolina Elisa Fierro Gutierrez (UGent) , Pieter Meysman, Aminael Sanchez Rodriguez (UGent) , Klaas Vandepoele (UGent) , Kathleen Marchal (UGent) and Kristof Engelen

(2014) BIOINFORMATICS. 30(9). p.1316-1318
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A network-based approach to identify substrate classes of bacterial glycosyltransferases

Aminael Sánchez-Rodríguez, Hanne LP Tytgat, Joris Winderickx, Jos Vanderleyden, Sarah Lebeer and Kathleen Marchal (UGent)

(2014) BMC GENOMICS. 15.
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A putative de-N-acetylase of the PIG-L superfamily affects fluoroquinolone tolerance in Pseudomonas aeruginosa

Veerle Liebens, Valerie Defraine, Annelies Van der Leyden, Valerie N De Groote, Carolina Fierro, Serge Beullens, Natalie Verstraeten, Cyrielle Kint, Ann Jans, Emanuela Frangipani, et al.

(2014) PATHOGENS AND DISEASE. 71(1). p.39-54
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Phenotypical and molecular responses of Arabidopsis thaliana roots as a result of inoculation with the auxin-producing bacterium Azospirillum brasilense

Stijn Spaepen, Stijn Bossuyt, Kristof Engelen, Kathleen Marchal (UGent) and Jos Vanderleyden

(2014) NEW PHYTOLOGIST. 201(3). p.850-861
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ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

Mushthofa Mushthofa (UGent) , Gustavo Adolfo Torres Torres (UGent) , Yves Van de Peer (UGent) , Kathleen Marchal (UGent) and Martine De Cock (UGent)

(2014) BIOINFORMATICS. 30(21). p.3086-3092
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- Conference Paper
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Ranked tiling

Thanh Le Van, Matthijs Van Leeuwen, Siegfried Nijssen, Ana Carolina Fierro, Kathleen Marchal (UGent) and Luc De Raedt

(2014) Lecture Notes in Artificial Intelligence. 8725. p.98-113
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Genome-scale co-expression network comparison across escherichia coli and salmonella enterica serovar typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles

P Zarrineh, A Sanchez-Rodriguez, N Hosseinkhan, Z Narimani, Kathleen Marchal (UGent) and A Masoudi-Nejad

(2014) PLOS ONE. 9(8).
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Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing

Sam Crauwels, Bo Zhu, Jan Steensels, Pieter Busschaert, Gorik De Samblanx, Kathleen Marchal (UGent) , Kris A Willems, Kevin J Verstrepen and Bart Lievens

(2014) APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 80(14). p.4398-4413
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An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference

Guillermin Agüero-Chapin, Aminael Sánchez-Rodríguez, Pedro I Hidalgo-Yanes, Yunierkis Pérez-Castillo, Reinaldo Molina-Ruiz, Kathleen Marchal (UGent) , Vitor Vasconcelos and Agostinho Antunes

(2013) Proceedings IWBBIO 2013 : International work-conference on bioinformatics and biomedical engineering. p.155-156
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EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

Lieven Verbeke (UGent) , Lore Cloots, Piet Demeester (UGent) , Jan Fostier (UGent) and Kathleen Marchal (UGent)

(2013) BIOINFORMATICS. 29(10). p.1308-1316
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- A2
Identifying differentially expressed genes in the absence of replication

Pushpke J Thilakarathne, Geert Verbeke, Kristof Engelen, Kathleen Marchal (UGent) and Dan Lin

(2013) INTERNATIONAL JOURNAL OF BIOINFORMATICS RESEARCH AND APPLICATIONS. 9(1). p.71-90
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Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles

Pieter Meysman, Aminael Sánchez-Rodríguez, Qiang Fu, Kathleen Marchal (UGent) and Kristof Engelen

(2013) MOLECULAR BIOLOGY AND EVOLUTION. 30(6). p.1302-1314
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PheNetic: network-based interpretation of unstructured gene lists in E. coli

Dries De Maeyer, Joris Renkens, Lore Cloots, Luc De Raedt and Kathleen Marchal (UGent)

(2013) MOLECULAR BIOSYSTEMS. 9(7). p.1594-1603
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Omics derived networks in bacteria

Aminael Sánchez-Rodríguez, Lore Cloots and Kathleen Marchal (UGent)

(2013) CURRENT BIOINFORMATICS. 8(4). p.489-495
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Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family

Pieter Meysman, Kathleen Marchal (UGent) and Kristof Engelen

(2013) CURRENT BIOINFORMATICS. 8(4). p.483-488
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MLVA as a tool for public health surveillance of human Salmonella Typhimurium : prospective study in Belgium and evaluation of MLVA loci stability

Véronique Wuyts, Wesley Mattheus, Guillaume De Laminne de Bex, Christa Wildemauwe, Nancy HC Roosens, Kathleen Marchal (UGent) , Sigrid CJ De Keersmaecker and Sophie Bertrand

(2013) PLOS ONE. 8(12).
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Synthetic biology and microdevices : a powerful combination

Lyn Venken, Kathleen Marchal (UGent) and Jos Vanderleyden

(2013) ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS. 9(4).
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Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Pablo Meyer, Geoffrey Siwo, Danny Zeevi, Eilon Sharon, Raquel Norel, Eran Segal, Gustavo Stolovitzky, the DREAM6 consortium, Yvan Saeys (UGent) and Kathleen Marchal (UGent)

(2013) GENOME RESEARCH. 23(11). p.1928-1937
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EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

Lieven Verbeke (UGent) , Piet Demeester (UGent) , Jan Fostier (UGent) and Kathleen Marchal (UGent)

(2013) Intelligent Systems for Molecular Biology, 21st Annual international conference, Abstracts.
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Identifying relevant pathways for different breast cancer subtypes using network based data integration

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

(2013) Regulatory and Systems Genomics, 6th Annual RECOMB/ISCB conference, Abstracts.
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Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation

Elham Aslankoohi, Bo Zhu, Mohammad Naser Rezaei, Karin Voordeckers, Dries De Maeyer, Kathleen Marchal (UGent) , Emmie Dornez, Christophe M Courtin and Kevin J Verstrepen

(2013) APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 79(23). p.7325-7333
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Exploring the complementarity of eQTL mapping methods (poster)

Lieven Verbeke (UGent) , Kathleen Marchal (UGent) and Jan Fostier (UGent)

(2012) 20e Annual Conference on Intelligent Systems for Molecular Biology, Abstracts. p.1-1
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- Journal Article
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Association of the vascular endothelial growth factor gene polymorphisms (-460C/T,+405G/C and+936T/C) with endometriosis: a meta-analysis

Shaohua Xu, Wei Wu, Hong Sun, Jing Lu, Beilei Yuan, Yankai Xia, Bart De Moor, Kathleen Marchal (UGent) , Xinru Wang, Peizhen Xu, et al.

(2012) ANNALS OF HUMAN GENETICS. 76(6). p.464-471
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Nucleosomes affect local transformation efficiency

Elham Aslankoohi, Karin Voordeckers, Hong Sun, Aminael Sanchez-Rodriguez, Elisa van der Zande, Kathleen Marchal (UGent) and Kevin J Verstrepen

(2012) NUCLEIC ACIDS RESEARCH. 40(19). p.9506-9512
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Follicle stimulating hormone receptor G-29A, 919A > G, 2039A > G polymorphism and the risk of male infertility: A meta-analysis

Wei Wu, Hongquan Cai, Hong Sun, Jing Lu, Dan Zhao, Yufeng Qin, Xiumei Han, Xiaobing Niu, Chuncheng Lu, Yankai Xia, et al.

(2012) GENE. 505(2). p.388-392
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Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology

Karin Voordeckers, Dries De Maeyer, Elisa van der Zande, Marcelo D Vinces, Wim Meert, Lore Cloots, Owen Ryan, Kathleen Marchal (UGent) and Kevin J Verstrepen

(2012) MOLECULAR MICROBIOLOGY. 86(1). p.225-239
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- Journal Article
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DNA structural properties in the classification of genomic transcription

Pieter Meysman, Kathleen Marchal (UGent) and Kristof Engelen

(2012) BIOINFORMATICS AND BIOLOGY INSIGHTS. 6. p.155-168
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- Conference Paper
- C3
An ASP-based simulation method for finding all synchronous and asynchronous attractors in genetic regulatory networks

Gustavo Adolfo Torres Torres (UGent) , Kathleen Marchal (UGent) , Yves Van de Peer (UGent) and Martine De Cock (UGent)

(2012) ISBC Student Council, 8th Symposium, Abstracts.
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- Conference Paper
- C3
Predicting long term behavior of genetic regulatory networks with answer set programming

Gustavo Adolfo Torres Torres (UGent) , Kathleen Marchal (UGent) , Yves Van de Peer (UGent) and Martine De Cock (UGent)

(2012) Proceedings of the 21st Belgian-Dutch conference on machine learning.
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- Journal Article
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A combined approach to study the protein glycosylation potential of Lactobacillus rhamnosus GG (LGG)

Hanne LP Tytgat, Aminael Sánchez-Rodríguez, Geert Schoofs, Tine LA Verhoeven, Sigrid CJ De Keersmaecker, Kathleen Marchal (UGent) , Jos Vanderleyden and Sarah Lebeer

(2012) COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES. 77(1). p.15-19
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- Book Chapter
Directed module detection in a large-scale expression compendium

Qiang Fu, Karen Lemmens, Aminael Sánchez-Rodríguez, Inge M Thijs, Pieter Meysman, Hong Sun, Ana Carolina Fierro, Kristof Engelen and Kathleen Marchal (UGent)

(2012) Bacterial molecular networks : methods and protocols. In Methods in Molecular Biology 804. p.131-165
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Mining local staircase patterns in noisy data

Thanh Le Van, Ana Carolina Fierro, Tias Guns, Matthijs Van Leeuwen, Siegfried Nijssen, Luc De Raedt and Kathleen Marchal (UGent)

(2012) 2012 IEEE 12th international conference on data mining workshops (ICDM 2012). p.139-146
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MotifSuite: workflow for probabilistic motif detection and assessment

Marleen Claeys, Valerie Storms, Hong Sun, Tom Michoel and Kathleen Marchal (UGent)

(2012) BIOINFORMATICS. 28(14). p.1931-1932
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Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Hong Sun, Tias Guns, Ana Carolina Fierro, Lieven Thorrez, Siegfried Nijssen and Kathleen Marchal (UGent)

(2012) NUCLEIC ACIDS RESEARCH. 40(12).
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- Journal Article
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An ensemble biclustering approach for querying gene expression compendia with experimental lists

Riet De Smet (UGent) and Kathleen Marchal (UGent)

(2011) BIOINFORMATICS. 27(14). p.1948-1956
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COMODO : an adaptive coclustering strategy to identify conserved coexpression modules between organisms

Peyman Zarrineh, Ana C Fierro, Aminael Sánchez-Rodríguez, Bart De Moor, Kristof Engelen and Kathleen Marchal (UGent)

(2011) NUCLEIC ACIDS RESEARCH. 39(7).
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A comparative transcriptome analysis of Rhizobium etli bacteroids: specific gene expression during symbiotic nongrowth

Maarten Vercruysse, Maarten Fauvart, Serge Beullens, Kristien Braeken, Lore Cloots, Kristof Engelen, Kathleen Marchal (UGent) and Jan Michiels

(2011) MOLECULAR PLANT-MICROBE INTERACTIONS. 24(12). p.1553-1561
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Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

Lore Cloots and Kathleen Marchal (UGent)

(2011) CURRENT OPINION IN MICROBIOLOGY. 14(5). p.599-607
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COLOMBOS : access port for cross-platform bacterial expression compendia

Kristof Engelen, Qiang Fu, Pieter Meysman, Aminael Sánchez-Rodríguez, Riet De Smet (UGent) , Karen Lemmens, Ana Carolina Fierro and Kathleen Marchal (UGent)

(2011) PLOS ONE. 6(7).
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Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil

Maarten Fauvart, Aminael Sánchez-Rodríguez, Serge Beullens, Kathleen Marchal (UGent) and Jan Michiels

(2011) JOURNAL OF BACTERIOLOGY. 193(12). p.3158-3159
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Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response

Sandra Van Puyvelde, Lore Cloots, Kristof Engelen, Frederik Das, Kathleen Marchal (UGent) , Jos Vanderleyden and Stijn Spaepen

(2011) MICROBIAL ECOLOGY. 61(4). p.723-728
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Query-based biclustering of gene expression data using Probabilistic Relational Models

Hui Zhao, Lore Cloots, Tim Van den Bulcke, Yan Wu, Riet De Smet (UGent) , Valerie Storms, Pieter Meysman, Kristof Engelen and Kathleen Marchal (UGent)

(2011) BMC BIOINFORMATICS. 12(suppl. 1).
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Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

Pieter Meysman, Hai Dang Thanh, Kris Laukens, Riet De Smet (UGent) , Yan Wu, Kathleen Marchal (UGent) and Kristof Engelen

(2011) NUCLEIC ACIDS RESEARCH. 39(2).
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An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference

Guillermin Aguero-Chapin, Aminael Sánchez-Rodríguez, Pedro I Hidalgo-Yanes, Yunierkis Pérez-Castillo, Reinaldo Molina-Ruiz, Kathleen Marchal (UGent) , Vitor Vasconcelos and Agostinho Antunes

(2011) PLOS ONE. 6(10).
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Stress response regulators identified through genome-wide transcriptome analysis of the (p) ppGpp-dependent response in Rhizobium etli

Maarten Vercruysse, Maarten Fauvart, Ann Jans, Serge Beullens, Kristien Braeken, Lore Cloots, Kristof Engelen, Kathleen Marchal (UGent) and Jan Michiels

(2011) GENOME BIOLOGY. 12(2).
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A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

Ines Thiele, Daniel R Hyduke, Benjamin Steeb, Guy Fankam, Douglas K Allen, Susanna Bazzani, Pep Charusanti, Feng-Chi Chen, Ronan MT Fleming, Chao A Hsiung, et al.

(2011) BMC SYSTEMS BIOLOGY. 5.
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- Conference Paper
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An ensemble method for querying gene expression compendia with experimental lists

Riet De Smet (UGent) and Kathleen Marchal (UGent)

(2010) Proceedings 2010 IEEE international conference on bioinformatics and biomedicine (BIBM 2010). p.314-318
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Module network inference from a cancer gene expression data set identifies microRNA regulated modules

Eric Bonnet (UGent) , Marianthi Tatari, Anagha Madhusudan Joshi (UGent) , Tom Michoel (UGent) , Kathleen Marchal (UGent) , Geert Berx (UGent) and Yves Van de Peer (UGent)

(2010) PLOS ONE. 5(4).
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- Conference Paper
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Regulation of cystathionine beta synthase by 1α,25-dihydroxyvitamin D₃

Carsten Kriebitzsch, Lieve Verlinden, Guy Eelen, Kathleen Marchal (UGent) , Bart De Moor, Ine Beullens, Mark Van Camp, Roger Bouillon and Annemieke Verstuyf

(2010) BONE. 46(suppl. 1). p.S51-S51
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Regulation of semaphorin 3 family members and their receptors by 1α,25-dihydroxyvitamin D₃

Lieve Verlinden, Carsten Kriebitzsch, Guy Eelen, Ine Beullens, Mark Van Camp, Biauw Keng Tan, Bart De Moor, Kathleen Marchal (UGent) , Roger Bouillon and Annemieke Verstuyf

(2010) BONE. 46(suppl. 1). p.S66-S66
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The potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Animael Sanchez-Rodriguez, Cindy Martens (UGent) , Kristof Engelen, Yves Van de Peer (UGent) and Kathleen Marchal (UGent)

(2010) BMC EVOLUTIONARY BIOLOGY. 10.
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Alternative experimental design with an applied normalization scheme can improve statistical power in 2D-DIGE experiments

Kristof Engelen, Alejandro Sifrim, Babs Van de Plas, Kris Laukens, Lutgarde Arckens and Kathleen Marchal (UGent)

(2010) JOURNAL OF PROTEOME RESEARCH. 9(10). p.4919-4926
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Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array

Maarten Vercruysse, Maarten Fauvart, Lore Cloots, Kristof Engelen, Inge M Thijs, Kathleen Marchal (UGent) and Jan Michiels

(2010) BMC GENOMICS. 11.
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The small regulatory RNA molecule MicA is involved in Salmonella enterica serovar Typhimurium biofilm formation

Gwendoline Kint, David De Coster, Kathleen Marchal (UGent) , Jos Vanderleyden and Sigrid CJ De Keersmaecker

(2010) BMC MICROBIOLOGY. 10.
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Integration of 'omics' data: does it lead to new insights into host-microbe interactions?

Gwendoline Kint, Carolina Fierro, Kathleen Marchal (UGent) , Jos Vanderleyden and Sigrid CJ De Keersmaecker

(2010) FUTURE MICROBIOLOGY. 5(2). p.313-328
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The effect of orthology and coregulation on detecting regulatory motifs

Valerie Storms, Marleen Claeys, Amiael Sanchez, Bart De Moor, Annemieke Verstuyf and Kathleen Marchal (UGent)

(2010) PLOS ONE. 5.
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The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium

Inge M Thijs, Hui Zhao, Ami De Weerdt, Kristof Engelen, David De Coster, Geert Schoofs, Michael McClelland, Jos Vanderleyden, Kathleen Marchal (UGent) and Sigrid CD De Keersmaecker

(2010) CELL RESEARCH. 20(8). p.966-969
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- Book Chapter
Systems microbiology : gaining insights in transcriptional networks

Riet De Smet, Karen Lemmens, Ana Carolina Fierro and Kathleen Marchal (UGent)

(2010) Infectious disease informatics. p.93-122
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- Conference Paper
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Cis-regulatory module detection using constraint programming

Tias Guns, Hong Sun, Kathleen Marchal (UGent) and Siegfried Nijssen

(2010) Proceedings 2010 IEEE international conference on bioinformatics and biomedicine (BIBM 2010). p.363-368
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Advantages and limitations of current network inference methods

Riet De Smet (UGent) and Kathleen Marchal (UGent)

(2010) NATURE REVIEWS MICROBIOLOGY. 8(10). p.717-729
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- Conference Paper
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The use of mixed models to identify differentially expressed genes when a single replicate per biological condition is present

PJ Thilakarathne, G Verbeke, K Engelen and Kathleen Marchal (UGent)

(2009) Proceedings of the 2009 international conference on bioinformatics and computational biology, BIOCOMP 2009. p.186-190
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Inferring the transcriptional network of Bacillus subtilis

Abeer Fadda, Ana Carolina Fierro, Karen Lemmens, Pieter Monsieurs, Kristof Engelen and Kathleen Marchal (UGent)

(2009) MOLECULAR BIOSYSTEMS. 5(12). p.1840-1852
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DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

Karen Lemmens, Tijl De Bie (UGent) , Thomas Dhollander, Sigrid CJ De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, et al.

(2009) GENOME BIOLOGY. 10(3).
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The condition-dependent transcriptional network in Escherichia coli

Karen Lemmens, Tijl De Bie (UGent) , Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen and Kathleen Marchal (UGent)

(2009) Annals of the New York Academy of Sciences. 1158. p.29-35
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ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules

Hong Sun, Tijl De Bie (UGent) , Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor and Kathleen Marchal (UGent)

(2009) BMC BIOINFORMATICS. 10(suppl. 1).
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ViTraM: visualization of transcriptional modules

Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor and Kathleen Marchal (UGent)

(2009) BIOINFORMATICS. 25(18). p.2450-2451
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A nonlinear mixed-effects model for estimating calibration intervals for unknown concentrations in two-color microarray data with spike-ins

Pushpike J Thilakarathne, Geert Verbeke, Kristof Engelen and Kathleen Marchal (UGent)

(2009) STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY. 8(1).
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- Conference Paper
- P1
Layout and post-processing of transcriptional modules

Hong Sun, Tim Van den Bulcke, Bart De Moor, Karen Lemmens, Kristof Engelen and Kathleen Marchal (UGent)

(2009) 2009 International joint conference on bioinformatics, systems biology and intelligent computing, Proceedings. p.116-121
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Module networks revisited: computational assessment and prioritization of model predictions

Anagha Madhusudan Joshi (UGent) , Riet De Smet (UGent) , Kathleen Marchal (UGent) , Yves Van de Peer (UGent) and Tom Michoel (UGent)

(2009) BIOINFORMATICS. 25(4). p.490-496
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Reverse-engineering transcriptional modules from gene expression data

Tom Michoel (UGent) , Riet De Smet (UGent) , Anagha Madhusudan Joshi (UGent) , Kathleen Marchal (UGent) and Yves Van de Peer (UGent)

(2009) Annals of the New York Academy of Sciences. 1158. p.36-43
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Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Tom Michoel (UGent) , Riet De Smet (UGent) , Anagha Madhusudan Joshi (UGent) , Yves Van de Peer (UGent) and Kathleen Marchal (UGent)

(2009) BMC Systems Biology. 3(49). p.1-13
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Microarray analysis of MCF-7 breast cancer cells treated with 1,25-dihydroxyvitamin D-3 or a 17-methyl-D-ring analog

Els Vanoirbeek, Guy Eelen, Lieve Verlinden, Kathleen Marchal (UGent) , Kristof Engelen, Bart De Moor, Ine Beullens, Suzanne Marcelis, Pierre De Clercq (UGent) , Roger Bouillon, et al.

(2009) ANTICANCER RESEARCH. 29(9). p.3585-3590
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- Conference Paper
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Microarray analysis of MCF-7 breast cancer cells treated with 1,25-(OH)(2)D-3 or the analog WY1112

Els Vanoirbeek, Guy Eelen, Ine Beullens, Mark Van Camp, Kristof Engelen, Kathleen Marchal (UGent) , Pierre De Clercq (UGent) , M Vandewalle, Roger Bouillon and Annemieke Verstuyf

(2008) ANTICANCER RESEARCH. 28(3A). p.1625-1626
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Evaluation of time profile reconstruction from complex two-color microarray designs

Ana C Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal (UGent) and Nicolas Pollet

(2008) BMC BIOINFORMATICS. 9.
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Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data

Koenraad Van Leemput, Tim Van den Bulcke, Thomas Dhollander, Bart De Moor, Kathleen Marchal (UGent) and Piet van Remortel

(2008) ARTIFICIAL LIFE. 14(1). p.49-63
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Expression of the BRCA1-interacting protein Brip1/BACH1/FANCJ is driven by E2F and correlates with human breast cancer malignancy

G Eelen, I Vanden Bempt, L Verlinden, M Drijkoningen, A Smeets, P Neven, MR Christiaens, Kathleen Marchal (UGent) , R Bouillon and A Verstuyf

(2008) ONCOGENE. 27(30). p.4233-4241
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- Miscellaneous
- open access
Bacterial networking

Kathleen Marchal (UGent) and Sigrid CJ De Keersmaecker

(2008) GENOME BIOLOGY. 9(11).
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- A1
Genome-wide expression analysis reveals TORC1-dependent and -independent functions of Sch9

Bart Smets, Pepijn De Snijder, Kristof Engelen, Eva Joossens, Ruben Ghillebert, Karin Thevissen, Kathleen Marchal (UGent) and Joris Winderickx

(2008) FEMS YEAST RESEARCH. 8(8). p.1276-1288
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Using ribosomal protein genes as reference : a tale of caution

Lieven Thorrez, Katrijn Van Deun, Léon-Charles Tranchevent, Leentje Van Lommel, Kristof Engelen, Kathleen Marchal (UGent) , Yves Moreau, Iven Van Mechelen and Frans Schuit

(2008) PLOS ONE. 3.
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Meta analysis of gene expression data within and across species

Ana Carolina Fierro, Filip Vandenbussche (UGent) , Kristof Engelen, Yves Van de Peer (UGent) and Kathleen Marchal (UGent)

(2008) CURRENT GENOMICS. 9(8). p.525-534
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Brominated furanones inhibit biofilm formation by Salmonella enterica serovar Typhimurium

Joost CA Janssens, Hans Steenackers, Stijn Robijns, Edith Gellens, Jeremy Levin, Hui Zhao, Kim Hermans, David De Coster, Tine L Verhoeven, Kathleen Marchal (UGent) , et al.

(2008) APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 74(21). p.6639-6648
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Validating module network learning algorithms using simulated data

Tom Michoel (UGent) , Steven Maere (UGent) , Eric Bonnet (UGent) , Anagha Madhusudan Joshi (UGent) , Yvan Saeys (UGent) , Tim Van den Bulcke, Koenraad Van Leemput, Piet Van Remortel, Martin Kuiper (UGent) , Kathleen Marchal (UGent) , et al.

(2007) BMC BIOINFORMATICS. 8(suppl. 2).
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- Journal Article
- A4
Combining omics data to unravel the regulatory network controlling Salmonella invasion of epithelial cells

Inge M Thijs, Sigrid CJ De Keersmaecker, A Fadda, Kristof Engelen, H Zhao, M McClelland, Kathleen Marchal (UGent) and Jos Vanderleyden

(2007) COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES. 72(1). p.55-59
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- Journal Article
- A1
Query-driven module discovery in microarray data

Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal (UGent) and Yves Moreau

(2007) BIOINFORMATICS. 23(19). p.2573-2580
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Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and biofilm formation

Sarah Lebeer, Sigrid CJ De Keersmaecker, Tine LA Verhoeven, Abeer A Fadda, Kathleen Marchal (UGent) and Jos Vanderleyden

(2007) JOURNAL OF BACTERIOLOGY. 189(3). p.860-871
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Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis

Inge MV Thijs, Sigrid CJ De Keersmaecker, Abeer A Fadda, Kristof Engelen, Hui Zhao, Michael McClelland, Kathleen Marchal (UGent) and Jos Vanderleyden

(2007) JOURNAL OF BACTERIOLOGY. 189(13). p.4587-4596
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Joint mapping of genes and conditions via multidimensional unfolding analysis

Katrijn Van Deun, Kathleen Marchal (UGent) , Willem J Heiser, Kristof Engelen and Iven Van Mechelen

(2007) BMC BIOINFORMATICS. 8.
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- Journal Article
- A1
1α,25-Dihydroxyvitamin D₃-induced down-regulation of the checkpoint proteins, Chk1 and Claspin, is mediated by the pocket proteins p107 and p130

Lieve Verlinden, Guy Eelen, Ruth Van Hellemont, Kristof Engelen, Ine Beullens, Mark Van Camp, Kathleen Marchal (UGent) , Chantal Mathieu, Roger Bouillon and Annemieke Verstuyf

(2007) JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY. 103(3-5). p.411-415
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The E2F-regulated gene Chk1 is highly expressed in triple-negative estrogen receptor-/progesterone receptor-/HER-2-breast carcinomas

Lieve Verlinden, Isabelle Vanden Bempt, Guy Eelen, Maria Drijkoningen, Ilse Verlinden, Kathleen Marchal (UGent) , Christiane De Wolf-Peeters, Marie-Rose Christiaens, Luc Michiels, Roger Bouillon, et al.

(2007) CANCER RESEARCH. 67(14). p.6574-6581
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CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data

Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal (UGent)

(2007) BIOINFORMATICS. 23(13). p.1700-1701
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- Book Chapter
Gene regulation bioinformatics of microarray data

Gert Thijs, Frank De Smet, Yves Moreau, Kathleen Marchal (UGent) and Bart De Moor

(2007) Genomics and proteomics engineering in medicine and biology. p.55-98
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- Conference Paper
- C1
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GeneReg: integration of experimental data on the DNA transcription process

David Pastor, Karen Lemmens, Álvaro Cortés-Calabuig, Kathleen Marchal (UGent) , Marc Denecker and Bart De Moor

(2007) Proceedings of the 19th Belgian-Dutch conference on artificial intelligence. p.260-267
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- Book Chapter
Divergence of regulatory sequences in duplicated fish genes

R Van Hellemont, Tine Blomme (UGent) , Yves Van de Peer (UGent) and Kathleen Marchal (UGent)

(2007) Gene and protein evolution. In Genome Dynamics 3. p.81-100
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A calibration method for estimating absolute expression levels from microarray data

Kristof Engelen, Bart Naudts, Bart De Moor and Kathleen Marchal (UGent)

(2006) BIOINFORMATICS. 22(10). p.1251-1258
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Inferring transcriptional modules from ChIP-chip, motif and microarray data

Karen Lemmens, Thomas Dhollander, Tijl De Bie (UGent) , Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor and Kathleen Marchal (UGent)

(2006) GENOME BIOLOGY. 7(5).
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More robust detection of motifs in coexpressed genes by using phylogenetic information

Pieter Monsieurs, Gert Thijs, Abeer A Fadda, Sigrid CJ De Keersmaecker, Jos Vanderleyden, Bart De Moor and Kathleen Marchal (UGent)

(2006) BMC BIOINFORMATICS. 7.
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SynTReN : a generator of synthetic gene expression data for design and analysis of structure learning algorithms

Tim Van den Bulcke, Koenraad Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor and Kathleen Marchal (UGent)

(2006) BMC BIOINFORMATICS. 7.
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Integration of omics data: how well does it work for bacteria?

Sigrid CJ De Keersmaecker, Inge MV Thijs, Jos Vanderleyden and Kathleen Marchal (UGent)

(2006) MOLECULAR MICROBIOLOGY. 62(5). p.1239-1250
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Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid

Sigrid CJ De Keersmaecker, Tine LA Verhoeven, Jos Desair, Kathleen Marchal (UGent) , Jos Vanderleyden and István Nagy

(2006) FEMS MICROBIOLOGY LETTERS. 259(1). p.89-96
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Predicting the clinical behavior of ovarian cancer from gene expression profiles

F De Smet, NL Pochet, K Engelen, T Van Gorp, P Van Hummelen, Kathleen Marchal (UGent) , F Amant, D Timmerman, BL De Moor and IB Vergote

(2006) INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER. 16(suppl. 1). p.147-151
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The effect of a sertoli cell-selective knockout of the androgen receptor on testicular gene expression in prepubertal mice

Evi Denolet, Karel De Gendt, Joke Allemeersch, Kristof Engelen, Kathleen Marchal (UGent) , Paul Van Hummelen, Karen AL Tan, Richard M Sharpe, Philippa TK Saunders, Johannes V Swinnen, et al.

(2006) MOLECULAR ENDOCRINOLOGY. 20(2). p.321-334
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- Journal Article
- A1
Inferring transcriptional networks by mining 'omics' data

Tim Van den Bulcke, Karen Lemmens, Yves Van de Peer (UGent) and Kathleen Marchal (UGent)

(2006) CURRENT BIOINFORMATICS. 1(3). p.301-313
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- Conference Paper
- P1
Discovering transcriptional modules from motif, chip-chip and microarray data

Tijl De Bie (UGent) , Pieter Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini and Kathleen Marchal (UGent)

(2005) Pacific symposium on biocomputing 2005. p.483-494
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- Journal Article
- A1
Characterization of the condensin component Cnap1 and protein kinase Melk as novel E2F target genes down-regulated by 1,25-dihydroxyvitamin D3

Lieve Verlinden, Guy Eelen, Ine Beullens, Mark Van Camp, Paul Van Hummelen, Kristof Engelen, Ruth Van Hellemont, Kathleen Marchal (UGent) , Bart De Moor, Floris Foijer, et al.

(2005) JOURNAL OF BIOLOGICAL CHEMISTRY. 280(45). p.37319-37330
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- Conference Paper
- C1
M@CBETH: optimizing clinical microarray classification

NLMM Pochet, FAL Janssens, F De Smet, Kathleen Marchal (UGent) , IB Vergote, JAK Suykens and BLR De Moor

(2005) 2005 IEEE Computational systems bioinformatics conference workshops and poster abstracts. p.89-90
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- Conference Paper
- C1
- open access
Identifying new drug targets to combat pathogenic infections: an interdisciplinary approach

Ilse Smets, Astrid Cappuyns, Kristel Bernaerts, Nadja Van Boxel, Kathleen Sonck, Sigrid De Keersmaecker, Pieter Monsieurs, Tim Van den Bulcke, Kathleen Marchal (UGent) , Janick Mathys, et al.

(2005) Proceedings of the 16th IFAC world congress.
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- Journal Article
- A1
Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium

Pieter Monsieurs, Sigrid CJ De Keersmaecker, William W Navarre, Martin W Bader, Frank De Smet, Michael McClelland, Ferric C Fang, Bart De Moor, Jos Vanderleyden and Kathleen Marchal (UGent)

(2005) JOURNAL OF MOLECULAR EVOLUTION. 60(4). p.462-474
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- Journal Article
- A1
M@CBETH: a microarray classification benchmarking tool

Nathalie LMM Pochet, Frizo AL Janssens, Frank De Smet, Kathleen Marchal (UGent) , Johan AK Suykens and Bart LR De Moor

(2005) BIOINFORMATICS. 21(14). p.3185-3186
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- Journal Article
- A1
PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability

Johnny Roosen, Kristof Engelen, Kathleen Marchal (UGent) , Janick Mathys, Gerard Griffioen, Elisabetta Cameroni, Johan M Thevelein, Claudio De Virgilio, Bart De Moor and Joris Winderickx

(2005) MOLECULAR MICROBIOLOGY. 55(3). p.862-880
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- Book Chapter
Advances in cluster analysis of microarray data

Qizheng Sheng, Yves Moreau, Frank De Smet, Kathleen Marchal (UGent) and Bart De Moor

(2005) Data analysis and visualization in genomics and proteomics. p.153-173
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- Journal Article
- A1
Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar Typhimurium HilA regulatory protein, including hilA itself

Sigrid CJ De Keersmaecker, Kathleen Marchal (UGent) , Tine LA Verhoeven, Kristof Engelen, Jos Vanderleyden and Corrella S Detweiler

(2005) JOURNAL OF BACTERIOLOGY. 187(12). p.4381-4391
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- Journal Article
- A1
Chemical synthesis of (S)-4,5-dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella Typhimurium

Sigrid CJ De Keersmaecker, Csaba Varszegi, Nadja van Boxel, Lothar W Habel, Kristine Metzger, Ruth Daniels, Kathleen Marchal (UGent) , Dirk De Vos and Jos Vanderleyden

(2005) JOURNAL OF BIOLOGICAL CHEMISTRY. 280(20). p.19563-19568
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- A1
- open access
A novel approach to identifying regulatory motifs in distantly related genomes

Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer (UGent) and Kathleen Marchal (UGent)

(2005) GENOME BIOLOGY. 6(13).
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- Journal Article
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The effects of 1α,25-dihydroxyvitamin D₃ on the expression of DNA replication genes

Guy Eelen, Lieve Verlinden, Mark van Camp, Paul van Hummelen, Kathleen Marchal (UGent) , Bart de Moor, Chantal Mathieu, Geert Carmeliet, Roger Bouillon and Annemieke Verstuyf

(2004) JOURNAL OF BONE AND MINERAL RESEARCH. 19(1). p.133-146
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- Journal Article
- A1
Annotation of the pRhico plasmid of Azospirillum brasilense reveals its role in determining the outer surface composition

Els Vanbleu, Kathleen Marchal (UGent) , Mark Lambrecht, Janick Mathys and Jos Vanderleyden

(2004) FEMS MICROBIOLOGY LETTERS. 232(2). p.165-172
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- A1
Genetic and physical map of the pLAFR1 vector

E Vanbleu, Kathleen Marchal (UGent) and J Vanderleyden

(2004) DNA SEQUENCE. 15(3). p.225-227
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- Journal Article
- A1
Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters

G Dirix, P Monsieurs, B Dombrecht, R Daniels, Kathleen Marchal (UGent) , J Vanderleyden and J Michiels

(2004) PEPTIDES. 25(9). p.1425-1440
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- Miscellaneous
Screening genomes of Gram-positive bacteria for double-glycine-motif-containing peptides

G Dirix, P Monsieurs, Kathleen Marchal (UGent) , J Vanderleyden and J Michiels

(2004) MICROBIOLOGY-SGM. 150(5). p.1121-1126
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- Journal Article
- A1
- open access
In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection

Kathleen Marchal (UGent) , Sigrid De Keersmaecker, Pieter Monsieurs, Nadja van Boxel, Karen Lemmens, Gert Thijs, Jos Vanderleyden and Bart De Moor

(2004) GENOME BIOLOGY. 5(2).
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- Book Chapter
Computational biology and toxicogenomics

Kathleen Marchal (UGent) , Frank De Smet, Kristof Engelen and Bart De Moor

(2004) Predictive toxicology. p.37-85
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- Journal Article
- A1
Differential regulation of the insulin-like growth factor II mRNA-binding protein genes by architectural transcription factor HMGA2

Jan R Brants, Torik AY Ayoubi, Kiran Chada, Kathleen Marchal (UGent) , Wim JM Van de Ven and Marleen MR Petit

(2004) FEBS LETTERS. 569(1-3). p.277-283
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Computational approaches to identify promoters and cis-regulatory elements in plant genomes

Stephane Rombauts (UGent) , Kobe Florquin (UGent) , Magali Lescot (UGent) , Kathleen Marchal (UGent) , Pierre Rouzé (UGent) and Yves Van de Peer (UGent)

(2003) PLANT PHYSIOLOGY. 132(3). p.1162-1176
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MARAN: normalizing micro-array data

Kristof Engelen, Bert Coessens, Kathleen Marchal (UGent) and Bart De Moor

(2003) BIOINFORMATICS. 19(7). p.893-894
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- Journal Article
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Genome-specific higher-order background models to improve motif detection

Kathleen Marchal (UGent) , Gert Thijs, Sigrid De Keersmaecker, Pieter Monsieurs, Bart De Moor and Jos Vanderleyden

(2003) TRENDS IN MICROBIOLOGY. 11(2). p.61-66
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- A1
Bioinformatics: organisms from Venus, technology from Jupiter, algorithms from Mars

Bart De Moor, Kathleen Marchal (UGent) , Janick Mathys and Yves Moreau

(2003) EUROPEAN JOURNAL OF CONTROL. 9(2-3). p.237-278
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- A1
- open access
INCLUSive : a web portal and service registry for microarray and regulatory sequence analysis

Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal (UGent) , Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys and Bart De Moor

(2003) NUCLEIC ACIDS RESEARCH. 31(13). p.3468-70-3470
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- open access
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes

Gert Thijs, Kathleen Marchal (UGent) , Magali Lescot (UGent) , Stephane Rombauts (UGent) , Bart De Moor, Pierre Rouzé (UGent) and Yves Moreau

(2002) JOURNAL OF COMPUTATIONAL BIOLOGY. 9(2). p.447-464
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INCLUSive: INtegrated Clustering, Upstream of sequence retrieval and motif Sampling

Gert Thijs, Yves Moreau, Frank De Smet, Janick Mathys, Magali Lescot (UGent) , Stephane Rombauts (UGent) , Pierre Rouzé (UGent) , Bart De Moor and Kathleen Marchal (UGent)

(2002) BIOINFORMATICS. 18(2). p.331-332
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- A1
- open access
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Magali Lescot (UGent) , Patrice Déhais (UGent) , Gert Thijs, Kathleen Marchal (UGent) , Yves Moreau, Yves Van de Peer (UGent) , Pierre Rouzé (UGent) and Stephane Rombauts (UGent)

(2002) NUCLEIC ACIDS RESEARCH. 30(1). p.325-327
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- Journal Article
- A1
- open access
Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales

Bruno Dombrecht, Kathleen Marchal (UGent) , Jos Vanderleyden and Jan Michiels

(2002) GENOME BIOLOGY. 3(12).
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- Conference Paper
- C1
- open access
Integrating quality-based clustering of microarray data with Gibbs sampling for the discovery of regulatory motifs

Yves Moreau, Gert Thijs, Kathleen Marchal (UGent) , Frank De Smet, Janick Mathys, Magali Lescot (UGent) , Stephane Rombauts (UGent) , Pierre Rouzé (UGent) and Bart De Moor

(2002) JOBIM 2002 : journées ouvertes biologie, informatique, mathématique.

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

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

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

Synthetic multimodal data modelling for data imputation

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

WSI based prediction of TP53 mutations identifies aggressive disease phenotype in prostate cancer

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

Antibiotic cycling affects resistance evolution independently of collateral sensitivity

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

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

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

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

OMEN : network-based driver gene identification using mutual exclusivity

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

Halvade somatic : somatic variant calling with Apache Spark

BLSSpeller to discover novel regulatory motifs in maize

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Pathway and network analysis of more than 2500 whole cancer genomes

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

Integrative pathway enrichment analysis of multivariate omics data

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

Pan-cancer analysis of whole genomes

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

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

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

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

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

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

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

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

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

Sex differences in oncogenic mutational processes

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

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

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

Associating expression and genomic data using co-occurrence measures

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

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

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

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

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

Managing evidence in food safety and nutrition

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

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

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

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

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

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:-

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

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

The evolutionary significance of polyploidy

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