Ghent University Academic Bibliography

Journal Article
A1
open access

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

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

(2023) MICROBIAL GENOMICS. 9(1).

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Journal Article
A1
open access

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

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

(2023) BMC GENOMICS. 24.

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Journal Article
A1
open access

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

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

(2022) FOODS. 11(21).

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Journal Article
A2
open access

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

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

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

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Journal Article
A1
open access

Antibiotic cycling affects resistance evolution independently of collateral sensitivity

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

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

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Journal Article
A1
open access

Halvade somatic : somatic variant calling with Apache Spark

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

(2022) GIGASCIENCE. 11.

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Miscellaneous
open access

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

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

(2022)

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Journal Article
A1
open access

BLSSpeller to discover novel regulatory motifs in maize

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

(2022) DNA RESEARCH. 29(4).

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

Taher Mohasseli, Razgar Seyed Rahmani (UGent) , 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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Journal Article
A1
open access

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

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

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

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Journal Article
A1
open access

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

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

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

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Journal Article
A1
open access

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

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

(2021) ISCIENCE. 24(7).

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Journal Article
A1
open access

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

(2021) MICROORGANISMS. 9(4).

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Journal Article
A1
open access

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 (UGent) , 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.

Academic Bibliography

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

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

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

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

Antibiotic cycling affects resistance evolution independently of collateral sensitivity

Halvade somatic : somatic variant calling with Apache Spark

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

BLSSpeller to discover novel regulatory motifs in maize

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

OMEN : network-based driver gene identification using mutual exclusivity

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

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

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

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

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

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