Author

Dirk Valkenborg

Hasselt UniversityORCID 0000-0002-1877-3496Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Assay:metabolomics· 2 Research Focus:batch correction / integration· 1 Research Focus:database / resource· 1 Research Focus:deconvolution· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Kris LaukensiD· 3 shared Pieter MeysmaniD· 3 shared Bart CuypersiD· 2 shared Wout BittremieuxiD· 2 shared Aida MrziciD· 1 shared Anna GambiniD· 1 shared Axel-Jan RousseauiD· 1 shared Basudha KhanaliD· 1 shared

Activity by Year

2020-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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3 shared papersBioinformatics

Kris LaukensORCID

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Author profile →

5 papers

Recent·Most cited

A new paradigm for biological sequence retrieval inspired by natural language processing and database research

Axel-Jan Rousseau, Sébastien Lemal, Yegor Korovin, Georgios Triantopoulos, Ingrid Brands, Maxim Biemans, Dirk Van Hyfte, Dirk Valkenborg

The paper introduces a new sequence retrieval method using pattern mining from cross-species omic data, showing it can retrieve homologous sequences with 50% identity without alignment.

bioRxiv · Nov 7, 2023 · PreprintBioinformatics

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

Bart Cuypers, Pieter Meysman, Ionas Erb, Wout Bittremieux, Dirk Valkenborg, Geert Baggerman, Inge Mertens, Shyam Sundar, Basudha Khanal, Cédric Notredame, Jean‐Claude Dujardin, Malgorzata A. Domagalska, Kris Laukens

This study uses multi-omics analysis to show that aneuploidy in Leishmania causes proportional changes in transcript and protein abundance, with post-transcriptional regulation compensating for some effects.

PLoS Pathogens · Sep 23, 2022Peer-reviewedSystems Biology

Constrained standardization of count data from massive parallel sequencing

Joris Van Houtven, Bart Cuypers, Pieter Meysman, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg

This paper evaluates and adapts the CONSTANd normalization method for use with count data from sequencing, showing its efficiency and ability to remove bias across different experimental conditions.

Journal of Molecular Biology · Mar 29, 2021Peer-reviewedBioinformatics

Masserstein: robust linear deconvolution by optimal transport

Michał Aleksander Ciach, Błażej Miasojedow, Grzegorz Skoraczyński, Szymon Majewski, Michał Piotr Startek, Dirk Valkenborg, Anna Gambin

The paper introduces a linear deconvolution method using optimal transport to improve accuracy in mass spectrometry by reducing sensitivity to measurement inaccuracies.

bioRxiv · Jun 2, 2020 · PreprintBioinformatics

MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra

Youzhong Liu, Aida Mrzic, Pieter Meysman, Thomas De Vijlder, Edwin P. Romijn, Dirk Valkenborg, Wout Bittremieux, Kris Laukens

MESSAR recommends metabolite substructures from tandem mass spectra without requiring predefined metabolite candidates.

PLoS ONE · Jan 16, 2020Peer-reviewedBioinformatics