Author

Meine D. Boer

Utrecht UniversityORCID 0009-0009-4620-6964Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 2 Assay:whole-genome sequencing· 2 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Research Focus:imputation· 1 Approach:statistical model· 1

Frequent Co-Authors

Bas E. DutilhiD· 2 shared Andreas Florian HaasiD· 1 shared Aristeidis LitosiD· 1 shared Chrats MelkonianiD· 1 shared Daniel Rios GarzaiD· 1 shared Erica Padial· 1 shared Haris ZafeiropoulosiD· 1 shared José Luis LópeziD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersGenomics

Bas E. DutilhORCID

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2 papers

Recent·Most cited

GenomicsbioRxivPreprintApr 27, 2026

Widespread synchronization of codon usage in functionally related genes

José Luis López, Aristeidis Litos, Malte Siemers…·Bas E. Dutilh

The paper identifies synchronized codon usage evolution between functionally related genes across bacterial genomes, revealing new functional associations.

DOI 10.64898/2025.12.10.693408

bacteria (other)whole-genome sequencing

𝕏 PostBluesky

BioinformaticsiSciencePeer-reviewedNov 7, 2024

Improving genome-scale metabolic models of incomplete genomes with deep learning

Meine D. Boer, Chrats Melkonian, Haris Zafeiropoulos…·Bas E. Dutilh

This paper introduces DNNGIOR, a deep learning method to improve genome-scale metabolic models of incomplete genomes by imputing missing reactions based on reaction frequency and phylogenetic distance.

14 citations

bacteria (other)whole-genome sequencing

𝕏 PostBluesky