Recent publications by UBC members

08 July 2026

Recent publications by UBC members

Below, you can find an overview of publications by UBC principal investigators during the period from February 2026 – July 2026

gplasCC: classification and recovery of plasmids from short-read sequencing data for any bacterial species.
NAR genomics and bioinformatics, 2026
Paganini JA et al. (With Anita Schurch)

Regulatory grammar in human promoters uncovered by MPRA-based deep learning.
Nature, 2026
Barbadilla-Martínez L et al. (With Jeroen de Ridder)

CAZome comparison in relation to host plant for selected <i>Sordariomycete</i> and <i>Dothidiomycete</i> plant pathogenic fungi.
Frontiers in fungal biology, 2026
Kandemir H et al. (With Ronald de Vries)

Beyond similarity: Unveiling the distinctive transcriptional regulatory roles of ARA1 in plant biomass utilization by Myceliophthora thermophila and related fungi.
New biotechnology, 2026
Benocci T et al. (With Ronald de Vries)

Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.
Metabolomics : Official journal of the Metabolomic Society, 2026
Wolthuis JC et al. (With Jeroen de Ridder)

Large-scale exome analyses reveal new rare variant contributions in amyotrophic lateral sclerosis.
Nature genetics, 2026
Hop PJ et al. (With Jan Veldink)

Genetically determined ancestry associates with morphological and molecular carotid plaque features.
Atherosclerosis, 2026
Fahim N et al. (With Sander van der Laan)

UV-induced mutations accumulate during early clonal expansion in aneuploid subtypes of pediatric B-cell precursor acute lymphoblastic leukemia.
Haematologica, 2026
Suurenbroek LC et al. (With Roland Kuiper)

The genome-scale sugar metabolic model from Neurospora crassa reveals lower gene redundancy than that of Aspergillus niger.
Current research in microbial sciences, 2026
Li J et al. (With Ronald de Vries)

Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development.
eLife, 2026
Bhardwaj V et al. (With Alexander van Oudenaarden)

A transcriptomic atlas of conserved responses in mushroom-forming fungi during interaction with competitors.
Microbiological research, 2026
van Maanen MH et al. (With Robin Ohm)

The H3K36me3 methyltransferase SETD2 contributes to PAF1C interactions with RNA Pol II and is required for neuronal differentiation.
The EMBO journal, 2026
Ambrosi C et al. (With Tuncay Baubec)

Machine learning identifies differences between breast milk and formula in the gut microbiome.
Gut microbiome (Cambridge, England), 2026
Chia Liu T et al. (With Alejandro Lopez Rincon)

Structural promiscuity in the human circulatory IgA1 clonal repertoire.
Proceedings of the National Academy of Sciences of the United States of America, 2026
Rolland AD et al. (With Albert Heck)

Structural basis of signal peptide recognition by the signal peptidase complex.
Nature communications, 2026
Manuel Liaci A et al. (With Friedrich Forster)

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.
Science advances, 2026
Meijer J et al. (With Bas E. Dutilh)

New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi.
BMC genomics, 2026
Pérez Gallego R et al. (With Laura Villanueva)

Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.
Bioinformatics (Oxford, England), 2026
Beeloo R et al. (With Bas E. Dutilh)

Impact of reducing colistin use on colistin resistance in Escherichia coli isolated from humans and poultry in Indonesia (COINCIDE): A protocol for a multisectoral, transdisciplinary One Health study.
One health (Amsterdam, Netherlands), 2026
Naing SY et al. (With Jaap Wagenaar)

LGL-1 and the RhoGAP protein PAC-1 redundantly polarize the Caenorhabditis elegans embryonic epidermis.
The Journal of cell biology, 2026
Jarosińska OD et al. (With Mike Boxem)

Towards modeling phage therapy.
PLoS computational biology, 2026
de Boer RJ et al. (With Rob de Boer)

Data-driven causal structure discovery to generate causal hypotheses and strengthen causal inference in exposome studies.
Environment international, 2026
Kakhaia S et al. (With Roel Vermeulen)

Untargeted metabolomic profiling of childhood asthma: An exploratory analysis of anthropogenic chemicals and the serum metabolome.
Environmental epidemiology (Philadelphia, Pa.), 2026
Oosterwegel MJ et al. (With Roel Vermeulen)

Expanding the human proteome with microproteins and peptideins.
Nature, 2026
Deutsch EW et al. (With Sebastiaan van Heesch)

Genetic basis of the circle of Willis characteristics in the healthy and intracranial aneurysm population.
European journal of human genetics : EJHG, 2026
Bakker MK et al. (With Ynte Ruigrok)

DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.
Communications biology, 2026
Xu X et al. (With Alexandre Bonvin)

Gene expression profiles of carotid plaques differ between patients with amaurosis fugax and those with cerebral transient ischemic attack or stroke.
Cardiovascular research, 2026
Lan T et al. (With Michal Mokry)

Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma.
Nature communications, 2026
Steemers AS et al. (With Ruben van Boxtel)

Identification of iso-diabolic acid-based tetraester and mixed ether/ester membrane-spanning lipids in members of the Bacillota provides insight into the biosynthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
Applied and environmental microbiology, 2026
Sahonero-Canavesi DX et al. (With Laura Villanueva)

Integrating experimental and computational approaches for protein–protein interaction discovery
nature reviews bioengineering, 2026
Anastasia Rapti et al. (With Alexandre Bonvin)

Investigating the relationship between ATP synthase and the TCA cycle by crosslinking mass spectrometry.
Nature communications, 2026
Pérez Pañeda L et al. (With Albert Heck)

Non-cell-autonomous mechanisms of tumor initiation and relapse by chromosomal instability.
Proceedings of the National Academy of Sciences of the United States of America, 2026
Lafirenze SJA et al. (With Geert Kops)

Embrace Open, Collaborative, Discovery-Based Exposomics.
Environmental science & technology, 2026
Schymanski EL et al. (With Roel Vermeulen)

Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.
Nature communications, 2026
Magnitov, M.D., van der Weide, R.H., Witvliet, A.F. et al.