{"id":9275,"date":"2026-07-08T12:36:51","date_gmt":"2026-07-08T10:36:51","guid":{"rendered":"https:\/\/ubc.uu.nl\/?p=9275"},"modified":"2026-07-09T13:26:26","modified_gmt":"2026-07-09T11:26:26","slug":"recent-publications-by-ubc-members-14","status":"publish","type":"post","link":"https:\/\/ubc.uu.nl\/recent-publications-by-ubc-members-14\/","title":{"rendered":"Recent publications by UBC members"},"content":{"rendered":"\t\t
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Below, you can find an overview of publications by UBC principal investigators during the period from February 2026 – July 2026<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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gplasCC: classification and recovery of plasmids from short-read sequencing data for any bacterial species.<\/strong><\/a>
NAR genomics and bioinformatics, 2026
Paganini JA et al. (With Anita Schurch<\/strong>)<\/div>\n
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Regulatory grammar in human promoters uncovered by MPRA-based deep learning.<\/strong><\/a>
Nature, 2026
Barbadilla-Mart\u00ednez L et al. (With Jeroen de Ridder<\/strong>)<\/div>\n
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CAZome comparison in relation to host plant for selected <i>Sordariomycete<\/i> and <i>Dothidiomycete<\/i> plant pathogenic fungi.<\/strong><\/a>
Frontiers in fungal biology, 2026
Kandemir H et al. (With Ronald de Vries<\/strong>)<\/div>\n
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Beyond similarity: Unveiling the distinctive transcriptional regulatory roles of ARA1 in plant biomass utilization by Myceliophthora thermophila and related fungi.<\/strong><\/a>
New biotechnology, 2026
Benocci T et al. (With Ronald de Vries<\/strong>)<\/div>\n
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Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.<\/strong><\/a>
Metabolomics : Official journal of the Metabolomic Society, 2026
Wolthuis JC et al. (With Jeroen de Ridder<\/strong>)<\/div>\n
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Large-scale exome analyses reveal new rare variant contributions in amyotrophic lateral sclerosis.<\/strong><\/a>
Nature genetics, 2026
Hop PJ et al. (With Jan Veldink<\/strong>)<\/div>\n
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Genetically determined ancestry associates with morphological and molecular carotid plaque features.<\/strong><\/a>
Atherosclerosis, 2026
Fahim N et al. (With Sander van der Laan<\/strong>)<\/div>\n
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UV-induced mutations accumulate during early clonal expansion in aneuploid subtypes of pediatric B-cell precursor acute lymphoblastic leukemia.<\/strong><\/a>
Haematologica, 2026
Suurenbroek LC et al. (With Roland Kuiper<\/strong>)<\/div>\n
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The genome-scale sugar metabolic model from Neurospora crassa<\/i> reveals lower gene redundancy than that of Aspergillus niger<\/i>.<\/strong><\/a>
Current research in microbial sciences, 2026
Li J et al. (With Ronald de Vries<\/strong>)<\/div>\n
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Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development.<\/strong><\/a>
eLife, 2026
Bhardwaj V et al. (With Alexander van Oudenaarden<\/strong>)<\/div>\n
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A transcriptomic atlas of conserved responses in mushroom-forming fungi during interaction with competitors.<\/strong><\/a>
Microbiological research, 2026
van Maanen MH et al. (With Robin Ohm<\/strong>)<\/div>\n
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The H3K36me3 methyltransferase SETD2 contributes to PAF1C interactions with RNA Pol II and is required for neuronal differentiation.<\/strong><\/a>
The EMBO journal, 2026
Ambrosi C et al. (With Tuncay Baubec<\/strong>)<\/div>\n
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Machine learning identifies differences between breast milk and formula in the gut microbiome.<\/strong><\/a>
Gut microbiome (Cambridge, England), 2026
Chia Liu T et al. (With Alejandro Lopez Rincon<\/strong>)<\/div>\n
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Structural promiscuity in the human circulatory IgA1 clonal repertoire.<\/strong><\/a>
Proceedings of the National Academy of Sciences of the United States of America, 2026
Rolland AD et al. (With Albert Heck<\/strong>)<\/div>\n
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Structural basis of signal peptide recognition by the signal peptidase complex.<\/strong><\/a>
Nature communications, 2026
Manuel Liaci A et al. (With Friedrich Forster<\/strong>)<\/div>\n
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Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.<\/strong><\/a>
Science advances, 2026
Meijer J et al. (With Bas E. Dutilh<\/strong>)<\/div>\n
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New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi.<\/strong><\/a>
BMC genomics, 2026
P\u00e9rez Gallego R et al. (With Laura Villanueva<\/strong>)<\/div>\n
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Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.<\/strong><\/a>
Bioinformatics (Oxford, England), 2026
Beeloo R et al. (With Bas E. Dutilh<\/strong>)<\/div>\n
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Impact of reducing colistin use on colistin resistance in Escherichia coli <\/em>isolated from humans and poultry in Indonesia (COINCIDE): A protocol for a multisectoral, transdisciplinary One Health study.<\/strong><\/a>
One health (Amsterdam, Netherlands), 2026
Naing SY et al. (With Jaap Wagenaar<\/strong>)<\/p>


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LGL-1 and the RhoGAP protein PAC-1 redundantly polarize the Caenorhabditis elegans embryonic epidermis.<\/strong><\/a>
The Journal of cell biology, 2026
Jarosi\u0144ska OD et al. (With Mike Boxem<\/strong>)<\/p>


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Towards modeling phage therapy.<\/strong><\/a>
PLoS computational biology, 2026
de Boer RJ et al. (With Rob de Boer<\/strong>)<\/p>


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


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


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Expanding the human proteome with microproteins and peptideins.<\/strong><\/a>
Nature, 2026
Deutsch EW et al. (With Sebastiaan van Heesch<\/strong>)<\/p>


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


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


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


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Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma.<\/strong><\/a>
Nature communications, 2026
Steemers AS et al. (With Ruben van Boxtel<\/strong>)<\/p>


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Identification of iso<\/em>-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.<\/strong><\/a>
Applied and environmental microbiology, 2026
Sahonero-Canavesi DX et al. (With Laura Villanueva<\/strong>)<\/div>\n
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Integrating experimental and computational approaches for protein\u2013protein interaction discovery<\/strong><\/a>
nature reviews bioengineering, 2026
Anastasia Rapti et al. (With Alexandre Bonvin<\/strong>)<\/div>\n
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Investigating the relationship between ATP synthase and the TCA cycle by crosslinking mass spectrometry.<\/strong><\/a>
Nature communications, 2026
P\u00e9rez Pa\u00f1eda L et al. (With Albert Heck<\/strong>)<\/div>\n
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Non-cell-autonomous mechanisms of tumor initiation and relapse by chromosomal instability.<\/strong><\/a>
Proceedings of the National Academy of Sciences of the United States of America, 2026
Lafirenze SJA et al. (With Geert Kops<\/strong>)<\/div>\n
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Embrace Open, Collaborative, Discovery-Based Exposomics.<\/strong><\/a>
Environmental science &amp; technology, 2026
Schymanski EL et al. (With Roel Vermeulen<\/strong>)<\/p>\n

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Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.<\/b><\/a>
Nature communications, 2026
<\/span>Magnitov, M.D., van der Weide, R.H.<\/b>, Witvliet, A.F. <\/span>et al.<\/i>  <\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

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, 2026Paganini JA et al. (With Anita Schurch)   Regulatory grammar in human promoters uncovered by MPRA-based deep learning.Nature, […]<\/p>\n","protected":false},"author":94,"featured_media":6628,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_angie_page":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"page_builder":"","_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[398,27,408],"tags":[],"class_list":["post-9275","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-activities","category-highlights","category-news_freestyle"],"acf":[],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2024\/08\/Screenshot-2024-08-15-at-11.48.41.png","_links":{"self":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts\/9275","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/users\/94"}],"replies":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/comments?post=9275"}],"version-history":[{"count":19,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts\/9275\/revisions"}],"predecessor-version":[{"id":9341,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts\/9275\/revisions\/9341"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/media\/6628"}],"wp:attachment":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/media?parent=9275"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/categories?post=9275"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/tags?post=9275"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}