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Jan 2025
Golubova D, Salmon M, Su H, Tansley C, Kaithakottil G, Linsmith G, Schudoma S, Swarbreck D, O’Connell M, Patron N
Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids inCalendula officinalis(pot marigold)
PrePrint
Publishers version: doi: 10.1101/2025.01.11.632544
Jan 2025
Bloomfield SJ, Hildebrand F, Zomer AL, Palau R, Mather AE
Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications
Journal Article
Publishers version: doi: 10.1099/mgen.0.001337
Jan 2025
Lee CZ, Worsley SF, Davies CS, Silan E, Burke T, Komdeur J, Hildebrand F, Dugdale HL, Richardson DS
Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance
Journal Article
Publishers version: doi: 10.1093/ismeco/ycaf008
Jan 2025
Hill R, McGowan J, Brabcová V, McTaggart S, Irish N, Barker T, Knitlhoffer V, Lucchini S, Baker K, Catchpole L, Watkins C, Gharbi K, Kaithakottil G, Tracey A, Wood JMD, Tomšovský M, Baldrian P, Swarbreck D, Hall N
Nuclear and Mitochondrial Genome Assemblies for the Endangered Wood-Decaying Fungus Somion occarium
Journal Article
Publishers version: doi: 10.1093/gbe/evaf003
Jan 2025
Diaz M, Aird H, Le Viet T, Gutiérrez AV, Larke-Mejia N, Omelchenko O, Moragues-Solanas L, Fritscher J, Som N, McLauchlin J, Hildebrand F, Jørgensen F, Gilmour M
Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes
Journal Article
Publishers version: doi: 10.1016/j.fm.2024.104649
Dec 2024
Feng S, Huang L, Pournara AV, Huang Z, Yang X, Zhang Y, Brazma A, Shi M, Papatheodorou I, Miao Z
Alleviating batch effects in cell type deconvolution with SCCAF-D
Journal Article
Publishers version: doi: 10.1038/s41467-024-55213-x
Dec 2024
Nasr E, Amato P, Bernt M, Bhardwaj A, Blankenberg D, Brites D, Cumbo F, Do K, Ferrari E, Griffin TJ, Gruening B, Hiltemann S, Hyde CJ, Jagtap P, Mehta S, Métris KL, Momin S, Oba A, Pavloudi C, Pechlivanis N, Péguilhan R, Price GR, Psomopoulos F, Rosic N, Schatz MC, Schiml VC, Siguret C, Soranzo N, Stubbs A, Van Heusden P, Vohra M, microGalaxy Community, Zierep P, Batut B
The Microbiology Galaxy Lab: A community-driven gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data
PrePrint
Publishers version: doi: 10.1101/2024.12.23.629682
Dec 2024
Rayner T, Saalbach G, Vickers M, Paajanen P, Martins C, Wouters RHM, Chinoy C, Mulholland F, Bal M, Isaac P, Novak P, Macas J, Ellis N, Steuernagel B, Domoney C
Rebalancing the seed proteome following deletion of vicilin-related genes in pea (Pisum sativum L.)
Journal Article
Publishers version: doi: 10.1093/jxb/erae518
Dec 2024
Long KA, Lister A, Jones MRW, Adamski NM, Ellis RE, Chedid C, Carpenter SJ, Liu X, Backhaus AE, Goldson A, Knitlhoffer V, Pei Y, Vickers M, Steuernagel B, Kaithakottil GG, Xiao J, Haerty W, Macaulay IC, Uauy C
Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution
PrePrint
Publishers version: doi: 10.1101/2024.12.19.629411
Dec 2024
Wright J, Baker K, Barker T, Catchpole L, Durrant A, Fraser F, Gharbi K, Harrison C, Henderson S, Irish N, Kaithakottil G, Leitch IJ, Li J, Lucchini S, Neve P, Powell R, Rees H, Swarbreck D, Watkins C, Wood J, McTaggart S, Hall A, MacGregor D
Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis
Journal Article
Publishers version: doi: 10.1038/s41597-024-04222-y
Dec 2024
McGowan J, Richards TA, Hall N, Swarbreck D
Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates
Journal Article
Publishers version: doi: 10.1371/journal.pgen.1011512
Dec 2024
Bottery MJ, van Rhijn N, Chown H, Rhodes JL, Celia-Sanchez BN, Brewer MT, Momany M, Fisher MC, Knight CG, Bromley MJ
Elevated mutation rates in multi-azole resistant Aspergillus fumigatus drive rapid evolution of antifungal resistance
Journal Article
Publishers version: doi: 10.1038/s41467-024-54568-5
Dec 2024
Gómez-Pérez D, Keller A
Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction
PrePrint
Publishers version: doi: 10.1101/2024.12.07.627346
Dec 2024
Kidenya BR, Mboowa G, Sserwadda I, Kanyerezi S, Nakafu E, Akaro IL, Mkinze B, Joloba ML, Seni J
Whole genome-based characterization of extended-spectrum β-lactamase-producing Enterobacter cloacae from orthopedic patients and environment of a tertiary referral hospital in Tanzania
Journal Article
Publishers version: doi: 10.1016/j.nmni.2024.101486
Dec 2024
Collí-Dulá RC, Papatheodorou I
Single-cell RNA sequencing offers opportunities to explore the depth of physiology, adaptation, and biochemistry in non-model organisms exposed to pollution
Journal Article
Publishers version: doi: 10.1016/j.cbd.2024.101339
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