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Resource: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Sandra Reuter,
- M. Estée Török,
- Matthew T.G. Holden,
- Rosy Reynolds,
- Kathy E. Raven,
- Beth Blane,
- Tjibbe Donker,
- Stephen D. Bentley,
- David M. Aanensen,
- Hajo Grundmann,
- Edward J. Feil,
- Brian G. Spratt,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. February 2016 26: 263-270; Published in Advance December 15, 2015, doi:10.1101/gr.196709.115
...applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) s drawn from England, Northern Ireland...
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Research: A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland
- Kathy E. Raven,
- Sandra Reuter,
- Rosy Reynolds,
- Hayley J. Brodrick,
- Julie E. Russell,
- M. Estée Török,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. October 2016 26: 1388-1396; Published in Advance August 15, 2016, doi:10.1101/gr.204024.116
...-adapted Enterococcus faecalis lineages. Nat Microbiol 1: 15033. Reuter S, TörökME, HoldenMTG, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H, et al. 2016. Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland. Genome Res 26: 263...
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Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...spRefine denoises and imputes spatial1 transcriptomics with a reference-free framework2 powered by genomic language model3 Tianyu Liu1,2, Tinglin Huang3, Wengong Jin4,5, Tinyi Chu2, Rex4 Ying3, Hongyu Zhao1,2*5 1Interdepartmental Program in Computational Biology &6 Bioinformatics, Yale University...
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Research: Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland
- Danesh Moradigaravand,
- Christine J. Boinett,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2016 26: 1101-1109; Published in Advance July 18, 2016, doi:10.1101/gr.205245.116
....1101/gr.205245.116 genome;gr.205245.116 1088-9051 Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland Moradigaravand et al. Emergence of MDR clones Recent independent emergence of multiple multidrug-resistant Serratia marcescens...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...1986 under the UK Home Office license PFF8CC5BE and were approved by the ethics 556 committee at the University of Aberdeen, Scotland, United Kingdom. 557 Stimulation of fish with viral mimic 558 Poly I:C (Sigma, P1530) was diluted to 5 mg/mL in PBS, aliquoted and stored at -20 °C. 559 Prior to being...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...of simulated datasets to systematically analyze the impact of various genetic parameters on 90 the prediction accuracy of different ML approaches in genomics. Building on this analysis, 91 ML was conducted with a focus on biological characteristics and hyperparameter optimization, 92 resulting in further...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...such as arithmetic coding is used to convert the data into a compressed bitstream (Mahoney 2000). Following this line, “DeepZip” (Goyal et al. 2018) estimated the probabilities by processing genomic sequences with gated recurrent units (GRUs) and long short-term memory units (LSTMs). Mahoney (2005) introduced...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...with varying degrees of true heritability, increasing from left to right. Heritability estimation using GREML and LDSC methods, after correcting for recent population structure using both approaches, is shown, along with display of average phenotype values in each administrative county in the United Kingdom...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
...Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom; 3Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7LG, United Kingdom ↵4 These authors contributed equally to this work. Corresponding author: shorsfield...
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