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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: 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
..., Carlsson AS, Ceplitis A, Crossa J, et al. 2024. Genomic selection in plant 567 breeding: Key factors shaping two decades of progress. Molecular Plant 17: 552–578. 568 Azodi CB, Tang J, Shiu S-H. 2020. Opening the Black Box: Interpretable Machine Learning for 569 Geneticists. Trends in Genetics 36: 442...
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Research: Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment
- Theodore Gouliouris,
- Kathy E. Raven,
- Danesh Moradigaravand,
- Catherine Ludden,
- Francesc Coll,
- Beth Blane,
- Plamena Naydenova,
- Carolyne Horner,
- Nicholas M. Brown,
- Jukka Corander,
- Direk Limmathurotsakul,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. April 2019 29: 626-634; Published in Advance March 21, 2019, doi:10.1101/gr.232629.117
...Copenhagen, Denmark. J Antimicrob Chemother 72: 40–47. doi:10.1093/jac/dkw360 ↵Raven KE, Reuter S, Reynolds R, Brodrick HJ, Russell JE, Török ME, Parkhill J, Peacock SJ. 2016. A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland. Genome Res 26: 1388...
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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: 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: 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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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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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...occurring in repetitive regions. SVs and TRs are inherently interconnected, as many SVs involve alterations in TR regions, such as expansions or contractions of repeat units. Recognizing this overlap is crucial for a comprehensive understanding of genomic variation. By analyzing SVs and TRs together, we can...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
..., University of Exeter, Penryn, TR10 9FE, United Kingdom ↵4 These authors contributed equally to this work. Corresponding authors: aujilongm@birc.au.dk, trine.bilde@bio.au.dk, mheide@birc.au.dkAbstractIn cooperatively breeding social animals, a few individuals account for all reproduction. In some taxa...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...

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