Deep Seq: Next Generation Sequencing Facility

Publications

2025

  1. Deacon, S. et al. (2025) ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor  diagnosis. Neuro-Oncol.27, 2035–2046.
  2. Gopaulchan, D. et al. (2025) A defined microbial community reproduces attributes of fine flavour chocolate fermentation. Nat. Microbiol.10, 2130–2152.
  3. McClure, C. P. et al. (2025) ‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2. Microb. Genomics11, 001451.
  4. Smith KE et al. (2025) An ecological, phenotypic, and genomic survey of duckweeds with their associated aquatic environments in the United Kingdom. AoB PLANTS17, plaf018.
  5. Cahyani, I. et al. (2025) An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride. Genome Res.35, 1154–1166.
  6. Patel, A. et al. (2025) Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors. Nat. Med.31, 1567–1577.
  7. Munro, R. et al. (2025) Enhancing nanopore adaptive sampling for PromethION using readfish at scale. Genome Res.35, 877–885.
  8. Crowley, D. et al. (2025) Programming of pluripotency and the germ line co-evolved from a Nanog ancestor.Cell Rep.44, 115396.
  9. Nash, A. et al. (2025) An evaluation of spraying as a delivery method for human mesenchymal stem cells suspended in low-methyl pectin solutions. Stem Cell Res. Ther.16, 246.

 

2024

  1. Morgan, H. L. et al. (2024) Paternal undernutrition and overnutrition modify semen composition and preimplantation embryo developmental kinetics in mice. BMC Biol. 22, 207.
  2. Bray SM et al. (2024) Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids. Cell Rep. 43, 114576.
  3. Simpson, L. et al. (2024) A single-cell atlas of pig gastrulation as a resource for comparative embryology. Nat. Commun. 15, 5210.
  4. Khoshkerdar, A. et al. (2024) Sub-Optimal Paternal Diet at the Time of Mating Disrupts Maternal Adaptations to Pregnancy in the Late Gestation Mouse. Nutrients 16, 1879.
  5. Hämälä, T. et al. (2024) Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat. Commun. 15, 5377.
  6. Munro, R., Wibowo, S., Payne, A. & Loose, M. (2024) Icarust, a real-time simulator for Oxford Nanopore adaptive sampling. Bioinformatics 40, btae141.
  7. Ho, W. K. et al. (2024) A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat. Commun. 15, 1901.

 

2023

  1. Brunner, F. S. et al. (2023) Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England. Water Res.247, 120804. 
  2. Apaa, T. et al. (2023) Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) Minacovirus. J. Gen. Virol.104, 001917.
  3. Weilguny, L. et al. (2023) Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nat. Biotechnol.41, 1018–1025.
  4. Apaa, T. et al. (2023) Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology. J. Gen. Virol.104, 001859.
  5. Child, H. T. et al. (2023) Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing. PLOS ONE18, e0284211.
  6. Bassano, I. et al. (2023) Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples. Microb. Genomics9, 001917.
  7. Blanchard, A. M. et al. (2023) Genome Reference Assembly for Bottlenecked Southern Australian Koalas. Genome Biol. Evol.15, evac176.
  8. Maciel-Guerra, A. et al. (2023) Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. ISME J.17, 21–35.
  9. Munro, R. et al. (2023) A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing. Front. Genet.14, 1138582.
  10. Edwards, A. et al. (2023) Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nat. Commun.14, 876

 

2022

  1. Tarlinton, R.E. et al. (2022) Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution. J. Gen. Virol. 103(6):001749
  2. Ashton, G.D. et al. (2022) Use of Bulk Segregant Analysis for Determining the Genetic Basis of Azole Resistance in the Opportunistic Pathogen Aspergillus fumigatus. Front. Cell Infect. Microbiol. 12:841138
  3. Patel, A. et al. (2022) Rapid-CNS2: rapid comprehensive adaptive nanopore-sequencing of CNS tumors, a proof-of-concept study. Acta Neuropathol. 143(5):609–612
  4. Rodriguez-Algarra, F. et al. (2022) Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. Genome Biol. 23(1):54
  5. Munro, R. et al. (2022) minoTour, real-time monitoring and analysis for nanopore sequencers. Bioinformatics. 38(4):1133–1135
  6. Francis, R.V. et al. (2022) The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. J. Infect. Dis. 225(1):10–18

 

2021

  1. Payne, A. et al. (2021) Barcode aware adaptive sampling for GridION and PromethION Oxford Nanopore sequencers. bioRxiv
  2. Tang, J.W. et al. (2021) The UK Leicester COVID-19 'exceedance' May–July 2020: An analysis of hospitalised cases. J. Infect. 83(1):e5–e7
  3. Mead, D. et al. (2021) The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758. Wellcome Open Res. 6:112
  4. Payne, A. et al. (2021) Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nat. Biotechnol. 39(4):442–450
  5. Chappell, J.G. et al. (2021) Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. J. Gen. Virol. 102(6):001595

 

2020

  1. Tighe, P.J. et al. (2020) Potent anti-SARS-CoV-2 Antibody Responses are Associated with Better Prognosis in Hospital Inpatient COVID-19 Disease. medRxiv
  2. Outhred, A.C. et al. (2020) Extensive homoplasy but no convergent evolution of repeat numbers at MIRU loci in modern Mycobacterium tuberculosis lineages. Front. Public Health. 8:455
  3. Miga, K.H. et al. (2020) Telomere-to-telomere assembly of a complete human X chromosome. Nature. 585(7823):79–84
  4. Grillo, M. et al. (2020) Stat3 oxidation-dependent regulation of gene expression impacts on developmental processes and involves cooperation with Hif-1α. PLoS ONE. 15(12):e024425

 

2019

  1. Workman, R.E. et al. (2019) Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat. Methods. 16(12):1297–1305
  2. Payne, A. et al. (2019) BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics. 35(13):2193–2198

 

2018 

Publications from 2018 and beyond

  1. Brown WR, Thomas G, Lee NC, Blythe M, Liti G, Warringer J, Loose MW. (2014) Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A. 2014  4;111(5):1903-8.
  2. Moreton J, Malla S, Aboobaker AA, Tarlinton RE, Emes RD (2014) Characterisation of the horse transcriptome from immunologically active tissues. PeerJ. Accepted for publication.
  3. Amer AHA, Wall RJ, Malla S, Sang F, Aboobaker A, Avery SV, Mellor IR, Rose M, Rowlands CJ, Grant TW, Bell DR (2014) Genes involved in the induction of liver growth by peroxisome proliferators. Toxicology research. Accepted for publication. 
  4. Hawkins, M., Malla, S., Blythe, M.J., Nieduszynski, C. A., Allers, T. (2013) Accelerated growth in the absence of DNA replication origins. Nature. Nov 28; 503 (7477): 544-7
  5. Hamilton, H.M., Wilson, R., Blythe, M., Nehring, R.B., N.C., Fonville, Louis, E.J., Rosenberg, S. M. (2013) Thymineless death is inhibited by CsrA in Escherichia coli lacking the SOS response. DNA Repair 12: 993–999.
  6. Mahdavi J, Royer PJ, Sjölinder HS, Azimi S, Self T, Stoof J, Wheldon LM, Brännström K, Wilson R, Moreton J, Moir JW, Sihlbom C, Borén T, Jonsson AB, Soultanas P, Ala'aldeen DA. (2013) Pro-inflammatory cytokines can act as intracellular modulators of commensal bacterial virulence. Open Biol. Oct 9; 3(10): 130048.
  7. Müller CA, Hawkins M, Retkute R, Malla S, Wilson R, Blythe MJ, Nakato R, Komata M, Shirahige K, de Moura AP, Nieduszynski CA. (2013)  The dynamics of genome replication using deep sequencing.  Nucleic Acids Res. Jan; 42(1): e3
  8. Jaber-Hijazi F, Lo PJ, Mihaylova Y, Foster JM, Benner JS, Tejada-Romero B, Chen C, Malla S, Solana J, Ruzov A, Aboobaker AA (2013) Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation. Dev Biol. Dec 1; 384(1): 141-53
  9. Ries L, Pullan ST, Delmas S, Malla S, Blythe MJ, Archer DB (2013) Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. BMC Genomics. Aug 9; 14: 541
  10. Kamila D, Blythe MJ, Malla S, Diane GP, Alessandro G, Pavan P, Moles A, Snart C, Ryder T,  Ortori CA, Barrett DA, Schuster E, Stöger R (2013) Transient exposure to low levels of insecticide affects metabolic networks of honeybee larvae. Plos One.  Jul 2; 8(7): e68191
  11. Novodvorska M,  Hayer K,  Pullan ST, Wilson R, Blythe MJ, Hein S, Stratford M, Archer DB (2013) Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing.  BMC Genomics. 14:246.
  12. Liti G, Nguyen AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Calas FD, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, and Nieduszynski CA (2013) High Quality de novo Sequencing and Assembly of the Saccharomyces arboricolus genome.  BMC Genomics. Jan 31; 14: 69.
  13. Brown K, Moreton J, Malla S, Aboobaker AA, Emes RD, Tarlinton RE (2012) Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing. Virology. 433(1): 55-63.
  14. Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A, Tucker GA and Archer DB (2012) Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genetics 8(8): e1002875.
  15. Blythe M, Malla S, Everall R, Shih Y-h, Lemay V, Moreton J, Wilson R and Aboobaker AA (2012) High Through-Put Sequencing of the Parhyale hawaiensis mRNAs and microRNAs to Aid Comparative Developmental Studies. PLoS ONE 7(3): e33784. 
  16. Solana J, Kao D, Mihaylova Y, Malla S, Wilson R, Aboobaker AA, (2011) Defining the molecular profile of planarian pluropotent stem cells using a combinatorial RNA-seq, RNAi and irradiation approach. Genome Biology, 22; 13(3): R19 
  17. Hooton SPT, Timms AR, Rowsell J, Wilson R and Connerton IF (2011) Salmonella Typhimurium-specific bacteriophage PhiSH19 and the origins of species specificity in the Vi01-like phage family. Virology Journal 8: 498.
  18. Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans, D, Jowett, J, Hall, A, Lemay, V, Lam, S and Aboobaker AA, (2010) A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology. PLoS One 5(12).

 

 

 

Deep Seq

Centre for Genetics and Genomics
The University of Nottingham
Queen's Medical Centre, Nottingham, NG7 2UH

telephone: +44 (0) 115 823 0363
email: deep.seq@nottingham.ac.uk