We have a funded PhD opportunity available through the Horsebet levy racing board.
Investigating cellular heterogeneity in tendon homeostasis and aging using single cell proteomics.
Deadline is 31st July. Project is a collaboration between the Peffers, Emmott and Thorpe labs on equine tendons funded by the HL.Start Oct 2026.
Funding:Fully funded for tuition fees, stipend and bench fees for a UK citizen. They may be a vet or none vet.3 year studentship funded by The Horserace Betting Levy Board.
Click here for more details on Findaphd.com
If you have queries on the above project, in the first instance please query Prof. Peffers (Prof. Peffers).
We also have multiple positions advertised on FindaPhd for students with access to their own funding for PhD studies, i.e. graduate studies loan, or international applicants who may have access to funding from their home country. These cover single-cell biology, viral proteases, antivirals, and viral post-translational modifications. Please click on the headings to expand.
Understanding post-translational modifications during viral infection
In this project, you will be working to understand how viruses such as coronaviruses, caliciviruses and picornaviruses interact with infected cells, with a focus on post-translational modifications. You will learn molecular virology, cell culture assays, and LC-MS/MS proteomic methods alongside bioinformatic analysis in R.
RNA viruses represent major pathogens of animals and humans, including SARS-CoV-2, norovirus, and pathogens with pandemic potential such as MERS-CoV and ‘Disease X’. Positive-sense RNA viruses, such as those above, replicate by generating a long polyprotein that is post-translationally cleaved by viral and in some cases cellular proteases into various fully- and partially-cleaved forms that come together to regulate viral infection. An additional layer of regulation can come from post-translational modification of viral proteins, such as phosphorylation, methylation or nucleotidylation. In this project you will build on and extend the groups extensive data to characterise post-translational modifications of viral and cellular proteins throughout positive-sense RNA virus infection, and characterise the pro- and antiviral roles they play, and if they serve a regulatory purpose in the viral life cycle.
There is flexibility in how this project develops, with two key directions this project can go – the viral characterisation aspect, or developing LC-MS/MS methods to better characterise rare PTMs. In the former case this would suit candidates with prior virology experience, and in the latter case with prior LC-MS/MS experience.
You will be based in Ed Emmott’s lab, part of the Centre for Proteome Research, and the Department of Biochemistry, Cell & Systems Biology at the University of Liverpool (https://www.liverpool.ac.uk/people/edward-emmott, https://emmottlab.org/), with access to cutting-edge equipment including a cellenONE for single-cell sample preparation, containment level 3 laboratories, and the latest generation Orbitrap Astral Zoom for mass spectrometry analysis.
References
1. Meyer B, Chiaravalli J, Gellenoncourt S, Brownridge P, Bryne DP, Daly LA, Grauslys A, Walter M, Agou F, Chakrabarti LA, Craik CS, Eyers CE, Eyers PA, Gambin Y, Jones AR, Sierecki E, Verdin E, Vignuzzi M, Emmott E. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun. 2021 Sep 21;12(1):5553. doi: 10.1038/s41467-021-25796-w. PMID: 34548480; PMCID: PMC8455558.
2. Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, Kharchenko P, Koller A, Slavov N. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 2021 Jan 27;22(1):50. doi: 10.1186/s13059-021-02267-5. PMID: 33504367; PMCID: PMC7839219.
3. Petelski AA, Emmott E, Leduc A, Huffman RG, Specht H, Perlman DH, Slavov N. Multiplexed single-cell proteomics using SCoPE2. Nat Protoc. 2021 Dec;16(12):5398-5425. doi: 10.1038/s41596-021-00616-z. Epub 2021 Oct 29. PMID: 34716448; PMCID: PMC8643348.
4. Huffman RG, Leduc A, Wichmann C, Di Gioia M, Borriello F, Specht H, Derks J, Khan S, Khoury L, Emmott E, Petelski AA, Perlman DH, Cox J, Zanoni I, Slavov N. Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. Nat Methods. 2023 May;20(5):714-722. doi: 10.1038/s41592-023-01830-1. Epub 2023 Apr 3. PMID: 37012480; PMCID: PMC10172113.
Single-cell proteomic analysis of RNA virus infections
In this project, you will be working to understand how viruses such as coronaviruses, caliciviruses and picornaviruses interact with infected cells, with a focus on single-cell proteomic studies and antiviral resistance. You will learn molecular virology, cell culture assays, and LC-MS/MS proteomic methods alongside bioinformatic analysis in R.
While we know individuals can respond very differently to the same viral infection, single-cell studies have shown this is even the case for different cells within the same infected individual. Single cell virology approaches which have traditionally employed microscopy, FACS, microfluidics or scRNAseq have been characterising this process, but often require either modification of the virus to express a reporter gene (e.g. GFP) or provide information only on RNA expression. For viruses whose replication is regulated by post-translational protein modfications, e.g. coronaviruses, caliciviruses, and picornaviruses, protein- and PTM-level readouts are essential. This is especially true when current antivirals are targeting viral enzymes or post-translational events (e.g. protease inhibitors). An understanding of this process at single-cell level offers the chance to better understand how viruses interact with inhibitors, evasion mechanisms, and ultimately improve treatment strategies and therapeutics.
In this project, you will apply single-cell proteomics by mass spectrometry to the study of viral infection. You will gain skills in LC-MS/MS proteomics, cellenONE-based sample preparation, and molecular virology approaches. You will be based in Ed Emmott’s lab, part of the Centre for Proteome Research, and the Department of Biochemistry, Cell & Systems Biology at the University of Liverpool (https://www.liverpool.ac.uk/people/edward-emmott, https://emmottlab.org/), with access to cutting-edge equipment including a cellenONE for single-cell sample preparation, containment level 3 laboratories, and the latest generation Orbitrap Astral Zoom for mass spectrometry analysis
References
1. Meyer B, Chiaravalli J, Gellenoncourt S, Brownridge P, Bryne DP, Daly LA, Grauslys A, Walter M, Agou F, Chakrabarti LA, Craik CS, Eyers CE, Eyers PA, Gambin Y, Jones AR, Sierecki E, Verdin E, Vignuzzi M, Emmott E. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun. 2021 Sep 21;12(1):5553. doi: 10.1038/s41467-021-25796-w. PMID: 34548480; PMCID: PMC8455558.
2. Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, Kharchenko P, Koller A, Slavov N. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 2021 Jan 27;22(1):50. doi: 10.1186/s13059-021-02267-5. PMID: 33504367; PMCID: PMC7839219.
3. Petelski AA, Emmott E, Leduc A, Huffman RG, Specht H, Perlman DH, Slavov N. Multiplexed single-cell proteomics using SCoPE2. Nat Protoc. 2021 Dec;16(12):5398-5425. doi: 10.1038/s41596-021-00616-z. Epub 2021 Oct 29. PMID: 34716448; PMCID: PMC8643348.
4. Huffman RG, Leduc A, Wichmann C, Di Gioia M, Borriello F, Specht H, Derks J, Khan S, Khoury L, Emmott E, Petelski AA, Perlman DH, Cox J, Zanoni I, Slavov N. Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. Nat Methods. 2023 May;20(5):714-722. doi: 10.1038/s41592-023-01830-1. Epub 2023 Apr 3. PMID: 37012480; PMCID: PMC10172113.
Understanding substrates of viral 3C/3C-like proteases
In this project, you will be working to understand how viruses such as coronaviruses, caliciviruses and picornaviruses interact with infected cells, focusing on substrates of viral proteases. You will learn molecular virology, cell culture assays, and LC-MS/MS proteomic methods alongside bioinformatic analysis in R.
Many of the viruses disrupting society today are distantly related: these include SARS-CoV-2, the agent behind the COVID-19 pandemic, and norovirus which causes epidemics of gastroenteritis. These viruses are members of the coronavirus and calicivirus families, and along with the picornavirus family share common elements, including an enzyme: a 3C or 3C-like protease, which cleaves viral and cellular proteins.
In this project, you will build on the labs prior work using cutting edge LC-MS/MS methods (e.g. Meyer et al. 2021 Nature Comms.) to understand which cellular proteins are cleaved by viral 3C or 3C-like proteases, and use molecular biology and virology approaches to understand the role of these proteins during authentic viral infection with a range of viruses. You will gain skills in R-based bioinformatic analysis, and ultimately characterise the pro- or antiviral roles of identified substrates. By understanding which host proteins are required for efficient viral infection, we can learn new ways to stymie virus replication that may ultimately have the potential to be developed into host-targeting antivirals.
For this project, you will be based in Ed Emmott’s lab, part of the Centre for Proteome Research, and the Department of Biochemistry, Cell & Systems Biology at the University of Liverpool (https://www.liverpool.ac.uk/people/edward-emmott, https://emmottlab.org/).
Email your CV, cover letter, project title to Prof. Emmott at e.emmott@liverpool.ac.uk. As this project is unfunded, please indicate how you plan on funding your studies.
References
1. Meyer B, Chiaravalli J, Gellenoncourt S, Brownridge P, Bryne DP, Daly LA, Grauslys A, Walter M, Agou F, Chakrabarti LA, Craik CS, Eyers CE, Eyers PA, Gambin Y, Jones AR, Sierecki E, Verdin E, Vignuzzi M, Emmott E. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun. 2021 Sep 21;12(1):5553. doi: 10.1038/s41467-021-25796-w. PMID: 34548480; PMCID: PMC8455558.
Understanding coronavirus polyprotein processing
In this project, you will be working to understand how coronaviruses replicate, and how this process is shared across multiple coronaviruses. You will learn molecular virology, cell culture assays, and LC-MS/MS proteomics and transcriptomics methods alongside bioinformatic analysis in R.
Coronaviruses are the causative agents of recent human pandemics and common human and animal diseases. Despite their importance, significant details of the coronavirus life cycle remain unknown. Coronaviruses produce the proteins required for genome replication by translating two long polyproteins: pp1a and pp1ab. Two viral proteases process both polyproteins into the components of the viral replication complex. This proteolytic cleavage results in over 100 theoretical fully and partially-cleaved products. The latter are termed ‘precursors’ and play vital roles in the replication of similar RNA virus families. For the coronaviruses, it has been speculated that early in infection, long partially-cleaved precursors direct antisense RNA synthesis. Late in infection, fully-cleaved polyprotein products direct sense RNA synthesis. However, experimental data and a mechanistic understanding of specific polyprotein cleavage products’ roles is lacking. Understanding this process may pave the way for the next generation of antiviral drugs.
In your PhD, you will work alongside our Wellcome-funded team to study how this process works for human and avian coronaviruses using a range of methods including reverse genetics, molecular biology, RNA sequencing, and LC-MS/MS-based proteomics. You will be based in Ed Emmott’s lab, part of the Centre for Proteome Research, and the Department of Biochemistry, Cell & Systems Biology at the University of Liverpool (https://www.liverpool.ac.uk/people/edward-emmott, https://emmottlab.org/).
Email your CV, cover letter, project title to Prof. Emmott at e.emmott@liverpool.ac.uk. As this project is unfunded, please indicate how you plan on funding your studies.
References
1. Emmott E, Sweeney TR, Goodfellow I. A Cell-based Fluorescence Resonance Energy Transfer (FRET) Sensor Reveals Inter- and Intragenogroup Variations in Norovirus Protease Activity and Polyprotein Cleavage. J Biol Chem. 2015 Nov 13;290(46):27841-53. doi: 10.1074/jbc.M115.688234. Epub 2015 Sep 11. PMID: 26363064; PMCID: PMC4646915.
2. Emmott E, de Rougemont A, Hosmillo M, Lu J, Fitzmaurice T, Haas J, Goodfellow I. Polyprotein processing and intermolecular interactions within the viral replication complex spatially and temporally control norovirus protease activity. J Biol Chem. 2019 Mar 15;294(11):4259-4271. doi: 10.1074/jbc.RA118.006780. Epub 2019 Jan 15. PMID: 30647130; PMCID: PMC6422069.
3. Schamoni-Kast K, Uetrecht C. From Science to Fiction – Connecting In Vivo and In Vitro Results in Polyprotein Processing of Coronaviruses. J Mol Biol. 2025 Nov 15;437(22):169370. doi: 10.1016/j.jmb.2025.169370. Epub 2025 Aug 5. PMID: 40754154.
4. Meyer B, Chiaravalli J, Gellenoncourt S, Brownridge P, Bryne DP, Daly LA, Grauslys A, Walter M, Agou F, Chakrabarti LA, Craik CS, Eyers CE, Eyers PA, Gambin Y, Jones AR, Sierecki E, Verdin E, Vignuzzi M, Emmott E. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun. 2021 Sep 21;12(1):5553. doi: 10.1038/s41467-021-25796-w. PMID: 34548480; PMCID: PMC8455558.
For the unfunded projects above, please email your CV, cover letter, project title to Prof. Emmott at e.emmott@liverpool.ac.uk. As these projects are unfunded, please indicate how you plan on funding your studies.
While we don’t have other funded positions at present, the time to check back for these is usually in the September to January window depending on the funding scheme (typically most are advertised in November or December with January deadlines).
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