Join the team! - The Emmott Lab

Join the team!

In the lab, you’ll have the opportunity to get hands-on training in cutting-edge proteomics methods such as single-cell proteomics (SCoPE2/pSCoPE), have access to one of the few cellenONE platforms in UK academia, hands-on access to outstanding mass spectrometry instrumentation as part of the Centre for Proteome Research, training to work on HG2/3 pathogens or clinical samples, and work alongside a team spanning virology, mass spec, bioinformatics and clinical proteomics.

Lab members also have access to additional training opportunities through the University and have used these to gain qualifications granting AFHEA or FHEA status, obtain commercialisation and science communication training, and complete more project-specific training in bioinformatics through courses run by the computational biology facility.

Work in this lab will suit you if you:

Want to do rigorous science, where we share our data, code, and reagents, letting others learn from, expand on, and validate our results.
In terms of research, you should be interested in one or several of the below:
- Find (+ssRNA) viruses neat! Both because they can cause a lot of damage, but also because they can be incredible tools to learn about normal cell biology. Specifically we care about how these viruses replicate and interest with their hosts
- Like mass spec (or want to learn), and how we can apply and develop new methods to study e.g. virus and cell or disease biology.
Aren’t afraid of doing/learning some coding so you can do your own analysis (with help!).
Want to have fun, with a supportive team who help and troubleshoot each others work (and when necessary, feed each other cake) while you are doing it!

Funded Positions:

Funded PhD opportunity! (UK students only due to funder restrictions).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 HBLB. 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, and how to apply on Findaphd.com

Other PhD positions – Others may become available through the Liverpool BBSRC or MRC DLA schemes for Oct 2027 start.
PDRA positions – None at present, next likely funded positions to be advertised in 2027.

Unfunded Positions:

For applicants interested in MRes, PhD student or PDRA positions with access to funding, or who have identified a suitable funding scheme they are competitive for, we have the following priority areas we are interested in recruiting in:

Bioinformatics of single-cell proteomics, and proteolytic cleavage data
Antiviral development/drug repurposing/mode of action/evasion
Viral biology (norovirus, coronavirus)

We have several Unfunded PhD projects advertised on FindAPhD.com (click to expand each project title):

Understanding post-translational modifications during viral infection

Advert on FindAPhD.comAbout the Project
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

Advert on FindAPhD.comAbout the Project
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

Understanding substrates of viral 3C/3C-like proteases

Advert on FindAPhD.comAbout the Project
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.

Understanding coronavirus polyprotein processing

Advert on FindAPhD.comAbout the Project
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.

Please contact Ed to discuss options, some of which are listed below. Please note that most of the fellowship schemes below are highly competitive, and you will need a strong prior record.

Other opportunities:

Fellowships and applying with/for your own funding (PhD &. Postdoc): If you have access to, or wish to pursue alternate sources of funding for PhD or postdoctoral positions in the lab, please contact Ed with a copy of your CV, and a description of your research interests and how these can fit with research in the lab. If a good fit, Ed can work with you to identify suitable research questions, and assist with funding applications. Please note fellowship applications take extensive work, so please get in touch well ahead of the relevant deadline.

Details on the application process for international students with access to funding who wish to pursue PhD study can be found here. A great source of potential fellowship schemes for interested applicants can be found at ECRcentral. Some specific Postdoctoral/PhD funding schemes include:

Wellcome Early Career Awards (Postdoctoral)

For those with up to 3 years postdoctoral experience, a Wellcome Early Career Award provides 5 years of funding for research expenses, your salary and helps you develop your own research identity as you move from a postdoctoral to an independent group leader position. See here for more details.

Royal Commision of 1851 Research Fellowships (Postdoctoral)

You must have a PhD and no more than three years postdoctoral experience. These cover your salary for a three year period, and £10k/yr research expenses. More information here.

Marie Curie Postdoctoral Fellowships

International applicants may be eligible for Marie Curie Postdoctoral Fellowships. Please see here for details. You must have a maximum of eight years postdoctoral experience (dated from your PhD viva), and you must not have worked in the UK for more than twelve months in the prior three years. Duration is 12-24 months for a standard fellowship, and 24-36 months for a global fellowship.

HFSP Postdoctoral fellowships

Annual fellowship call, 3 year fellowships including research expenses. You must have a PhD, and these cover salary and research expenses for three years. In the third year you have the option to move country to your/your spouses home country or another HFSPO country. There are two types: cross-disciplinary fellowships for applicants with a PhD from a non-biological discipline who want to embark on a project in the life sciences, and long-term fellowships, for those from a life sciences background. More details here.

Royal Society Newton International Fellowships (Postdoctoral)

International applicants may be eligible for Royal Society Newton International Fellowships which provide 2 years of funding for postdoctoral projects. Applicants must not be UK citizens, and must be working outside the UK at the time of application. Full eligibility notes available here.

Royal Society Career Development Fellowships , Wellcome Accelerator awards

Royal Society Career Development Fellowships are a newly-launched scheme from the Royal Society specifically aimed at supporting researchers of Black or mixed-Black heritage. Applicants must have a PhD (or have one by the time funding starts) and at most 24 months of postdoctoral experience. Funding is for four years, covers your costs including visa and relocation costs if required and research expenses. Open to non-UK nationals. Wellcome Accelerator awards are a similar scheme from Wellcome, aimed at UK-based researchers from a Black, Bangladeshi or Pakistani background. Applicants must have a PhD by the time funding starts, funding is for two years and covers research expenses.

Swiss National Science Foundation Postdoctoral Mobility

These awards support researchers with links to Switzerland (please see scheme for full details) to spend two years gaining skills in an international lab, prior to a final year in Switzerland. The final year is applied for separately. Funds include salary and research support. Full details available here.

EMBO Postdoctoral Fellowships

These cover your salary and relocation costs for 12-24 months. More details here. You must have a PhD, must be moving country, and cannot have done your PhD studies in the UK.

MRC Clinical Research Training Fellowship (Postdoctoral)

These support clinicians with a PhD, who completed their PhD usually ~5 years prior, without significant research experience since., and who wish to pursue a research career. More details here.

NIHR Research Career Funding options (PhD, Postdoctoral)

We have strong ongoing and prior collaborations with the directorate of Infection & Immunity at Liverpool Clinical Laboratories, and NIHR funding may suit clinically-trained applicants who want to conduct applied research in the area of virology. More details here.

Bekker NAWA Programme

This programme supports Polish PhD students or Postdocs who wish to spend 3-24 months in a foreign laboratory. It covers your living expenses related to the stay. More details here.

Commenwealth Scholarships (PhD)

International applicants from Commonwealth countries may be eligible for Commonwealth Scholarships to support PhD studies. The exact funding schemes available depend on the applicant country of citizenship. Currently the only open scheme is for candidates applying from countries defined by OECD Development Assistance Committee (DAC) as least developed or vulnerable states.

Summer Studentships: If you are a second or third year BSc student interested in a summer placement in the lab, please contact Ed early in the academic year. There are funding streams you can apply to, for example, from the Microbiology Society, as well as internal schemes for University of Liverpool students. However, the deadlines for these are generally early in the spring before the placement, so please make contact early. It is usually Ed who will need to apply on your behalf, so you need to discuss this with Ed with plenty of time before the deadline.

Please note we are now at capacity for summer 2026.

Masters and Undergraduate Projects: There are projects available in the lab on the MRes Biological and Biomedical Sciences MRes course. Please refer to the course page for details of the course, and email Ed if you would like further details of the available projects.

Positions (General): All current positions (funded or unfunded) will be advertised here, on Ed’s linkedin or the lab bluesky account (@emmottlab.bsky.social), and through University recruitment as they become available. PhD student positions will also be advertised on findaphd.com.