PhD: Leveraging sequencing technologies to advance identification of bacterial pathogens
University of Liverpool
Location
Leveraging sequencing technologies to advance identification of bacterial pathogens University of Liverpool Added Nov 10 Liverpool, UK
Type
Full-time
Posted
Nov 10, 2025
Mission
What you will drive
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• PhDs **
• Leveraging sequencing technologies to advance identification of bacterial pathogens
** PhDs
##
***
* Leveraging sequencing technologies to advance identification of bacterial pathogens
##
University of Liverpool
**
Institute of Systems, Molecular and Integrative Biology
Dr Yu Wan
Prof N Williams
Prof Steve Paterson
**
Applications accepted all year round
** Self-Funded PhD Students Only
Register interest
Register interest
Liverpool
United Kingdom
Bacteriology
Bioinformatics
Data Science
Genomics
Microbiology
Software Engineering
*
## About the Project
This four-year PhD project aims to advance sequencing-based bioinformatics methods for identification and characterisation of bacterial pathogens in diverse clinical and surveillance samples. Methodological and knowledge breakthroughs from this study will improve the diagnosis, monitoring, prevention, and control of bacterial infectious diseases, addressing the pressing threat of antimicrobial resistance.
Identification of bacterial pathogens is essential for diagnosis, outbreak investigation, infection prevention and control, and surveillance. High-throughput sequencing has become a powerful tool in bacterial genomics, facilitating high-resolution tracking of pathogen transmission and patterns of antimicrobial resistance (AMR). While short-read sequencing (such as Illumina sequencing) has been widely used in diagnostic laboratories, since the last decade long-read sequencing technologies (such as PacBio’s Single Molecule Real-time Sequencing and Oxford Nanopore Technologies’s nanopore sequencing) have revolutionised bacterial genomics by improving genome assembly, variant detection, and reconstruction of complex genomic features. Integrating both short-read and long-read sequencing approaches can improve the accuracy of pathogen identification, enabling high-resolution characterisation of pathogens. This four-year PhD project focuses on advancing bioinformatics methods for identification and characterisation of bacterial pathogens in high-throughput sequencing data.
**Aims**
1. Develop bioinformatics methods for pathogen identification and characterisation.
2. Advance understandings of pathogen and AMR dissemination.
**Project structure**
· Year 1: Conduct a pilot study to generate sequencing data from available isolates and explore current methods for understanding the spread of bacterial pathogens and AMR.
· Years 2 and 3: Develop bioinformatics methods and experimental protocols to improve pathogen identification and characterisation.
· Years 3 and 4: Apply the new methods to investigate the epidemiology of pathogens and AMR.
· Year 4: Write-up.
** **
**Training**
*Mandatory training*
· Graduate School First Year Skills Workshop
· Graduate School Career Skills Workshop
· Departmentally provided subject specific skills training
· Poster presentation on an annual University Postgraduate Poster Day
** **
*Scientific skills*
· Experiments for microbiology and DNA sequencing
· Advanced bioinformatics and programming
· Collation and sharing of sequence data
· Statistics and infectious disease epidemiology
*Transferable skills*
· Communications
· Critical thinking
· Multidisciplinary collaboration within a diverse research environment
· Time management
Career development
**Please email the following information to supervisor Dr Yu Wan (**[email protected]**), with a citation of this project’s title and reference number:**
· **Cover letter, enclosing a motivation statement, research interests, expertise, relevant experience, probable start date, a study plan, and contact details of two referees**
· **Curriculum vitae**
· **University transcripts relevant to this PhD project**
**A list of your accessible publications (preferably, peer-reviewed first/last-author journal articles, and we accept other types of publications, such as blogs, forum posts, software documentation, etc) or a 1000-word sample of scientific writing**
Candidates should register and apply through the University of Liverpool Application Portal. You'll receive an email acknowledgment once you have submitted your application. We will be in touch by email with further details about what happens next. This application may close once a suitable candidate is found
Biological Sciences (4)
Computer Science (8)
## Funding Notes
The Hill Abram Prize Endowment provides the successful candidate with a waiver of tuition fees, charged at the UK and Republic of Ireland student rate, for up to four years if the project begins before 31 July 2026.
## References
1. E. Jauneikaite, K. S. Baker, J. G. Nunn, et al., Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities. The Lancet Microbe (2023). https://doi.org/10.1016/S2666-5247(23)00282-3.
2. R. R. Wick, L. M. Judd, K. E. Holt, Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLOS Computational Biology 19, e1010905 (2023). https://doi.org/10.1371/journal.pcbi.1010905.
3. D. M. Aanensen, C. C. Carlos, P. Donado-Godoy, et al., Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae. Clinical Infectious Diseases 73, S255–S257 (2021). https://doi.org/10.1093/cid/ciab795.
##
Register your interest for this project
Recipient
University of Liverpool
Dr Yu Wan
Prof N Williams
The university will respond to you directly. You will have a FindAPhD account to view your sent enquiries and receive email alerts with new PhD opportunities and guidance to help you choose the right programme.
Recipient *
First name
Last name
Email address *
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Dominican Republic (+1-809)
East Timor (+670)
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Equatorial Guinea (+240)
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French Guiana (+592)
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French Sthern Terr. (+262)
Gabon (+241)
Georgia (+995)
Germany (+49)
Ghana (+233)
Gibraltar (+350)
Greece (+30)
Greenland (+299)
Grenada (+1-473)
Guadeloupe (+590)
Guam (+1-671)
Guatemala (+...
Profile
What makes you a great fit
•
-->
*
*
** Don't miss our weekly PhD newsletter | Sign up now** Don't miss our weekly PhD newsletter | Sign up now**
FindAPhD **
• PhDs **
• Leveraging sequencing technologies to advance identification of bacterial pathogens
** PhDs
##
***
* Leveraging sequencing technologies to advance identification of bacterial pathogens
##
University of Liverpool
**
Institute of Systems, Molecular and Integrative Biology
Dr Yu Wan
Prof N Williams
Prof Steve Paterson
**
Applications accepted all year round
** Self-Funded PhD Students Only
Register interest
Register interest
Liverpool
United Kingdom
Bacteriology
Bioinformatics
Data Science
Genomics
Microbiology
Software Engineering
*
## About the Project
This four-year PhD project aims to advance sequencing-based bioinformatics methods for identification and characterisation of bacterial pathogens in diverse clinical and surveillance samples. Methodological and knowledge breakthroughs from this study will improve the diagnosis, monitoring, prevention, and control of bacterial infectious diseases, addressing the pressing threat of antimicrobial resistance.
Identification of bacterial pathogens is essential for diagnosis, outbreak investigation, infection prevention and control, and surveillance. High-throughput sequencing has become a powerful tool in bacterial genomics, facilitating high-resolution tracking of pathogen transmission and patterns of antimicrobial resistance (AMR). While short-read sequencing (such as Illumina sequencing) has been widely used in diagnostic laboratories, since the last decade long-read sequencing technologies (such as PacBio’s Single Molecule Real-time Sequencing and Oxford Nanopore Technologies’s nanopore sequencing) have revolutionised bacterial genomics by improving genome assembly, variant detection, and reconstruction of complex genomic features. Integrating both short-read and long-read sequencing approaches can improve the accuracy of pathogen identification, enabling high-resolution characterisation of pathogens. This four-year PhD project focuses on advancing bioinformatics methods for identification and characterisation of bacterial pathogens in high-throughput sequencing data.
**Aims**
1. Develop bioinformatics methods for pathogen identification and characterisation.
2. Advance understandings of pathogen and AMR dissemination.
**Project structure**
· Year 1: Conduct a pilot study to generate sequencing data from available isolates and explore current methods for understanding the spread of bacterial pathogens and AMR.
· Years 2 and 3: Develop bioinformatics methods and experimental protocols to improve pathogen identification and characterisation.
· Years 3 and 4: Apply the new methods to investigate the epidemiology of pathogens and AMR.
· Year 4: Write-up.
** **
**Training**
*Mandatory training*
· Graduate School First Year Skills Workshop
· Graduate School Career Skills Workshop
· Departmentally provided subject specific skills training
· Poster presentation on an annual University Postgraduate Poster Day
** **
*Scientific skills*
· Experiments for microbiology and DNA sequencing
· Advanced bioinformatics and programming
· Collation and sharing of sequence data
· Statistics and infectious disease epidemiology
*Transferable skills*
· Communications
· Critical thinking
· Multidisciplinary collaboration within a diverse research environment
· Time management
Career development
**Please email the following information to supervisor Dr Yu Wan (**[email protected]**), with a citation of this project’s title and reference number:**
· **Cover letter, enclosing a motivation statement, research interests, expertise, relevant experience, probable start date, a study plan, and contact details of two referees**
· **Curriculum vitae**
· **University transcripts relevant to this PhD project**
**A list of your accessible publications (preferably, peer-reviewed first/last-author journal articles, and we accept other types of publications, such as blogs, forum posts, software documentation, etc) or a 1000-word sample of scientific writing**
Candidates should register and apply through the University of Liverpool Application Portal. You'll receive an email acknowledgment once you have submitted your application. We will be in touch by email with further details about what happens next. This application may close once a suitable candidate is found
Biological Sciences (4)
Computer Science (8)
## Funding Notes
The Hill Abram Prize Endowment provides the successful candidate with a waiver of tuition fees, charged at the UK and Republic of Ireland student rate, for up to four years if the project begins before 31 July 2026.
## References
1. E. Jauneikaite, K. S. Baker, J. G. Nunn, et al., Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities. The Lancet Microbe (2023). https://doi.org/10.1016/S2666-5247(23)00282-3.
2. R. R. Wick, L. M. Judd, K. E. Holt, Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLOS Computational Biology 19, e1010905 (2023). https://doi.org/10.1371/journal.pcbi.1010905.
3. D. M. Aanensen, C. C. Carlos, P. Donado-Godoy, et al., Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae. Clinical Infectious Diseases 73, S255–S257 (2021). https://doi.org/10.1093/cid/ciab795.
##
Register your interest for this project
Recipient
University of Liverpool
Dr Yu Wan
Prof N Williams
The university will respond to you directly. You will have a FindAPhD account to view your sent enquiries and receive email alerts with new PhD opportunities and guidance to help you choose the right programme.
Recipient *
First name
Last name
Email address *
## It looks like you alredy have a FindAPhD Account
Log in to save time sending your enquiry and view previously sent enquiries
Dialling code Optional
Afghanistan (+93)
Albania (+355)
Algeria (+213)
American Samoa (+1-684)
Andorra (+376)
Angola (+244)
Anguilla (+1-264)
Antarctica (+672)
Antigua and Barbuda (+1-268)
Argentina (+54)
Armenia (+374)
Aruba (+297)
Australia (+61)
Austria (+43)
Azerbaijan (+994)
Bahamas (+1-242)
Bahrain (+973)
Bangladesh (+880)
Barbados (+1-246)
Belarus (+375)
Belgium (+32)
Belize (+501)
Benin (+229)
Bermuda (+1-441)
Bhutan (+975)
Bolivia (+591)
Bosnia and Herzegovina (+387)
Botswana (+267)
Bouvet Island (+47)
Brazil (+55)
British Ind. Ocean Terr. (+246)
Brunei Darussalam (+673)
Bulgaria (+359)
Burkina Faso (+226)
Burundi (+257)
Cambodia (+855)
Cameroon (+237)
Canada (+1)
Cape Verde (+238)
Caribbean Netherlands (+599)
Cayman Islands (+1-345)
Central African Rep. (+236)
Chad (+235)
Chile (+56)
China (+86)
Christmas Island (+61)
Cocos: Keeling (+61)
Colombia (+57)
Comoros (+269)
Cook Islands (+682)
Costa Rica (+506)
Cote d Ivoire (+225)
Croatia (+385)
Cuba (+53)
Curacao (+599)
Cyprus (+357)
Czechia (+420)
Democratic Republic of the Congo (+243)
Denmark (+45)
Djibouti (+253)
Dominica (+1-767)
Dominican Republic (+1-809)
East Timor (+670)
Ecuador (+593)
Egypt (+20)
El salvador (+503)
Equatorial Guinea (+240)
Eritrea (+291)
Estonia (+372)
Ethiopia (+251)
Falkland Islands (+500)
Faroe Islands (+298)
Fiji (+679)
Finland (+358)
France (+33)
French Guiana (+592)
French Polynesia (+689)
French Sthern Terr. (+262)
Gabon (+241)
Georgia (+995)
Germany (+49)
Ghana (+233)
Gibraltar (+350)
Greece (+30)
Greenland (+299)
Grenada (+1-473)
Guadeloupe (+590)
Guam (+1-671)
Guatemala (+...