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PhD in Decoding and Designing DNA Replication Origins with Genome Language Models

Project 1838 · Earlham Institute · Graduate Programme

Application workspace

Save this opportunity and prepare around its actual requirements. Confirm deadlines and eligibility at the original source.

Read the research report View the recruitment source
Country or region
United Kingdom
Application deadline
2026-11-30 (confirm the exact time with the source)
Funding
NRPDTP offers eligible international applicants a competitive four-year award covering full tuition and a living stipend, plus £5,000 per year for research training. International students are capped at 30% of annual programme intake, not a project quota or individual probability. £21,805 is the 2026/27 stipend reference. The project advert says shortlisted for funding while Funding Notes say the project is awarded; the applicant's award, 2027/28 stipend and final fee coverage remain unconfirmed. Eligible personal visa/IHS costs may be reimbursed up to £3,500 after registration with evidence; dependants are excluded and upfront or excess costs remain.

The research opportunity

PhD in Decoding and Designing DNA Replication Origins with Genome Language Models

Project overview

The NIEDUSZYNSKI_E27DTP project at the Earlham Institute asks how DNA replication origins are encoded and regulated, and whether genome language models can predict their function. It is a four-year, full-time PhD within the Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP), based at Earlham in Norwich, UK, with doctoral registration and applications routed through the University of East Anglia (UEA). The advertised start date is 1 October 2027 and the deadline is 30 November 2026, with no time or time zone stated. Current application availability has not been confirmed.

Research question and doctoral work

The project asks how cells select replication origins and how origin function is encoded. The doctoral work includes developing predictive genome-language models of origin function, designing hundreds of synthetic DNA sequences, and testing their performance in yeast using advanced molecular biology and nanopore sequencing. The advert also identifies high-throughput experimental approaches and training in machine learning, genome engineering, automation, CRISPR-based genome editing, next-generation sequencing and data analysis. It does not specify the final model architecture, datasets or assay design.

An annotated candidate origin, an origin used by an individual cell, population initiation frequency and replication timing are related but distinct prediction targets. The work needs to connect model outputs to what the measurements support and test when predictions are reliable. Single-molecule observations in human cells can inform measurement limits, but do not validate a yeast model. Broad clinical use or transfer across organisms is not established.

Supervisors, host and training

The project page names Conrad Nieduszynski (conrad.nieduszynski@earlham.ac.uk) as lead supervisor and Carolina Grandellis (Carolina.Grandellis@earlham.ac.uk) as co-supervisor. Nieduszynski leads an Earlham research group; Grandellis heads the Earlham Biofoundry. The Li and Hall groups are named as collaborators, but their formal supervisory roles are not specified; the Hall link points to Anthony Hall. Earlham is the research host and UEA is the doctoral registration and application route. The specific registering School and course identifier remain unconfirmed.

See Nieduszynski’s current Earlham profile.

Earlham’s data-biology, sequencing and genomics platforms and the NBI Graduate School offer an interdisciplinary setting, but the advert does not promise dedicated technical staff, instrument time or a personal GPU allocation. NRPDTP provides training-needs assessment, a personal development plan and career training. All students complete a three-month PIPS professional internship during the four-year programme; it is normally outside the immediate thesis topic.

Eligibility, application and dates

The minimum academic requirement is a UK-equivalent 2:1 Honours Bachelor’s degree. NRPDTP may consider a 2:2 undergraduate degree where the applicant also has a relevant qualifying Master’s degree or substantial relevant research or non-academic experience; this is assessed individually. Chinese qualifications are assessed individually, and no standard Chinese percentage cutoff for this PhD is established.

English requirements can be met with IELTS 6.5 overall and at least 6.0 in each component; TOEFL iBT 88 (reading 20, writing 19, listening 19, speaking 21); or iBT26 4.5 overall (reading, writing and listening 3.5 each; speaking 4, including Home Edition). The table gives two-year validity. English may be an offer condition, and English-medium study in China does not automatically waive the requirement.

Apply through UEA using the NRPDTP Personal Statement and Research Statement proformas; omission leads to rejection. Applicants may submit up to three projects, with a separate application for each. Materials include degree certificates and transcripts, postgraduate records if applicable, a roughly 1–2-page CV, at least two referees (including one academic referee), and identity, immigration or English documents where applicable. Non-English academic records require official translations. Proposed supervisors, friends and relatives cannot act as referees, and the statements must be written by the applicant.

The advert lists interviews for 2–4 February 2027. Current application availability has not been confirmed; check with admissions before relying on the advertised deadline. The partners state that selection does not distinguish on the basis of gender, marital or civil partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background. To improve accessibility and attract applicants from underrepresented groups, NRPDTP requires its bespoke statement templates, designed to let applicants show their experience and potential through suitable examples and evidence.

Funding

NRPDTP policy allows eligible international applicants to compete for a four-year award covering full tuition and a living stipend, plus £5,000 per year in research training support. International students are capped at 30% of annual programme intake; this is not a project quota or an individual probability. £21,805 is the 2026/27 stipend reference, not a confirmed 2027/28 rate. The advert says the project is shortlisted for funding, while its Funding Notes say it is awarded a four-year studentship; neither statement confirms an individual award or its final fee terms. Eligible personal visa/IHS costs may be reimbursed up to £3,500 after enrolment with evidence; dependants are excluded, and upfront or excess costs remain.

Points to confirm

Confirm the UEA registering School and course identifier, individual award and fee terms, 2027 stipend, visa/IHS reimbursement process, supervisory roles, datasets, experimental assays and computing allocation. Further information is available from the NRPDTP website.

Research and application brief

Report generated: . This date does not confirm that recruitment remains open.

Information updated: . Recheck the original notice before applying.

Show report contents

PhD in Decoding and Designing DNA Replication Origins with Genome Language Models

Quick Decision

A strong opportunity, subject to confirming the research fit. This Earlham Institute opportunity connects computational prediction with the biological interpretation of DNA replication origins in yeast. Its value is the combination of replication research, genomic measurement and a formal co-supervisor who leads the Earlham Biofoundry. The official project listed on 18 October 2026 names Conrad Nieduszynski and Carolina Grandellis, starts on 1 October 2027 and closes on 30 November 2026, without a published time or time zone. Eligible international candidates can compete for the NRPDTP four-year tuition-and-maintenance package. The first discussion should establish a bounded thesis question, the computational/experimental balance and allocated support, rather than assume that a language model already captures the rules of chromosome function. Current exact project

This timing comes from the saved 18 October 2026 project information; current application availability has not been confirmed.

Research Problem and Doctoral Work

A replication origin is a biological starting point for DNA copying. The project asks how origin function is encoded and regulated, and whether genome language models can help explain it. The scientific question links computational prediction to the interpretation of yeast genomic measurements, including nanopore observations. A generally reliable predictive model and a context-independent account of origin function remain research questions, rather than established outputs of this studentship.

The difficult part is connecting the model's target to what the biological measurements actually observe. An annotated candidate origin, an origin used in an individual cell, the frequency of initiation across a population and the time at which replication occurs are related but different quantities. A prediction can appear accurate against one definition without explaining another. The group's recent single-molecule research is useful here because it shows how population averages can conceal dispersed or infrequent events. Evidence from human cells informs measurement reasoning; it does not automatically establish rules for the yeast model. Recent original replication study

At doctoral level, a defensible contribution could be a clearly defined prediction task with biologically interpretable comparisons and an honest account of uncertainty. The analysis should distinguish association in training data from functional evidence, and recognise possible overlap between model-development data and evaluation material. The advertisement does not identify the final model architecture, datasets, computing allocation or the student's initial biological comparison.

The advertised doctoral tasks also include developing models of origin function, designing hundreds of synthetic DNA sequences, and testing their performance in yeast using advanced molecular biology and nanopore sequencing. The project combines high-throughput experimental approaches; machine learning, genome engineering, automation, CRISPR-based genome editing, next-generation sequencing and data analysis are listed training areas. The specific assay and sequence of tasks are not stated.

The practical role spans computation and experimental interpretation. Machine learning, automation, sequencing and data analysis are advertised training categories. The student should expect to learn how measurement limitations affect the conclusions, rather than treat sequence-model output as a substitute for evidence. The project could develop valuable quantitative genomics skills even if the eventual result is a carefully bounded explanation of when predictions fail. Clinical benefit and transfer of results to unrelated organisms are not established outcomes.

School, Programme and Field Context

Earlham Institute is the research host. Its current research-degree guidance explicitly directs applicants to University of East Anglia PhD registration and the UEA application system. The exact registering school and course identifier for this award still need confirming. Participation by several research groups does not create a joint degree. Earlham registration guidance

The institute's relevant strengths are its data-driven biology, sequencing, bioinformatics and laboratory-automation environment. Its postgraduate page describes access to experienced researchers, student representation and the NBI Graduate School. The exact project additionally identifies the Biofoundry and genomics platforms. Advertised access is a positive resource signal, but not a guarantee of unrestricted instrument slots, dedicated technical staff or individual GPU time. Earlham postgraduate environment

NRPDTP combines one main four-year research project with training and a mandatory three-month PIPS professional internship, normally outside the immediate PhD topic. Training needs analysis and a personal development plan tailor specialist and transferable learning. Programme structure, Training programme

UEA is joint 381 overall in QS 2027. That is a university-level ranking, not an Earlham or replication-group ranking. For this project, the substantive judgement should centre on supervisory expertise, usable genomic measurements and the integration of biological and computational training. Public material does not establish a project-specific supervision frequency or progression calendar. QS university context

Supervisor and Lab Assessment

The current Earlham profile identifies Conrad Nieduszynski as Group Leader, with research in replication, genome evolution and stability, combining genomic technologies and mathematical reasoning. The exact project calls him Dr, whereas an earlier recruitment heading used Prof. Group Leader is the confirmed role; a corresponding professorial rank remains unconfirmed. The public scientific contact is conrad.nieduszynski@earlham.ac.uk. Current supervisor profile

Dr Carolina Grandellis (Carolina.Grandellis@earlham.ac.uk), named as co-supervisor on the current project page, is Head of the Earlham Biofoundry. Her role supports relevant automation and interdisciplinary training. Li and Hall are also linked as contributing groups, but are not thereby all formal co-supervisors; the current project's Hall link points to Anthony Hall. Other platform projects or grants are not this student's personal funding. Co-supervisor profile

Three genuine Nieduszynski-coauthored recent original studies inform the assessment, with different evidence depth:

Carrington and Colleagues (2025): Measurement and Prediction Labels

The earlier evidence assessment of this Genome Biology study covered the primary abstract, selected results, discussion and conclusions. Single-molecule observations reveal dispersed initiation events missed in population-level maps. The authors explicitly note that sequencing depth samples origins rather than exhaustively cataloguing them. This supports careful definition of training labels and biological ground truth; it is human-cell research, not validation of a yeast language model. Original journal study

Schindler and Colleagues (2023): Context-Dependent Biological Responses

The earlier evidence assessment of this Cell study covered the complete original abstract, primary summary/highlights and authorship. Functional characterisation of a yeast neochromosome found substantial host responses, including ploidy changes. The finding illustrates why a predicted genomic property cannot alone establish the broader biological response. Nieduszynski is a coauthor in a large collaboration, not its sole lead. Full methods, results and supplementary data were not reviewed. Original abstract

Díez-Santos and Colleagues (2025): Single-Molecule Interpretation

The official supervisor bibliography and the creator-supplied study/dataset description identify single-molecule replication observations in fission yeast, including repetitive regions. This is directly relevant to distinguishing initiation, termination and pausing. The earlier evidence assessment covered the complete creator description through the NLM dataset registry; the preprint article itself and deposited data were not read or downloaded. Peer-reviewed publication was not independently established. Original study's dataset description

Thus the evidence comprises two peer-reviewed journal studies and one original preprint, not three fully read papers. The wider genome-language-model reference in the advertisement was not independently reviewed. Clarify daily supervisory roles, technical mentoring, meeting and feedback expectations, and whether the initial work is predominantly computational or experimental before judging the training fit.

Funding, Application, and Living Cost

NRPDTP policy available in October 2026 offers eligible international candidates a fully funded four-year award covering tuition, maintenance and research support. International appointments are capped at 30% of the programme's annual intake; this is not an individual's chance or a guaranteed number assigned to this topic. Personal selection remains competitive. The project description's “shortlisted for funding” and funding note's “awarded” differ in strength; neither means that an applicant has already received a personal offer. Current funding framework

Maintenance follows the UKRI minimum; £21,805 is the 2026/27 annual reference, not the confirmed 2027/28 amount. £5,000 annually is research training support, not additional disposable living income. For October 2027 starters, the programme contributes up to £3,500 per student towards eligible visa and IHS costs, reimbursed against appropriate evidence after enrolment and registration. Dependants are excluded, and the cap does not remove the need to fund upfront costs or any balance.

A dated UEA accommodation reference lists Village at £178.50 weekly and Crome at £209.50 weekly for 2026/27. Listed 41-week totals are £7,318.50 and £8,589.50. Applying those weekly rates to 52 weeks gives an illustrative £9,282–£10,894 rent range, leaving £10,911–£12,523 from the quoted stipend before other expenses. This is arithmetic for comparison, not a 52-week contract, a complete budget or a 2027 room offer. Official accommodation reference

October 2026 visa references are £558 for a Student visa application and £776 per visa year for student IHS. Visa duration and rounding affect the upfront total. Financial-evidence rules differ from a personal annual budget: the present outside-London maintenance figure is £1,171 monthly for up to nine months, with applicable evidence rules. China is on the differential-evidence list, but UKVI can still request evidence; the underlying funding requirement is not waived. Visa route, Financial evidence, IHS

Applicant Fit and Preparation

The project requires at least a UK-equivalent 2:1 Honours Bachelor's degree. NRPDTP assesses equivalent overseas qualifications and may consider applicants with a UK Lower Second-class (2:2) undergraduate degree who also hold a Master's meeting the school's requirements, or have significant relevant research or non-academic experience. This exception requires individual assessment. UEA's broader alternative entry routes remain distinct from this competition's specific criteria. This provides a positive in-principle route for Chinese applicants, alongside international tuition support, without inventing a uniform Chinese percentage cutoff. NRPDTP eligibility

The project specifies IELTS 6.5 overall, at least 6.0 in every component. UEA's Science research table additionally lists TOEFL iBT 88, with reading 20, writing 19, listening 19 and speaking 21; its iBT26 equivalents are 4.5 overall, with reading/writing/listening 3.5 and speaking 4. Home Edition is included, and the table gives two-year validity. Tests and exemptions must match the eventual offer; Chinese English-medium education alone does not automatically establish exemption. English can be an offer condition rather than already satisfied at application. Current English equivalencies

NRPDTP and its partners state that selection does not distinguish on the basis of gender, marital or civil partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background. To improve accessibility and attract applicants from underrepresented groups, the programme requires bespoke Personal Statement and Research Statement templates so applicants can present their experience and potential with suitable examples and evidence.

NRPDTP requires both its Personal Statement and Research Statement proformas; omitting them leads to rejection. Apply through UEA, with up to three projects and a separate application for each. The current checklist includes degree certificates and transcripts, postgraduate records if studied, a roughly 1–2-page CV, at least two referees including one academic, and relevant identity/immigration and English documents. Proposed project supervisors, friends and relatives cannot be referees. Non-English academic records require official translations. Earlham's general guide describes an own-authored research statement for advertised projects; use the competition's current templates and their field limits rather than its generic free-form statement or self-funded proposal instructions. Application requirements

Useful preparation includes quantitative reasoning, programming/data-analysis experience and a willingness to understand biological measurement. These are preparation suggestions, not extra advertised mandatory software or laboratory credentials. A purely AI-engineering interest without engagement with replication biology, or a purely wet-lab expectation without interest in modelling, leaves an important mismatch. A research discussion should explain what the prediction means, what evidence would contradict it and what training is needed.

Next Actions and Questions to Verify

Before Applying

Contact Nieduszynski about the first biological question, available datasets and the balance of computation and laboratory interpretation. Confirm Grandellis's supervisory role, the support expected from the Li and Hall groups, and the registering UEA school/course identifier. Use the current templates and prepare before 30 November, without assuming an unpublished midnight deadline. The programme timeline places interviews on 2–4 February 2027, with outcome notification in the week commencing 22 February. Key dates

At Interview

Ask how the first model's target will be defined and how measurement uncertainty will be distinguished from prediction error. Discuss access to computing, genomic platforms and technical mentoring, expectations for biological interpretation, data/IP conditions and regular supervision. The evidence supports a strong replication and automation environment, not guaranteed individual access to every listed facility.

Before Accepting

Obtain the individual four-year award terms, 2027 maintenance rate, tuition coverage, continuation conditions and the £3,500 reimbursement process in writing. Clarify relocation costs, accommodation availability, visa/CAS timing and any subject-specific approvals stated in the offer. Recruitment information reflects 18 October 2026 sources; later availability should be confirmed with admissions. A topic-specific nationality restriction or particular clearance requirement is not established by these sources; the individual offer governs.

The training could support computational genomics, research-software, sequencing-analysis and interdisciplinary bioscience careers. PIPS can expose students to policy, education or industry beyond the immediate thesis, but does not guarantee a named employer, job or salary. Its value depends on whether the student gains rigorous judgement about genomic data and reproducible modelling alongside the specialist biology. Professional internship framework

Evidence and Sources

Project, supervisors and original research

School, programme and training

Funding, application, costs and careers

Sources

The listing may come from a university or recruitment platform. Check the notice and official sources in the report for current application requirements. View the recruitment source

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