The Spanish National Centre for Biotechnology (CNB), a leading research institute in Madrid, is inviting applications for a fully funded PhD position in Computational Microbial Biotechnology under the prestigious PIF2025 Fellowship. This position is part of the AMBIZIONE Project, a cutting-edge international initiative focused on the rational design of synthetic microbial communities (SynComs) through a combination of computational modeling and experimental research.

About the AMBIZIONE Project

AMBIZIONE (Advanced Microbiome Biotechnology Zips ONE HEALTH) is an innovative research program integrating ecological, biochemical, and evolutionary data to design microbial communities for applications in human health, agriculture, and environmental sustainability.

The project uses a wide range of state-of-the-art technologies, including:

• Advanced statistical analysis
• Metabolic modeling
• Multi-omics (OMICS) technologies
• Complex network analysis
• Artificial intelligence and machine learning

The ultimate aim is to build a robust SynCom design platform that can transform microbiome engineering for practical real-world solutions.

PhD Role and Key Responsibilities

As a PhD researcher in this project, you will:

• Develop theoretical and computational models for microbial community design
• Collaborate with multidisciplinary teams at CNB and partner institutions
• Contribute to high-impact publications and conference presentations
• Progressively shape and develop your own research ideas
• Actively participate in laboratory and institutional activities

Candidate Profile – Who Can Apply?

Ideal candidates should have:

• Bachelor’s or Master’s degree in Physics, Mathematics, Computer Science, or other quantitative fields
• Strong programming skills in Python, R, Julia, or C
• Experience with software development tools (Git, Nextflow, Snakemake)
• Interest in biological systems and microbiome research
• Fluency in English and excellent communication abilities

Funding and Benefits

Selected candidates will receive:

• 4-year fully funded PhD position under the PIF2025 Fellowship
• Competitive salary: €1,623.26/year (1st year) and €2,029.07/year (2nd–4th years)
• Coverage of lab fees and research expenses
• Access to national and international research collaborations
• Training in scientific research and career development
• Official enrollment in the PhD program at Universidad Autónoma de Madrid

Application Process

1. Prepare Your Documents:
   • Motivation Letter outlining your research interest and fit for the project
   • Updated CV with academic qualifications and technical expertise
2. Submit Your Application:
   Email your application to the project supervisors:
   • Alberto Pascual-García – alberto.pascualgrcia@gmail.com
   • Javier Nogales – jnogales@cnb.csic.es
     Subject line: PhD AMBIZIONE

Deadline: Applications remain open until the PIF2025 Fellowship deadline (expected September 2025). Early submission is strongly advised.

Why Apply?

This is an exceptional opportunity to join one of Europe’s leading microbiome research teams, work with cutting-edge computational and experimental methods, and contribute to groundbreaking advancements in synthetic microbial biotechnology.

PhD Research Focus: OPISCOW Project

The PhD candidate will work on the OPISCOW Project – Origin, Prevalence, and Impact of Complex Structural Variation in cattle. This exciting research aims to:

• Estimate the de novo mutation rate of structural variants (SVs) in bovine genomes
• Utilize PacBio HiFi long-read sequencing on 50 parent-offspring trios
• Map data to a bovine telomere-to-telomere (T2T) genome assembly
• Build haplotype-resolved genome assemblies
• Contribute to the global bovine pangenome initiative

Key Responsibilities

As a PhD student in this genomics project, your role will include:

• Analyzing high-throughput long-read sequencing datasets
• Identifying and characterizing structural variants and mutation rates
• Performing genome assembly and sequence alignment
• Engaging in collaborative international research projects
• Presenting your findings in top journals and scientific conferences

Candidate Requirements

To qualify for this PhD program, applicants must have:

• A Master’s degree (MSc) in genomics, genetics, bioinformatics, or related disciplines
• Programming skills in Python, R, or similar languages
• Experience working with high-performance computing (HPC) clusters
• Strong interest in computational and statistical genomics
• Proficiency in English communication and scientific writing

Why Choose ETH Zurich?

ETH Zurich stands out as a global leader in research and education, offering:

• A world-class environment for genomics and data science
• Excellent research infrastructure and laboratory facilities
• A competitive PhD salary and comprehensive benefits
• A collaborative and inclusive research community
• Exceptional support for career development and publishing opportunities

Important Dates & Application Process

• Start Date: September 1, 2025 (flexible; earlier start possible)
• Application Review Begins: May 20, 2025
• PhD Duration: 4 years (fully funded)

How to Apply:

Submit the following documents through the official ETH Zurich application portal:

1. Motivation letter
2. Updated CV (Curriculum Vitae)
3. Academic transcripts and degree certificates
4. Contact details of two academic referees

Contact Information

For inquiries about the position (not for applications), reach out to:
Prof. Hubert Pausch
Email: hubert.pausch@usys.ethz.ch

Commitment to Diversity & Inclusion

ETH Zurich is proud to be an equal opportunity employer. The university promotes diversity and cultivates an inclusive research culture where every individual can thrive and contribute to innovative science.

About the Research Assistant Role

This is a unique opportunity to work at the crossroads of biology, computer science, and engineering. As a Pre-Doctoral Research Assistant, you’ll collaborate with an interdisciplinary team to design and implement custom imaging systems, Raspberry Pi-based automation tools, and machine learning pipelines for advanced research in plant-microbe interactions.

Key Responsibilities

• Develop imaging systems using Raspberry Pi and open-source tools
• Create pipelines for image acquisition, processing, and machine learning
• Collaborate with biologists to support experimental research
• Produce technical documentation, SOPs, and user manuals
• Present findings at lab meetings and contribute to scientific publications

About The Sainsbury Laboratory (TSL)

TSL is a world-renowned research institute focused on plant health, microbial interactions, and sustainable agriculture. With top-tier facilities and a collaborative culture, TSL offers an ideal environment for early-career scientists to thrive.

Project Highlights

As part of this innovative research role, you’ll contribute to:

• Monitoring microbial growth in real-time within incubators
• Automated phenotyping of plants in controlled environments
• Building custom imaging and sensing systems for plant-microbe studies
• Applying machine learning (e.g., TensorFlow, PyTorch) for biological data analysis

Required Qualifications

• Bachelor’s degree in Computer Science, Bioinformatics, Computational Biology, or related field
• Proficiency in Python or equivalent programming languages
• A basic understanding of plant biology
• Strong problem-solving, analytical, and communication skills

Desirable Skills (Bonus Points)

• Hands-on experience with Raspberry Pi development
• Familiarity with OpenCV, image processing, or computer vision tools
• Knowledge of machine learning frameworks (TensorFlow, PyTorch)
• Previous experience in a research or laboratory automation setting

Position Details

• Job Title: Pre-Doctoral Research Assistant
• Salary: £23,881 (TSL Grade 3, Spine Point 11)
• Contract: 1-Year Full-Time
• Location: The Sainsbury Laboratory, Norwich, Norfolk, UK
• Start Date: Immediate (flexible start options available)

Why Join TSL?

• 30 days of annual leave + UK public holidays
• Access to cutting-edge research facilities
• Mentorship from leading plant science experts
• Support for scientific writing and grant applications
• A vibrant and inclusive research community
• Generous pension scheme and training opportunities

How to Apply

• Application Reference Code: DM01-2025
• Deadline: Applications will be reviewed starting 15th May 2025
• Final closing date: 15th June 2025 or until the position is filled

Submit your application via the APPLY NOW button, including:

• CV (max 2 pages)
• Cover letter (1 page) explaining your motivation and fit
• Contact information for 2–3 referees

For queries, contact: HR@TSL.ac.uk

About The Sainsbury Laboratory (TSL)

Located in the beautiful Norfolk countryside, The Sainsbury Laboratory is a globally recognized leader in plant-microbe interaction research. TSL is dedicated to sustainable agriculture and plant health, providing a dynamic, inclusive, and innovative environment for scientists at all career stages.