Project: Alignment-free read recruitment for pangenome-based genotyping of complex genomic loci

Join a place where ambitious science thrives.

Application closing date: October 29, 2026

Human Technopole (Milan) is a rapidly expanding life science institute where international researchers and cutting-edge technologies converge to accelerate biomedical discovery. Our mission is to transform bold scientific ideas into advances that improve human health.

Within this mission, the Soranzo Research Group investigates human genetic variation and its impact on complex traits and diseases. By integrating large-scale genomic datasets with functional genomic and immunological assays, the group aims to systematically map how genetic variation propagates across multiple layers of gene regulation to understand inter-individual variability.

We are seeking a highly motivated Master’s student to support an alignment-free "fishing" strategy development to recruit locus-specific reads directly from raw sequencing data, bypassing reference bias in highly polymorphic genomic regions.

Your mission

As an intern, you will have the opportunity to contribute to activities such as:

• Apply, extend or build tools to identify highly specific k-mers from pangenomic assemblies and sequenced samples (e.g. kfilt)
• Develop and implement efficient algorithms to extract reads from raw sample FASTQ files belonging to target complex loci (e.g., MHC, AMY1).
• Build and integrate a fast, reference-agnostic front-end for the COSIGT/PANVAR pangenome genotyping pipeline.
• Benchmark performance on diverse modern human populations as well as ancient DNA datasets.
• Participate in regular research group meetings, presenting your progress and discussing scientific findings.
• Work alongside experienced researchers in an interdisciplinary and international environment.

Grow your skills

You will enhance your scientific and professional skills by working with:

• Algorithm development at the intersection of computer science and computational pangenomics.
• Advanced k-mer data structures and graph-based pangenomic representations.
• High-performance scientific programming and optimization for large-scale raw sequencing datasets.
• Researchers with deep expertise in computational genomics, population genetics, and algorithm design.
• Human Technopole supports career development through mentoring, scientific seminars, and dedicated learning opportunities.

What you'll bring

We are looking for candidates with a strong computational background and an interest in applying algorithm design to complex biological problems.

Essential

• Currently enrolled in an MSc program in Bioinformatics, Computational Biology, Computer Science, Biotechnology, or a related discipline.
• Strong programming skills in Python and/or Go/C++.
• Familiarity with k-mer data structures and sequence analysis formats (e.g., FASTQ, BAM).
• Working knowledge of Unix environments and version control (Git).
• Good command of written and spoken English.

Preferred

• Background or interest in pangenomics, sequence alignment, and graph algorithms.
• Familiarity with handling complex structural variation or ancient DNA.

Organizational and interpersonal skills

• Strong analytical and problem-solving skills.
• Excellent communication and teamwork skills.
• Strong organizational skills with attention to detail.
• Ability to work independently while contributing effectively to an interdisciplinary research environment.
• Curiosity, critical thinking, and willingness to learn.
• Commitment to working in a diverse, inclusive, and international research setting.

Why Human Technopole

HT offers an international and dynamic workplace where researchers collaborate across disciplines to tackle ambitious scientific challenges. Interns benefit from close supervision by experienced scientists, access to training initiatives, networking opportunities and hands-on experience with cutting-edge computational research in a collaborative and inclusive environment.

How to apply

Submit:

• CV
• Motivation letter (in English)

For scientific enquiries regarding the position, please contact davide.bolognini@fht.org.

Internship duration: 12 months

Number of positions: 1

The position is based in Milan, Italy.