Computational sciences applied to biology and medicine are at the very core of the mission of HT. The Centre for Computational Biology has the goal of developing new mathematical and computational approaches for the analysis and interpretation of medical and biological data. Computational biology at HT is not just about developing new methods for data analysis, but more importantly, also about asking fundamental questions about biology and human health that can be addressed only using computational approaches, from mathematical modelling of dynamical systems to machine learning and Artificial Intelligence.
The Human Technopole Foundation is looking for a Bioinformatics Core Manager of the Omics Data Analysis and Integration Unit of the Centre for Computational Biology, a core group providing advanced bioinformatics support.
This newly created unit will support the data analysis efforts of the different research groups in the Centre for Computational Biology and report directly to the Head of the Centre, Prof. Andrea Sottoriva. The unit will work with research teams in a collaborative fashion, performing bioinformatics analysis on a variety of data types, ranging from genomic and transcriptomic data, to epigenetics and single-cell profiling. The unit will rely on data generated by the Data Generation and Experimental Validation team of the Centre, in conjunction with the High Throughput Genomics Core Facility of HT. The unit will also be involved in the analysis of data generated by external collaborators as well as publicly available data, when required.
The successful candidate will be responsible for maintaining the data analysis infrastructure of the Centre and coordinating a team of five to eventually around nine bioinformaticians with different specialised expertise. Besides lab management duties, the candidate will also directly support members of the Centre with advanced bioinformatics analysis of their samples, ensuring reproducibility and robustness of analyses. The work will involve the development and maintenance of analysis pipelines for next-generation sequencing of samples from humans and model systems, such as RNA-seq, whole-genome and whole-exome sequencing, ATAC-seq, ChIP-seq and Hi-C, as well as post-genomic applications, such as genome-wide pooled CRISPR screens. Particular focus will be put on the development of integrative analysis pipelines, as well as single-cell profiling with scRNA-seq, scATAC-seq and scCNV. The candidate will be expected to ensure that the computational pipelines are state-of-the-art and steadily incorporating new analytical methods and tools designed by the Centre’s researchers, and to coordinate the setting up of new analysis pipelines as new technologies are adopted by HT.
Key tasks and responsibilities
The Manager of the Omics Data Analysis and Integration Unit of the Centre for Computational Biology will be responsible for:
- Coordination and maintenance of the state-of-the-art bioinformatics analysis infrastructure, including:
- Development of analysis pipelines to process samples for multi-omic profiling, including whole-genome and whole-exome sequencing, transcriptome sequencing, ATAC-seq, ChIP-seq and Hi-C and genome-wide pooled CRISPR screens,
- Setup and maintenance of single-cell analysis pipelines for scRNA-seq, scATAC-seq and scCNV,
- Setting up and maintaining pipelines for long-read sequencing technologies, and
- Developing reproducible pipelines based on Nextflow and Docker systems;
- Data analysis and data sharing, including:
- Analysis of data from patient samples and model systems and provision of results and QC to the relevant researchers in the Centre,
- Helping with the access to and analysis of public datasets that may be relevant to the Centre’s activities,
- Aiding data sharing and reproducibility of bioinformatics analyses, and
- Design of data management and sharing plans, as well as GDPR compliance;
- Effectively managing a Scientific Service Unit, including:
- Leading a team of technical posts within the unit with different computational expertise,
- Recruiting, training and mentoring of (junior) staff, and
- Responsibility for implementing priorities and resource planning for the unit;
- Collaboration with different HT facilities and units, such as:
- The HT High Throughput Genomics Core Facility and the Data Generation and Experimental Validation unit,
- The HT Computational Genomics Facility (processing data with established pipelines),
- The Image Analysis Facility (integrating ‘omics data with imaging),
- The HT Scientific Computing to coordinate the computational needs of the Centre, and
- Other HT groups to implement new pipelines for novel technologies;
- Integrative activities for the Centre, such as:
- Organisation of introductions and assistance for new users of the unit,
- Management of scientific computing access charges with periodic review to ensure sustainability and competitiveness,
- Building effective links and collaborations within HT,
- Developing links with other national and international genomics facilities,
- Support of third-party fundraising, where possible,
- Closely following technological developments that could benefit the Centre;
- Preparation for centre reviews by external experts;
- PhD or equivalent qualification in a relevant subject, e.g. computational biology, computer science, physics or a related field of science;
- +5 years of hands-on experience in bioinformatics applied to next-generation sequencing data, and ideally also single-cell sequencing and/or long-read technologies;
- Experience in a lead/managerial role in a centre, laboratory or facility;
- Proven leadership, communication, team building and problem-solving skills.
- Documented experience with setting up bioinformatics pipelines and robust standard operating procedures for quality assurance;
- Experience in the analysis of human samples;
- Excellent computational, programming and trouble-shooting skills;
- Familiarity with container systems and NextFlow/SnakeMake pipelines;
- HPC and Unix systems savvy;
- Ability to interact effectively with other teams and work synergistically to drive projects forward;
- Highly organised and meticulous;
- Fluency in English – HT is an international research institute;
Please apply by sending:
i) a CV
ii) a motivation letter in English
iii) names and contacts of 2 referees
The remuneration package is internationally competitive and comprise a highly competitive salary, pension scheme, medical and other social benefits and support for relocation and installation. The contract is meant to be permanent.
Importantly, international candidates coming to Italy for the first time, or Italian nationals returning after residing abroad, benefit from very attractive income tax benefits.
For any inquiry about the call, please feel free to contact Prof Andrea Sottoriva at email@example.com (this email address should not be used to send applications).
HT offers a highly collaborative, international culture to foster top quality, interdisciplinary research by promoting a vibrant environment consisting of independent research groups with access to outstanding graduate students, postdoctoral fellows and core facilities.
HT is an inclusive employer that fosters diversity and engages systematically to ensure that equal employment opportunities are provided without regard to age, race, creed, religion, sex, disability, medical condition, sexual orientation, gender identity or expression, national or ethnic origin or any other legally recognized status entitled to protection under applicable laws. HT offers attractive conditions and benefits appropriate to a leading, internationally competitive, research organisation that promotes a collegial and open atmosphere.
The Human Technopole Foundation is based in Milan