Manager of the Omics Data Analysis and Integration Unit

HT - Human Technopole

Manager of the Omics Data Analysis and Integration Unit

HT - Human Technopole

Milan, Italy

Job descripton


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 is looking for a Manager of the Omics Data Analysis and Integration Unit of the Centre for Computational Biology, a core group providing advance bioinformatics support.

This newly created unit will support the data analysis efforts of the research groups in the Centre for Computational Biology and will be composed of 7 to 9 members. 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 and publicly available data when required.

The successful candidate will be responsible for maintaining the data analysis infrastructure of the centre and coordinate a team of bioinformaticians with different specialised expertise. 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 successful candidate and their team will perform bioinformatics analysis in collaboration with the research groups of the Centre. Besides lab management duties, the candidate will also be directly involved in the analysis of the data.

A key mission of the Manager or the Omics Data Analysis and Integration Unit will be to support members of the centre with advanced bioinformatics analysis of their samples. The selected candidate will also be expected to ensure that the computational pipelines are state-of-the-art and steadily incorporating new analytical methods and tools designed by the researchers of the centre, and they will coordinate the setting up of new analysis pipelines as new technologies are adopted by HT. They will also be involved in the recruitment, training and mentoring of staff. Ensuring reproducibility and robustness of bioinformatics analyses will a core task of this role.

The successful candidate will report directly to the Head of the Centre for Computational Biology, Prof Andrea Sottoriva. International candidates, women and members of ethnic minorities are particularly encouraged to apply.

Key tasks and responsibilities

The Manager of the Omics Data Analysis and Integration Unit of the Centre for Computational Biology will be responsible for:

  • Coordinate and maintain the bioinformatics analysis infrastructure 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;
  • Setting up and maintain single-cell analysis pipelines for scRNA-seq, scATAC-seq and scCNV;
  • Setting up and maintain pipelines for long-read sequencing technologies;
  • Develop reproducible pipelines based on Nextflow and Docker systems;
  • Interact with a team of technical posts within the unit with different computational expertise;
  • Analyse data from patient samples and model systems and provide results and QC to the relevant researchers in the centre;
  • Work with the HT High Throughput Genomics Core Facility and the Data Generation and Experimental Validation unit for data processing;
  • Work with the HT Computational Genomics Facility to process data with established pipelines;
  • Work closely with the Image Analysis Facility to integrate ‘omics data with imaging;
  • Help accessing and analysing public datasets that may be relevant to the centre’s activities;
  • Be responsible for implementing priorities and resource planning for the unit;
  • Aid data sharing and reproducibility of bioinformatics analyses;
  • Ensure the pipelines and analyses are world-class;
  • Coordinate the computational needs of the centre with HT Scientific Computing;
  • Manage scientific computing access charges with periodic review to ensure sustainability and competitiveness;
  • Cooperate with other groups to implement new pipelines for novel technologies;
  • Design data management and sharing plans, as well as GDPR compliance;
  • Closely follow technological developments that could benefit the centre;
  • Organise introductions and assistance for new users of the unit;
  • Help select, lead and mentor junior staff;
  • Prepare for centre reviews by external experts;
  • Participate actively in the overall development of HT core facilities;
  • Build effective links and collaborations within HT;
  • Develop links with other national and international genomics facilities;
  • Support third-party fundraising where possible.

Job requirements

  • +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;
  • PhD or equivalent qualification in a relevant subject, e.g. computational biology, computer science, physics or a related field of science;
  • +2 years experience in a lead/managerial role in a centre, laboratory or facility;
  • Documented experience with setting up bioinformatics pipelines and robust standard operating procedures for quality assurance;
  • Experience in the analysis of human samples;
  • Excellent computational skills, outstanding programming abilities and trouble-shooting;
  • 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 meticolous;
  • Fluency in English – HT is an international research institute;
  • Proven leadership, communication, team building and problem-solving skills.

Application Instructions

Please apply by sending:

  1. a CV;
  2. a motivation letter in English;
  3. 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 initial contract is for 5 years and it is renewable.

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 (this email address should not be used to send applications).

Additional information

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.

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EuroJobsites is a registered company number: 4694396 VAT number: GB 880 9055 04

Registered address: EuroJobsites Ltd, Unit 8, Kingsmill Business Park, Kingston Upon Thames, London, KT1 3GZ, United Kingdom

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