Bioinformaticians, Neurogenomics Centre

HT - Human Technopole

Bioinformaticians, Neurogenomics Centre

HT - Human Technopole

Milan, Italy

Job description

APPLICATION CLOSING DATE: 18.10.2022

Human Technopole (HT) is a new interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health. HT is composed of five Centres: Computational Biology, Structural Biology, Genomics, Neurogenomics and Health Data Science. The Centres work together to enable interdisciplinary research and to create an open, collaborative environment that will help promote life science research both nationally and internationally.

HT is looking for 2 bioinformaticians for the Centre for Neurogenomics, respectively in the CEll REference BRain Atlas (CEREBRA) Scientific Support unit and the Software Development and Data Curation Scientific Support unit.

The Software Development and Data Curation Scientific Support Unit develops, implements and maintains state-of-the-art computational tools for the analysis of data generated by cutting edge biological applications. In particular, the unit focuses on the development and implementation of pipelines for transcriptomics/epigenomics data processing, including single cell multiomics, by orchestrating the software components for data analysis and by maintaining software platforms for interactive data analysis and visualization. The unit will design and develop novel quantitative models based on the integration of high resolution multiomics and clinical data.

CEll REference BRain Atlas (CEREBRA) Scientific Support Unit is a team with expertise in bioinformatics and neuroscience, with a special focus on innovative computational approaches for the annotation, analysis and integration of single cell multiomics data related to the human brain and its disease-associated experimental models. CEREBRA will bring together and integrate publicly available and in-house generated single cell omics brain and brain organoids datasets, enabling their fluent accessibility to researchers through the generation of bespoke data portals, streamlining their cross referencing by integrated and joint analysis in a reference atlas.

Both units, which are parts of the Neurogenomics research Centre, conform their activity to the highest standards of reproducibility and transparency of the FAIR paradigm (Findable, Accessible, Interoperable and Reusable). The units benefit from a state-of-the-art High-Performance Computing infrastructure, and from close interaction with an expert community of computational and experimental biologists within the Neurogenomics Centre, the Computational Biology and Genomics Centres and the transformative core facilities of HT in the areas of genomics and high throughput disease modelling.

Bioinformatician of the Software Development and Data Curation Unit

The successful candidate will work in the Software Development and Data Curation Unit and will be involved in the development and implementation of high-performance computational solutions to deploy novel statistical methods for the analysis of single-cell data, including transcriptomics and epigenomics analyses, differentially expressed and regulated genes, developmental trajectories, cell populations, and clinical metadata.

She/he will have the following tasks and responsibilities

  • Designing and develop of novel statistical models and applications for the analysis of omics data.
  • Supporting researchers and collaborators by performing statistical analysis and providing advice on the best suited statistical models.
  • Developing and maintaining computational analytical pipelines.
  • Testing and implementing innovative analysis tools from the international scientific community.
  • Communicating, explaining and contextualising statistical results to a wide variety of collaborators with varying degrees of statistical know-how.
  • Maintaining and documenting software, following best practices of software engineering (e.g., revisioning and containerization).

Bioinformatician of the CEREBRA Unit

The successful candidate will be involved in the setting-up, maintenance and constant evolution of a Reference Atlas of single cell multiomics data from the human brain and brain organoids, contributing to the generation of a key resource to streamline the interrogation and interpretation of experimental results related to the development and function of the human brain in physiological and pathological conditions.

She/he will have the following tasks and responsibilities

  • Establishing and maintaining reproducible and well-documented bioinformatic pipelines for the standardised analysis of internal and external single cell multi-omics datasets.
  • Collecting relevant internal and external single cell datasets and curate/harmonize their annotation and metadata.
  • Developing survey, test and implement bioinformatics algorithms both in house and by the community for the integration of heterogenous omics datasets in a reference atlas.
  • Contributing to the design and development of bespoke data portals and data navigation/visualization solutions.
  • Maintaining and documenting software, following best practices of software engineering (e.g., revisioning and containerization).

Job requirements

For both positions preferential requirements

  • MSc in a quantitative field (bioinformatics, computer science, statistics, mathematics, physics, engineering or similar). A PhD degree and/or years of work experience in a data science/software engineering related role will be considered a plus;
  • Proven and extensive knowledge of at least one of the following programming languages: Python (preferable), R, java, javascript, C++, C#;
  • Strong organization skills and attention to detail; propensity to structure analytical steps in well-documented and reproducible workflows;
  • Excellent problem-solving, analytical and critical thinking skills; collaborative attitude and ability to work in teams with colleagues of heterogeneous scientific backgrounds;
  • Proficiency with code versioning systems (e.g., git, SVN) and familiarity with container technologies (e.g., Docker, Singularity, Podman); experience working in a Unix/Linux environment;
  • Experience in bioinformatics workflow systems (i.e., Nextflow, Snakemake, CWL) will be considered a plus;
  • Ability to manage competing priorities in a fast-paced environment and to work independently;
  • Fluency in English – HT is an international research institute.

For the Bioinformatician of the Software Development and Data Curation Unit

  • Knowledge of statistical methods for the analysis of complex data, with demonstrable hands-on experience. Particularly relevant expertise in this context includes Bayesian inference methods, Machine Learning (including Deep Learning) and Artificial Intelligence approaches, probabilistic modelling;
  • Experience with single-cell omics data and/or molecular and population genomics will be considered a plus.

For the Bioinformatician (CEREBRA Unit)

  • Previous experience in the analysis of single cell omics datasets and an interest in neurobiology (or previous experience in the field) will be considered a plus;
  • Expertise in the following areas will be considered a plus: web frameworks for data visualization, dashboards, database, data management.

Special consideration will be given to candidates who are part of the protected categories list, according to L. 68/99.

Application Instructions

To apply, please send the following

  • a CV.
  • a motivation letter in English.
  • names and contacts of 2 referees.

For any informal inquiry about the position, please feel free to contact Giuseppe Testa at giuseppe.testa@humantechnopole1.recruitee.com (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 recognised 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 compensation package granted will be internationally competitive and comprise a pension scheme, medical and other social benefits and support for (inter)national mobility and installation, applicable for candidates outside the Lombardy region.

Candidates coming to Italy for the first time, or returning after residing abroad, benefit from very attractive income tax benefits.

Number of positions offered: 2
Contract offered: CCNL Chimico Farmaceutico, Employee level, fixed-term contract 5 years.

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