Bioinformatician/Sr. Bioinformatician

Human Technopole (HT) is looking for a Bioinformatician for the Functional Genomics Computation Unit in the Centre for Genomics – Functional Programme.

HT is a new interdisciplinary research institute, created and supported by the Italian government, whose aim is to develop innovative strategies to promote human health and aging through a multidisciplinary and integrated approach, combining genomics, computational and structural biology and neuroscience, as well as data and decisions sciences.

The mission of the Centre for Genomics – Functional Programme will be to elucidate key biological questions including “how the genome is regulated in each cell, tissue and organ in health and disease”, “what are the molecules and networks that drive biological activity in cells, tissues, organs”, and “how to modify genome regulation and genome output in health and diseases”. We will identify and characterize functional and regulatory non-coding genomic element networks in different cells and tissues of the human body, with the goal to identify the grammar of the genome, which will ultimately provide deeper understanding of genome function and enable biology and genomics medicine.
To address these challenges, the Centre develops original technologies to identify and functionally characterize regulatory elements, long non-coding RNA, genome conformation, interactomes of biological molecules in living cells and computational approaches to study genome regulation. These approaches will be broadly used to map the function and regulation of human genome in health and diseases across human diversity and ultimately derive actionable targets.

We are looking for a Bioinformatician in the Functional Genomics Computation Unit, a new state-of-the-art unit for the analysis of large volumes functional genomics deriving from a variety of technologies and approaches. This unit will support the data analysis efforts of the research groups in the Functional Genomics Programme. The Unit will rely on data generated by the research teams and units in the Centre and 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 Unit will benefit from a large High-Performance Computing and Data Storage infrastructure, and from close interaction with an expert community of computational biologists within the Genomics Centre, other Research Centres, and of core facilities at HT.

The post will be responsible for setting up and running state-of-the-art computational workflows for functional genomics and will be involved in functional analysis of key datasets. A key mission will be to ensure the processing and delivery of analysed data for large-scale projects, including through bespoke collaborations with Investigators of the Research Programme and other Research Centres. They will also be expected to contribute to the development of new methods and the rapid standardization/implementation of new computational approaches for emerging technologies. Reproducibility and robustness of bioinformatics analyses, using standardised and modular workflows, will be at the core of this role.

The successful candidate will currently report directly to Dr. Piero Carninci, Head of the Centre for Genomics – Functional Programme.

Key tasks and responsibilities

• Setting up and operating bioinformatics analysis pipelines to process transcriptomics and functional genomics data, using short- and long-read technologies, including but not limited to genomics analysis from bulk, single cell genomics and multiomics datasets.
• Design, set up and maintain data analysis pipelines and software for genomics analysis downstream of the pipelines (eg identification of promoters, enhancers, regulatory elements; interactomes; annotation of transcripts and promoter, termination and splicing variants, RNA modifications etc.).
• Manage import, storage and use of external datasets (eg: ENCODE, Human Cell Atlas, FANTOM), including control of appropriate access rights and data annotation.
• Manage storage and maintenance of genetic and genomic datasets produced by the research groups, curation of data for depositions in public repositories. Data harmonization of genomic resources; curation of metadata of experiments
• Processing and analysis of datasets for faculty groups or for cross-centre and external collaborative projects.
• Curation of functional genomics elements, from projects of the Center, the broader HT and broader collaborations.
• Provide support, training and supervision to member of the department (students and staff) on scientific computing and functional genomics tools and analyses
• Participate in preparing accessible resources/databases for the community-wide fruition of the data generated within the research programs;
• Support grant applications, project reports and papers on a case by case basis
• Support development of accessible resources for the community-wide fruition of the data generated within the research program, including liaising with the major existing databases from the relevant communities to maximize integration, impact etc.

• A PhD and experience in the areas of main responsibilities, with particular emphasis on computational biology and bioinformatics, proven experience in functional genomics data analysis of large-scale research programs including a diverse range of data types, including large-scale sequencing data.
• have direct experience in functional genomics projects, in which you have taken the lead of bioinformatics analysis.
• Advanced skills in computational biology-data analysis with appropriate publication and track record.
• Coding Standards and Best Practices. Familiarity with bioinformatics, computational biology, programming and familiarity with tools broadly used for functional genomics analysis and strong understanding of functional genomics, gene regulation, lncRNAs and related areas; the ideal candidate would have:

1. Experience using high performance cluster computing.
2. Knowledge of at least one widely used programming languages for genomic data processing and analysis (eg. R, Python).
3. Experience processing and analysing genome/transcriptome sequencing data.

• Excellent computational and trouble-shooting skills.
• Fluency in English – HT is an international research institute.

Advantageous requirements :

The following skills and experiences are not essential, but would be advantageous:

• Experience with long-read and direct RNA sequencing would be a strong advantage.
• Direct experience with other types of RNA sequencing assays and analyses (e.g. single-cell sequencing, isoform-level analyses, Ribo-seq) and/or chromatin-level assays (e.g. HiC, ChiP-seq, ATAQseq).
• Experience in finding, retrieving and processing public datasets (eg. Encode, GTEx, Epimap).
• Experience in developing approaches to process and analyse data from novel experimental assays.
• Advanced experience of repoduceable research (eg. git) and/or repoduceable software development (eg. R package development).
• Experience in pipeline development (eg. nextflow, snakemake).
• Experience analysing imaging/microscopy data.

Required personal skills:

• Ability to manage competing priorities in a fast-paced environment and to work independently.
• Strong interpersonal skills demonstrated by the ability to lead and gain the assistance and cooperation of others in a team endeavor. Proven ability to train, lead and mentor colleagues;
• Ability to build trust through operating with transparency and creating an open and positive environment.
• Ability to work in a multi-cultural, multi-ethnic environment with sensitivity and respect for diversity.

Above all, we are looking for a candidate with the willingness to learn, develop and improve their computational skills in tandem with the needs and interests of the research groups in the department.

Application Instructions:

To apply, please send the following:

• a CV.
• a motivation letter in English relating your track record to the specifics of the call.
• names and contacts of 2 referees.

For specific enquires concerning the role only, please contact Piero Carninci, Head of the Genomics Research Centre: piero@humantechnopole1.recruitee.com (this email address should not be used to send applications).

Additional information:

HT offers a highly collaborative, international culture. The working language at HT is English. HT will 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, equal opportunity employer offering attractive conditions and benefits appropriate to a leading, internationally competitive, research organization and seeks to promote a collegial and open atmosphere. The compensation package granted will be internationally competitive and comprise pension scheme, medical and other social benefits.

Number of positions offered: 1

Contract offered: CCNL Chimico Farmaceutico, Employee level - contract duration to be determined.

The position is based in Milan.