Senior Bioinformatics Engineer, Iorio Group

APPLICATION CLOSING DATE: March 15^th, 2023

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: Neurogenomics, Computational Biology, Structural Biology, Genomics, and Health Data Science. The Centers work together to enable interdisciplinary research and to create an open, collaborative environment that will help promote life science research both nationally and internationally.

The Iorio Group in the Computational Biology Research Centre at Human Technopole in Milan works at the interface of biology, machine learning, statistics and information theory with the goal of understanding and predicting how genomic alterations and molecular traits from other omics contribute to pathological processes, biological circuits’ rewiring and have an impact on therapeutic response in human cancers and other diseases. Our research aims at advancing human health by designing algorithms, computational tools and novel analytical methods for the integration and the analysis of pharmacogenomics and functional-genomics datasets, with the objective of identifying new therapeutic targets, biomarkers and drug repositioning opportunities.

We are seeking an experienced Bioinformatics Engineer to provide computational support to projects focusing on cancer pharmacogenomics and engaged in analysing data from genome-editing, pharmaco/functional-genomics and single cell transcriptomics screens.

The selected candidate will report to Francesco Iorio and will be actively interacting with the other research centres at Human Technopole, as well as national and international collaborators, such as those involved in the Cancer Dependency Map partnership, whose broad goal is to systematically identify cancer vulnerabilities and dependencies that could be exploited therapeutically.

We strongly support the training of our lab members.

The successful candidate will be able to implement and use new computational pipelines for pre-processing and quality control assessment of data from genome-editing screens, whole exome and whole genome sequencing databases, scRNA and bulk transcriptomic profiling, as well as developing new analytical methods and tools on an individual project needs’ basis.

Key tasks and responsibilities:

This will involve:

• Extending existing software, writing, documenting and maintaining code packages on public/internal repositories.
• Curating genomic data from publicly available repositories and from the characterization of panels of cancer in-vitro and PDx models and designing new meta-descriptors and annotations for drug/genetic-perturbation screens’ data.
• Collaborating with expert biologists and other groups’ members to define amounts and types of meta-data used in each project.
• Designing prototype software applications and tools to make data/results internally accessible in a user-friendly way.
• Assisting PhD students and post-docs in assembling fully computable scientific manuscripts.
• Interacting with the software and web development team to coordinate data/software/results flows in the public domain and design custom software packages and interfaces for front-ends and web-apps.
• Designing new algorithms.

Training colleagues, other staff, and institute’s visitors to use the developed software and organizing usability test sessions, workshops and courses.

Essential requirements:

• PhD in a relevant subject area (Physics, Computer Science, Engineering, Statistics, Mathematics, Computational Biology, Bioinformatics).
• At least a couple of years of research experience post-PhD.
• Experience in analysis of Next-Generation Sequencing (NGS) data focusing on DNA-seq, RNA-seq and scRNA-seq and scRNA-seq.

Advantageous requirements:

• Full working proficiency with software versioning systems (eg. Git, GitHub, svn).
• Experience in creating, documenting, and maintaining software packages.
• Experience with cluster farms.
• Basic knowledge of statistics and combinatorics.
• Full working proficiency in UNIX/Linux.
• Experience with genomic data curation and data management from large-scale in-vitro drug/functional-genomic screens (advantageous).
• Ability to devise novel quantitative models, and use relevant mathematics-heavy literature (advantageous).
• Experience with data from high throughput assays and from functional genetic screens (advantageous).
• Full working proficiency in a compiled language (e.g. C, C++, D, Fortran) (advantageous).

Other key competences:

• Fluent English.
• Ability to communicate ideas and results effectively.
• Ability to work independently and to organise own workload.
• Ability to work with others in a collegial manner and to communicate effectively internally at all levels and with select external individuals.
• Ability to work in a multi-cultural, multi-ethnic environment with sensitivity and respect for diversity.

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.

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 organisation 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, Fixed-term 5 years - employee level

The position is based in Milan.