Closed for Applications
Early Stage Researcher (ESR7)
PhD fellowship in network-based approaches for multi-omics data analysis
“E-MUSE Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration” MSCA-ITN-2020 European Training Network
Alma Mater Studorium – Universita di Bologna (UNIBO),
Via Zamboni 33, Bologna 40126, Italy
Applied physics, systems biology, network theory, data analysis
30th June 2021 23:59 - Europe/Brussels
Envisaged Job Starting Date
full-time employment (based on COVID-19 evolution and restrictions, possibility to start remotely, once situation allows the presence is required)
€3 413.88 gross salary/month
+ €600 gross mobility allowance/month and €500 gross family allowance/month (if applicable)
Taxation and Social (including Pension) Contribution deductions based on National and company regulations will apply.
The objective of the research project is the integration and embedding of multi-omics data into a Systems network framework, and to develop new advanced statistical and mathematical methods (based on Machine Learning and Network Theory) for integrated analysis of multiple omics datasets to characterize complex microbial ecosystems. The ESR will deal with omics experimental data and combine them with relevant information about bacterial and metagenomics networks (e.g. protein interaction, biochemical pathways, metabolic networks). Starting from these reconstructed networks, several methods will be applied to identify key players (nodes, pathways, communities) related to the experimental conditions studied.
It is expected to clarify the relationships between different omics measurements, and to identify the key players with a relevant role in the studied processes (i.e. a signature or a subnetwork community), or to rank the different network elements based on their structural and functional role (prioritization). These network-based techniques will be combined with the basics of Machine Learning for the pursued research aims: multivariate linear and nonlinear regression, feature extraction, clustering and classification.
In total, 2 months will be spent at Vrije Universiteit Amsterdam in Netherlands (systems modelling), 2 months at Agencia Estatal Consejo Superior Deinvestigaciones Cientificas in Spain (systems modelling) and 2 months at the Szegedi Tudomanyegyetemusz in Hungary (data analysis through artificial intelligence models).
Enrolment in Doctoral degree
Alma Mater Studorium – Universita di Bologna (UNIBO) (https://www.unibo.it/en)
Required Education Level
The candidate is required to have a master degree in Physics, Computer science, Mathematics, Statistics or related fields giving access to PhD school and NOT to have any kind of PhD degree. Previous research experience (which must be no longer than 4 years) although appreciated, is not mandatory.
Skills / Qualifications
• networking and good communications skills (writing and presentation skills)
• willingness to travel abroad for the purpose of research, training and dissemination
• good skills in programming of high-level languages like Python, R, Matlab (not mandatory but highly recommended)
English: B2, good oral and written communication skills in English are compulsory
The project will take place at the Laboratory of Applied Physics and Systems Biophysics, Department of Physics and Astronomy (DIFA) of the Alma Mater Studiorum - University of Bologna, Italy. DIFA is one Department of the Science School and one of the most scientifically productive Physics Departments in Italy. DIFA has a large computing facility, available to the Biophysics group (14-core HPC, GPU server, mirrored storage server with >100 Tb storage), and to the whole Department (OPH HPC facility, >200 cores).
The lead supervisor Prof. Daniel Remondini is the director of the lab, with specific expertises on biomedical data analysis (Machine Learning, Deep Learning), complex network theory and its applications to BioMedicine. He is a supervisor of 8 PhD students in Physics (5 ongoing, 2 with a PostDoc position abroad and 1 with a Research Assistant position in Bologna) and 1 ITN PhD student, supervisor of 3 PostDoc Students, and of >50 Undergraduate and Master Thesis students in Physics. The co-supervisor, Dr. Enrico Giampieri is a researcher with specific expertises on scientific computing, including networks, stochastic processes and statistics in High Performance Computing environment and supervisor of >10 Undergraduate and Master Thesis students in Physics.
Host Institution Description
The Alma Mater Studiorum, (https://www.unibo.it/it) the oldest university in the Western world, paves the way for innovation through an increasingly rich programme catalogue, cutting-edge research and a constant and increasingly broad international perspective.
Since its origins in 1088, Alma Mater has been student-centred hosting prominent figures from science and the arts. Based in five campuses (Bologna, Cesena, Forlì, Ravenna, Rimini), with a branch in Buenos Aires, it offers a teaching catalogue diversified and tailored to the needs of present-day society: over 200 degree programmes among its 32 Departments and 11 Schools are offered to over 81,000 students. 5,000 graduates are enrolled in PhDs and 3rd cycle programmes.
As a comprehensive research university Alma Mater invests in the multidisciplinary cross-cultural approach and in the inseparable connection between research and teaching. One of the most active universities leading and participating in European research and academic cooperation projects, Bologna has formed knowledge alliances with industry and public/private organizations. It is a hub of international networks. Beyond its close European links, it enjoys multiple connections with America, Africa, Asia and Australia.
Research and Innovation are a priority of the University mission.
With regard to Innovation, UNIBO filed 86 new patent applications in 2017, of which 25 are new registrations, thereby giving rise to an active patent portfolio of over 370 patents related to more than 140 inventions. It also has an active portfolio of more than 20 patented plant varieties, 80% of which are increased in value through active licenses with geographic coverage in countries in different parts of the world. UNIBO set up or accredited 27 spin-off companies up to 2017 and can also count Almacube, as business incubator that managed 15 incubated companies in 2017.
With regard to the capability of attracting funding for research and innovation, UNIBO is very active both at National and European level in all the research areas. Activities related to competitive funding programs are supported by the Research Division, with more than 10 years experience and about 50 people assisting the research groups in the whole project lifecycle. A Research Development Office deals with the pre-award phase and the UNIBO strategic positioning at local, national and international level, through integrated networking and lobby activities in each specific research area. While the Programs&Projects Office supports the UNIBO researchers in the implementation phase of the projects with technical, legal, financial and administrative expertise. These Offices strictly cooperate between each other and in strictly connection with the Knowledge Transfer Office, for the Innovation Management expertise and the IP protection and exploitation, and the take up and commercialization of project results.
Thanks to its scientific excellence and a central Project Management support working closely, UNIBO has gained a considerable experience in International and European research projects, successfully participated in FP7: with 274 projects funded in 2007-2013; (58 of them as coordinator) and 87,8ML Euros of funding. In Horizon 2020, UNIBO is so far involved in 223 funded projects (57 as coordinator) with more than 92 ML Euros of funding. UNIBO is also partner of the EIT Knowledge & Innovation Communities (“EIT DIGITAL”, “Climate KIC”, “EIT Raw Materials”) and many of the most important EU initiatives related to the Horizon 2020 framework program (ie. ETPs, EIPs, JPIs, etc).