The UNICAM team is the founder of the Bioshape and Data Science Lab (BDSLab) at the School of Sciences and Technology of the University of Camerino. The Lab produces open source tools that are available at Lab's Github page
The components of the team are:
- Prof. Luca Tesei, Principal Investigator
- Prof. Emanuela Merelli, Component of the Research Unit
The Lab started working on RNA secondary structures in 2014 and focused on algebraic-based languages and structural abstractions. The Lab is also active on using comparative tools and machine learning in order to classify secondary structures with respect to phylogenetic classification and function and on discovering underlying similarities between the folding of proteins and of RNAs.
In RNA2Fun UNICAM will be responsible for WP1, creation and management of the dataset, providing, processing and receiving data from all the other WPs. UNICAM will also strongly collaborate with UCBM in WP2 for developing the methodologies of evaluation of predicted RNA secondary structures, using its expertise in comparison methods and possibly developing supporting tools. Moreover, the expertise in data analysis will support the study on the relationships between primary and secondary structures of WP2. UNICAM will also work on WP3, in collaboration with UCBM and SAPIENZA, to predict and evaluate RNA secondary structuress of identified portions of lncRNA validated structures. Finally UNICAM will be responsible for WP5 about management and dissemination of the results of this project.
The UCBM team is part of the Research Unit of Non Linear Physics and Mathematical Modeling, Engineering Dep., Campus Bio-Medico Univ. of Rome. The group research lines involve the study, via theoretical and computational advanced multiscale tools, of various classes of physical objects and phenomena, with special focus on biological and biomedical topics.
The components of the team are:
- Prof. Letizia Chiodo, Responsible of the Research Unit
- Prof. Christian Cherubini, Component of the Research Unit
- Nicole Luchetti, junior post-doc, Component of the Research Unit (start 1st November 2024)
In RNA2Fun UCBM will work at WP1, supporting the activities of UNICAM. UCBM will mostly work at WP2, in particular at creating secondary structure models to be tested via the established protocol, and will collaborate with UNICAM at analysing and interpreting the correlation among RNAs characteristics.
UCBM will be also in charge of WP3, working in close collaboration with UNICAM and SAPIENZA to determine reliable secondary structures of the lncRNA pCharme and of other lncRNAs of election.
The SAPIENZA team will work at the Dept. of Biology and Biotech. “Charles Darwin” (BBCD, Sapienza University, Rome). Research at BBCD focuses on macromolecules approached through methods to determine their structure, dynamics, functions and evolution. Prof. Monica Ballarino is scientific director of the ncRNA lab, established in 2012 with the aim to study ncRNAs with physio-pathological relevance.
The components of the team are:
- Prof. Monica Ballarino, Responsible of the Research Unit
- Marco Simula, PhD Student in Genetics and Molecular Biology, Component of the Research Unit
In RNA2Fun SAPIENZA will work at WP4 in close collaboration with UNICAM and UCBM to carry on the WP4 activities. The team will add biological skills and knowledge for populating the dataset with interesting RNA secondary structuress (WP1) and improving their computational modelling (WP2 and WP3) with experimental data.
The recent work of SAPIENZA on the characterization of functional lncRNA-protein interactions, perfectly fits with the aim of the proposed WPs and represents the last tile to satisfy the required and needed interdisciplinarity. Most importantly, for the success of the proposed research, SAPIENZA has access to all the infrastructures in Sapienza required for the cellular activities.