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BioPhys - Computational Biology

BioPhys - Computational Biology



Settore ERC

LS2_4 - Gene regulation


The main goal of the BioPhys network  is  the study of problems and systems of Biological interest with the tools and ideas typical of theoretical physics. Our main focus is in Molecular Biology, a research context which has seen an impressive development in these last years  and is nowadays of central relevance, both for the deep scientific questions which it raises and for the large number of potential biomedical applications.

In this framework, our research project is organized in three main directions:

1. Numerical simulations of systems of biological interest.  (protein folding, biomolecules aggregation, protein-protein interactions...)
2. Neural Networks and related systems. (Study of Brain connectivity, emergence of spatio-temporal patterns....)
3. Regulatory Networks  (Gene Regulatory Networks, Immune Networks, Chromatin organization....)

The common theme and the unifying setting of these research lines is the use of theoretical physics methods to model and analyse these problems. In particular methods borrowed from the statistical mechanics of disordered systems (Spin Glasses, Hopfield model...);  computational tools typical of the simulation of many-body physical systems (Montecarlo Simulations, Molecular Dynamics,...);  advanced mathematical tools (Graph theory, Network Theory, Stochastic Equations....)
The most relevant aspect of our research network is the strong interaction of all the units with biologist. All the problems that we address stem from precise biological questions to which we try to give quantitative and testable answers.  

2012-2015 "Grant di Ateneo" GeneRNet
"Computational and experimental approaches to identify and model biologically relevant Gene Regulatory Networks"


Prodotti della ricerca


  • Protein degradation sets the fraction of active ribosomes at vanishing growth
    2022-01-01 Calabrese L.; Grilli J.; Osella M.; Kempes C.P.; Lagomarsino M.C.; Ciandrini L.
  • A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell
    2022-01-01 Ruiz Tejada Segura, Mayra L.; Abou Moussa, Eman; Garabello, Elisa; Nakahara, Thiago S.; Makhlouf, Melanie; Mathew, Lisa S.; Wang, Li; Valle, Filippo; Huang, Susie S.Y.; Mainland, Joel D.; Caselle, Michele; Osella, Matteo; Lorenz, Stephan; Reisert, Johannes; Logan, Darren W.; Malnic, Bettina; Scialdone, Antonio; Saraiva, Luis R.
  • The Dynamics of Aerotaxis in a Simple Eukaryotic Model
    2021-01-01 Biondo M.; Panuzzo C.; Ali S.M.; Bozzaro S.; Osella M.; Bracco E.; Pergolizzi B.
  • Initial cell density encodes proliferative potential in cancer cell populations
    2021-01-01 Enrico Bena C.; Del Giudice M.; Grob A.; Gueudre T.; Miotto M.; Gialama D.; Osella M.; Turco E.; Ceroni F.; De Martino A.; Bosia C.
  • Concurrent processes set E. coli cell division
    2018-01-01 Micali, Gabriele; Grilli, Jacopo; Osella, Matteo; Cosentino Lagomarsino, Marco
  • Dissecting the Control Mechanisms for DNA Replication and Cell Division in E. coli
    2018-01-01 Micali, Gabriele; Grilli, Jacopo; Marchi, Jacopo; Osella, Matteo; Cosentino Lagomarsino, Marco
  • Relevant parameters in models of cell division control
    2017-01-01 Grilli, Jacopo; Osella, Matteo; Kennard, Andrew S; Lagomarsino, Marco Cosentino
  • Step by Step, Cell by Cell: Quantification of the Bacterial Cell Cycle
    2017-01-01 Osella, Matteo; Tans, Sander J; Cosentino Lagomarsino, Marco
  • Emergent statistical laws in single-cell transcriptomic data
    2023-01-01 Lazzardi, Silvia; Valle, Filippo; Mazzolini, Andrea; Scialdone, Antonio; Caselle, Michele; Osella, Matteo
  • Multiomics Topic Modeling for Breast Cancer Classification
    2022-01-01 Valle F.; Osella M.; Caselle M.
  • The impact of whole genome duplications on the human gene regulatory networks
    2021-01-01 Mottes F.; Villa C.; Osella M.; Caselle M.
  • A Topic Modeling Analysis of TCGA Breast and Lung Cancer Transcriptomic Data
    2020-01-01 Valle, Filippo; Osella, Matteo; Caselle, Michele
  • A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome
    2020-01-01 Riba, Andrea; Fumagalli, Maria Rita; Caselle, Michele; Osella, Matteo
  • Investigating the epi-miRNome: Identification of epi-miRNAs using transfection experiments
    2019-01-01 Reale E.; Taverna D.; Cantini L.; Martignetti L.; Osella M.; De Pitta C.; Virga F.; Orso F.; Caselle M.
  • Biophysical Analysis of miRNA-Dependent Gene Regulation
    2018-01-01 Riba, Andrea; Osella, Matteo; Caselle, Michele; Zavolan, Mihaela
  • Statistics of Shared Components in Complex Component Systems
    2018-01-01 Mazzolini, Andrea; Gherardi, Marco; Caselle, Michele; Cosentino Lagomarsino, Marco; Osella, Matteo
  • Heaps' law, statistics of shared components, and temporal patterns from a sample-space-reducing process
    2018-01-01 Mazzolini, Andrea; Colliva, Alberto; Caselle, Michele; Osella, Matteo
  • Modelling the evolution of transcription factor binding preferences in complex eukaryotes
    2017-01-01 Rosanova, Antonio; Colliva, Alberto; Osella, Matteo; Caselle, Michele
  • Stochastic timing in gene expression for simple regulatory strategies
    2017-01-01 Co, Alma Dal; Lagomarsino, Marco Cosentino; Caselle, Michele; Osella, Matteo
  • Interplay of microRNA and epigenetic regulation in the human regulatory network.
    2014-01-01 Osella M;Riba A;Testori A;Corà D;Caselle M
  • Gene autoregulation via intronic microRNAs and its functions.
    2012-01-01 Bosia C; Osella M; El Baroudi M; Corà D; Caselle M.
  • The role of incoherent microRNA-mediated feedforward loops in noise buffering
    2011-01-01 Caselle M; Osella M; Bosia C; El Baroudi M; Cora D
  • Gene autoregulation via intronic microRNAs and its functions
    2011-01-01 El Baroudi M; Bosia C; Osella M; Cora' D; Caselle M
  • A Curated Database of miRNA Mediated Feed-Forward Loops Involving MYC as Master Regulator.
    2011-01-01 El Baroudi M; Corà D; Bosia C; Osella M; Caselle M.
  • The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering
    2011-01-01 Matteo Osella; Carla Bosia; Davide Cora'; Michele Caselle
  • Entropic contributions to the splicing process
    2009-01-01 M. Osella; M. Caselle
  • Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer
    2019-01-01 Cantini L.; Bertoli G.; Cava C.; Dubois T.; Zinovyev A.; Caselle M.; Castiglioni I.; Barillot E.; Martignetti L.
  • Molecular inverse comorbidity between alzheimer’s disease and lung cancer: New insights from matrix factorization
    2019-01-01 Greco A.; Valle J.S.; Pancaldi V.; Baudot A.; Barillot E.; Caselle M.; Valencia A.; Zinovyev A.; Cantini L.
  • Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data
    2019-01-01 Cantini L.; Caselle M.
  • A review of computational approaches detecting microRNAs involved in cancer
    2017-01-01 Cantini, L; Caselle, M; Forget, A; Zinovyev, A; Barillot, E; Martignetti, L
  • MicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes
    2015-01-01 Cantini, Laura; Isella, Claudio; Petti, Consalvo; Picco, Gabriele; Chiola, Simone; Ficarra, Elisa; Caselle, Michele; Medico, Enzo
  • Detection of gene communities in multi-networks reveals cancer drivers
    2015-01-01 Cantini, Laura; Medico, Enzo; Fortunato, Santo; Caselle, Michele

Ultimo aggiornamento: 05/09/2023 15:42
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