The group
The group includes the PI, yours truly, and students with a passion for AI, computational modeling, statistics, and affine topics. Lab members belong to several institutions.
Current members
- I. Cazzaniga, Research Fellow (CNR)
- F. Bacic Toplek, Post-doctoral research collaborator (CNR)
- S. Naik, Pre-doctoral research collaborator (CNR)
Where we work
We are located in the Department of Biosciences of the University of Milan. Due to the nature of computational work, we collaborate both in person and online.
Joining opportunities
- Interested in joining? Drop me an email.
- There are usually opportunities for theses (final triennale/specialistica), and occasionally PhD.
- Selection procedures are advertised in the official CNR website (see e.g. sections Concorsi e opportunità, Selezioni online and Concorsi e selezioni).
Alumni
- F. Ballabio, formerly a post-doc with our group; now a post-doc at Helmholtz Center Munich.
- C. Caprai, formerly a research fellow; now a PhD student at Sorbonne University and Institut Pasteur.
- F. Santoro, formerly a research fellow.
Recently supervised students
- G. Salvaneschi, Student of the Quantitative Biology Master Course at the University of Milan, “Benchmarking a novel clustering algorithm for the detection and characterisation of alternative pockets in GPCRs from large-scale molecular dynamics simulations”, 110/110 cum laude, now a SEMM PhD at Human Technopole.
- S. Eissa, Student of the Quantitative Biology Master Course at the University of Milan: “From Geometry to Forces: Algorithmic Differentiation of Collective Variables in Molecular Dynamics Simulations”.
- C. Caprai, Student of the Quantitative Biology Master Course at the University of Milan: “Large Scale Molecular Dynamics Approaches to Data-Driven Binding Mode Identification and Classification”, 110/110 cum laude.
- I. Cazzaniga, Student of the Quantitative Biology Master Course at the University of Milan: “Temperature dependence of the intrinsic dimension of the protein dynamics manifold”, 110/110 cum laude.
- M. Ansari, Student of the Quantitative Biology Master Course at the University of Milan: “Deep Protein Language Models for Property Prediction and Data-Driven Sequence Design: an Application to Hemolytic Peptides”.
- O. Simbari, Laurea Magistrale in Ingegneria Biomedica, University of Pavia: “Automazione di simulazioni molecolari su calcolatore ad alte prestazioni per supporto e generazione di ipotesi farmacologiche”, 110/110 cum laude.
- C. Pacini, Laurea Triennale in Fisica, University of Milan: “Local latent space dimension of the dynamics of biopolymers”.
- I. Boniardi, Corso di laurea in Chimica e Tecnologie Farmaceutiche, University of Milan: “Identificazione di un nuovo hotspot di instabilità della Gelsolina”.
- E. Fagnani, Master degree in Molecular Biotechnology and Bioinformatics, University of Milan: “In silico and in vitro characterization of Type I BIR domains inhibitors in cancer therapy”, 110/110 cum laude.
- I. Bussoli, Corso di Laurea Magistrale in Scienze Statistiche, Università degli Studi di Padova: “Eventi di legame rari in Dinamica Molecolare: il caso del dominio SH2 e del peptide pYEEI”.
Courses
In the past I’ve lectured for courses including:
- Fondamenti di Informatica Laboratorio (Dept. of Engineering and Computers Science, University of Pavia, Italy)
- Molecular Simulations (Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain)
- High Performance Computing (Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain)
- Fonts i tecnologies de la informació (Biologia Humana, Universitat Pompeu Fabra, Barcelona, Spain)
Some course material is linked below (likely outdated):
- Automated ligand parametrization at the High Throughput Molecular Dynamics workshop (session 2), PRBB Barcelona, 7 Nov. 2013
- Coarse graining at the High Throughput Molecular Dynamics workshop (session 2), PRBB Barcelona, 8 Nov. 2013
- High performance computing (HPC), Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, 2012
- Introduction to database modeling, part of the course Fonts i Tecnologies (spanish, biology undergraduate), Universitat Pompeu Fabra, 2011
- Slides for the High performance computing (HPC) course: class 7, class 8 (master Bioinformatics for Health Sciences), Universitat Pompeu Fabra, 2010
- Slides for the Molecular Simulations (MSI) course: preparing simulations (class 2); free energy of deca-alanin (class 23-24) (master Bioinformatics for Health Sciences), Universitat Pompeu Fabra, 2010
- Slides for the course Fondamenti Informatica Laboratorio (Università di Pavia, 2002-2008)