CBU@MBC

Computational Biology Unit
Molecular Biotechnology Center
University of Torino, Italy
Via Nizza 52
I - 10126 TORINO, Italy

Welcome to the website of the Computational Biology Unit (CBU) of the University of Torino’s inter-faculty Molecular Biotechnology Center (MBC). We're an interdisciplinary reseach team interested in diverse topics regarding computational biology and bioinformatics. Although we have started our collaboration already years ago, the CBU was officially formed in 2006 when the Molecular Biotechnology Center was inaugurated to pool the University's diverse biotechnology research groups and form a center of excellence for interdisciplinary teaching.

People

We are an interdisciplinary team with expertise in molecular biology, medicine, bioinformatics, computer science, mathematics and physics.

Researchers:

	Name: Ferdinando Di Cunto Background: medicine, molecular biology Research interests: cytokinesis, neuronal differentiation, computational biology Homepage: http://www.personalweb.unito.it/ferdinando.dicunto/ [italian] E-mail: ferdinando.dicunto -AT- unito.it
	Name: Mario Giacobini Background: mathematics, computer science Research interests: artificial evolution, artificial life, complex systems, game theory Homepage: http://www.biocut.unito.it/giacobini/ E-mail: mario.giacobini -AT- unito.it
	Name: Paolo Provero Background: physics, bioinformatics Research interests: computational biology, regulatory networks Homepage: under construction E-mail: paolo.provero -AT- unito.it

PhD Students:

	Name: Ugo Ala Background: physics, bioinformatics Research interests: co-expression networks, network analysis Homepage: under construction E-mail: ugo.ala -AT- unito.it
	Name: Rosario M. Piro Background: physics, grid computing, bioinformatics Research interests: disease gene prediction, network analysis, grid computing Homepage: http://www.biocut.unito.it/piro/ E-mail: rosario.piro -AT- unito.it
	Name: Christian Damasco Background: Research interests: Homepage: under construction E-mail: christian.damasco -AT- unito.it
	Name: Antonio Lembo Background: argricultural and plant biotechnologies Research interests: survival analysis in cancer, predictive signatures, miRNAs Homepage: under construction E-mail: antonio.lembo -AT- unito.it

Undergraduate Students:

Name: Elena Grassi
Background: medicine, system administration, programming
Research interests: data-mining, microarray data analysis, genomic annotations
Homepage: http://www.medito.eu.org/vodka [italian]
E-mail: grassi.e -AT- gmail.com

Visiting Researchers/Students:

Name: Christian Darabos
Background: computer science, Bio-inspired/Natural Computation, bioinformatics
Research interests: dynamics of phenomena on gene regulatory networks
Homepage: http://www-iis.unil.ch/~cdarabos/
E-mail: christian.darabos -AT- unil.ch

News @ CBU and MBC

June 22^nd 2007

New webpage online.

Events

The following is a list of events, conferences, summer schools, etc. we are involved in (since 2007):

Upcoming events:

Past events:

Evo*2008 (EvoStar2008) joint events on Evolutionary Computing
EuroGP, EvoCOP and EvoBIO conferences and EvoWorkshops, March 26^th - 28^th, 2008, Napoli (Naples), Italy.
CBU member: Mario Giacobini
Role: EvoWorkshops2008 coordinator

IX Annual Congress 2007 of the Italian Life Sciences Federation (FISV)
September 26^th-29^th, 2007, Riva del Garda, Italy.
CBU member: Ugo Ala
Role: speaker; "Human-Mouse Conserved Coexpression Networks Predict Candidate Disease Genes"

Corso Estivo in Computazione Evolutiva e Vita Artificiale (SECEVitA 2007)
Summer school on Evolutionary Computation and Artificial Life, August 31^st - September 4^th, 2007.
And Workshop Italiano di Vita Artificiale e Computazione Evolutiva (WIVACE 2007)
Italian Workshop on Artificial Life and Evolutionary Computation, September 5^th - 7^th, 2007.
Baia Samuele, Sampieri (Ragusa), Sicily, Italy.
CBU member: Mario Giacobini
Role: lecturer (SECEVitA 2007) and organizing committee (WIVACE 2007)

Open Grid Forum 20 (OGF20)
May 7^th - 11^th, 2007, Manchester, UK.
CBU member: Rosario M. Piro
Role: RUS-WG chair, Joint UR and RUS Session chair.

Evo*2007 (EvoStar2007) joint events on Evolutionary Computing
EuroGP, EvoCOP and EvoBIO conferences and EvoWorkshops, April 11^th - 13^th, 2007, Valencia, Spain.
CBU member: Mario Giacobini
Role: EvoWorkshops2007 chair

Research

The research of the Computational Biology Unit (CBU) focuses on large-scale analysis of transcriptional regulation and gene expression. We develop data-mining strategies to extract biologically relevant information from the enormous amount of data present in the public databases and repositories. This leads to new hypotheses that can be experimentally tested, in particular on the biological or pathological processes in which individual genes or pathways are involved.

The unit also collaborates with several experimental laboratories, within the MBC and elsewhere, providing computational and data-mining expertise.

Publications

Papers:

Find our papers at PubMed.

Posters:

Generation And Analysis Of Human-Mouse Conserved Coexpression Networks
Authors: U. Ala, R. Piro, E. Grassi, C. Damasco, L. Silengo, H. Brunner, P. Provero and F. Di Cunto
IX Annual Congress 2007 of the Italian Life Sciences Federation (FISV), Riva del Garda, Italy, September 26-29, 2007. [ppt]

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data
Authors: L. Miozzi, U. Ala, R. Piro, F. Rosa, F. Di Cunto and P. Provero
The 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology, EMBL Heidelberg, October 14-17, 2006. [ppt]

Identification of candidate disease genes from conserved coexpression
Authors: P. Provero, U. Ala, R.M. Piro, E. Grassi, C. Damasco, L. Silengo, M. Oti, F. Di Cunto
16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July 19-23, 2008.
Outstanding Poster Award, sponsored by the Sudarsky Center for Computational Biology

Prediction of Human Disease Genes by Analysis of Conserved Coexpression
Authors: U. Ala, R. M. Piro, E. Grassi, C. Damasco, L. Silengo, M. Oti, P. Provero and F. Di Cunto.
7th European Conference on Computational Biology (ECCB'08), Cagliari, Italy, September 22-26, 2008. [pdf]

Theses:

A method for prioritizing candidate genes for human hereditary diseases based on co-expression
Author: Rosario M. Piro
Master's thesis, University of Turin, April 2006.

Web Resources

Downloads

Courses

The following are a few links to courses and course materials:

Corso di Abilità Informatiche [website in italian]
Computer course for undergraduate studies in Biotechnologies.

Metodi di Intelligenza Artificiale [website in italian]
Optional course on artificial intelligence for undergraduate studies in Biotechnologies.

Modulo di Statistica ed Informatica (Corsi di Fisica applicata e statistica e Fisica e statistica medica) [websites in italian]
Course in statistics and computer science for undergraduate studies in Veterinary Medicine.

Course of Graphs and Search (website under construction)
Master in Bioinformatics.

Facilities

The following is a brief description of our most important computing facilities (powered by Aethia):

CrickCluster:

Operating system:	Debian GNU/Linux
Batch system:	Torque 1.01
Nodes:	8 (one master and seven worker nodes)
CPUs (master):	1 x Intel(R) Xeon(TM) CPU 3.00GHz
CPUs (worker):	4 x Intel(R) Xeon(TM) CPU 3.00GHz (total: 28)
Memory (master):	1 GB RAM
Memory (worker):	2 GB RAM

Santiago:

Operating system:	Debian GNU/Linux
CPUs:	2 x AMD Opteron (64 bit)
Memory:	16 GB RAM

Ramon:

Operating system:	Ubuntu Linux 9.04
CPUs:	2 x Quad-Core AMD Opteron (64 bit)
Memory:	32 GB RAM

Links

Our group is related to or collaborates with:

	University of Torino, Italy
	Department of Genetics, Biology and Biochemistry (University of Torino)
	Interfaculty School of Biotechnologies (University of Torino)
	Fondazione per le Biotecnologie, Torino, Italy
	Fondazione per la Ricerca Biomedica, Torino, Italy
	Centro Interdipartimentale Sistemi Complessi in Biologia e Medicina Molecolare (SysBioM), Torino, Italy
	INFN FB11 Group - Biological applications of theoretical physics methods, Italy
	Aethia Srl, Colleretto Giacosa (TO), Italy

Contact us

To contact us, write to:

Computational Biology Unit
Molecular Biotechnology Center
Via Nizza 52
I - 10126 TORINO, Italy

or contact one of our team members by e-mail.

How to reach us:

It is fairly easy to find us:

By train:
Right in front of the entrance of the main station (Torino Porta Nuova), take bus/tram number 1 (direction: Artom) or 35 (direction: Amendola) to the bus stop "Piazza Nizza" (three or four bus stops from Porta Nuova depending on what bus you take). From there, follow Via Nizza for a few meters, you will find MBC to your right.
(For a map, see YahooMaps & TuttoCittà)

By plane:
From the airport Torino Caselle, take the bus to Torino Porta Nuova. From there follow the instructions for arrival by train.