| Network
of Excellence |
CARiMan |
The
Internet Portal for Computer Aided Risk Management |
Dr.
Stefano Volinia
Lab. di Genomica Funzionale
Dip. di Morfologia ed Embriologia
Università degli Studi di Ferrara
Via Fossato di Mortara 64/b
44100 Ferrara (ITALY)
Tel +39-0532-291714
Fax
+39-0532-291533
Cell
+39-340-5836717
s.volinia@unife.it
Università di Ferrara (UniFE)
Name
of institution: Sez. di Istologia - Dip. di Morfologia ed Embriologia -
Universita' Department, service, laboratory or equivalent: Lab. of Functional
Genomics Address: Istologia - Universita' - via Fossato di Mortara 64/b - 44100
- Ferrara - FE Zip Code: 44100 Phone: 0532-291714 Fax: 0532-291533 E-mail:
s.volinia@unife.it Head of department/institution: Prof Angelo Caruso Total
employees number: 30
E-Mail: S.Volinia@unife.it
Major equipment: DNA Microarrays Scanner, Packard DNA sequencer, ABI DNA
microarrayer, BioRobotics MicroGrid Pro ABI PRISM® 7000 Sequence Detection
System Laser Capture Microdissection system, Arcturus Computer: Bioinformatics
Servers and Private Lan
Current
Research:
1
- Automatic detection of differentially regulated biological functions from
microarrays results. Once a table of ESTs and relevant statistical scores is
entered, the application will return a scoring of GO terms related to the
differential expression present within the experiment, including p-values.
2
- Cross-comparison of microarrays results obtained from different platforms (academical
and commercial) The Gene Ontology analysis will be applied to enable
cross-comparisons of microarrays datasets generated from independent
laboratories.
3
- Establishment of a WWW resource to automatically generate and evaluate scoring
of molecular functions, biological processes and cellular components from the
results of an expression profiling experiment. The resource's tools can be
applied to different biological problems, from multiple groups to time course
experiments.
4
- Statistical analysis of the Gene Ontology results. Bootstrap analysis is
performed to define p-values and false detection rates within each dataset.
5
- Automatic association of differential expression to genome maps. Once a table
of ESTs and relevant statistical scores is entered, the application will return
a scoring of the differential expression present within the experiment related
to the chromosomal location of the genes, including p-values.
6
- Cross-comparison of microarrays results obtained from different platforms (academical
and commercial) The application will be applied to enable at a genomic sequence
level cross-compariso ns of microarrays datasets generated from independent
laboratories.
7-
Establishment of a WWW resource to automatically generate a differential
transcriptional map from the results of an expression profiling experiment. The
resource's tools can be applied to different biological problems, from multiple
groups to time course experiments.
8
- Statistical analysis of the Genome-Differential Transcription results.
Bootstrap
analysis is performed to define p-values within each dataset.
9
- Extension of the analysis to most available microarrays platforms. The
applications within the resource can be used for DNA microarrays,
oligonucleotide microarrays and possibly SAGE datasets. Platforms deposited in
GEO and ArrayExpress will be implemented.
10
- Use of the microarrays data stored in public database to annotate a host of
hereditary human diseases for regulated cell functions and chromosomal
differential expression.
Contribution to CARiMan
Project
Manager (PM) for JPA RC Risk in Cancer.
CV of Stefano Volinia
The
PI has been involved in developing bioinformatics applications since 1988
(identification of statistically anomalous oligonucleotides in DNA databases).
Lately he has been responsible for developing a WWW based resource at Harvard
Medical School for the identification of protein-protein interaction and protein
phosphorylation sites (Yaffe et al 2001, Zacchi et al, 2002). Alongside with the
development of in-house scripts for DNA microarrays analysis and management (Francioso
et al 2002, Carinci et al 2002), he started about 6 months ago the construction
of a web application for association of Gene Ontology terms to expression
profiles, and specifically for the identification of regulated molecular
functions and cellular processes. The Web site (alpha-version) is accessible at
the URL http://nbiol28.unife.it/GOal/.
Education
Universita'
di Ferrara B. Sc 1987
Biological
Sciences Universita' di Ferrara Ph. D 1992
Genetics
University of London, UK. MSc 1993
Computer
Science Training Imperial Cancer Research Fund, London, UK. Fellow 1988-1989
Molecular Genetics
Ludwig
Institute for Cancer Research, London, UK. Senior Fellow 1990-1994 Cell Biology
Beth
Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. Human
Frontier Fellow 1996-1998 Cell Biology / Bioinformatics
Employment
and Experience
Present
Position: Histology, Assistant Professor. Lecturer in Molecular Cytology
(Biotechnology), Biology and Histology (Faculty of Medicine).
Research
and Professional Experience
01/01/88-
Research Fellow at Imperial Cancer Research Fund, London, Molecular Analysis of
Mammalian Mutation (Prof. A.-M. Frischauf). Huntington's Disease mapping and
cloning.
01/10/90-
Senior Research Fellow, Ludwig Institute for Cancer Research, London, Receptor
Studies (Prof. M.D. Waterfield). PI 3-kinases cloning and characterization.
07/02/95- Postdoc at Dept of Biochemistry and Molecular Biology (Universita' di
Ferrara). Cellular role of class II PI 3-kinases.
22/04/96-
Human Frontier Science Program Long Term Fellowship, at Division of Signal
Transduction, Beth Israel Deaconess Medical Center, Harvard Medical School,
Boston, USA (Prof. L. C. Cantley). Phosphodependent protein interactions.
Bioinformatics.
01/10/96-to
date Assistant Professor, Histology, Facolta' di Medicina e Chirurgia,
Universita' di Ferrara. Functional Genomics.
01/10/2001-30/04/2003
Telethon Institute for Genetics and Medicine, TIGEM, Naples, Italy.
01/01/2003
to date. Microarrays Bioinformatics, Head, ICC, Rovigo.
1.Publications
Yaffe
MB, Leparc GG, Lai J, Obata T, Volinia S, Cantley LC. A motif-based profile
scanning approach for genome-wide prediction of signaling pathways. Nat
Biotechnol 2001 19(4):348-53. Visnjic D, Crljen V, Curic J, Batinic D, Volinia
S, Banfic H. The activation of nuclear phosphoinositide 3-kinase C2beta in
all-trans-retinoic acid-differentiate d HL-60 cells. FEBS Lett 2002 Oct
9;529(2-3):268-74.
Francioso
F, Carinci F, Tosi L, Scapoli L, Pezzetti F, Passerella E, Evangelisti R,
Pastore A, Pelucchi S, Piattelli A, Rubini C, Fioroni M, Carinci P, Volinia S.
Identification of differentially expressed genes in human salivary gland tumors
by DNA microarrays. Mol Cancer Ther 2002 1(7):533-8.
Carinci
F, Bodo M, Tosi L, Francioso F, Evangelisti R, Pezzetti F, Scapoli L, Martinelli
M, Baroni T, Stabellini G, Carinci P, Bellucci C, Lilli C, Volinia S. Expression
profiles of craniosynostosis-derived fibroblasts. Mol Med 2002 8(10):638-44.
Crljen
V, Volinia S, Banfic H. Hepatocyte growth factor activates phosphoinositide
3-kinase C2 beta in renal brush-border plasma membranes. Biochem J 2002
365:791-9.
Zacchi
P, Gostissa M, Uchida T, Salvagno C, Avolio F, Volinia S, Ronai Z, Blandino G,
Schneider C, Del Sal G. The prolyl isomerase Pin1 reveals a mechanism to control
p53 functions after genotoxic insults. Nature 2002 419(6909):853-7.
Carinci
F, Francioso F, Rubini C, Fioroni M, Tosi L, Pezzetti F, Venturoli L, Volinia S,
Piattelli A. Genetic portrait of malignant granular cell odontogenic tumour.
Oral Oncol 2003 39(1):69-77.
Carinci
F, Francioso F, Piattelli A, Rubini C, Fioroni M, Evangelisti R, Arcelli D, Tosi
L, Pezzetti F, Carinci P, Volinia S. Genetic expression profiling of six
odontogenic tumors. J Dent Res. 2003 Jul;82(7):551-7.
| Network
of Excellence |
CARiMan |
The
Internet Portal for Computer Aided Risk Management |