Curriculum Vitae
Dott. ssa Francesca Cordero
Department of clinical and biological sciences University of Torino
Regione Gonzole, 10149 Orbassano (TO) (Italy)
Department of computer science University of Torino
Corso Svizzera 185, 10149 Torino (Italy)
Personal information
Nationality Italian;
Date of birth 19 December 1980;
Place of birth Ivrea (TO) ITALY;
Address via Marucca, 35 Burolo (TO) ITALY;
Phone Number 3491701932;
E-mail :[email protected]
Web Page : www.di.unito.it/∼fcordero
Academic Degree
• December 2009 - present fellowship (Borsa di studio) at Department of Clinical and Biological Sciences, in University of Torino.
• December 2007 - November 2009 post-PhD fellowship (Assegno di ricerca) at Department of Clinical and Biological Sciences, in University of Torino.
• 15 July 2008 ”Ph.D.” in Computer Science at University of Torino Ph.D. thesis title Graphical models for the prediction of transcrip-
tion factor binding sites Advisor Prof Marco Botta
Co-Advisor Prof Gary D. Stormo
• Novembre 2004/2007 PhD in Computer Science at University of Torino.
• 8 July 2004 Laurea in Biological science at University of Torino Laurea thesis title Identificazione di geni estrogeno responsivi con
metodi computazionali
Advisor Prof Raffaele A. Calogero Co-Advisor Prof Michele De Bortoli
• July 1999 High school degree at Liceo Scientifico ”A.Gramsci” Ivrea (TO).
PhD Schools
• Bertinoro International Spring School 2005 (BISS 2005).
• Computational and statistical aspects of microarray analysis. Bres- sanone June 2005.
Fellowships
• November 2009 awarded fellowship (Borsa di studio) for project in the field of medical science. The duration of this fellowship was 12 months. Title of the project ”Identificazione di nuovi bersagli terapeu- tici espressi dalle cellule staminali tumorali mammarie”.
• December 2007 awarded post-PhD fellowship (Assegno di ricerca) for project in the field of medical science. The duration of this fellowship was 24 months. Title of the project ”Ottimizzazione della cura di lesioni tumorali precoci: integrazione di molecole antisenso e vaccini a DNA nel modello murino del carcinoma mammario BALB-neuT”.
• November 2004 awarded PhD fellowship of ”Fondazione CRT - Pro- getto Langrange”. The duration of this fellowship was 24 months.
Research Training
April - October 2006 visiting scholar (six months) in research group of prof.
Gary Stormo in the Department of Genetics, Center for Genome Sciences, Washington University Medical School in St. Louis, (USA).
Research interests
• Computational Biology;
• System Biology;
• Reverse engineering of cellular systems;
• Microarray data analysis and mining.
Publications
In Refereed International Journal
[JuPensa09] Pensa RG, Boulicaut J-F, Cordero F, Atzori M. Co-clustering Numerical Data under User-defined Constraints Statistical Analy- sis and Data Mining Wiley-Blackwell. Accepted: November 2009.
ISSN: 1932-1864.
[JuDellaBeffa08] Della Beffa C, Cordero F, Calogero RA.Dissecting an alter- native splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays BMC Genomics 2008 Nov 28;9:571. ISSN: 1471-2164.
[JuCordero07] Cordero F, Botta M, Calogero RA.Microarray data analy- sis and mining approaches Functional Genomics and Proteomics 2007 Dec;6(4):265-81. Epub 2008 Jan 22. ISSN: 1473-9550.
[JuCalogero07] Calogero RA, Cordero F, Forni G, Cavallo F Inflamma- tion and breast cancer. Inflammatory component of mammary carcino- genesis in ErbB2 transgenic mice Breast Cancer Res. 2007 Aug 10;9(4):211 ISSN: 1465-542X.
[JuSanger07] Sanger R, Cordero F, Calogero RA oneChannelGUI: a graph- ical interface to Bioconductor tools, designed for life scientists who are not familiar with R language Bioinformatics 2007 Sep 17. ISSN:
1367-4803.
[JuSaviozzi06] Saviozzi S, Cordero F, Lo Iacono M, Novello S, Scagliotti G, Calogero AR Selection of suitable reference genes for accurate normal- ization of gene expression profile studies in non-small cell lung cancer BMC Cancer 2006 6:2006. ISSN: 1471-2407.
[JuCavallo05] Cavallo F, Astolfi A, Iezzi M, Cordero F, Lollini PL, Forni G, Calogero RA An integrated approach of immunogenomics and bioin- formatics to identify new Tumor Associated Antigens (TAA) for mam- mary cancer immunological prevention BMC Bioinformatics 2005 Dic 1. ISSN: 1471-2105.
[JuLazzarato04] Lazzarato F, Franceschinis G, Botta M, Cordero F, Calogero RA RRE: a tool for the extraction of non-coding regions surround- ing annotated genes from genomic datasets Bioinformatics 2004 Nov 1;20(16):2848-50. 2004 Apr 29. ISSN 1367-4803.
Proceeding of Refereed International Conferences
[PrVisconti10] Visconti A, Cordero F, Botta M, Calogero RA Gene Ontology rewrited for computing gene functional similarity. In Proceeding of the third International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2010) IEEE Computer Society Press. [To appear]
[PrCordero09a] Cordero F, Manini D, Gribaudo M, Balbo G An intuitive object-oriented methodology to model biological pathways. In Proceed- ing of the fourth Sysbiohealth Symposium Loncomia Innovazione Press. pp 62-64 November 25-27, 2009, Milano, Italy. ISBN 978-88- 903154-6-6
[PrCordero09b] Cordero F, Pensa RG, Visconti A, Ienco D, Botta M Ontology- driven Co-clustering of Gene Expression Data. In Proceedings of the 11th Conference of the Italian Association for Artificial Intel- ligence (AI*IA) LNAI 5883 Springer pp 426-435. December 9-12, 2009, Reggio Emilia, Italy. ISSN: 0302-9743.
[PrCordero09c] Cordero F, Manini D, Gribaudo M. Modeling Biological Pathways: an Object-oriented like Methodology Based on Mean Field Analysis In Proceedings of the Third International Conference on Advanced Engineering Computing and Applications in Sci- ences(ADVCOM) IEEE Computer Society Press. October 2009, Sliema,Malta.
[PrNapione09] Napione L, Manini D, Cordero F, Horvath A, Picco A, De Pierro M, Pavan S, Sereno M, Veglio A, Bussolino F and Balbo G On the use of Stochastic Petri Nets in the analysis of a signal transduction pathways for angiogenesis process In Proceedings Lectures Notes
in Bioinformatics of the Computational Methods of System Biology LNBI 5688 Springer-Verlag, pp. 281-295, 2009 Bologna Italy.
ISSN: 0302-9743.
[PrLenzken09] Lenzken SC, Vivarelli S, Zolezzi F, Cordero F, Della Beffa C, Calogero RA and Barabino S Genome-wide Search For Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS). In Proceeding of CISIS (International Conference on Complex, Intelligent and Software Intensive Systems IEEE. Fukuoka, Japan, March 16-19 2009, p. 20-27
[PrCordero09d] Cordero F, Visconti A, and Botta M A new protein motif ex- traction framework based on constrained co-clustering In Proceedings of the 24th Annual ACM Symposium on Applied Computing ACM Press, March 2009, Hololulu, Hawaii USA.
Refereed International Conferences and Posters
[PoCordero08a] Cordero F, Visconti A and Botta M A web interface to ex- tract protein motifs by constrained co-clustering RECOMB Satellite on Regulatory Genomics 2008 Boston MIT Broad Oct 28 Nov 2 2008, Boston.
[PoCordero08b] Cordero F., Visconti A. and Botta M. A motif extraction framework applied on RNA secondary structure Alternative Splicing Workshop, October 3, 2008, Milano
[PoCordero07] Cordero F. and Gary D Stormo. Crystal structure and phylogenetic data to infer the binding motif for new protein The 4th Annual RECOMB Satellite on Regulatory Genomics 2007 Boston MIT Broad Oct. 11-13 2007, Boston.
[PoAltobelli06] G. Altobelli, D. Cora; , F. Cordero, M. Caselle and M. De Bortoli Identifying Networks of Estrogen-Responsive Genes in Breast Cancer Cells The 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology Oct. 14-17 2006, Hei- delberg
[PoCordero06] Cordero F., Saviozzi S, Di Renzo MF, Oliveiro M, Cirenei N, Calogero RA Microarray cross-platforms differential expression vali- dation Bioinformatics Italian Society-BITS 2006 Bologna 28-29 April 2006. Poster, Abstract 38.
[PoCavallo06] Cavallo F, Astolfi A, Iezzi M, Cordero F, Lollini PL, Forni G, Calogero RA An integrated approach of immunogenomics and bioinfor- matics to identify new Tumor Associates Antigen (TAA) for mammary cancer immuno-prevention. Models and Methods for Human Genomics FIMA International Conference, Ayas-Champoluc, Aosta Valley, January 23-27, 2006
[PoCardamone05] Cardamone M, Cordero F, Lazzarato F, Cicatiello D, Scafoglio C, Cimino D, Basile A, Weisz A, Calogero RA, De Bortoli M.
Bioinformatic and functional analysis of ERE-contain Genes EMBO Conference, Nuclear receptors from chromatin to disease Riva del Garda, 29 Sept - 1Oct 2005
Talks in international conferences
• An intuitive object-oriented methodology to model biological pathways In the fourth Sysbiohealth Symposium, November 2009 Milano, Italy
• Modeling Biological Pathways: an Object-oriented like Methodology Based on Mean Field Analysis In the Third International Conference on Ad- vanced Engineering Computing and Applications in Sciences(ADVCOM) October 2009, Sliema, Malta.
• On the use of Stochastic Petri Nets in the analysis of a signal transduc- tion pathways for angiogenesis process In Bioinformatics of the Com- putational Methods of System Biology, September 2009 Bologna Italy.
• A motif extraction framework applied on RNA secondary structure in Alternative Splicing Workshop, October 2008, Milano
Invited Speaker
• Seminar on next generation sequencing algorithms at Complex Systems PhD course, March 2010, University of Torino.
• 4th Annual Meeting, Mini-workshop on Regulatory Networks, 5 Febru- ary 2010 at Department of Biology, University of Torino.
• RNA sequencing Seminar, Taking RNA studies to the next level, 1 De- cember 2009, University La Sapienza, Roma.
Academic Teaching
• A.A. 2009/2010
Professore a contratto: ”Programmazione” in Master degree in ”In- formatica Giuridica”, University of Piemonte Orientale.
• A.A. 2004/2005 2005/2006 2006/2007 Courses
Laboratorio del corso di bioinformatica (Master degree in ”Scienze Biologiche” and ”Informatica”).
Laboratorio del corso di biologia molecolare (Master degree in ”Medic- ina”).
• A.A. 2007/2008 2008/2009 Courses
Ciclo di semiari propedeutici alla bioinformatica (Master degree in ”Scienze Biologiche” and ”Informatica”).
Laboratorio del corso di bioinformatica (Master degree in ”Scienze Biologiche” and ”Informatica”).
Laboratorio del corso di biologia molecolare (Master degree in ”Medic- ina”).
• Instructor in Data Analysis Workshop - GeneChip EXON 1.0 ST array Practical Data Analysis Course, Dept. Clinical and Biological Sciences, Orbassano (TO) June 24-26, 2008
• Instructor in Data Analysis Workshop - GeneChip EXON 1.0 ST array Practical Data Analysis Course, Dept. Clinical and Biological Sciences, Orbassano (TO) November 19-21, 2008
• Instructor in Data Analysis Workshop - GeneChip EXON 1.0 ST array Practical Data Analysis Course, Dept. Clinical and Biological Sciences, Orbassano (TO) December 9-11, 2009
Research Activities: a short description
The research topics developed in the last years are:
• System Biology: Quantitative analysis and Reverse engineer- ing of cellular systems
The major goal of system biology concerns the modelling, simulation and numerical analysis of biological systems. This field is becoming in- creasingly significant in biology and medicine environments. Indeed it is a of great interest the deep understanding of all the mechanisms un- derlying the kinetics of biochemical reactions characterizing biological pathways, in terms of concentration of substrates and products as well as rates of reactions. I have worked on the development of a method- ology that allows to perform qualitative and quantitative analysis of a selected portion of signal transduction events involved in angiogene- sis process [PrNapione09]. This approach is based on the use of Petri Nets (PN) and in some cases their variant called Stochastic Petri Nets (SPNs), that provide a detailed representation of the biological model.
Moreover a simplification process is applied in order to obtain a model where the number of parameters is reduced and the analysis results tractable from the computational point of view.
Moreover I have worked on the development of a object-oriented method- ology, based on the Mean Field Analysis, that offers an intuitive way to describe the behavior of biological systems characterized by a huge number of interacting objects. To underline the intuitive and the ap- plicability of this formalism we model the lac operon gene regulatory
mechanism and glycolysis pathway [PrCordero09a] [PrCordero09b]. A graphical tool adressed to biologists that exploits this approach is in construction.
• Identification of Transcriptional Factor Binging Sites
The Gene regulation is partly mediated by the binding of protein tran- scription factors (TFs) to the cis-regulatory regions of the genome.
Transcriptional factors interpret the genome’s regulatory code by bind- ing to specific sequences to induce or repress gene expression. This is why accurate genome-wide characterization of TF binding sites (TF- BSs) is a necessary prerequisite for deciphering expression patterns of complex genes. In [JuCordero08] we reviewed some of the state-of-the- art methods for TFBS identification.
In my PhD thesis [ThCordero08] a method was developed allowing one to infer the binding site of a TF from DNA-protein interaction struc- tures. In this work, the interaction information is obtained from X-ray diffraction and Nuclear Magnetic Resonance (NMR) experiments. The probabilistic representation of the DNA-protein interaction is improved by using probabilistic graphical models. Both Markov Random Fields and Bayesian Networks have been built starting from the crystal data.
This was the first time that extensive structural information has been exploited to predict TFBSs. More recently, I started to explore whether conditioned graphical models and the boolean features framework could be used to improve the prediction accuracy.
• Microarray analysis
Microarray based transcription profiling is now a consolidated method- ology and has widespread use in areas such as pharmacogenomics, di- agnostics and drug target identification. Large-scale microarray stud- ies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data anal- ysis and mining. When microarrays became a methodology of general use, considerable effort was made to produce algorithms and methods for the identification of differentially expressed genes. In this topic I
worked on both the develop of graphical interface in R for data analysis of one channel microarrays (i.e. Affymetrix and Applied Biosystems) [JuSanger07] and on the definition of analysis work-flow for GeneChip Exon [JuDellaBeffa08]. Moreover I mined genome-wide transcription data to search putative tumor associated antigen in mammary cancer [JuCavallo05] [JuCalogero07].
For what concern the data mining I also worked on a constraints co- clustering techniques [JuPensa10] specifically applied on gene expres- sion data [PrCordero09b], in this context about the definition of con- straint we re-written the Gene Ontology (RGO) [PrCordero10] aiming at obtaining a more compact and informative ontology, leading to closer biological regulated GO terms. The RGO will help researcher to easily identify the genes belonging to the same network module without the need of additional data.
Il sottoscritto dichiara inoltre di essere informato che , ai sensi e per gli effetti di cui all’art. 13 D.Lgs 30.06.2003 n. 196, i dati personali forniti dai candidati saranno raccolti presso la Divisione Attivit´a Istituzionali/Ufficio Concorsi e trattati per le finalit´a di gestione della procedura di valutazione comparativa e dell’eventuale procedimento di assunzione in servizio.
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