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Rosario M. Piro

Department of Theoretical Bioinformatics
German Cancer Research Center
[Deutsches Krebsforschungszentrum (DKFZ)]
Heidelberg, Germany

This is the academic website of Rosario M. Piro, postdoctoral fellow in the Network Modeling Group at the Dep. of Theoretical Bioinformatics of the German Cancer Research Center (DKFZ).

Research interests:

Bioinformatics - with a particular focus on cancer metabolism and its regulation, cancer genetics/genomics, network analysis, and disease gene prediction.
Grid Computing - with a particular focus on grid accounting, resource usage prediction and economic approaches to job scheduling and workload balancing.
Philosophy of Biology - with a particular focus on gene concepts and notions of essentialism, information and genetic programs in biology.

Education:

Undergradute studies (Vordiplom and Laurea) in physics at the University of Heidelberg (Germany) and the University of Torino (Italy).

Graduate studies (Laurea Specialistica) in physics at the University of Torino and the Italian National Institute of Nuclear Physics - Section of Torino (INFN Torino). Field of study: Grid Computing in High Energy Physics; Economic Models for the Distributed Grid Accounting System (DGAS) of the European DataGrid (EDG).

Graduate studies (Master's degree) in bioinformatics at the University of Torino and the Fondazione per le Biotecnologie (Foundation for Biotechnologies, Torino). Field of Study: Prioritization of candidate genes for human hereditary diseases.

PhD in molecular medicine with focus on bioinformatics at the Molecular Biotechnology Center and the Department of Genetics, Biology and Biochemistry of the University of Torino.

Work experience:

Student researcher/programmer (10/1997 to 7/1999 and 10/2000 to 3/2001) in the Division of Molecular Biophysics of the German Cancer Research Center (Deutsches Krebsforschungszentrum - DKFZ, Heidelberg). Responsibilities included the maintenance and improvement - in the C and Fortran programming languages - of programs for genetic sequence analysis and their adoption to HUSAR (Heidelberg Unix Sequence Analysis Resources).

Software developer at DCS Software e Servizi S.r.l. (6/2003 to 9/2004). Development of web and stand-alone applications for lawyers associations ("ordini degli avvocati"), e.g. for the management of and online access to sentences in digital form, in particular for the lawyers associations of Milan, Turin and Florence.

Researcher/programmer for INFN Torino (2/2005 to 8/2008) within the Middleware Reengineering & Integration task (JRA1) of the EGEE and EGEE-II projects (Enabling Grids for E-sciencE), within the Operations Service Activity (SA1) of the EGEE-III project, and within the JRA1 Accounting Activity of the OMII-Europe project (Open Middleware Infrastructure Institute for Europe). Research and development as well as improvement of grid middleware for resource usage accounting, namely the Distributed Grid Accounting System (DGAS). Coordination of the OMII-Europe project's JRA1 Accounting Activity task (4/2006 to 11/2006).

Bioinformatics

Department of Theoretical Bioinformatics
German Cancer Research Center
[Deutsches Krebsforschungszentrum (DKFZ)]
Heidelberg, Germany

I'm currently a postdoctoral fellow in the Network Modeling Group at the Dep. of Theoretical Bioinformatics of the German Cancer Research Center (DKFZ).
My research is focused on cancer genetics and changes in metabolic networks in cancer, but I'm also interested in topics related to the identification and the prioritization of candidate genes for human hereditary disorders.

Publications:

see here.

Posters:

• PathWave Update: Identifying Regulatory Changes in Metabolic Pathways
  Authors: R. M. Piro, G. Schramm, et al.
  International Conference on Systems Biology (ICSB-2011), Heidelberg/Mannheim, Germany, Aug. 28-Sept. 1, 2011. [pdf]

• Disease gene prediction based on tissue-specific conserved coexpression
  Authors: R. M. Piro, U. Ala, et al.
  European Conference on Computational Biology (ECCB2010), Ghent, Belgium, September 26-29, 2010. [pdf]

• Tissue-specific conserved coexpression for disease gene prediction and hypotheses generation
  Authors: R. M. Piro, U. Ala, et al.
  European Human Genetics Conference (ESHG2010), Göteborg, Sweden, June 12-15, 2010. [pdf]
  Poster Award Candidate (61 candidates out of over 1,400 accepted posters).
  Abstract published in: Eur J Hum Genet 18(Suppl.1):275, 2010.

• 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]

• 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.

• 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]

Lectures/Courses:

• Abilità Informatiche (esecitazioni) - Secondo Modulo [italian]
  Laurea di Primo Livello, Scuola Universitaria Interfacoltà in Biotecnologie, Università degli Studi di Torino.
  A.A. 2007/2008, A.A. 2008/2009, A.A. 2009/2010 and A.A. 2010/2011 (first semester):
  Lab. 1 [pdf], Lab. 4 [pdf (testo), zip (files)], Lab. 7 [pdf], Lab. 10 [pdf (testo), zip (files)], Lab. 13 [pdf].
  Introduzione al CD Linux live: [pdf].

• Phenotype analysis in humans using OMIM
  Master's Course in Bioinformatics, University of Torino and Fondazione per le Biotecnologie, May 26th, 2007. [pdf]

Philosophy of Biology

I have recently developed an interest in the philosophy of biology, with a particular focus on evolution, gene concepts and notions of essentialism, and information and genetic programs in biology, although my philosophical research is mainly centered around biological questions that I study in bioinformatics, with the purpose of complementing these studies.

Publications:

see here.

Grid Computing

Istituto Nazionale di Fisica Nucleare
Sezione di Torino (INFN Torino), Italy
[until August 2008]

Research and middleware development:

I worked at INFN Torino as one of the developers of the Distributed Grid Accounting System (DGAS), that has been developed within the European DataGrid (EDG) and Enabling Grids in E-sciencE (EGEE) projects (see below) and has participated in the EGEE-II/III and OMII-Europe projects.
My research in the field of grid accounting was focused on topics regarding resource usage prediction and the application of economic models to the grid scheduling problem (workload balancing, economic brokering).

Project participations:

European DataGrid (EDG) - 4/2002 to 3/2004
Enabling Grids for E-sciencE (EGEE) - 4/2004 - 3/2006
Open Middleware Infrastructure Institute for Europe (OMII-Europe) - 4/2006 to 11/2006
Enabling Grids for E-sciencE II and III (EGEE-II/III) - 12/2006 - 8/2008

Open Grid Forum & Resource Usage Service:

As an individual member of the Open Grid Forum (OGF) I was interested in standardization, above all regarding issues related to accounting in grid environments and served for several years as one of the chairs of the Resource Usage Service (RUS) working group, contributing also to the Usage Record (UR) working group.

Publications:

see here.

Presentations:

• Consistency of Accounting Information with DGAS
  EGEE JRA1 All Hands Meeting, Helsinki/Espoo, Finland, June 18-20, 2007. [pdf, ppt]

• Joint UR And RUS Session (on aggregation of usage records)
  Open Grid Forum 20 (OGF20), Manchester, UK, May 10, 2007. [pdf]
  (held as a chair of the joint session of the OGF UR and RUS working groups)

• DGAS - Basic concepts and proposals for the UR format
  GridWorld/Global Grid Forum 18 (GGF18), Washington, DC, September 11-14, 2006. [pdf]
  (Note: due to time constraints only the proposals for version 2 of the GGF Usage Record where presented and discussed, the entire talk is provided here for completeness.)

• APEL & DGAS - A vertical infrastructure for Grid Accounting (joint talk with APEL developer Dave Kant, RAL)
  EGEE JRA1 All Hands Meeting, CERN, March 23, 2006. [pdf]

• Distributed Grid Accounting System - Brief Overview & DGAS2APEL Interface
  4th EGEE Conference, Pisa, Italy, October 24-28, 2005. [pdf]

• DataGrid Accounting System - Brief overview & DGAS2APEL interface
  Joint OSG/EGEE Grid Operations Workshop, Culham, UK, September 28th, 2005. [pdf]

• DataGrid Accounting System - Basic concepts and current status
  eIRG Workshop on e-Infrastructures, Amsterdam, Netherlands, May 13, 2005. [pdf]

• Simulation of Price-sensitive Resource Brokering and the Hybrid Pricing Model with DGAS-Sim
  13th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises (WETICE-2004), track on Emerging Technologies for Next generation GRID (ETNGRID 2004), Modena, Italy, June 14-16, 2004. [pdf]

• Accounting economico e bilanciamento del carico di lavoro per la European DataGrid (italian)
  Internal Meeting with Eurix Group and Oracle Italia, Torino/Italy, December, 2003. [pdf, sxi]

• DGAS, An Economy-based Accounting Infrastructure for the DataGrid
  4th International Workshop on Grid Computing (GRID2003), held in conjunction with SC2003, Phoenix, Arizona (USA), November 17th, 2003. [pdf, sxi]

• DGAS-Sim, Simulation of economic brokering with the Hybrid Pricing Model
  EDG WP1 Meeting, Rome, November 6-7, 2003. [pdf, sxi]

• DGAS-Sim, Simulation of economic brokering
  EDG WP1 Meeting, Prague, July 7-8, 2003. [pdf, sxi]

Other documents:

• Evaluation and Design Plan of a RUS Interface for DGAS
  Technical report. DRAFT (Version 0.2) - September 22, 2006. [pdf]

Publications

Bioinformatics (and related) - Papers:

• Computational approaches to disease-gene prediction: rationale, classification and successes
  Authors: Rosario M. Piro, Ferdinando Di Cunto
  FEBS Journal 279(5):678-696, 2012. [available at: Wiley]

• An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction
  Authors: Rosario M. Piro^*, Ugo Ala^*, Ivan Molineris^* et al. (*= joint first authors)
  European Journal of Human Genetics 19(11):1173-1180, 2011. [available at: Nature Publishing Group]

• Evaluation of candidate genes from orphan FEB and GEFS+ loci by analysis of human brain gene expression atlases
  Authors: Rosario M. Piro, et al.
  PLoS ONE 6(8):e23149, 2011. [available at: PLoS]

• Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR
  Authors: Rosario M. Piro, et al.
  Bioinformatics 26(18):i618-624, 2010. [presented at the European Conference on Computational Biology 2010 (ECCB10), September 26-29, Ghent, Belgium; available at: Oxford Journals]

• Generation of Functional Hepatocytes from Mouse Germline Cell-derived Pluripotent
  Stem Cells in vitro
  Authors: Sharmila Fagoonee et al.
  Stem Cells and Development 19(8):1183-1194, 2010. doi:10.1089/scd.2009.0496 [available at: Liebert Online]

• Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis
  Authors: Uga Ala^*, Rosario M. Piro^*, et al. (*= joint first authors)
  PLoS Computational Biology 4(3):e1000043, 2008. doi:10.1371/journal.pcbi.1000043 [available at: PLoS]

• Functional Annotation and Identification of Candidate Disease Genes by Computational Analysis of Normal Tissue Gene Expression Data
  Authors: Laura Miozzi, Rosario M. Piro, et al.
  PLoS ONE 3(6):e2439, 2008. doi:10.1371/journal.pone.0002439 [available at: PLoS]

Bioinformatics - Thesis:

• Computational analysis of spatially mapped gene expression and conserved co-expression for disease gene prediction
  PhD thesis, University of Torino, January 2011.

• A method for prioritizing candidate genes for human hereditary diseases based on co-expression
  Master's thesis, University of Torino, April 2006.

Philosophy of Biology - Papers:

• Are all genes regulatory genes?
  Author: Rosario M. Piro
  Biology & Philosophy 26(4):595-602, 2011. [available at: SpringerLink; final draft: pdf]

Grid Computing - Book chapters:

• Accounting as a Requirement for Market-Oriented Grid Computing
  Authors: Andrea Guarise, Rosario M. Piro.
  Chapter 9 in: Buyya, R. and Bubendorfer, K. (eds.), Market-Oriented Grid and Utility Computing (Wiley Series on Parallel and Distributed Computing), Wiley Press, Hoboken, New Jersey, USA, 2010. [available at: Wiley]

• Resource Usage Accounting in Grid Computing
  Author: Rosario M. Piro.
  Chapter 18 in: Udoh, E. and Wang, F. (eds.), Handbook of Research on Grid Technologies and Utility Computing: Concepts for Managing Large-Scale Application (Encyclopedia of Grid Computing Technologies and Applications), Information Science Reference (IGI Global), Hershey, PA, USA, 2009. [available at: IGI Global]

Grid Computing - Papers:

• Using historical accounting information to predict the resource usage of grid jobs
  Authors: Rosario M. Piro, Andrea Guarise, Giuseppe Patania, Albert Werbrouck.
  Future Generation Computer Systems 25(5):499-510, 2009. [available at: ScienceDirect]

• The gLite Workload Management System
  Authors: P. Andreetto et al.
  Computing in High Energy and Nuclear Physics (CHEP'07), Victoria, Canada, September 2-7, 2007
  and: Journal of Physics: Conference Series 119(6):062007, 2008. [doi: 10.1088/1742-6596/119/6/062007]

• Tracing Resource Usage Over Heterogeneous Grid Platforms: A Prototype RUS Interface for DGAS
  Authors: Rosario M. Piro^*, Michele Pace^*, et al. (*= joint first authors)
  Proceedings of the 3rd International Conference on e-Science and Grid Computing (eScience 2007), pp. 93-101, Bangalore, India, December 10-13, 2007. [available at: IEEE]

• An Integrated Framework for VO-oriented Authorization, Policy-based Management and Accounting
  Authors: V. Ciaschini et al.
  Computing in High Energy and Nuclear Physics (CHEP'06), T.I.F.R. Mumbai, India, February 13-17, 2006. [paper and poster available at: CHEP'06 publications]

• Flexible Job Submission Using Web Services: the gLite WMProxy Experience
  Authors: G. Avellino et al.
  Computing in High Energy and Nuclear Physics (CHEP'06), T.I.F.R. Mumbai, India, February 13-17, 2006. [paper available at: CHEP'06 publications]

• CREAM: A simple, Grid-accessible, Job Management System for local Computational Resources
  Authors: P. Andreetto et al.
  Computing in High Energy and Nuclear Physics (CHEP'06), T.I.F.R. Mumbai, India, February 13-17, 2006. [paper available at: CHEP'06 publications]

• Price-sensitive Resource Brokering with the Hybrid Pricing Model and Widely Overlapping Price Domains
  Authors: Rosario M. Piro, Andrea Guarise, Albert Werbrouck.
  Concurrency and Computation: Practice and Experience 18(8):837-850, 2006. [preprint: pdf, ps; final version available at: Wiley]

• The DataGrid Workload Management System: Challenges And Results
  Authors: G. Avellino et al.
  Journal of Grid Computing 2:353-367, 2004. [available at: SpringerLink]

• Simulation of Price-sensitive Resource Brokering and the Hybrid Pricing Model with DGAS-Sim
  Authors: Rosario M. Piro, Andrea Guarise, Albert Werbrouck.
  13th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises (WETICE-2004) (track on Emerging Technologies for Next generation GRID (ETNGRID 2004)), Modena, Italy, June 14-16, 2004. [available at: IEEE]

• An Economy-based Accounting Infrastructure for the DataGrid
  Authors: Rosario M. Piro, Andrea Guarise, Albert Werbrouck.
  Proceedings of the 4th International Workshop on Grid Computing (GRID2003), Phoenix, Arizona (USA), November 17th, 2003. [available at: IEEE]

Grid Computing - Articles:

• Un sistema di accounting economico per le grid computazionali / European DataGrid (italian)
  Author: Rosario M. Piro.
  NetworkNews Italia, numero 137, 5 dicembre 2003. [draft: pdf, ps; final: pdf/zip (2 pages), ps/zip (2 pages)]

Grid Computing - Thesis:

• Simulation of Economy-based Load Balancing in Computational Grids for Large-scale Scientific Applications
  Laurea Specialistica thesis, University of Torino, April 2004. [pdf, 144 pages, 1.80MB]

Miscellaneous - Thesis:

• Development of a hardware and software-based Test System for the Power Supply Units of the CMS Silicon Strip Tracker
  Laurea thesis, University of Torino, January 2002.

Downloads

DGAS-Sim:

DGAS-Sim(ulator) is a simple simulation tool of the architecture of the EDG Workload Management System (only the components involved in the scheduling process), written in Java, to study the impact of different resource pricing schemes on workload balancing.
DGAS-Sim is released under the terms of the EU DataGrid Software License.

Stable releases:
edg-dgas-sim-0.1.0.tgz [source code, 50.2kB] date: April, 2004.
Development releases:
edg-dgas-sim-0.0.3dev.tgz [source code, 33.3kB] date: September 24, 2003.

nnet:

nnet is a C++ library for artificial neural networks. Feed-forward networks with back-propagation are supported. Other network architectures may be derived from generic classes for neurons, synapses (connections) and networks.
nnet is released under the terms of the GNU General Public License (Version 2 or later).
It can also be downloaded from http://sourceforge.net/projects/nnet/.

Stable releases:
nnet-0.1.0.tgz [source code, 43.5kB] date: April 2, 2003.
Development releases:
there is currently no development on nnet.

Contact

For contacting me, please write to:

Rosario M. Piro
Department of Theoretical Bioinformatics (B080)
German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 580
69120 Heidelberg, Germany
E-mail: r.piro -AT- dkfz.de
Phone: +49 (0) 6221 42 36 12

Impressum/Legal notice according to German legislation

Responsible for the content of this website according to § 5 TMG (German Act for Telecommunications Media Services) and § 55 Abs. 2 RStV (German Interstate Broadcasting Agreement):
Rosario M. Piro
Department of Theoretical Bioinformatics (B080)
German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 580
69120 Heidelberg, Germany
E-mail: r.piro -AT- dkfz.de
Phone: +49 (0) 6221 42 36 12

Liability for the content of linked websites:
This website contains links to external websites on whose content I have no influence and for which I thus cannot take any responsibility. The responsibility for the content of linked websites lies with the providers or administrators of the respective websites. Linked websites have been checked for a possible infringement of laws upon creation of the link. No infringement could be identified when the links were created. A permanent control of the content of the linked websites is not reasonable without a tangible suspicion of the violation of a law. If I should be notified or otherwise become aware of violations of law by the content of a linked website, I will immediately remove the corresponding link.

Rosario M. Piro
Last updated: 2012-03-26