Rosario M. Piro, PhD

Assistant Professor of Bioinformatics
Principle Investigator: Computational Neuropathology & Oncology (CNO) Research Group

Freie Universität Berlin, Germany Charité-Universitätsmedizin Berlin
Dep. of Mathematics and Computer Science Institute of Medical Genetics
Institute of Computer Science and Human Genetics
and Institute of Bioinformatics
Personal website @ FU


Research interests:

Bioinformatics / computational biology - medical bioinformatics with a primary focus on
(i) computational neuropathology, including cancer genetics/genomics of brain tumors as well as network analysis and the identification and prioritization of candidate genes for human hereditary disorders of the central nervous system; and
(ii) computational oncology in general, including the development and evolution of cancers in other organs or tissues.

Philosophy of biology - philosophical issues (loosly) associated with my primary research focus on computational biology; areas of interest include evolution (e.g. in the context of cancer), gene concepts and notions of essentialism, information and genetic programs in biology.

Past research focus:
Grid computing - distributed computing with a particular focus on grid accounting, resource usage prediction and economic approaches to job scheduling and workload balancing.


Education:

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.

Graduate studies (Master's degree) in bioinformatics at University of Torino. Field of Study: Prioritization of candidate genes for human hereditary diseases.

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).

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


Professional experience:

Since March 2015: Assistant Professor (Juniorprofessor) of Bioinformatics at the Dep. of Mathematics and Computer Sciene of Freie Universität Berlin and the Institute of Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin, Germany.

Postdoctoral fellow (9/2013 to 2/2015) in the Division of Molecular Genetics of the German Cancer Research Center (DKFZ) and the German Consortium for Translational Cancer Research (DKTK).

Postdoctoral fellow (3/2011 to 8/2013) in the Division of Theoretical Bioinformatics of the German Cancer Research Center (DKFZ).

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). Coordination of the OMII-Europe project's JRA1 Accounting Activity task (4/2006 to 11/2006).
[Previously: member of the European DataGrid (EDG) project (4/2002 to 3/2004) as an undergraduate student for INFN Torino and University of Torino.]
Tasks: Research and development as well as improvement of grid middleware for resource usage accounting, namely the Distributed Grid Accounting System (DGAS). For several years co-chair of the Resource Usage Service (RUS) working group and member of the Usage Record (UR) working group of the Open Grid Forum (OGF) to promote standardization, above all regarding issues related to accounting in grid environments.

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.

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).


About me in numbers

Erdős number: 4

[1] Peter J. Cameron coauthored with Paul Erdős [0]
[2] Christoph Buchheim coauthored with Peter J. Cameron
[3] Marcus Oswald coauthored with Christoph Buchheim
[4] Rosario M. Piro coauthored with Marcus Oswald

Einstein number: 5

[1] Valentine Bargmann coauthored with Albert Einstein [0]
[2] Luciano Girardello coauthored with Valentine Bargmann
[3] Marco Billó coauthored with Luciano Girardello
[4] Paolo Provero coauthored with Marco Billó
[5] Rosario M. Piro coauthored with Paolo Provero

Crick number: <=9 (in analogy to Erdős and Einstein)

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Publications

Computational biology (and related) - papers:

  • No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients
    Authors: Hutter S, Piro RM, et al.
    Human Genetics 135(5):469-475, 2016. [available at: SpringerLink]

  • Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants
    Authors: Hutter S, Piro RM, et al.
    Acta Neuropathologica 128(3):449-452, 2014. [available at: SpringerLink]

  • Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
    Authors: Piro RM, et al.
    BMC Systems Biology 8:56, 2014. [available at: BioMed Central]

  • Genome sequencing of SHH medulloblastoma predicts genotype-related response to Smoothened inhibition
    Authors: Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, et al.
    Cancer Cell 25(3):393-405, 2014. [available at: Cell Press]

  • Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
    Authors: Mack SC*, Witt H*, Piro RM, et al. (*= first authors)
    Nature 506(7489):445-450, 2014. [available at: Nature Publishing Group]

  • Stem cell characteristics in glioblastoma are maintained by the ecto-nucleotidase E-NPP1
    Authors: Bageritz J, Puccio L, Piro RM, et al.
    Cell Death & Differentiation 21(6):929-940, 2014. [available at: Nature Publishing Group]

  • BCAT1 promotes cell proliferation through amino acid catabolism in gliomas carrying wild-type IDH1
    Authors: Tönjes M, Barbus S, Park YJ, Wang W, Schlotter M, Lindroth AM, Pleier SV, Bai AH, Karra D, Piro RM, et al.
    Nature Medicine 19(7):901-908, 2013. [available at: Nature Publishing Group]

  • Meningeal hemangiopericytoma and solitary fibrous tumors carry the NAB2-STAT6 fusion and can be diagnosed by nuclear expression of STAT6 protein
    Authors: Schweizer L*, Koelsche C*, Sahm F*, Piro RM*, et al. (*= first authors)
    Acta Neuropathologica 125(5):651-658, 2013. [available at: SpringerLink]

  • Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations
    Authors: Reuss DE*, Piro RM*, Jones DTW*, et al. (*= first authors)
    Acta Neuropathologica 125(3):351-358, 2013. [available at: SpringerLink]

  • Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities
    Authors: Piro RM, et al.
    Bioinformatics 29(4):468-475, 2013. [available at: Oxford Journals]

  • Network medicine: linking disorders
    Author: Piro RM.
    Human Genetics 131(12):1811-1820, 2012. [available at: SpringerLink]

  • Computational approaches to disease-gene prediction: rationale, classification and successes
    Authors: Piro RM, Di Cunto F.
    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: Piro RM*, Ala U*, Molineris I*, et al. (*= 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: Piro RM, 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: Piro RM, 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: Fagoonee S, Hobbs RM, De Chiara L, Cantarella D, Piro RM, 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: Ala U*, Piro RM*, et al. (*= 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: Miozzi L, Piro RM, et al.
    PLoS ONE 3(6):e2439, 2008. doi:10.1371/journal.pone.0002439 [available at: PLoS]

Computational biology - theses:

  • 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: Piro RM.
    Biology & Philosophy 26(4):595-602, 2011. [available at: SpringerLink; final draft: pdf]

Philosophy of biology - book reviews:

  • Né Kupiec né Sonigo
    Author: Piro RM.
    LN LibriNuovi 52(10.1):12-22, 2010. [Italian; out of print, see for example Book Depository; pdf]

Grid computing - book chapters:

  • Accounting as a Requirement for Market-Oriented Grid Computing
    Authors: Guarise A, Piro RM.
    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: Piro RM.
    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: Piro RM, Guarise A, Patania G, Werbrouck A.
    Future Generation Computer Systems 25(5):499-510, 2009. [available at: ScienceDirect]

  • The gLite Workload Management System
    Authors: Andreetto P, 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: Piro RM*, Pace M*, et al. (*= 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: Ciaschini V, 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: Avellino G, 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: Andreetto P, 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: Piro RM, Guarise A, Werbrouck A.
    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: Avellino G, 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: Piro RM, Guarise A, Werbrouck A.
    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: Piro RM, Guarise A, Werbrouck A.
    Proceedings of the 4th International Workshop on Grid Computing (GRID2003), Phoenix, Arizona (USA), November 17th, 2003. [available at: IEEE]

Grid computing - popular science articles:

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

Grid computing - technical reports:

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

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]

Physics - 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.

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Downloads

PathWave:

PathWave enables the identification of disease-specific regulation patterns by combining gene expression data and network topology. By analyzing regulatory patterns at multiple scales, PAthWave is capabale to detect both global deregulation of pathways and localized regulatory switches that may still have a singificant impact on metabolic fluxes. PathWave is available here, or from our collaboration partners at Hans Knöll Institute (HKI), Jena:

CITING PATHWAVE: please cite Piro et al. (2014) for PathWave version 2.1, Schramm et al. (2010) for PathWave version 1.0, and both papers (Schramm et al. 2010; Piro et al. 2014) for PathWave in general.

  1. Schramm G, et al. (2010) PathWave: Discovering patterns of differentially regulated enzymes in metabolic pathways. Bioinformatics 26(9):1225-1231.
  2. Piro RM, et al. (2014) Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. BMC Systems Biology 8:56.

CGPACE:

CGPACE (Candidate Gene Prioritization by Analysis of Co-Expression) is the latest version of the software I developed and continusously improved for the following papers:

  1. Piro RM, et al. (2010) Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR. Bioinformatics 26(18):i618-624.
  2. Piro RM, et al. (2011) Evaluation of candidate genes from orphan FEB and GEFS+ loci by analysis of human brain gene expression atlases. PLoS ONE 6(8):e23149.
  3. Piro RM, et al. (2013) Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. Bioinformatics 29(4):468-475.

Note: despite its name, CGPACE can be used for data other than gene expression profiles (e.g. total binding affinities/TBAs in paper 3).

Please cite paper 1 when using CGPACE with a Pearson correlation coefficient and paper 3 when using it with the Relative Intensity Overlap (RIO), the use for TBAs and/or a noisy-OR gate for data integration.

See the publications for descriptions of the algorithm, the RIO, the noisy-OR and the use for TBAs; contact me in case of further questions.

CGPACE is released under the terms of the GNU General Public License (Version 2 or later).

Stable releases:
CGPACE-5-2012-12-03.tgz [source code, 57kB]; date: December, 2012.

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.

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Contact

For contacting me, please write to:

Prof. Dr. Rosario M. Piro

Dep. of Mathematics and Computer Science
Institute of Computer Science
Freie Universität Berlin
Takustr. 9
14195 Berlin, Germany
Phone: +49 (0)30 838 55114

E-mail: r.piro -AT- fu-berlin.de
Website: Piro @ FU-Mathematik und Informatik

or:
Institute of Medical and Human Genetics
Charité-Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin, Germany

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):

Prof. Dr. Rosario M. Piro
Dep. of Mathematics and Computer Science
Freie Universität Berlin
Takustr. 9
14195 Berlin, Germany
E-mail: r.piro -AT- fu-berlin.de

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.

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