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

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Freie Universität Berlin (since 2015):

    W = winter semester, S = summer semester.

  • Algorithmische Bioinformatik (Algorithmic Bioinformatics) (lectures) [German]
    B.Sc. in Bioinformatics; W 2015/2016

  • Genetik und Genomforschung (Genetics and Genome Research) (lectures) [German]
    B.Sc. in Bioinformatics; W 2016/2017

  • Genomics (lectures)
    M.Sc. in Bioinformatics; W 2015/2016, W 2016/2017, W 2017/2018 (upcoming)

  • Medical Bioinformatics (lectures)
    M.Sc. in Bioinformatics; S 2016, S 2017
    see course website at Charité

  • Medical Genomics (practical course)
    M.Sc. in Bioinformatics; S 2015, S 2016, S 2017
    see course website at Charité

German Cancer Research Center (2011 - 2015):

  • Current Topics in Bioinformatics and Computational Cell Biology (seminar)
    M.Sc. in Molecular Biology; single sessions; W 2011/2012, W 2012/2013

  • Bioinformatik √úbungen (Programming in Perl) (lectures + excercises) [german]
    B.Sc. in Molecular Biology; single lectures; W 2012/2013

Università degli Studi di Torino (2007 - 2011):

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

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

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Computational biology:

  • Identification of Mutational Signatures Active in Individual Tumors
    NETTAB 2017 - Methods, Tools & Platforms for Personalized Medicine in the Big Data Era, Palermo, Italy, October 16-18, 2017 (talk accepted). [conference website]

  • Computational medicine: identification of causes of genetic disorders (invited keynote)
    Confluence-2017 - 7th International IEEE Conference on Cloud Computing, Data Science & Engineering, Noida, India, January 12-13, 2017. [conference website]

  • Computational Neuropathology & Oncology (invited talk)
    IMPRS-CBSC Spring Colloqium, Max Planck Institute (MPI) for Molecular Genetics, Berlin, Germany, March 9, 2016. [seminar website]

  • Identification of metabolic switches in glioblastomas of IDH1-mutation carriers by integration of information on somatic mutations into gene expression-based pathway analysis
    Workshop on Integration of OMICS Datasets into Metabolic Pathway Analysis (IOMPA 2011) (held in conjunction with the International Conference on Systems Biology, ICSB 2011), Heidelberg, Germany, July 17, 2011. [conference website]

  • Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR
    9th European Conference on Computational Biology (ECCB2010), Ghent, Belgium, September 26-29, 2010. [conference website]

Grid computing:

  • 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]

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Computational biology:

  • Identification of the genetic basis of human disorders
    Authors: Piro RM, et al.
    "IT For Life Science @ Bayer" Workshop, BayArena, Leverkusen, Germany, May 26-27, 2014.

  • Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities
    Authors: Piro RM, Molineris I, et al.
    Int. Conf. on the Systems Biology of Human Disease, Heidelberg, Germany, June 12-14, 2013. [pdf]

  • PathWave 2.1: a user-friendly R package for detecting differential regulation and switches in metabolic and signaling pathways
    Authors: Piro RM, Wiesberg S, et al.
    EMBO Conference Series: From Functional Genomics to Systems Biology, EMBL, Heidelberg, Germany, Nov. 17-20, 2012. [pdf]

  • PathWave Update: Identifying Regulatory Changes in Metabolic Pathways
    Authors: Piro RM, Schramm G, 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: Piro RM, Ala U, 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: Piro RM, Ala U, 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: Ala U, Piro RM, et al.
    7th European Conference on Computational Biology (ECCB'08), Cagliari, Italy, September 22-26, 2008. [pdf]

  • Identification of candidate disease genes from conserved coexpression
    Authors: Provero P, Ala U, Piro RM, et al.
    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: Miozzi L, Ala U, Piro RM, et al.
    The 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology, EMBL Heidelberg, October 14-17, 2006. [ppt]

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