Stefano De Pretis

Post Doc

Research Lines

Genomic Science




Center for Genomic Science of IIT@SEMM Fondazione Istituto Italiano di Tecnologia Via Adamello 16


Postdoc Junior at IIT@SEMM at Center for Genomic Science in the Epigenomic Unit (10/2012-present)


Ph.D. in Bioinformatics, University of Sannio, 2012

(Visiting student at Harvard Medical School, June 2011-February 2012)

Thesis: "Dynamical systems in the fate decision of Embryonic Stem Cells: the role of excitability and bistability." (Prof. Giancarlo Mauri)

M.S. in Bioinformatics, University of Milano Bicocca, 2008

Thesis: "Stochastic Simulations with MesoRD and their applications on small Genetic Networks." (Prof. Luca De Gioia)

B.S. in Molecular Biotechnology, University of Milano Bicocca, 2005

Thesis: "NMR Studies of Characterization of Low-Molecular weight Heparins. Identification and Quantification of Biological Active Structures." (Dr. Marco Guerrini - Ronzoni Institute for Chemical and Biochemical Research, B.S. Molecular Biotechnology)


RNA production and degradation dynamics

IIT Publications

  • 2017
  • De Pretis S.iit, Kress T.R.iit, Morelli M.J.iit, Sabo A.iit, Locarno C.iit, Verrecchia A., Doni M., Campaner S.iit, Amati B.iit, Pelizzola M.iit

    Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation

    Genome Research, vol. 27, (no. 10), pp. 1658-1664
  • Mukherjee N., Calviello L., Hirsekorn A., De Pretis S.iit, Pelizzola M.iit, Ohler U.

    Integrative classification of human coding and noncoding genes through RNA metabolism profiles

    Nature Structural and Molecular Biology, vol. 24, (no. 1), pp. 86-96
  • 2016
  • Marzi M.J.iit, Ghini F.iit, Cerruti B.iit, De Pretis S.iit, Bonetti P.iit, Giacomelli C.iit, Gorski M.M., Kress T.iit, Pelizzola M.iit, Muller H.iit, Amati B.iit, Nicassio F.iit

    Degradation dynamics of micrornas revealed by a novel pulse-chase approach

    Genome Research, vol. 26, (no. 4), pp. 554-565
  • Marzi M. J., Ghini F., Cerruti B., de Pretis S.iit, Nicassio F.iit

    Insights into function and regulation of microRNAs by decoding degradation dynamics

    Keystone Symposia: Small RNA Silencing: Little Guides, Big Biology (A6)
  • Bianchi V.iit, Ceol A.iit, Ogier A.G.E., De Pretis S.iit, Galeota E.iit, Kishore K.iit, Bora P.iit, Croci O.iit, Campaner S.iit, Amati B.iit, Morelli M.J.iit, Pelizzola M.iit

    Integrated systems for NGS data management and analysis: Open issues and available solutions

    Frontiers in Genetics, vol. 7, (no. MAY)
  • Melloni G.E.M.iit, de Pretis S.iit, Riva L.iit, Pelizzola M.iit, Ceol A.iit, Costanza J.iit, Muller H.iit, Zammataro L.iit

    LowMACA: Exploiting protein family analysis for the identification of rare driver mutations in cancer

    BMC Bioinformatics, vol. 17, (no. 1)
  • 2015
  • De Pretis S.iit, Kress T.iit, Morelli M.J.iit, Melloni G.E.M.iit, Riva L.iit, Amati B.iit, Pelizzola M.iit

    INSPEcT: A computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

    Bioinformatics, vol. 31, (no. 17), pp. 2829-2835
  • Kishore K.iit, de Pretis S.iit, Lister R., Morelli M.J.iit, Bianchi V.iit, Amati B.iit, Ecker J.R., Pelizzola M.iit

    methylPipe and compEpiTools: A suite of R packages for the integrative analysis of epigenomics data

    BMC Bioinformatics, vol. 16, (no. 1)
  • Pelizzola M.iit, Morelli M.J.iit, Sabo A.iit, Kress T.R.iit, de Pretis S.iit, Amati B.iit

    Selective transcriptional regulation by Myc: Experimental design and computational analysis of high-throughput sequencing data

    Data in Brief, vol. 3, pp. 40-46
  • Austenaa L.M.I., Barozzi I., Simonatto M., Masella S., Della Chiara G., Ghisletti S., Curina A., de Wit E., Bouwman B.A.M., de Pretis S.iit, Piccolo V., Termanini A., Prosperini E., Pelizzola M.iit, de Laat W., Natoli G.

    Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

    Molecular Cell, vol. 60, (no. 3), pp. 460-474
  • 2014
  • de Pretis S.iit, Pelizzola M.iit

    Computational and experimental methods to decipher the epigenetic code

    Frontiers in Genetics, vol. 5, (no. SEP)
  • Melloni G.E.M.iit, Ogier A.G.E., de Pretis S.iit, Mazzarella L., Pelizzola M.iit, Pelicci P.G., Riva L.iit

    DOTS-Finder: A comprehensive tool for assessing driver genes in cancer genomes

    Genome Medicine, vol. 6, (no. 6)
  • Sabo A.iit, Kress T.R.iit, Pelizzola M.iit, De Pretis S.iit, Gorski M.M., Tesi A.iit, Morelli M.J.iit, Bora P.iit, Doni M., Verrecchia A., Tonelli C., Faga G., Bianchi V.iit, Ronchi A.iit, Low D., Muller H.iit, Guccione E., Campaner S.iit, Amati B.iit

    Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

    Nature, vol. 511, (no. 7510), pp. 488-492