Mattia Pelizzola

IIT Publications

• 2020
• Furlan M.^iit, Tanaka I.^iit, Leonardi T.^iit, de Pretis S.^iit, Pelizzola M.^iit
  DOI

  Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts

  Frontiers in Genetics, vol. 11
• Furlan M., de Pretis S., Pelizzola M.^iit
  DOI

  Dynamics of transcriptional and post-transcriptional regulation

  Briefings in Bioinformatics
• Dassi E., Baranov P.V., Pelizzola M.^iit
  DOI

  Editorial: Computational Epitranscriptomics: Bioinformatic Approaches for the Analysis of RNA Modifications

  Frontiers in Genetics, vol. 11
• Furlan M., Galeota E., Del Gaudio N., Dassi E., Caselle M., de Pretis S., Pelizzola M.^iit
  DOI

  Genome-wide dynamics of RNA synthesis, processing and degradation without RNA metabolic labeling

  Genome Research
• de Pretis S.^iit, Furlan M.^iit, Pelizzola M.^iit
  DOI

  INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species

  Frontiers in Genetics, vol. 11
• Galeota E.^iit, Kishore K.^iit, Pelizzola M.^iit
  DOI

  Ontology-driven integrative analysis of omics data through Onassis

  Scientific Reports, vol. 10, (no. 1)
• Biasini A., Abdulkarim B., de Pretis S.^iit, Tan J.Y., Arora R., Wischnewski H., Dreos R., Pelizzola M.^iit, Ciaudo C., Marques A.C.
  DOI

  Translation is required for miRNA-dependent decay of endogenous transcripts

  EMBO Journal
• 2019
• Lepesant J.M.J., Iampietro C., Galeota E., Auge B., Aguirrenbengoa M., Merce C., Chaubet C., Rocher V., Haenlin M., Waltzer L., Pelizzola M.^iit, Di Stefano L.
  DOI

  A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons

  Nucleic Acids Research
• Tesi A.^iit, de Pretis S.^iit, Furlan M.^iit, Filipuzzi M., Morelli M.J.^iit, Andronache A.^iit, Doni M., Verrecchia A., Pelizzola M.^iit, Amati B., Sabo A.
  DOI

  An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation

  EMBO Reports, vol. 20, (no. 9)
• Furlan M.^iit, Galeota E.^iit, de Pretis S.^iit, Caselle M., Pelizzola M.^iit
  DOI

  M6A-dependent RNA dynamics in T cell differentiation

  Genes, vol. 10, (no. 1)
• Lobo J., Costa A.L., Cantante M., Guimaraes R., Lopes P., Antunes L., Braga I., Oliveira J., Pelizzola M.^iit, Henrique R., Jeronimo C.
  DOI

  M6A RNA modification and its writer/reader VIRMA/YTHDF3 in testicular germ cell tumors: A role in seminoma phenotype maintenance

  Journal of Translational Medicine, vol. 17, (no. 1)
• Madaro L., Torcinaro A., De Bardi M., Contino F. F., Pelizzola M.^iit, Diaferia G. R., Imeneo G., Bouchè M., Puri P. L., De Santa F.
  DOI

  Macrophages fine tune satellite cell fate in dystrophic skeletal muscle of mdx mice

  PLoS Genetics
• 2018
• Yizhar-Barnea O., Valensisi C., Jayavelu N.D., Kishore K.^iit, Andrus C., Koffler-Brill T., Ushakov K., Perl K., Noy Y., Bhonker Y., Pelizzola M.^iit, Hawkins R.D., Avraham K.B.
  DOI

  DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium

  Scientific Reports, vol. 8, (no. 1)
• Kishore K.^iit, Pelizzola M.^iit
  DOI

  Identification of differentially methylated regions in the genome of Arabidopsis thaliana

  Methods in molecular biology (Clifton, N.J.), vol. 1675, pp. 61-69
• Jantsch M.F., Quattrone A., O'Connell M., Helm M., Frye M., Macias-Gonzales M., Ohman M., Ameres S., Willems L., Fuks F., Oulas A., Vanacova S., Nielsen H., Bousquet-Antonelli C., Motorin Y., Roignant J.-Y., Balatsos N., Dinnyes A., Baranov P., Kelly V., Lamm A., Rechavi G., Pelizzola M.^iit, Liepins J., Holodnuka Kholodnyuk I., Zammit V., Ayers D., Drablos F., Dahl J.A., Bujnicki J., Jeronimo C., Almeida R., Neagu M., Costache M., Bankovic J., Banovic B., Kyselovic J., Valor L.M., Selbert S., Pir P., Demircan T., Cowling V., Schafer M., Rossmanith W., Lafontaine D., David A., Carre C., Lyko F., Schaffrath R., Schwartz S., Verdel A., Klungland A., Purta E., Timotijevic G., Cardona F., Davalos A., Ballana E., OCarroll D., Ule J., Fray R.
  DOI

  Positioning Europe for the EPITRANSCRIPTOMICS challenge

  RNA Biology, vol. 15, (no. 6), pp. 829-831
• 2017
• Donato E.^iit, Croci O.^iit, Sabo A.^iit, Muller H.^iit, Morelli M.J.^iit, Pelizzola M.^iit, Campaner S.^iit
  DOI

  Compensatory RNA polymerase 2 loading determines the efficacy and transcriptional selectivity of JQ1 in Myc-driven tumors

  Leukemia, vol. 31, (no. 2), pp. 479-490
• Pistore C., Giannoni E., Colangelo T., Rizzo F., Magnani E., Muccillo L., Giurato G., Mancini M., Rizzo S., Riccardi M., Sahnane N., Del Vescovo V., Kishore K.^iit, Mandruzzato M., MacChi F., Pelizzola M.^iit, Denti M.A., Furlan D., Weisz A., Colantuoni V., Chiarugi P., Bonapace I.M.
  DOI

  DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells

  Oncogene, vol. 36, (no. 40), pp. 5551-5566
• 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
  DOI

  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.
  DOI

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

  Nature Structural and Molecular Biology, vol. 24, (no. 1), pp. 86-96
• Galeota E.^iit, Pelizzola M.^iit
  DOI

  Ontology-based annotations and semantic relations in large-scale (epi)genomics data

  Briefings in Bioinformatics, vol. 18, (no. 3), pp. 403-412
• 2016
• Pelizzola M.^iit

  Computational epigenomics

  Handbook of Neurobehavioral Genetics and Phenotyping, Publisher: Wiley
• 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
  DOI

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

  Genome Research, vol. 26, (no. 4), pp. 554-565
• 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
  DOI

  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
  DOI

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

  BMC Bioinformatics, vol. 17, (no. 1)
• Polena H., Boudou F., Tilleul S., Dubois-Colas N., Lecointe C., Rakotosamimanana N., Pelizzola M., Andriamandimby S.F., Raharimanga V., Charles P., Herrmann J.-L., Ricciardi-Castagnoli P., Rasolofo V., Gicquel B., Tailleux L.
  DOI

  Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination

  Scientific Reports, vol. 6
• 2015
• Robinson M.D., Pelizzola M.^iit
  DOI

  Computational epigenomics: Challenges and opportunities

  Frontiers in Genetics, vol. 5, (no. FEB)
• 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
  DOI

  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
  DOI

  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
  DOI

  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.
  DOI

  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
  DOI

  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
  DOI

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

  Genome Medicine, vol. 6, (no. 6)
• Almouzni G., Altucci L., Amati B.^iit, Ashley N., Baulcombe D., Beaujean N., Bock C., Bongcam-Rudloff E., Bousquet J., Braun S., Paillerets B.B.D., Bussemakers M., Clarke L., Conesa A., Estivill X., Fazeli A., Grgurevic N., Gut I., Heijmans B.T., Hermouet S., Houwing-Duistermaat J., Iacobucci I., Ilas J., Kandimalla R., Krauss-Etschmann S., Lasko P., Lehmann S., Lindroth A., Majdic G., Marcotte E., Martinelli G., Martinet N., Meyer E., Miceli C., Mills K., Moreno-Villanueva M., Morvan G., Nickel D., Niesler B., Nowacki M., Nowak J., Ossowski S., Pelizzola M.^iit, Pochet R., Potocnik U., Radwanska M., Raes J., Rattray M., Robinson M.D., Roelen B., Sauer S., Schinzer D., Slagboom E., Spector T., Stunnenberg H.G., Tiligada E., Torres-Padilla M.-E., Tsonaka R., Soom A.V., Vidakovic M., Widschwendter M.
  DOI

  Relationship between genome and epigenome - challenges and requirements for future research

  BMC Genomics, vol. 15, (no. 1)
• 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
  DOI

  Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

  Nature, vol. 511, (no. 7510), pp. 488-492
• Looney T.J., Zhang L., Chen C.-H., Lee J.H., Chari S., Mao F.F., Pelizzola M., Zhang L., Lister R., Baker S.W., Fernandes C.J., Gaetz J., Foshay K.M., Clift K.L., Zhang Z., Li W.-Q., Vallender E.J., Wagner U., Qin J.Y., Michelini K.J., Bugarija B., Park D., Aryee E., Stricker T., Zhou J., White K.P., Ren B., Schroth G.P., Ecker J.R., Xiang A.P., Lahn B.T.
  DOI

  Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells

  Genome Research, vol. 24, (no. 2), pp. 267-280
• 2013
• Schmitz R.J., Schultz M.D., Urich M.A., Nery J.R., Pelizzola M.^iit, Libiger O., Alix A., McCosh R.B., Chen H., Schork N.J., Ecker J.R.
  DOI

  Patterns of population epigenomic diversity

  Nature, vol. 495, (no. 7440), pp. 193-198
• Chang K.N., Zhong S., Weirauch M.T., Hon G., Pelizzola M.^iit, Li H., Carol Huang S-S., Schmitz R.J., Urich M.A., Kuo D., Nery J.R., Qiao H., Yang A., Jamali A., Chen H., Ideker T., Ren B., Bar-Joseph Z., Hughes T.R., Ecker J.R.
  DOI

  Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

  eLife, vol. 2013, (no. 2)
• 2012
• Hon G.C., Hawkins R.D., Caballero O.L., Lo C., Lister R., Pelizzola M., Valsesia A., Ye Z., Kuan S., Edsall L.E., Camargo A.A., Stevenson B.J., Ecker J.R., Bafna V., Strausberg R.L., Simpson A.J., Ren B.
  DOI

  Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

  Genome Research, vol. 22, (no. 2), pp. 246-258
• Dowen R.H., Pelizzola M.^iit, Schmitz R.J., Lister R., Dowen J.M., Nery J.R., Dixon J.E., Ecker J.R.
  DOI

  Widespread dynamic DNA methylation in response to biotic stress

  Proceedings of the National Academy of Sciences of the United States of America, vol. 109, (no. 32)
• 2011
• Liu Z., Hu Z., Pan X., Li M., Togun T.A., Tuck D., Pelizzola M., Huang J., Ye X., Yin Y., Liu M., Li C., Chen Z., Wang F., Zhou L., Chen L., Keefe D.L., Liu L.
  DOI

  Germline competency of parthenogenetic embryonic stem cells from immature oocytes of adult mouse ovary

  Human Molecular Genetics, vol. 20, (no. 7), pp. 1339-1352
• Lister R., Pelizzola M., Kida Y.S., Hawkins R.D., Nery J.R., Hon G., Antosiewicz-Bourget J., Ogmalley R., Castanon R., Klugman S., Downes M., Yu R., Stewart R., Ren B., Thomson J.A., Evans R.M., Ecker J.R.
  DOI

  Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

  Nature, vol. 471, (no. 7336), pp. 68-73
• Pelizzola M., Molinaro A.
  DOI

  Methylated DNA immunoprecipitation genome-wide analysis

  Methods in molecular biology (Clifton, N.J.), vol. 791, pp. 113-123
• Pelizzola M., Ecker J.R.
  DOI

  The DNA methylome

  FEBS Letters, vol. 585, (no. 13), pp. 1994-2000
• 2010
• Harris R.A., Wang T., Coarfa C., Nagarajan R.P., Hong C., Downey S.L., Johnson B.E., Fouse S.D., Delaney A., Zhao Y., Olshen A., Ballinger T., Zhou X., Forsberg K.J., Gu J., Echipare L., O'Geen H., Lister R., Pelizzola M., Xi Y., Epstein C.B., Bernstein B.E., Hawkins R.D., Ren B., Chung W.-Y., Gu H., Bock C., Gnirke A., Zhang M.Q., Haussler D., Ecker J.R., Li W., Farnham P.J., Waterland R.A., Meissner A., Marra M.A., Hirst M., Milosavljevic A., Costello J.F.
  DOI

  Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

  Nature Biotechnology, vol. 28, (no. 10), pp. 1097-1105
• Hawkins R.D., Hon G.C., Lee L.K., Ngo Q., Lister R., Pelizzola M., Edsall L.E., Kuan S., Luu Y., Klugman S., Antosiewicz-Bourget J., Ye Z., Espinoza C., Agarwahl S., Shen L., Ruotti V., Wang W., Stewart R., Thomson J.A., Ecker J.R., Ren B.
  DOI

  Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

  Cell Stem Cell, vol. 6, (no. 5), pp. 479-491
• Sirri A., Bianchi V., Pelizzola M., Mayhaus M., Ricciardi-Castagnoli P., Toniolo D., D'Adamo P.
  DOI

  Temporal gene expression profile of the hippocampus following trace fear conditioning

  Brain Research, vol. 1308, pp. 14-23
• 2009
• Koga Y., Pelizzola M., Cheng E., Krauthammer M., Sznol M., Ariyan S., Narayan D., Molinaro A.M., Halaban R., Weissman S.M.
  DOI

  Genome-wide screen of promoter methylation identifies novel markers in melanoma

  Genome Research, vol. 19, (no. 8), pp. 1462-1470
• Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., Tonti-Filippini J., Nery J.R., Lee L., Ye Z., Ngo Q.-M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Millar A.H., Thomson J.A., Ren B., Ecker J.R.
  DOI

  Human DNA methylomes at base resolution show widespread epigenomic differences

  Nature, vol. 462, (no. 7271), pp. 315-322
• Halaban R., Krauthammer M., Pelizzola M., Cheng E., Kovacs D., Sznol M., Ariyan S., Narayan D., Bacchiocchi A., Molinaro A., Kluger Y., Deng M., Tran N., Zhang W., Picardo M., Enghild J.J.
  DOI

  Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: Clinical implications

  PLoS ONE, vol. 4, (no. 2)
• 2008
• Foti M., Granucci F., Pelizzola M., Pavelka N., Beretta O., Vizzardelli C., Urbano M., Zanoni I., Capuano G., Mingozzi F., Trottein F., Aebischer T., Ricciardi-Castagnoli P.
  DOI

  Gene Profiling of Dendritic cells during Host-Pathogen Interactions

  Handbook of Dendritic Cells, vol. 1, pp. 175-197, Publisher: Wiley-VCH Verlag GmbH
• Pelizzola M., Koga Y., Urban A.E., Krauthammer M., Weissman S., Halaban R., Molinaro A.M.
  DOI

  MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment

  Genome Research, vol. 18, (no. 10), pp. 1652-1659
• Tailleux L., Waddel S.J., Pelizzola M., Mortellaro A., Withers M., Tanne A., Castagnoli P.R., Gicquel B., Stoker N.G., Butcher P.D., Foti M., Neyrolles O.
  DOI

  Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

  PLoS ONE, vol. 3, (no. 1)
• Pavelka N., Fournier M.L., Swanson S.K., Pelizzola M., Ricciardi-Castagnoli P., Florens L., Washburn M.P.
  DOI

  Statistical similarities between transcriptomics and quantitative shotgun proteomics data

  Molecular and Cellular Proteomics, vol. 7, (no. 4), pp. 631-644
• 2007
• Splendiani A., Brandizi M., Even G., Beretta O., Pavelka N., Pelizzola M., Mayhaus M., Foti M., Mauri G., Ricciardi-Castagnoli P.
  DOI

  The Genopolis Microarray Database

  BMC Bioinformatics, vol. 8, (no. SUPPL. 1)
• 2006
• Pelizzola M., Pavelka N., Foti M., Ricciardi-Castagnoli P.
  DOI

  AMDA: An R package for the automated microarray data analysis

  BMC Bioinformatics, vol. 7
• Foti M., Granucci F., Pelizzola M., Beretta O., Ricciardi-Castagnoli P.
  DOI

  Dendritic cells in pathogen recognition and induction of immune responses: A functional genomics approach

  Journal of Leukocyte Biology, vol. 79, (no. 5), pp. 913-916
• Vizzardelli C., Pavelka N., Luchini A., Zanoni I., Bendickson L., Pelizzola M., Beretta O., Foti M., Granucci F., Nilsen-Hamilton M., Ricciardi-Castagnoli P.
  DOI

  Effects of dexamethazone on LPS-induced activation and migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis

  European Journal of Immunology, vol. 36, (no. 6), pp. 1504-1515
• Foti M., Granucci F., Pelizzola M., Pavelka N., Beretta O., Vizzardelli C., Urbano M., Zanoni I., Capuano G., Mingozzi F., Ricciardi-Castagnoli P.
  DOI

  Transcriptional Profiling of Dendritic Cells in Response to Pathogens

  Immunogenomics and Human Disease, pp. 461-486, Publisher: John Wiley & Sons, Ltd
• 2005
• Aebischer T., Bennett C.L., Pelizzola M., Vizzardelli C., Pavelka N., Urbano M., Capozzoli M., Luchini A., Ilg T., Granucci F., Blackburn C.C., Ricciardi-Castagnoli P.
  DOI

  A critical role for lipophosphoglycan in proinflammatory responses of dendritic cells to Leishmania mexicana

  European Journal of Immunology, vol. 35, (no. 2), pp. 476-486
• 2004
• Pavelka N., Pelizzola M., Vizzardelli C., Capozzoli M., Splendiani A., Granucci F., Ricciardi-Castagnoli P.
  DOI

  A power law global error model for the identification of differentially expressed genes in microarray data

  BMC Bioinformatics, vol. 5
• Trottein F., Pavelka N., Vizzardelli C., Angeli V., Zouain C.S., Pelizzola M., Capozzoli M., Urbano M., Capron M., Belardelli F., Granucci F., Ricciardi-Castagnoli P.
  DOI

  A Type I IFN-Dependent Pathway Induced by Schistosoma mansoni Eggs in Mouse Myeloid Dendritic Cells Generates an Inflammatory Signature

  Journal of Immunology, vol. 172, (no. 5), pp. 3011-3017