Mattia Pelizzola
Researcher
Researcher

About
Education
2006: PhD “Complexity in post-genomic biology”. University of Torino, Advisor M. Caselle.
2003: MS “Bioinformatics”. University of Milano-Bicocca, Advisor P. Ricciardi-Castagnoli.
2001: MSc “Industrial Biotechnologies”. University of Milano-Bicocca.
Working experience
2011 Researcher. Team leader of the Epigenomics and Transcriptional Regulation unit at the Center for Genomic Science, c/o IFOM-IEO Campus, Milano.
2009 Postdoctoral Research Associate. Genomic Analysis Lab, Salk Institute, Advisor J.R. Ecker.
2007 Postdoctoral Research Associate. Biostatistic Division, Yale University, Advisor A. Molinaro.
2001 Computational biologist. Genopolis Consortium (University of Milano-Bicocca), Italy.
1999 Molecular biologist. University of Milano-Bicocca, Italy.
Interests
epigenomics transcriptional regulation DNA and RNA methylation RNA metabolism next generation sequencing integrative genomicsSelected Publications
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2020
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DOI
Genome-wide dynamics of RNA synthesis, processing and degradation without RNA metabolic labeling
Genome Research -
2017DOI
Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation
Genome Research, vol. 27, (no. 10), pp. 1658-1664 -
DOI
Ontology-based annotations and semantic relations in large-scale (epi)genomics data
Briefings in Bioinformatics, vol. 18, (no. 3), pp. 403-412 -
2015DOI
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
IIT Publications
- 2020
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DOI
Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts
Frontiers in Genetics, vol. 11 -
DOI
Dynamics of transcriptional and post-transcriptional regulation
Briefings in Bioinformatics -
DOI
Editorial: Computational Epitranscriptomics: Bioinformatic Approaches for the Analysis of RNA Modifications
Frontiers in Genetics, vol. 11 -
DOI
Genome-wide dynamics of RNA synthesis, processing and degradation without RNA metabolic labeling
Genome Research -
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 -
DOI
Ontology-driven integrative analysis of omics data through Onassis
Scientific Reports, vol. 10, (no. 1) -
DOI
Translation is required for miRNA-dependent decay of endogenous transcripts
EMBO Journal - 2019
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DOI
A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons
Nucleic Acids Research -
DOI
An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation
EMBO Reports, vol. 20, (no. 9) -
DOI
M6A-dependent RNA dynamics in T cell differentiation
Genes, vol. 10, (no. 1) -
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) -
DOI
Macrophages fine tune satellite cell fate in dystrophic skeletal muscle of mdx mice
PLoS Genetics - 2018
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DOI
DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium
Scientific Reports, vol. 8, (no. 1) -
DOI
Identification of differentially methylated regions in the genome of Arabidopsis thaliana
Methods in molecular biology (Clifton, N.J.), vol. 1675, pp. 61-69 -
DOI
Positioning Europe for the EPITRANSCRIPTOMICS challenge
RNA Biology, vol. 15, (no. 6), pp. 829-831 - 2017
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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 -
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 -
DOI
Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation
Genome Research, vol. 27, (no. 10), pp. 1658-1664 -
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 -
DOI
Ontology-based annotations and semantic relations in large-scale (epi)genomics data
Briefings in Bioinformatics, vol. 18, (no. 3), pp. 403-412 - 2016
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Computational epigenomics
Handbook of Neurobehavioral Genetics and Phenotyping, Publisher: Wiley -
DOI
Degradation dynamics of micrornas revealed by a novel pulse-chase approach
Genome Research, vol. 26, (no. 4), pp. 554-565 -
DOI
Integrated systems for NGS data management and analysis: Open issues and available solutions
Frontiers in Genetics, vol. 7, (no. MAY) -
DOI
LowMACA: Exploiting protein family analysis for the identification of rare driver mutations in cancer
BMC Bioinformatics, vol. 17, (no. 1) -
DOI
Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination
Scientific Reports, vol. 6 - 2015
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DOI
Computational epigenomics: Challenges and opportunities
Frontiers in Genetics, vol. 5, (no. FEB) -
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 -
DOI
methylPipe and compEpiTools: A suite of R packages for the integrative analysis of epigenomics data
BMC Bioinformatics, vol. 16, (no. 1) -
DOI
Selective transcriptional regulation by Myc: Experimental design and computational analysis of high-throughput sequencing data
Data in Brief, vol. 3, pp. 40-46 -
DOI
Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination
Molecular Cell, vol. 60, (no. 3), pp. 460-474 - 2014
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DOI
Computational and experimental methods to decipher the epigenetic code
Frontiers in Genetics, vol. 5, (no. SEP) -
DOI
DOTS-Finder: A comprehensive tool for assessing driver genes in cancer genomes
Genome Medicine, vol. 6, (no. 6) -
DOI
Relationship between genome and epigenome - challenges and requirements for future research
BMC Genomics, vol. 15, (no. 1) -
DOI
Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis
Nature, vol. 511, (no. 7510), pp. 488-492 -
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
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DOI
Patterns of population epigenomic diversity
Nature, vol. 495, (no. 7440), pp. 193-198 -
DOI
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
eLife, vol. 2013, (no. 2) - 2012
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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 -
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
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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 -
DOI
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
Nature, vol. 471, (no. 7336), pp. 68-73 -
DOI
Methylated DNA immunoprecipitation genome-wide analysis
Methods in molecular biology (Clifton, N.J.), vol. 791, pp. 113-123 -
DOI
The DNA methylome
FEBS Letters, vol. 585, (no. 13), pp. 1994-2000 - 2010
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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 -
DOI
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
Cell Stem Cell, vol. 6, (no. 5), pp. 479-491 -
DOI
Temporal gene expression profile of the hippocampus following trace fear conditioning
Brain Research, vol. 1308, pp. 14-23 - 2009
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DOI
Genome-wide screen of promoter methylation identifies novel markers in melanoma
Genome Research, vol. 19, (no. 8), pp. 1462-1470 -
DOI
Human DNA methylomes at base resolution show widespread epigenomic differences
Nature, vol. 462, (no. 7271), pp. 315-322 -
DOI
Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: Clinical implications
PLoS ONE, vol. 4, (no. 2) - 2008
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DOI
Gene Profiling of Dendritic cells during Host-Pathogen Interactions
Handbook of Dendritic Cells, vol. 1, pp. 175-197, Publisher: Wiley-VCH Verlag GmbH -
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 -
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) -
DOI
Statistical similarities between transcriptomics and quantitative shotgun proteomics data
Molecular and Cellular Proteomics, vol. 7, (no. 4), pp. 631-644 - 2007
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DOI
The Genopolis Microarray Database
BMC Bioinformatics, vol. 8, (no. SUPPL. 1) - 2006
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DOI
AMDA: An R package for the automated microarray data analysis
BMC Bioinformatics, vol. 7 -
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 -
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 -
DOI
Transcriptional Profiling of Dendritic Cells in Response to Pathogens
Immunogenomics and Human Disease, pp. 461-486, Publisher: John Wiley & Sons, Ltd - 2005
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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
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DOI
A power law global error model for the identification of differentially expressed genes in microarray data
BMC Bioinformatics, vol. 5 -
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
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