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List of works by Mattia Pelizzola

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

scientific article published in February 2005

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

scientific article

A type I IFN-dependent pathway induced by Schistosoma mansoni eggs in mouse myeloid dendritic cells generates an inflammatory signature

scientific article published on March 2004

AMDA: an R package for the automated microarray data analysis

scientific article

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

scientific article

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

scientific article published on 22 July 2016

Computational and experimental methods to decipher the epigenetic code

scientific article

Computational epigenomics: challenges and opportunities

scientific article published on 5 March 2015

Computational methods for RNA modification detection from nanopore direct RNA sequencing data

publication published on 24 September 2021

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

scientific article published in Scientific Reports

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

scientific article published on 05 June 2017

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

scientific article

Degradation dynamics of microRNAs revealed by a novel pulse-chase approach.

scientific article published on 28 January 2016

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

scientific article

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

scientific article

Dynamics of transcriptional regulation from total RNA-seq experiments: Supplemental Figures and Methods

article

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

scientific article published on June 2006

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

scientific article published on 25 September 2020

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

scientific article published on 02 June 2009

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

scientific article

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

scientific article published on 7 December 2011

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

scientific article

Human DNA methylomes at base resolution show widespread epigenomic differences

scientific article

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

scientific article published on 7 May 2015

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

scientific article

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

scientific article published on 13 September 2017

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

scientific article

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

scientific article

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

scientific article published on 9 February 2016

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

scientific article published on 2 September 2008

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

scientific article published on 18 October 2019

Methylated DNA immunoprecipitation genome-wide analysis

scientific article published in January 2011

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

scientific article published on 12 September 2016

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

scientific article

Ontology-driven integrative analysis of omics data through Onassis

scientific article published on 20 January 2020

Patterns of population epigenomic diversity.

scientific article published on 6 March 2013

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

scientific article

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

scientific article published on 18 June 2014

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.

scientific article

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

scientific article

Statistical similarities between transcriptomics and quantitative shotgun proteomics data

scientific article

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

scientific article published on 05 December 2013

Temporal gene expression profile of the hippocampus following trace fear conditioning

scientific article published on 24 October 2009

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

scientific article published on 11 June 2013

The DNA methylome

scientific article

The genopolis microarray database

scientific article

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

scientific article published on 22 October 2015

Translation is required for miRNA-dependent decay of endogenous transcripts

scientific article published on 10 December 2020

Widespread dynamic DNA methylation in response to biotic stress ⬇️

scientific article published on June 25, 2012

m6A-Dependent RNA Dynamics in T Cell Differentiation

article

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

scientific article

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