– de Pretis S, Kress T, Morelli MJ, Melloni GEM, Riva L, Amati B, Pelizzola M. “INSPEcT: a Computational Tool to Infer RNA Synthesis, Processing and Degradation Dynamics from RNA- and 4sU-seq Time Course Experiments.” Bioinformatics (IF 7.3; 18 citations). 2015, PMID: 25957348. In this study we provided the first software able to comprehensively quantify the RNA dynamics through the integrative analysis of total and nascent RNAs.
– Sabo A*, Kress TR*, Pelizzola M*, de Pretis S, et al. “Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.” Nature (IF 40.1; 212 citations). 2014, PMID: 25043028. * denotes equal contribution. In this study we comprehensively characterized MYC-dependent transcriptional and epigenetic land- scapes, thus revising the recent concept of MYC as transcriptional amplifier.
– Lister R*, Pelizzola M*, Kida YS, Hawkins RD, Nery JR, Hon G, et al. “Hotspots of aberrant epige- nomic reprogramming in human induced pluripotent stem cells.” Nature (IF 40.1; 1351 citations). 2011, PMCID: PMC3100360. * denotes equal contribution. In this study, which was recognized by ScienceWatch as the #4 hottest paper of 2011, we characterized the limits of epigenome reprogramming in the generation of iPSCs.
– Lister R*, Pelizzola M*, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. “Human DNA methylomes at base resolution show widespread epigenomic differences.” Nature (IF 40.1; 3344 citations). 2009, PMCID: PMC2857523. * denotes equal contribution. In this study, which was nominated as the #2 scientific discovery of the year 2009 by the TIME Magazine, we described for the first time whole-genome DNA methylation maps for human, and the occurrence and reprogramming of non-CpG methylation in pluripotent cells.