About the PI

Simone Sidoli

Simone Sidoli is an Assistant Professor at the Department of Biochemistry at the Albert Einstein College of Medicine.

He approached mass spectrometry (MS) as a trainee in the laboratory of Prof. Careri at the University of Parma (Italy), his hometown. There, he established methods to detect allergens in aliments, as food and food safety are critical aspects of the economy of Parma. Next, he moved to the University of Southern Denmark (Odense, DK) for his PhD, joining the prestigious Protein Research Group. In the group of Ole N. Jensen, he developed methods for protein analysis, processing large datasets and learned to maintain state-of-the-art instrumentation. Together with the Biotech Research & Innovative Center (BRIC) in Copenhagen, he studied the histone PTM landscape of embryonic stem cells using his own developed middle-down MS workflow. Middle-down MS performs unbiased identification and quantification of co-existing histone marks.

In 2014, he joined Ben Garcia’s lab, located within the Epigenetics Institute at the University of Pennsylvania (Philadelphia, PA, USA). In this amazing environment, hosting many worldwide famous experts in epigenetics, he investigated human disease systems by developing a proteomics and computational pipeline to link cell signaling cascades (protein phosphorylation) with chromatin changes (histone modifications). He also applied this methodology to identify the regulated proteome during host viral infection. These methods include improvements in quantification accuracy of histone PTMs, enhancement of throughput, quantification of chromatin accessibility and follow-up optimization of the middle-down MS strategy. Simone is now a member of the American Society of Mass Spectrometry (ASMS), HUman Proteome Organization (HUPO) and the New York Academy of Sciences (NYAS).

Selected publications (full list in PubMed)

A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins Sidoli S, Lopes M, Lund PJ, Goldman N, Fasolino M, Coradin M, Kulej K, Bhanu NV, Vahedi G and Garcia BA (Scientific Reports, 2019)

One minute analysis of histone post-translational modifications by direct injection mass spectrometry Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen K, Agosto L, Cunha JPC and Garcia BA (Genome Research, 2019)

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C and Garcia BA (Epigenetics & Chromatin, 2017)