Domenico Simone

Domenico Simone

Title:
Postdoctoral Scientist
Office:
305
Address: Innovation Hall
Email:
[email protected]

I am interested in the evaluation of computational methods for the analysis of metagenomic datasets and their application in a wide range of topics. Current projects include the profiling of the microbiome associated with mental diseases and other non-healthy conditions in humans and other animals.

Education

PhD, Biochemistry, Molecular Biology and Bioinformatics, University of Bari (Italy)
Master Degree, Molecular and Cellular Biology, University of Bari (Italy)

Publications

Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X; MSeqDR Consortium Participants; MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,; Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory  Enns, Giuseppe Gasparre,; Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,; Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,; Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. Thorburn, Johan Van Hove, Lynne Wolfe, and Lee-Jun Wong. Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Mol Genet Metab. 2015 Mar;114(3):388-96. doi: 10.1016/j.ymgme.2014.11.016. Epub 2014 Dec 4. Review. PubMed PMID: 25542617; PubMed Central PMCID: PMC4512182.

Bevilacqua V, Pietroleonardo N, Giannino E, Stroppa F, Simone D, Pesole G, Picardi E. EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. BMC Bioinformatics. 2014;15 Suppl 15:S7. doi: 10.1186/1471-2105-15-S15-S7. Epub 2014 Dec 3. PubMed PMID: 25474441; PubMed Central PMCID: PMC4271567.

Diroma MA, Calabrese C, Simone D, Santorsola M, Calabrese FM, Gasparre G, Attimonelli M. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics. 2014;15 Suppl 3:S2. doi:
10.1186/1471-2164-15-S3-S2. Epub 2014 May 6. PubMed PMID: 25077682; PubMed Central PMCID: PMC4083402.

Calabrese C*, Simone D*, Diroma MA, Santorsola M, Guttà C, Gasparre G, Picardi E, Pesole G, Attimonelli M. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. 2014 Nov 1;30(21):3115-7. doi: 10.1093/bioinformatics/btu483. Epub 2014 Jul 14. PubMed PMID: 25028726; PubMed Central PMCID: PMC4201154.

Simone D, Bay DC, Leach T, Turner RJ. Diversity and evolution of bacterial twin arginine translocase protein, TatC, reveals a protein secretion system that  is evolving to fit its environmental niche. PLoS One. 2013 Nov 13;8(11):e78742. doi: 10.1371/journal.pone.0078742. eCollection 2013. PubMed PMID: 24236045; PubMed Central PMCID: PMC3827258.

Triscari-Barberi T, Simone D, Calabrese FM, Attimonelli M, Hahn KR, Amoako KK, Turner RJ, Fedi S, Zannoni D. Genome sequence of the polychlorinated-biphenyl degrader Pseudomonas pseudoalcaligenes KF707. J Bacteriol. 2012 Aug;194(16):4426-7. doi: 10.1128/JB.00722-12. PubMed PMID: 22843571; PubMed
Central PMCID: PMC3416219.

Calabrese FM, Simone D, Attimonelli M. Primates and mouse NumtS in the UCSC Genome Browser. BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S15. doi: 10.1186/1471-2105-13-S4-S15. PubMed PMID: 22536961; PubMed Central PMCID: PMC3314570.

Lang M, Sazzini M, Calabrese FM, Simone D, Boattini A, Romeo G, Luiselli D, Attimonelli M, Gasparre G. Polymorphic NumtS trace human population relationships. Hum Genet. 2012 May;131(5):757-71. doi: 10.1007/s00439-011-1125-3. Epub 2011 Dec 8. PubMed PMID: 22160368.

Rubino F, Piredda R, Calabrese FM, Simone D, Lang M, Calabrese C, Petruzzella V, Tommaseo-Ponzetta M, Gasparre G, Attimonelli M. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res. 2012 Jan;40(Database issue):D1150-9. doi: 10.1093/nar/gkr1086. Epub 2011 Dec 1. PubMed PMID: 22139932; PubMed Central PMCID: PMC3245114.

Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. doi: 10.1186/1471-2164-12-517. PubMed PMID: 22013967; PubMed Central PMCID: PMC3228558.

Kurelac I, Lang M, Zuntini R, Calabrese C, Simone D, Vicario S, Santamaria M, Attimonelli M, Romeo G, Gasparre G. Searching for a needle in the haystack: comparing six methods to evaluate heteroplasmy in difficult sequence context. Biotechnol Adv. 2012 Jan-Feb;30(1):363-71. doi: 10.1016/j.biotechadv.2011.06.001. Epub 2011 Jun 13. PubMed PMID: 21689740.