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SVM²: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data.
Chiara M, Pesole G, Horner DS. Chiara M, et al. Nucleic Acids Res. 2012 Oct;40(18):e145. doi: 10.1093/nar/gks606. Epub 2012 Jun 25. Nucleic Acids Res. 2012. PMID: 22735696 Free PMC article.
Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G. Picardi E, et al. Nucleic Acids Res. 2010 Aug;38(14):4755-67. doi: 10.1093/nar/gkq202. Epub 2010 Apr 12. Nucleic Acids Res. 2010. PMID: 20385587 Free PMC article.
Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity within Fusarium fujikuroi.
Chiara M, Fanelli F, Mulè G, Logrieco AF, Pesole G, Leslie JF, Horner DS, Toomajian C. Chiara M, et al. Genome Biol Evol. 2015 Oct 15;7(11):3062-9. doi: 10.1093/gbe/evv198. Genome Biol Evol. 2015. PMID: 26475319 Free PMC article.
A-GAME: improving the assembly of pooled functional metagenomics sequence data.
Chiara M, Placido A, Picardi E, Ceci LR, Horner DS, Pesole G. Chiara M, et al. BMC Genomics. 2018 Jan 12;19(1):44. doi: 10.1186/s12864-017-4369-z. BMC Genomics. 2018. PMID: 29329522 Free PMC article.
SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).
Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. Formenti G, et al. Gigascience. 2019 Jan 1;8(1):giy142. doi: 10.1093/gigascience/giy142. Gigascience. 2019. PMID: 30496513 Free PMC article.
De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters.
Chiara M, Horner DS, Spada A. Chiara M, et al. PLoS One. 2013 Dec 6;8(12):e80961. doi: 10.1371/journal.pone.0080961. eCollection 2013. PLoS One. 2013. PMID: 24324652 Free PMC article.
Gene coexpression patterns during early development of the native Arabidopsis reproductive meristem: novel candidate developmental regulators and patterns of functional redundancy.
Mantegazza O, Gregis V, Chiara M, Selva C, Leo G, Horner DS, Kater MM. Mantegazza O, et al. Plant J. 2014 Sep;79(5):861-77. doi: 10.1111/tpj.12585. Epub 2014 Jul 28. Plant J. 2014. PMID: 24923650
Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity.
D'Erchia AM, Atlante A, Gadaleta G, Pavesi G, Chiara M, De Virgilio C, Manzari C, Mastropasqua F, Prazzoli GM, Picardi E, Gissi C, Horner D, Reyes A, Sbisà E, Tullo A, Pesole G. D'Erchia AM, et al. Mitochondrion. 2015 Jan;20:13-21. doi: 10.1016/j.mito.2014.10.005. Epub 2014 Nov 1. Mitochondrion. 2015. PMID: 25446395
Draft genome sequence of Acinetobacter sp. neg1 capable of degrading ochratoxin A.
Fanelli F, Chiara M, Liuzzi VC, Haidukowski M, Tristezza M, Caterina M, D'Erchia AM, Pesole G, Horner DS, Mule G. Fanelli F, et al. FEMS Microbiol Lett. 2015 Apr;362(7):fnv004. doi: 10.1093/femsle/fnv004. Epub 2015 Jan 18. FEMS Microbiol Lett. 2015. PMID: 25790508
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