Chiara M, Fanelli F, Mulè G, Logrieco AF, Pesole G, Leslie JF, Horner DS, Toomajian C. Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity within Fusarium fujikuroi. Genome Biol Evol. 2015 Oct 15;7(11):3062-9.Placido A, Hai T, Ferrer M, Chernikova TN, Distaso M, Armstrong D, Yakunin AF, Toshchakov SV, Yakimov MM, Kublanov IV, Golyshina OV, Pesole G, Ceci LR, Golyshin PN. Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase. Appl Microbiol Biotechnol. 2015 Dec;99(23):10031-46.
Chiara M, Caruso M, D’Erchia AM, Manzari C, Fraccalvieri R, Goffredo E, Latorre L, Miccolupo A, Padalino I, Santagada G, Chiocco D, Pesole G, Horner DS, Parisi A. Comparative Genomics of Listeria Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer. Genome Biol Evol. 2015 Jul 15;7(8):2154-72.
Fanelli F, Chiara M, Liuzzi VC, Haidukowski M, Tristezza M, Caterina M, D’Erchia AM, Pesole G, Horner DS, Mule G. Draft genome sequence of Acinetobacter sp. neg1 capable of degrading ochratoxin A. FEMS Microbiol Lett. 2015 Apr;362(7).
Mechelli R, Manzari C, Policano C, Annese A, Picardi E, Umeton R, Fornasiero A, D’Erchia AM, Buscarinu MC, Agliardi C, Annibali V, Serafini B, Rosicarelli B, Romano S, Angelini DF, Ricigliano VA, Buttari F, Battistini L, Centonze D, Guerini FR, D’Alfonso S, Pesole G, Salvetti M, Ristori G. Epstein-Barr virus genetic variants are associated with multiple sclerosis. Neurology. 2015 Mar 31;84(13):1362-8.
Fosso, B., Santamaria, M., Marzano, M., Alonso-Alemany, D., Valiente, G., Donvito, G., Monaco, A., Notarangelo, P., and Pesole, G. (2015). BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC bioinformatics 16, 203.
Manzari, C., Fosso, B., Marzano, M., Annese, A., Caprioli, R., D’Erchia, A., Gissi, C., Intranuovo, M., Picardi, E., Santamaria, M., et al. (2015). The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy. Biol Invasions 17, 923-940.
Balech, B., Vicario, S., Donvito, G., Monaco, A., Notarangelo, P., and Pesole, G. (2015). MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information. Bioinformatics 31, 2571-2573.
Kissling, W.D., Hardisty, A., García, E.A., Santamaria, M., De Leo, F., Pesole, G., Freyhof, J., Manset, D., Wissel, S., Konijn, J. & Los, W. (2015): Towards global interoperability for supporting biodiversity research on Essential Biodiversity Variables (EBVs). Biodiversity accepted (2015).
Delić, D., Balech, B., Radulović, M., Lolić, B., Karačić, A., Vukosavljević, V., Đurić, G., and Cvetković, T. (2015). Vmp1 and stamp genes variability of ‘Candidatus phytoplasma solani’ in Bosnian and Herzegovinian grapevine. Eur J Plant Pathol, 1-5.
Manzari C, Chiara M, Costanza A, Leoni C, Volpicella M, Picardi E, D’Erchia AM, Placido A, Trotta M, Horner DS, Pesole G, Ceci LR. Draft genome sequence of Sphingobium sp. strain ba1, resistant to kanamycin and nickel ions. FEMS Microbiol Lett. 2014 Oct 7.
Chiara M, D’Erchia AM, Manzari C, Minotto A, Montagna C, Addante N, Santagada G, Latorre L, Pesole G, Horner DS, Parisi A. Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy Products from a Processing Plant in Southern Italy. Genome Announc. 2014 Apr 10;2(2).
Griggio F, Voskoboynik A, Iannelli F, Justy F, Tilak MK, Turon X, Pesole G, Douzery EJ, Mastrototaro F, Gissi C. Ascidian mitogenomics: comparison of evolutionary rates in closely related taxa provides evidence of ongoing speciation events. Genome Biol Evol. 2014 Mar;6(3):591-605. doi: 10.1093/gbe/evu041. Erratum in: Genome Biol Evol. 2014 Apr;6(4):931. Xavier, Turon [corrected to Turon, Xavier].
Alonso E., Bellisari L, De Leo F, Hardisty A, Keuchkerian S, Konijn J, Los W, Manset D, Spinelli O, Vicario S. A roadmap of global research data infrastructures supporting biodiversity and ecosystem science Produced by the project CReATIVE-B Coordination of Research e-Infrastructures Activities Toward an International Virtual Environment for Biodiversity Funded by the European Commission with Grant agreement n°: 284441 (2014) 1-27
Santamaria, M., Fosso, B., Consiglio, A., De Caro, G., Grillo, G., Licciulli, F., Liuni, S., Marzano, M., Alonso-Alemany, D., Valiente, G., et al. (2012). Reference databases for taxonomic assignment in metagenomics. Briefings in bioinformatics 13, 682-695.
Fosso B, Marzano M, Santamaria M (2015). e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling. In: RNA Bioinformatics. 2015
Santamaria M, De Leo F, Pesole G (2014). Protocolli di laboratorio e strumenti bioinformatici innovativi per l’analisi composizionale dei microbiomi ambientali. In: Le innovazioni tecnologiche nel settore della caratterizzazione e bonifica dei siti contaminati. 2014
Tomasino M.P., Piredda R., Sánchez P., Duarte B., Fosso B., Caçador I., Amaral-Zettler L., Pesole G., Zingone A. “Exploring spatial and temporal distribution of harmful microalgae with HTS-based DNA-metabarcoding data”. A New Age of Discovery for Aquatic Microeukaryotes. January 26- 29, 2016, EMBL-Heidelberg, Germany (submtitted).Piredda R., D’Erchia A.M., Manzari C., Pesole G., Tomasino M.P., Montresor M., Kooistra W.H.C.F., Sarno D., Zingone A. “Seasonal diversity of marine planktonic protists in the Gulf of Naples inferred from V4 and V9 regions in the 18S rDNA.” ASLO- Aquatic Sciences Meeting, February 22 – 27, 2015, Granada, Spain.
Balech, B., Vicario, S., Donvito, G., Monaco, A., Notarangelo, P., and Pesole, G. MSA-PAD: Novel DNA Multiple Sequence Alignment Guided by PFAM Conserved Domains. Joint NETTAB and Integrative Bioinformatics Meetings, October 14-16, 2015, Bari, Italy.
Fosso B, Santamaria M, Lovero D, Corrado G, Vizza E, Passaro N, Crescenzi M, and Pesole G. “MetaShot: a complete workflow for the characterization of human microbiome from shotgun metagenomic data.” (Oral presentation). NETTAB & IB, 14-16 Ottobre 2015, Bari, Italy
Francavilla A, Marzano M, Favoino E, D’Erchia AM, Fosso B, Intranuovo M, Lovero D, Manzari C, Notarnicola M, Polimeno L, Santamaria M and Pesole G. “Effect of n3-polyunsaturated fatty acids (PUFA) and Orlistat on Colorectal Cancer (CRC)-associated microbiome”. (Poster) Human Gut Microbiome and Diseases, 25-26 Luglio 2015, Milan, Italy
Fosso B, Santamaria M, Marzano M, Alonso-Alemany D, Valiente G, Donvito G, Monaco A, Notarangelo P, Pesole G. “BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS”. (Poster) Bioinformatics ITalian Society (BITS) Annual meeting 2015, 3-5 Giugno 2015, Milan, Italy.
Fosso B, Santamaria M, Marzano M, Alonso-Alemany D, Valiente G, Donvito G, Monaco A, Notarangelo P, Pesole G. “BioMaS (Bioinformatic analysis of Metagenomic ampliconS): a user-friendly web resource for amplicon-based metagenomics”. (Oral presentation) ESF-EMBO Symposium Symbiomes: Systems Biology of Host-Microbiome Interactions, Pultusk (Poland), 5-10 Giugno 2015.
Fosso B, Santamaria M, Marzano M, Donvito G, Monaco A, Notarangelo P, Maggi GP, Pesole G. “BioMaS: a friendly web service for an accurate taxonomic assessment of microbiomes through target-oriented metagenomics”. (Poster) IHMC 2015 (5th International Human Microbiome Congress), Luxembourg 31 March – 2 Aprile 2015.
Fosso B, Santamaria M, Lovero D, Corrado G, Vizza E, Passaro N, Crescenzi M, and Pesole G. “MetaShot: a complete workflow for the characterization of the human associated microbiome from shotgun metagenomic data”. (Poster) IHMC 2015 (5th International Human Microbiome Congress), Luxembourg 31 March – 2 Aprile 2015.
Fosso B, Donvito G, Monaco A, Notarangelo P, Santamaria M, Pesole G. “BioMaS: a web service for the taxonomic characterization of bacterial and fungal microbiome”. (Oral Presentation). BIP-day 2014, Bari, Italy, 19 Dicembre 2014
Santamaria M, Fosso B, Manzari C, Marzano M, Intranuovo M, Valletti A, Mastropasqua F, Aiello I, Annese A, Balech B, Pousis C, Sgaramella G, De Filippis T, Picardi E, D’Erchia AM, Pesole G. “Analysis of the gut microbiome through a novel Illumina MiSeq sequencing-based strategy and ad hoc developed bioinformatics resources”. (Poster) 7th International Immunonutrition Workshop, Carovigno, Brindisi, Italy, 1-3 Maggio 2014
Fosso B, Donvito G, Monaco A, Notarangelo P, Santamaria M, Pesole G. “BioMas: a web service for bioinformatics analysis of Metagenomic AmpliconS”. (Poster) Bioinformatics ITalian Society (BITS) Annual meeting 2014. Febbraio 26-28, Rome, Italy.
Zagato E, Schioppa T, Spadoni I, Saccheri F, Guglietta S, Penna G, Marzano M, Fosso B, Pesole G, Rescigno M. “Role of bacteria and mucus system in intestinal tumorigenesis”. (Poster) Keystone Symposium on Inflammation, Infection and Cancer, Fairmont Chateau Whistler, Whistler, British Columbia, Canada, 9-14 Marzo 2014.
Fosso B, Santamaria M, Marzano M, Sabino L, Alonso-Alemany D, Valiente G and Pesole G. “BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic ampliconS”. (Oral Presentation). GDRE Comparative Genomics. Barcellona, Barcellona, Spagna (25-26 Novembre 2013);
Manzari C, Fosso B, Marzano M, Annese A, Intranuovo M, D’Erchia AM, Gissi C, Picardi E, Santamaria M, Caprioli R, Scorrano S, Stabili L, Piraino S, Pesole G. “Aquatic microbiome diversity under the influence of jellyfish bloom through the application of an Illumina-based protocol”. (Poster) VECTORS Annual Meeting 2013. Atene, Grecia (4-8 Novembre 2013);
Fosso B, Santamaria M, Marzano M, Sabino L, and Pesole G. “BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic ampliconS”. (Oral presentation). 3rd Annual Project Meeting -BioVeL. Budapest, Bulgaria (1-4 Ottobre 2013
Fosso B, Santamaria M, Marzano M, Sabino L, Pesole G. “BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic ampliconS”. (Poster). Biodiversity Informatics Horizons 2013. Roma, Italia (3-6 Settembre 2013);
Fosso B, Santamaria M, Marzano M, Liuni S, Valiente G, Pesole G. “BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic Amplicons”. (Poster). Next Generation Sequencing & Epigenomics Workshop 2012. Bari, Italia (5-7 Dicembre 2012);
Santamaria M, Fosso B, Marzano M, Manzari C, D’Erchia AM and Pesole G. “Experimental and computational strategies for exploring Biodiversity through Metagenomic approaches”. (Poster) International Workshop: Molecular Tools for monitoring invasive species. Lecce, Italia (12-14 Settembre 2012);
Fosso B, Santamaria M, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, and Pesole G. “ITSoneDB: a Specialized ITS1 Database for Amplicon-based Metagenomic Characterization of Environmental Fungal Communities”. (Poster). BITS Annual Meeting 2012. Catania, Italia (2-4 Maggio 2012);