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Items: 1 to 50 of 86

1.

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.

Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR 3rd, Ciofi C, Kwok PY, Pollard KS, Bruneau BG.

Nat Ecol Evol. 2019 Aug;3(8):1241-1252. doi: 10.1038/s41559-019-0945-8. Epub 2019 Jul 29.

PMID:
31358948
2.

The art of adapting to extreme environments: The model system Pseudoalteromonas.

Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R.

Phys Life Rev. 2019 Apr 4. pii: S1571-0645(19)30066-1. doi: 10.1016/j.plrev.2019.04.003. [Epub ahead of print] Review.

PMID:
31072789
3.

Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria.

Zoledowska S, Presta L, Fondi M, Decorosi F, Giovannetti L, Mengoni A, Lojkowska E.

Microorganisms. 2019 Apr 5;7(4). pii: E101. doi: 10.3390/microorganisms7040101.

4.

Tn-Core: A Toolbox for Integrating Tn-seq Gene Essentiality Data and Constraint-Based Metabolic Modeling.

diCenzo GC, Mengoni A, Fondi M.

ACS Synth Biol. 2019 Jan 18;8(1):158-169. doi: 10.1021/acssynbio.8b00432. Epub 2018 Dec 27.

PMID:
30525460
5.

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.

Checcucci A, diCenzo GC, Ghini V, Bazzicalupo M, Becker A, Decorosi F, Döhlemann J, Fagorzi C, Finan TM, Fondi M, Luchinat C, Turano P, Vignolini T, Viti C, Mengoni A.

ACS Synth Biol. 2018 Oct 19;7(10):2365-2378. doi: 10.1021/acssynbio.8b00158. Epub 2018 Oct 3.

PMID:
30223644
6.

Multidisciplinary approaches for studying rhizobium-legume symbioses.

diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A.

Can J Microbiol. 2019 Jan;65(1):1-33. doi: 10.1139/cjm-2018-0377. Epub 2018 Sep 11. Review.

7.

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp.

Maggini V, Miceli E, Fagorzi C, Maida I, Fondi M, Perrin E, Mengoni A, Bogani P, Chiellini C, Mocali S, Fabiani A, Decorosi F, Giovannetti L, Firenzuoli F, Fani R.

FEMS Microbiol Ecol. 2018 Aug 1;94(8). doi: 10.1093/femsec/fiy118.

PMID:
29912319
8.

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti.

diCenzo GC, Benedict AB, Fondi M, Walker GC, Finan TM, Mengoni A, Griffitts JS.

PLoS Genet. 2018 Apr 19;14(4):e1007357. doi: 10.1371/journal.pgen.1007357. eCollection 2018 Apr.

9.

G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs.

Di Salvo M, Pinatel E, Talà A, Fondi M, Peano C, Alifano P.

BMC Bioinformatics. 2018 Feb 6;19(1):36. doi: 10.1186/s12859-018-2049-x.

10.

Modelling the Kinetic Response to Nutrient Fluctuations.

Fondi M.

Trends Microbiol. 2018 Jan;26(1):4-5. doi: 10.1016/j.tim.2017.11.009. Epub 2017 Nov 24.

PMID:
29239769
11.

Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models.

Vignolini T, Mengoni A, Fondi M.

Methods Mol Biol. 2018;1716:177-196. doi: 10.1007/978-1-4939-7528-0_8.

PMID:
29222754
12.

Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance.

Perrin E, Fondi M, Bosi E, Mengoni A, Buroni S, Scoffone VC, Valvano M, Fani R.

BMC Genomics. 2017 Oct 30;18(1):834. doi: 10.1186/s12864-017-4222-4.

13.

Perspectives and Challenges in Microbial Communities Metabolic Modeling.

Bosi E, Bacci G, Mengoni A, Fondi M.

Front Genet. 2017 Jun 21;8:88. doi: 10.3389/fgene.2017.00088. eCollection 2017.

14.

Constraint-based metabolic modelling of marine microbes and communities.

Fondi M, Fani R.

Mar Genomics. 2017 Aug;34:1-10. doi: 10.1016/j.margen.2017.06.003. Epub 2017 Jun 23. Review.

PMID:
28648476
15.

New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens.

Miceli E, Presta L, Maggini V, Fondi M, Bosi E, Chiellini C, Fagorzi C, Bogani P, Di Pilato V, Rossolini GM, Mengoni A, Firenzuoli F, Perrin E, Fani R.

Genome Announc. 2017 Jun 22;5(25). pii: e00565-17. doi: 10.1128/genomeA.00565-17.

16.

Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections.

Presta L, Bosi E, Mansouri L, Dijkshoorn L, Fani R, Fondi M.

Sci Rep. 2017 Jun 16;7(1):3706. doi: 10.1038/s41598-017-03416-2.

17.

Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens.

Fondi M, Pinatel E, Talà A, Damiano F, Consolandi C, Mattorre B, Fico D, Testini M, De Benedetto GE, Siculella L, De Bellis G, Alifano P, Peano C.

Front Microbiol. 2017 May 12;8:835. doi: 10.3389/fmicb.2017.00835. eCollection 2017.

18.

Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex.

Maggini V, Presta L, Miceli E, Fondi M, Bosi E, Chiellini C, Fagorzi C, Bogani P, Di Pilato V, Rossolini GM, Mengoni A, Firenzuoli F, Perrin E, Fani R.

Genome Announc. 2017 May 18;5(20). pii: e00351-17. doi: 10.1128/genomeA.00351-17.

19.

Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach.

Mocali S, Chiellini C, Fabiani A, Decuzzi S, de Pascale D, Parrilli E, Tutino ML, Perrin E, Bosi E, Fondi M, Lo Giudice A, Fani R.

Sci Rep. 2017 Apr 12;7(1):839. doi: 10.1038/s41598-017-00876-4.

20.

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.

Bosi E, Fondi M, Orlandini V, Perrin E, Maida I, de Pascale D, Tutino ML, Parrilli E, Lo Giudice A, Filloux A, Fani R.

BMC Genomics. 2017 Jan 17;18(1):93. doi: 10.1186/s12864-016-3382-y.

21.

Pseudoalteromonas haloplanktis produces methylamine, a volatile compound active against Burkholderia cepacia complex strains.

Sannino F, Parrilli E, Apuzzo GA, de Pascale D, Tedesco P, Maida I, Perrin E, Fondi M, Fani R, Marino G, Tutino ML.

N Biotechnol. 2017 Mar 25;35:13-18. doi: 10.1016/j.nbt.2016.10.009. Epub 2016 Oct 29.

PMID:
27989956
22.

Phenotypic and genomic characterization of the antimicrobial producer Rheinheimera sp. EpRS3 isolated from the medicinal plant Echinacea purpurea: insights into its biotechnological relevance.

Presta L, Bosi E, Fondi M, Maida I, Perrin E, Miceli E, Maggini V, Bogani P, Firenzuoli F, Di Pilato V, Rossolini GM, Mengoni A, Fani R.

Res Microbiol. 2017 Apr;168(3):293-305. doi: 10.1016/j.resmic.2016.11.001. Epub 2016 Nov 22.

PMID:
27884784
23.

Modelling microbial metabolic rewiring during growth in a complex medium.

Fondi M, Bosi E, Presta L, Natoli D, Fani R.

BMC Genomics. 2016 Nov 24;17(1):970.

24.

A novel synthetic medium and expression system for subzero growth and recombinant protein production in Pseudoalteromonas haloplanktis TAC125.

Sannino F, Giuliani M, Salvatore U, Apuzzo GA, de Pascale D, Fani R, Fondi M, Marino G, Tutino ML, Parrilli E.

Appl Microbiol Biotechnol. 2017 Jan;101(2):725-734. doi: 10.1007/s00253-016-7942-5. Epub 2016 Oct 27.

PMID:
27796433
25.

Arthrobacter sp. EpRS66 and Arthrobacter sp. EpRS71: Draft Genome Sequences from Two Bacteria Isolated from Echinacea purpurea Rhizospheric Soil.

Presta L, Fondi M, Perrin E, Maida I, Miceli E, Chiellini C, Maggini V, Bogani P, Di Pilato V, Rossolini GM, Mengoni A, Fani R.

Front Microbiol. 2016 Sep 12;7:1417. doi: 10.3389/fmicb.2016.01417. eCollection 2016. No abstract available.

26.

Essential Oil from Origanum vulgare Completely Inhibits the Growth of Multidrug-Resistant Cystic Fibrosis Pathogens.

Pesavento G, Maggini V, Maida I, Lo Nostro A, Calonico C, Sassoli C, Perrin E, Fondi M, Mengoni A, Chiellini C, Vannacci A, Gallo E, Gori L, Bogani P, Bilia AR, Campana S, Ravenni N, Dolce D, Firenzuoli F, Fani R.

Nat Prod Commun. 2016 Jun;11(6):861-4.

PMID:
27534136
27.

Draft Genome Sequences of the Antimicrobial Producers Pseudomonas sp. TAA207 and Pseudomonas sp. TAD18 Isolated from Antarctic Sediments.

Presta L, Inzucchi I, Bosi E, Fondi M, Perrin E, Maida I, Miceli E, Tutino ML, Lo Giudice A, de Pascale D, Fani R.

Genome Announc. 2016 Jul 28;4(4). pii: e00728-16. doi: 10.1128/genomeA.00728-16.

28.

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.

diCenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, Finan TM, Galardini M, Fondi M.

Nat Commun. 2016 Jul 22;7:12219. doi: 10.1038/ncomms12219.

29.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.

Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3801-9. doi: 10.1073/pnas.1523199113. Epub 2016 Jun 10.

30.

Draft Genome Sequence of Flavobacterium sp. Strain TAB 87, Able To Inhibit the Growth of Cystic Fibrosis Bacterial Pathogens Belonging to the Burkholderia cepacia Complex.

Presta L, Inzucchi I, Bosi E, Fondi M, Perrin E, Miceli E, Tutino ML, Lo Giudice A, de Pascale D, Fani R.

Genome Announc. 2016 May 19;4(3). pii: e00410-16. doi: 10.1128/genomeA.00410-16.

31.

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.

Fondi M, Karkman A, Tamminen MV, Bosi E, Virta M, Fani R, Alm E, McInerney JO.

Genome Biol Evol. 2016 May 13;8(5):1388-400. doi: 10.1093/gbe/evw077.

32.

Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds.

Presta L, Bosi E, Fondi M, Maida I, Perrin E, Miceli E, Maggini V, Bogani P, Firenzuoli F, Di Pilato V, Rossolini GM, Mengoni A, Fani R.

Genome Announc. 2016 May 5;4(3). pii: e00346-16. doi: 10.1128/genomeA.00346-16.

33.

Genomic and phenotypic characterization of the species Acinetobacter venetianus.

Fondi M, Maida I, Perrin E, Orlandini V, La Torre L, Bosi E, Negroni A, Zanaroli G, Fava F, Decorosi F, Giovannetti L, Viti C, Vaneechoutte M, Dijkshoorn L, Fani R.

Sci Rep. 2016 Feb 23;6:21985. doi: 10.1038/srep21985.

34.

Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities.

Papaleo MC, Fondi M, Maida I, Perrin E, Bevivino A, Dalmastri C, Fani R.

Open Microbiol J. 2015 Aug 31;9:98-109. doi: 10.2174/1874285801509010098. eCollection 2015.

35.

Efflux-mediated resistance to a benzothiadiazol derivative effective against Burkholderia cenocepacia.

Scoffone VC, Ryabova O, Makarov V, Iadarola P, Fumagalli M, Fondi M, Fani R, De Rossi E, Riccardi G, Buroni S.

Front Microbiol. 2015 Aug 5;6:815. doi: 10.3389/fmicb.2015.00815. eCollection 2015.

36.

Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers.

Perrin E, Fondi M, Maida I, Mengoni A, Chiellini C, Mocali S, Cocchi P, Campana S, Taccetti G, Vaneechoutte M, Fani R.

J Microbiol Methods. 2015 Oct;117:108-12. doi: 10.1016/j.mimet.2015.07.025. Epub 2015 Jul 30.

PMID:
26235543
37.

Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.

Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, de Jesus Lopes Ribeiro AL, Marino LB, Centárová I, Svetlíková Z, Blaško J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikušová K, Alzari PM, Manganelli R, de Carvalho LP, Riccardi G, Cole ST, Pasca MR.

Chem Biol. 2015 Jul 23;22(7):917-27. doi: 10.1016/j.chembiol.2015.05.016. Epub 2015 Jun 18.

38.

A genomic and transcriptomic approach to investigate the blue pigment phenotype in Pseudomonas fluorescens.

Andreani NA, Carraro L, Martino ME, Fondi M, Fasolato L, Miotto G, Magro M, Vianello F, Cardazzo B.

Int J Food Microbiol. 2015 Nov 20;213:88-98. doi: 10.1016/j.ijfoodmicro.2015.05.024. Epub 2015 Jun 1.

PMID:
26051958
39.

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea.

Maida I, Chiellini C, Mengoni A, Bosi E, Firenzuoli F, Fondi M, Fani R.

Environ Microbiol. 2016 Sep;18(8):2357-65. doi: 10.1111/1462-2920.12911. Epub 2015 Jul 22.

PMID:
26013664
40.

MeDuSa: a multi-draft based scaffolder.

Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M.

Bioinformatics. 2015 Aug 1;31(15):2443-51. doi: 10.1093/bioinformatics/btv171. Epub 2015 Mar 25.

PMID:
25810435
41.

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology.

Fondi M, Liò P.

Microbiol Res. 2015 Feb;171:52-64. doi: 10.1016/j.micres.2015.01.003. Epub 2015 Jan 7. Review.

42.

Network Analysis of Plasmidomes: The Azospirillum brasilense Sp245 Case.

Orlandini V, Emiliani G, Fondi M, Maida I, Perrin E, Fani R.

Int J Evol Biol. 2014;2014:951035. doi: 10.1155/2014/951035. Epub 2014 Dec 29.

43.

Preface. Bacterial pangenomics.

Mengoni A, Fondi M, Galardini M.

Methods Mol Biol. 2015;1231:v-vi. No abstract available.

PMID:
25513663
44.

Genome-scale metabolic network reconstruction.

Fondi M, Liò P.

Methods Mol Biol. 2015;1231:233-56. doi: 10.1007/978-1-4939-1720-4_15.

PMID:
25343869
45.

Defining orthologs and pangenome size metrics.

Bosi E, Fani R, Fondi M.

Methods Mol Biol. 2015;1231:191-202. doi: 10.1007/978-1-4939-1720-4_13.

PMID:
25343867
46.

Methods for assembling reads and producing contigs.

Orlandini V, Fondi M, Fani R.

Methods Mol Biol. 2015;1231:151-61. doi: 10.1007/978-1-4939-1720-4_10.

PMID:
25343864
47.

Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs.

Mengoni A, Maida I, Chiellini C, Emiliani G, Mocali S, Fabiani A, Fondi M, Firenzuoli F, Fani R.

Res Microbiol. 2014 Oct;165(8):686-94. doi: 10.1016/j.resmic.2014.09.008. Epub 2014 Oct 2.

PMID:
25283726
48.

Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage.

Spagnoletti M, Ceccarelli D, Rieux A, Fondi M, Taviani E, Fani R, Colombo MM, Colwell RR, Balloux F.

MBio. 2014 Aug 19;5(4). pii: e01356-14. doi: 10.1128/mBio.01356-14.

49.

Enly: Improving Draft Genomes through Reads Recycling.

Fondi M, Orlandini V, Corti G, Severgnini M, Galardini M, Pietrelli A, Fuligni F, Iacono M, Rizzi E, De Bellis G, Fani R.

J Genomics. 2014 Apr 5;2:89-93. doi: 10.7150/jgen.7298. eCollection 2014.

50.

Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill.

Emiliani G, Mengoni A, Maida I, Perrin E, Chiellini C, Fondi M, Gallo E, Gori L, Maggini V, Vannacci A, Biffi S, Firenzuoli F, Fani R.

Evid Based Complement Alternat Med. 2014;2014:650905. doi: 10.1155/2014/650905. Epub 2014 May 26.

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