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Items: 29

1.

A resource of variant effect predictions of single nucleotide variants in model organisms.

Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P.

Mol Syst Biol. 2018 Dec 20;14(12):e8430. doi: 10.15252/msb.20188430.

2.

pyseer: a comprehensive tool for microbial pangenome-wide association studies.

Lees JA, Galardini M, Bentley SD, Weiser JN, Corander J.

Bioinformatics. 2018 Dec 15;34(24):4310-4312. doi: 10.1093/bioinformatics/bty539.

3.

Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species.

Golanowska M, Potrykus M, Motyka-Pomagruk A, Kabza M, Bacci G, Galardini M, Bazzicalupo M, Makalowska I, Smalla K, Mengoni A, Hugouvieux-Cotte-Pattat N, Lojkowska E.

Front Microbiol. 2018 Aug 31;9:1940. doi: 10.3389/fmicb.2018.01940. eCollection 2018.

4.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR.

Nat Microbiol. 2018 Apr;3(4):514-522. doi: 10.1038/s41564-018-0123-9. Epub 2018 Mar 19.

PMID:
29556107
5.

Phenotype inference in an Escherichia coli strain panel.

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P.

Elife. 2017 Dec 27;6. pii: e31035. doi: 10.7554/eLife.31035.

6.

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA.

Cell Syst. 2017 Mar 22;4(3):291-305.e7. doi: 10.1016/j.cels.2016.12.013. Epub 2017 Feb 8.

7.

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.

8.

Mixed Nodule Infection in Sinorhizobium meliloti-Medicago sativa Symbiosis Suggest the Presence of Cheating Behavior.

Checcucci A, Azzarello E, Bazzicalupo M, Galardini M, Lagomarsino A, Mancuso S, Marti L, Marzano MC, Mocali S, Squartini A, Zanardo M, Mengoni A.

Front Plant Sci. 2016 Jun 13;7:835. doi: 10.3389/fpls.2016.00835. eCollection 2016.

9.

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.

Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K.

Nucleic Acids Res. 2016 Jan 4;44(D1):D620-3. doi: 10.1093/nar/gkv1251. Epub 2015 Nov 19.

10.

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.

Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A.

PLoS Comput Biol. 2015 Sep 4;11(9):e1004478. doi: 10.1371/journal.pcbi.1004478. eCollection 2015 Sep.

11.

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
12.

Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.

Golanowska M, Galardini M, Bazzicalupo M, Hugouvieux-Cotte-Pattat N, Mengoni A, Potrykus M, Slawiak M, Lojkowska E.

Genome Announc. 2015 Mar 19;3(2). pii: e00109-15. doi: 10.1128/genomeA.00109-15.

13.

Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS.

Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A.

J Genomics. 2015 Feb 1;3:36-9. doi: 10.7150/jgen.9204. eCollection 2015.

14.

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

Bacci G, Ceccherini MT, Bani A, Bazzicalupo M, Castaldini M, Galardini M, Giovannetti L, Mocali S, Pastorelli R, Pantani OL, Arfaioli P, Pietramellara G, Viti C, Nannipieri P, Mengoni A.

Antonie Van Leeuwenhoek. 2015 Mar;107(3):785-97. doi: 10.1007/s10482-014-0372-4. Epub 2015 Jan 7.

PMID:
25563635
15.

Preface. Bacterial pangenomics.

Mengoni A, Fondi M, Galardini M.

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

PMID:
25513663
16.

From pangenome to panphenome and back.

Galardini M, Mengoni A, Mocali S.

Methods Mol Biol. 2015;1231:257-70. doi: 10.1007/978-1-4939-1720-4_16.

PMID:
25343870
17.

Mapping contigs using CONTIGuator.

Galardini M, Mengoni A, Bazzicalupo M.

Methods Mol Biol. 2015;1231:163-76. doi: 10.1007/978-1-4939-1720-4_11.

PMID:
25343865
18.

High-throughput phenomics.

Viti C, Decorosi F, Marchi E, Galardini M, Giovannetti L.

Methods Mol Biol. 2015;1231:99-123. doi: 10.1007/978-1-4939-1720-4_7.

PMID:
25343861
19.

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.

20.

Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58.

Galardini M, Bazzicalupo M, Biondi E, Brambilla E, Brilli M, Bruce D, Chain P, Chen A, Daligault H, Davenport KW, Deshpande S, Detter JC, Goodwin LA, Han C, Han J, Huntemann M, Ivanova N, Klenk HP, Kyrpides NC, Markowitz V, Mavrommatis K, Mocali S, Nolan M, Pagani I, Pati A, Pini F, Pitluck S, Spini G, Szeto E, Teshima H, Woyke T, Mengoni A.

Stand Genomic Sci. 2013 Dec 15;9(2):325-33. doi: 10.4056/sigs.3797438. eCollection 2013 Dec 20.

21.

DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.

Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S.

Genomics. 2014 Jan;103(1):1-10. doi: 10.1016/j.ygeno.2013.11.005. Epub 2013 Dec 4.

22.

The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti.

Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG.

Mol Microbiol. 2013 Oct;90(1):54-71. doi: 10.1111/mmi.12347. Epub 2013 Aug 19.

23.

Draft Genome Sequence of Chromate-Resistant and Biofilm-Producing Strain Pseudomonas alcaliphila 34.

Santopolo L, Marchi E, Decorosi F, Galardini M, Brilli M, Giovannetti L, Viti C.

Genome Announc. 2013 Jan;1(1). pii: e00125-12. doi: 10.1128/genomeA.00125-12. Epub 2013 Feb 21.

24.

Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti.

Galardini M, Pini F, Bazzicalupo M, Biondi EG, Mengoni A.

Genome Biol Evol. 2013;5(3):542-58. doi: 10.1093/gbe/evt027.

25.

The success of acinetobacter species; genetic, metabolic and virulence attributes.

Peleg AY, de Breij A, Adams MD, Cerqueira GM, Mocali S, Galardini M, Nibbering PH, Earl AM, Ward DV, Paterson DL, Seifert H, Dijkshoorn L.

PLoS One. 2012;7(10):e46984. doi: 10.1371/journal.pone.0046984. Epub 2012 Oct 29.

26.

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes.

Galardini M, Biondi EG, Bazzicalupo M, Mengoni A.

Source Code Biol Med. 2011 Jun 21;6:11. doi: 10.1186/1751-0473-6-11.

27.

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.

Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Land M, Hauser L, Woyke T, Mikhailova N, Ivanova N, Daligault H, Bruce D, Detter C, Tapia R, Han C, Teshima H, Mocali S, Bazzicalupo M, Biondi EG.

BMC Genomics. 2011 May 12;12:235. doi: 10.1186/1471-2164-12-235.

28.

Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?

Pini F, Galardini M, Bazzicalupo M, Mengoni A.

Genes (Basel). 2011 Nov 29;2(4):1017-32. doi: 10.3390/genes2041017.

29.

Genomics of biological wastewater treatment.

Siezen RJ, Galardini M.

Microb Biotechnol. 2008 Sep;1(5):333-40. doi: 10.1111/j.1751-7915.2008.00059.x. No abstract available.

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