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Items: 13

1.

Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital.

Manara S, Pasolli E, Dolce D, Ravenni N, Campana S, Armanini F, Asnicar F, Mengoni A, Galli L, Montagnani C, Venturini E, Rota-Stabelli O, Grandi G, Taccetti G, Segata N.

Genome Med. 2018 Nov 13;10(1):82. doi: 10.1186/s13073-018-0593-7.

2.

Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

Malacarne G, Pilati S, Valentini S, Asnicar F, Moretto M, Sonego P, Masera L, Cavecchia V, Blanzieri E, Moser C.

Front Plant Sci. 2018 Sep 21;9:1385. doi: 10.3389/fpls.2018.01385. eCollection 2018.

3.

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ.

Cell Host Microbe. 2018 Jul 11;24(1):146-154.e4. doi: 10.1016/j.chom.2018.06.007.

PMID:
30001517
4.

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N.

Cell Host Microbe. 2018 Jul 11;24(1):133-145.e5. doi: 10.1016/j.chom.2018.06.005.

5.

Profiling microbial strains in urban environments using metagenomic sequencing data.

Zolfo M, Asnicar F, Manghi P, Pasolli E, Tett A, Segata N.

Biol Direct. 2018 May 9;13(1):9. doi: 10.1186/s13062-018-0211-z.

6.

Correction for Pinto et al., "Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Strains from a Freshwater Ecosystem".

Pinto F, Tett A, Armanini F, Asnicar F, Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N.

Genome Announc. 2018 Mar 8;6(10). pii: e00169-18. doi: 10.1128/genomeA.00169-18. No abstract available.

7.

Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem.

Pinto F, Tett A, Armanini F, Asnicar F, Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N.

Genome Announc. 2018 Feb 1;6(5). pii: e00009-18. doi: 10.1128/genomeA.00009-18. Erratum in: Genome Announc. 2018 Mar 8;6(10 ):.

8.

Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater.

Pinto F, Tett A, Armanini F, Asnicar F, Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N.

Genome Announc. 2017 Nov 22;5(47). pii: e01294-17. doi: 10.1128/genomeA.01294-17.

9.

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis.

Tett A, Pasolli E, Farina S, Truong DT, Asnicar F, Zolfo M, Beghini F, Armanini F, Jousson O, De Sanctis V, Bertorelli R, Girolomoni G, Cristofolini M, Segata N.

NPJ Biofilms Microbiomes. 2017 Jun 22;3:14. doi: 10.1038/s41522-017-0022-5. eCollection 2017.

10.

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling.

Asnicar F, Manara S, Zolfo M, Truong DT, Scholz M, Armanini F, Ferretti P, Gorfer V, Pedrotti A, Tett A, Segata N.

mSystems. 2017 Jan 17;2(1). pii: e00164-16. doi: 10.1128/mSystems.00164-16. eCollection 2017 Jan-Feb.

11.

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N.

Nat Microbiol. 2016 May 27;1(7):16070. doi: 10.1038/nmicrobiol.2016.70.

PMID:
27572971
12.

Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, Segata N.

Nat Methods. 2016 May;13(5):435-8. doi: 10.1038/nmeth.3802. Epub 2016 Mar 21.

PMID:
26999001
13.

Compact graphical representation of phylogenetic data and metadata with GraPhlAn.

Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N.

PeerJ. 2015 Jun 18;3:e1029. doi: 10.7717/peerj.1029. eCollection 2015.

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