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Items: 16

1.

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
2.

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.

3.

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.

4.

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.

5.

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 ):.

6.

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.

7.

Accessible, curated metagenomic data through ExperimentHub.

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L.

Nat Methods. 2017 Oct 31;14(11):1023-1024. doi: 10.1038/nmeth.4468. No abstract available.

8.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E, Segata N, Lebeer S.

mSystems. 2017 Aug 22;2(4). pii: e00061-17. doi: 10.1128/mSystems.00061-17. eCollection 2017 Jul-Aug.

9.

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome.

Beghini F, Pasolli E, Truong TD, Putignani L, Cacciò SM, Segata N.

ISME J. 2017 Dec;11(12):2848-2863. doi: 10.1038/ismej.2017.139. Epub 2017 Aug 22.

10.

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission.

Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F, James K, Ferretti P, Gorfer V, Ferrario C, Milani C, Mangifesta M, Anzalone R, Zolfo M, Viappiani A, Pasolli E, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Fedi S, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Soffiati M, Tateo S, Pedrotti A, Segata N, van Sinderen D, Ventura M.

Microbiome. 2017 Jun 26;5(1):66. doi: 10.1186/s40168-017-0282-6.

11.

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.

12.

Microbial strain-level population structure and genetic diversity from metagenomes.

Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N.

Genome Res. 2017 Apr;27(4):626-638. doi: 10.1101/gr.216242.116. Epub 2017 Feb 6.

13.

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

Pasolli E, Truong DT, Malik F, Waldron L, Segata N.

PLoS Comput Biol. 2016 Jul 11;12(7):e1004977. doi: 10.1371/journal.pcbi.1004977. eCollection 2016 Jul.

14.

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
15.

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N.

Nat Methods. 2015 Oct;12(10):902-3. doi: 10.1038/nmeth.3589. No abstract available. Erratum in: Nat Methods. 2016 Jan;13(1):101.

PMID:
26418763
16.

Active learning methods for electrocardiographic signal classification.

Pasolli E, Melgani F.

IEEE Trans Inf Technol Biomed. 2010 Nov;14(6):1405-16. doi: 10.1109/TITB.2010.2048922.

PMID:
21056938

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