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DiMeTrack

Assembly-based discovery of uncharacterized human microbiomemembers and their tracking across individuals and time

Total Cost €

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EC-Contrib. €

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Partnership

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Project "DiMeTrack" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITA DEGLI STUDI DI TRENTO 

Organization address
address: VIA CALEPINA 14
city: TRENTO
postcode: 38122
website: www.unitn.it

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Italy [IT]
 Project website http://segatalab.cibio.unitn.it/
 Total cost 180˙277 €
 EC max contribution 180˙277 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2015
 Funding Scheme MSCA-IF-EF-RI
 Starting year 2016
 Duration (year-month-day) from 2016-10-01   to  2018-12-01

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITA DEGLI STUDI DI TRENTO IT (TRENTO) coordinator 180˙277.00

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 Project objective

In this proposal we aim to expose and characterize members of the human-associated microbial dark matter and exploit the novel information to dramatically enhance the resolution of metagenomic profiling and develop accurate predictive/diagnostic tools. As a first step we will discover currently uncharacterized human microbiome members from metagenomic data through novel application of assembly-based approaches on a large compendium of newly generated and available shotgun metagenomes (Aim 1). The new identified genomes will be phylogenetically and taxonomically characterized and investigated to track strain-level individual and temporal genetic variability (Aim 2). The new genomes will be then used to develop a next generation host condition prediction approach through a genome-level machine learning tool (Aim 3). The three main objectives of the proposal are functional to the characterization of microbial dark matter from human microbiome and its use for strain-level microbiology tasks and metagenomic prediction/association tools. DiMeTrack focuses specifically on shotgun metagenomics and tracking across time and individual on many samples from publicly available databases and generated at the host laboratory. By discovering previously uncharacterized microorganisms and unravelling their roles in specific biological phenomena (e.g., mother-to-neonate transmission) and association with disease states, we fulfil the Horizon 2020 policies in supporting research and innovation that improve our understanding of the causes and mechanisms underlying healthy and diseased people and improve our ability to monitor and detect diseases. The profile and the future research plan of the applicant fits well with these research areas. In addition, after working in United States for a few years, he wants to be reintegrated in a research position in EU.

 Publications

year authors and title journal last update
List of publications.
2019 Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar, Edoardo Pasolli, Federica Armanini, Moreno Zolfo, Francesco Beghini, Serena Manara, Nicolai Karcher, Chiara Pozzi, Sara Gandini, Davide Serrano, Sonia Tarallo, Antonio Francavilla, Gaetano Gallo, Mario Trompetto, Giulio Ferrero, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Jakob Wirbel, Petra Schrotz-King, Cornelia M. Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller, Francesca Cordero, Emmanuel Dias-Neto, João Carlos Setubal, Adrian Tett, Barbara Pardini, Maria Rescigno, Levi Waldron, Alessio Naccarati, Nicola Segata
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
published pages: 667-678, ISSN: 1078-8956, DOI: 10.1038/s41591-019-0405-7
Nature Medicine 25/4 2019-06-11
2017 Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, Lorenza Putignani, Simone M Cacciò, Nicola Segata
Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome
published pages: 2848-2863, ISSN: 1751-7362, DOI: 10.1038/ismej.2017.139
The ISME Journal 11/12 2019-05-27
2017 Adrian Tett, Edoardo Pasolli, Stefania Farina, Duy Tin Truong, Francesco Asnicar, Moreno Zolfo, Francesco Beghini, Federica Armanini, Olivier Jousson, Veronica De Sanctis, Roberto Bertorelli, Giampiero Girolomoni, Mario Cristofolini, Nicola Segata
Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis
published pages: , ISSN: 2055-5008, DOI: 10.1038/s41522-017-0022-5
npj Biofilms and Microbiomes 3/1 2019-05-22
2017 Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron
Accessible, curated metagenomic data through ExperimentHub
published pages: 1023-1024, ISSN: 1548-7091, DOI: 10.1038/nmeth.4468
Nature Methods 14/11 2019-05-22
2018 Serena Manara, Edoardo Pasolli, Daniela Dolce, Novella Ravenni, Silvia Campana, Federica Armanini, Francesco Asnicar, Alessio Mengoni, Luisa Galli, Carlotta Montagnani, Elisabetta Venturini, Omar Rota-Stabelli, Guido Grandi, Giovanni Taccetti, Nicola Segata
Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital
published pages: , ISSN: 1756-994X, DOI: 10.1186/s13073-018-0593-7
Genome Medicine 10/1 2019-05-22
2017 Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Adriano Boscaini, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata
Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi , Isolated from Alpine Lentic Freshwater
published pages: , ISSN: 2169-8287, DOI: 10.1128/genomea.01294-17
Genome Announcements 5/47 2019-05-22
2018 Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Adriano Boscaini, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata
Draft Genome Sequences of Novel Pseudomonas , Flavobacterium , and Sediminibacterium Species Strains from a Freshwater Ecosystem
published pages: , ISSN: 2169-8287, DOI: 10.1128/genomea.00009-18
Genome Announcements 6/5 2019-05-22
2018 Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Valentina Gorfer, Sabina Fedi, Federica Armanini, Duy Tin Truong, Serena Manara, Moreno Zolfo, Francesco Beghini, Roberto Bertorelli, Veronica De Sanctis, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Alice Viappiani, Moran Yassour, Hera Vlamakis, Ramnik Xavier, Carmen Maria Collado, Omry Koren, Saverio Tateo, Massimo Soffiati, Anna Pedrotti, Marco Ventura, Curtis Huttenhower, Peer Bork, Nicola Segata
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
published pages: 133-145.e5, ISSN: 1931-3128, DOI: 10.1016/j.chom.2018.06.005
Cell Host & Microbe 24/1 2019-05-22
2017 Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, Nicola Segata
Microbial strain-level population structure and genetic diversity from metagenomes
published pages: 626-638, ISSN: 1088-9051, DOI: 10.1101/gr.216242.116
Genome Research 27/4 2019-05-22
2019 Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi, Maria Carmen Collado, Benjamin L. Rice, Casey DuLong, Xochitl C. Morgan, Christopher D. Golden, Christopher Quince, Curtis Huttenhower, Nicola Segata
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
published pages: 649-662.e20, ISSN: 0092-8674, DOI: 10.1016/j.cell.2019.01.001
Cell 176/3 2019-05-22

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