F
Francesco Strozzi
Researcher at Parco Tecnologico Padano
Publications - 42
Citations - 8765
Francesco Strozzi is an academic researcher from Parco Tecnologico Padano. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 21, co-authored 41 publications receiving 6735 citations.
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Journal ArticleDOI
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Journal ArticleDOI
A unified catalog of 204,938 reference genomes from the human gut microbiome.
Alexandre Almeida,Alexandre Almeida,Stephen Nayfach,Stephen Nayfach,Miguel Boland,Francesco Strozzi,Martin Beracochea,Zhou Jason Shi,Katherine S. Pollard,Ekaterina A. Sakharova,Donovan H. Parks,Philip Hugenholtz,Nicola Segata,Nikos C. Kyrpides,Nikos C. Kyrpides,Robert D. Finn +15 more
TL;DR: The Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes, is presented, providing comprehensive resources for microbiome researchers.
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +22 more
TL;DR: This protocol describes the use of the Trinity platform for de novo transcriptome assembly from RNA-Seq data in non-model organisms and presents Trinity’s supported companion utilities for downstream applications, including RSEM for transcript abundance estimation and R/Bioconductor packages for identifying differentially expressed transcripts across samples.
Journal ArticleDOI
The ruminal microbiome associated with methane emissions from ruminant livestock.
TL;DR: The microbiome analysis is consistent with known pathways for H2 production and methanogenesis, but not yet in a predictive manner, and the production and utilisation of formate by the ruminal microbiota is poorly understood and may be a source of variability between animals.
Journal ArticleDOI
A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions
R. John Wallace,Goor Sasson,Philip C. Garnsworthy,Ilma Tapio,Emma Gregson,Paolo Bani,Pekka Huhtanen,Ali R. Bayat,Francesco Strozzi,Filippo Biscarini,Timothy J. Snelling,N. Saunders,Sarah L. Potterton,Jim Craigon,Andrea Minuti,Erminio Trevisi,Maria Luisa Callegari,Fiorenzo Piccioli Cappelli,E.H. Cabezas-Garcia,Johanna Vilkki,C. S. Pinares-Patiño,K. Fliegerová,Jakub Mrázek,Hana Sechovcová,Jan Kopečný,Aurélie Bonin,Frédéric Boyer,Pierre Taberlet,Fotini Kokou,Eran Halperin,John L. Williams,Kevin J. Shingfield,Itzhak Mizrahi +32 more
TL;DR: The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.