Marco Fondi

发表

Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network

Pietro Liò, Matteo Brilli, Alessio Mengoni, 2008, BMC Bioinformatics.

Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models.

Alessio Mengoni, Marco Fondi, Tiziano Vignolini, 2018, Methods in molecular biology.

MeDuSa: a multi-draft based scaffolder

Pietro Liò, Pierluigi Crescenzi, Marie-France Sagot, 2015, Bioinform..

A Systems Biology View on Bacterial Response to Temperature Shift

Marco Fondi, Emanuele Bosi, Angelina Lo Giudice, 2016 .

Methods for assembling reads and producing contigs.

Marco Fondi, Renato Fani, Valerio Orlandini, 2015, Methods in molecular biology.

Tn-Core: A Toolbox for Integrating Tn-seq Gene Essentiality Data and Constraint-Based Metabolic Modeling.

Alessio Mengoni, Marco Fondi, George C diCenzo, 2018, ACS synthetic biology.

Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data

Alessio Mengoni, Marco Fondi, George C. diCenzo, 2017, bioRxiv.

The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis

Matteo Brilli, Alessio Mengoni, Marco Fondi, 2010, BMC Systems Biology.

Metabolic Network Reconstruction and Modeling

Marco Fondi, M. Fondi, 2018, Methods in Molecular Biology.

G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs

Marco Fondi, Pietro Alifano, Adelfia Talà, 2018, BMC Bioinformatics.

On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes

Matteo Brilli, Marco Fondi, Renato Fani, 2007, BMC Bioinformatics.

The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case

Matteo Brilli, Marco Fondi, Renato Fani, 2007, BMC Evolutionary Biology.

Large-scale analysis of plasmid relationships through gene-sharing networks.

Marco Fondi, Renato Fani, Manu Tamminen, 2012, Molecular biology and evolution.

The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks.

Marco Fondi, Renato Fani, R. Fani, 2010, Environmental microbiology.

Origin and evolution of metabolic pathways.

Marco Fondi, Renato Fani, R. Fani, 2009, Physics of life reviews.

Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach

Marco Fondi, Renato Fani, Emanuele Bosi, 2017, Scientific Reports.

Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome

Matteo Brilli, Alessio Mengoni, Marco Fondi, 2010, BMC Evolutionary Biology.

Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia

Marco Fondi, Renato Fani, Livia Leoni, 2011, PloS one.

The mosaicism of plasmids revealed by atypical genes detection and analysis

Marco Fondi, Renato Fani, Emanuele Bosi, 2011, BMC Genomics.

A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land

Marco Fondi, Renato Fani, Simonetta Gribaldo, 2009, Biology Direct.

Origin and evolution of operons and metabolic pathways.

Marco Fondi, Renato Fani, R. Fani, 2009, Research in microbiology.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Marco Fondi, Emanuele Bosi, Jonathan M Monk, 2016, Proceedings of the National Academy of Sciences.

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

James O. McInerney, Marco Fondi, Renato Fani, 2016, Genome biology and evolution.