Articles

Treu L, Tsapekos P, Peprah M, Campanaro S, Giacomini A, Corich V, Kougias PG,
Angelidaki I. Microbial profiling during anaerobic digestion of cheese whey in
reactors operated at different conditions
. Bioresour Technol. 2019.

Zhu X, Campanaro S, Treu L, Kougias PG, Angelidaki I. Novel ecological
insights and functional roles during anaerobic digestion of saccharides unveiled
by genome-centric metagenomics
. Water Res. 2019.

Porté H, Kougias PG, Alfaro N, Treu L, Campanaro S, Angelidaki I. Process
performance and microbial community structure in thermophilic trickling biofilter
reactors for biogas upgrading.
Sci Total Environ. 2019.

Lemos Junior WJF, Fioravante Guerra A, da Silva Duarte V, Treu L, Tarrah A,
Campanaro S, Luchese RH, Giacomini A, Corich V. Draft genome sequence data of Lactobacillus paracasei strain DTA83 isolated from infant stools. Data Brief.
2019.

Nigris S, Baldan E, Tondello A, Zanella F, Vitulo N, Favaro G, Guidolin V,
Bordin N, Telatin A, Barizza E, Marcato S, Zottini M, Squartini A, Valle G,
Baldan B. Biocontrol traits of Bacillus licheniformis GL174, a culturable
endophyte of Vitis vinifera cv. Glera
. BMC Microbiol. 2018.

Di Francesco A, Fedrigo M, Santovito D, Natarelli L, Castellani C, De Pascale
F, Toscano G, Fraiese A, Feltrin G, Benazzi E, Nocco A, Thiene G, Valente M,
Valle G, Schober A, Gerosa G, Angelini A. MicroRNA signatures in cardiac biopsies and detection of allograft rejection. J Heart Lung Transplant. 2018.

Fontana A, Kougias PG, Treu L, Kovalovszki A, Valle G, Cappa F, Morelli L,
Angelidaki I, Campanaro S. Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics. Microbiome. 2018

De Iudicibus S, Lucafò M, Vitulo N, Martelossi S, Zimbello R, De Pascale F,
Forcato C, Naviglio S, Di Silvestre A, Gerdol M, Stocco G, Valle G, Ventura A,
Bramuzzo M, Decorti G. High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients. Int J Mol Sci. 2018.

Treu L, Kougias PG, de Diego-Díaz B, Campanaro S, Bassani I,
Fernández-Rodríguez J, Angelidaki I. Two-year microbial adaptation during
hydrogen-mediated biogas upgrading process in a serial reactor configuration
.
Bioresour Technol. 2018.

Ambrosino L, Ruggieri V, Bostan H, Miralto M, Vitulo N, Zouine M, Barone A,
Bouzayen M, Frusciante L, Pezzotti M, Valle G, Chiusano ML. Multilevel
comparative bioinformatics to investigate evolutionary relationships and
specificities in gene annotations: an example for tomato and grapevine
. BMC
Bioinformatics. 2018

Saleem M, Lavagnolo MC, Campanaro S, Squartini A. Dynamic membrane bioreactor
(DMBR) for the treatment of landfill leachate; bioreactor’s performance and
metagenomic insights into microbial community evolution
. Environ Pollut. 2018.

Giaretta S, Treu L, Vendramin V, da Silva Duarte V, Tarrah A, Campanaro S,
Corich V, Giacomini A. Comparative Transcriptomic Analysis of Streptococcus
thermophilus TH1436 and TH1477 Showing Different Capability in the Use of
Galactose
. Front Microbiol. 2018.

Zampieri G, Tran DV, Donini M, Navarin N, Aiolli F, Sperduti A, Valle G.
Scuba: scalable kernel-based gene prioritization. BMC Bioinformatics. 2018.

da Silva Duarte V, Dias RS, Kropinski AM, Campanaro S, Treu L, Siqueira C,
Vieira MS, da Silva Paes I, Santana GR, Martins F, Crispim JS, da Silva Xavier A,
Ferro CG, Vidigal PMP, da Silva CC, de Paula SO. Genomic analysis and immune
response in a murine mastitis model of vB_EcoM-UFV13, a potential biocontrol
agent for use in dairy cows
. Sci Rep. 2018.

Treu L, Campanaro S, Kougias PG, Sartori C, Bassani I, Angelidaki I.
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by
Genome-Centric Metagenomics
. Front Microbiol. 2018.

Lemos Junior WJF, da Silva Duarte V, Treu L, Campanaro S, Nadai C, Giacomini
A, Corich V. Whole genome comparison of two Starmerella bacillaris strains with
other wine yeasts uncovers genes involved in modulating important winemaking
traits
. FEMS Yeast Res. 2018.

Kougias PG, Campanaro S, Treu L, Tsapekos P, Armani A, Angelidaki I. Spatial
Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading
Uncultured Bacteria as Revealed by Genome-Centric Metagenomics
. Appl Environ
Microbiol. 2018.

da Silva Duarte V, Giaretta S, Campanaro S, Treu L, Armani A, Tarrah A,
Oliveira de Paula S, Giacomini A, Corich V. A Cryptic Non-Inducible Prophage
Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496
. Viruses.
2018.

Vitulo N, Dalla Valle L, Skobo T, Valle G, Alibardi L. Downregulation of
lizard immuno-genes in the regenerating tail and myogenes in the scarring limb suggests that tail regeneration occurs in an immuno-privileged organ.
Protoplasma.
2017.

Pagliarani C, Vitali M, Ferrero M, Vitulo N, Incarbone M, Lovisolo C, Valle
G, Schubert A. The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine. Plant Physiol. 2017.

Salvalaio M, D’Avanzo F, Rigon L, Zanetti A, D’Angelo M, Valle G, Scarpa M,
Tomanin R. Brain RNA-Seq Profiling of the Mucopolysaccharidosis Type II Mouse Model. Int J Mol Sci. 2017.

Marrano A, Birolo G, Prazzoli ML, Lorenzi S, Valle G, Grando MS.
SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.). PLoS One. 2017.

Vannozzi A, Donnini S, Vigani G, Corso M, Valle G, Vitulo N, Bonghi C, Zocchi
G, Lucchin M. Transcriptional Characterization of a Widely-Used Grapevine
Rootstock Genotype under Different Iron-Limited Conditions
. Front Plant Sci. 2017.

Bertoldi L, Forcato C, Vitulo N, Birolo G, De Pascale F, Feltrin E, Schiavon
R, Anglani F, Negrisolo S, Zanetti A, D’Avanzo F, Tomanin R, Faulkner G, Vezzi A, Valle G. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. BMC Bioinformatics. 2017.

Vitulo N, Dalla Valle L, Skobo T, Valle G, Alibardi L. Transcriptome analysis
of the regenerating tail vs. the scarring limb in lizard reveals pathways leading
to successful vs. unsuccessful organ regeneration in amniotes
. Dev Dyn. 2017.

Fadeev E, De Pascale F, Vezzi A, Hübner S, Aharonovich D, Sher D. Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island. Front Microbiol. 2016.

Rosselli R, Romoli O, Vitulo N, Vezzi A, Campanaro S, de Pascale F, Schiavon
R, Tiarca M, Poletto F, Concheri G, Valle G, Squartini A. Direct 16S rRNA-seq
from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon
. Sci Rep. 2016.

Alboresi A, Perin G, Vitulo N, Diretto G, Block M, Jouhet J, Meneghesso A,
Valle G, Giuliano G, Maréchal E, Morosinotto T. Light Remodels Lipid Biosynthesis in Nannochloropsis gaditana by Modulating Carbon Partitioning between Organelles. Plant Physiol. 2016.

Campagna D, Gasparini F, Franchi N, Vitulo N, Ballin F, Manni L, Valle G,
Ballarin L. Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri. BMC Genomics. 2016.

4: Kopf A, Bicak M, Kottmann R, …, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L’Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, …, Field D, Glöckner FO. The ocean sampling day consortium. Gigascience. 2015.

Corteggiani Carpinelli E, Telatin A, Vitulo N, Forcato F, D’Angelo M, Schiavon R, Vezzi A, Giacometti G M, Morosinotto T, Valle G. Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Molecular Plant. 2013

Campagna D, Telatin A, Forcato C, Vitulo N, Valle G. PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. Bioinformatics. 2013

Campanaro S, Pascale FD, Telatin A, Schiavon R, Bartlett DH, Valle G. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain. BMC Genomics. 2012

Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012

Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Šimková H, Kubaláková M, Perrotta G, Facella P, Lopez L, Pietrella M, Gianese G, Doležel J, Giuliano G, Cattivelli L, Valle G, Stanca AM. First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One. 2011

Belgrano A, Rakicevic L, Mittempergher L, Campanaro S, Martinelli VC, Mouly V, Valle G, Kojic S, Faulkner G. Multi-tasking role of the mechanosensing protein Ankrd2 in the signaling network of striated muscle. PLoS One. 2011

Maccagnan A, Riva M, Feltrin E, Simionati B, Vardanega T, Valle G, Cannata N. Combining ontologies and workflows to design formal protocols for biological laboratories. Autom Exp. 2010

Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G. Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res. 2010

Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics. 2010

Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pè ME, Horner DS. High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics. 2009

Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010

Benna C, Peron S, Rizzo G, Faulkner G, Megighian A, Perini G, Tognon G, Valle G, Reggiani C, Costa R, Zordan MA. Post-transcriptional silencing of the Drosophila homolog of human ZASP: a molecular and functional analysis. Cell Tissue Res. 2009

Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G. PASS: a program to align short sequences. Bioinformatics. 2009

Feltrin E, Campanaro S, Diehl AD, Ehler E, Faulkner G, Fordham J, Gardin C, Harris M, Hill D, Knoell R, Laveder P, Mittempergher L, Nori A, Reggiani C, Sorrentino V, Volpe P, Zara I, Valle G, Deegan J. Muscle Research and Gene Ontology: New standards for improved data integration. BMC Med Genomics. 2009

von Nandelstadh P, Ismail M, Gardin C, Suila H, Zara I, Belgrano A, Valle G, Carpen O, Faulkner G. A class III PDZ binding motif in the myotilin and FATZ families binds enigma family proteins: a common link for Z-disc myopathies. Mol Cell Biol. 2009

Campanaro S, Treu L, Valle G. Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates. BMC Evol Biol. 2008

Manavski SA, Valle G. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 2008

Todesco S, Campagna D, Levorin F, D’Angelo M, Schiavon R, Valle G, Vezzi A. PABS: an online platform to assist BAC-by-BAC sequencing projects. Biotechniques. 2008

Lauro FM, Tran K, Vezzi A, Vitulo N, Valle G, Bartlett DH. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure. J Bacteriol. 2008

Campanaro S, Picelli S, Torregrossa R, Colluto L, Ceol M, Del Prete D, D’Angelo A, Valle G, Anglani F. Genes involved in TGF beta1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map. BMC Genomics. 2007

Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, … Valle G,…; The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007

Vitulo N, Vezzi A, Romualdi C, Campanaro S, Valle G. A global gene evolution analysis on Vibrionaceae family using phylogenetic profile. BMC Bioinformatics. 2007

Vitulo N, Vezzi A, Galla G, Citterio S, Marino G, Ruperti B, Zermiani M, Albertini E, Valle G, Barcaccia G. Characterization and evolution of the cell cycle-associated mob domain-containing proteins in eukaryotes. Evol Bioinform Online. 2007