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Article ; Online: Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis.

Sales, Gabriele / Calura, Enrica

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2284, Page(s) 207–229

Abstract: RNA sequencing has become a powerful tool for profiling the expression level of small RNAs from both solid tissues and liquid biopsies. In conjunction with pathway analysis, it offers exciting possibilities for the identification of disease specific ... ...

Abstract	RNA sequencing has become a powerful tool for profiling the expression level of small RNAs from both solid tissues and liquid biopsies. In conjunction with pathway analysis, it offers exciting possibilities for the identification of disease specific biomarkers. In this chapter, we describe a workflow for processing this type of sequencing data. We start by removing technical sequences (adapters) and by performing quality control, a critical task that is necessary to identify possible issues caused by sample preparation and library sequencing. We then describe read alignment and gene-level abundance estimation. Building on these results, we normalize expression profiles and compute differentially expressed microRNAs between sample groups of interest. We conclude by showing how to employ pathway analysis to identify molecular signatures corresponding to biological processes that are significantly altered by the action for microRNAs.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Databases, Genetic ; Gene Expression Profiling/methods ; Gene Expression Regulation/genetics ; Gene Library ; Gene Regulatory Networks/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; MicroRNAs/analysis ; MicroRNAs/genetics ; Sequence Analysis, RNA/methods ; Signal Transduction/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2021-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1307-8_12
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Article ; Online: NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data.

Agostinis, Federico / Romualdi, Chiara / Sales, Gabriele / Risso, Davide

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 9, Page(s) 2648–2650

Abstract: Summary: We present NewWave, a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA sequencing data. To achieve scalability, NewWave uses mini-batch optimization and can work with out-of-memory ... ...

Abstract	Summary: We present NewWave, a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA sequencing data. To achieve scalability, NewWave uses mini-batch optimization and can work with out-of-memory data, enabling users to analyze datasets with millions of cells. Availability and implementation: NewWave is implemented as an open-source R package available through the Bioconductor project at https://bioconductor.org/packages/NewWave/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Software ; RNA-Seq ; Whole Exome Sequencing
Language	English
Publishing date	2022-03-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac149
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Article ; Online: Single-Cell RNAseq Analysis of lncRNAs.

Cagnin, Stefano / Alessio, Enrico / Bonadio, Raphael Severino / Sales, Gabriele

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2348, Page(s) 71–90

Abstract: Mammalian genomes are pervasively transcribed and a small fraction of RNAs produced codify for proteins. The importance of noncoding RNAs for the maintenance of cell functions is well known (e.g., rRNAs, tRNAs), but only recently it was first ... ...

Abstract	Mammalian genomes are pervasively transcribed and a small fraction of RNAs produced codify for proteins. The importance of noncoding RNAs for the maintenance of cell functions is well known (e.g., rRNAs, tRNAs), but only recently it was first demonstrated the involvement of microRNAs (miRNAs) in posttranscriptional regulation and then the activity of long noncoding RNAs (lncRNAs) in the regulation of miRNAs, DNA structure and protein function. LncRNAs have an expression more cell specific than other RNAs and basing on their subcellular localization exert different functions. In this book chapter we consider different protocols to evaluate the expression of lncRNAs at the single cell level using genome-wide approaches. We considered the skeletal muscle as example because the most abundant tissue in mammals involved in the regulation of metabolism and body movement. We firstly described how to isolate the smallest complete contractile system responsible for muscle metabolic and contractile traits (myofibers). We considered how to separate long and short RNAs to allow the sequencing of the full-length transcript using the SMART technique for the retrotranscription. Because of myofibers are multinucleated cells and because of it is better to perform single cell sequencing on fresh tissues we described the single-nucleus sequencing that can be applied to frozen tissues. The chapter concludes with a description of bioinformatics approaches to evaluate differential expression from single-cell or single-nucleus RNA sequencing.
MeSH term(s)	Computational Biology/methods ; Gene Expression Regulation ; Gene Library ; MicroRNAs/genetics ; Muscle Fibers, Skeletal/metabolism ; Polyadenylation ; RNA Processing, Post-Transcriptional ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods
Chemical Substances	MicroRNAs ; RNA, Long Noncoding ; RNA, Messenger
Language	English
Publishing date	2021-06-23
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1581-2_5
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Article ; Online: Gene expression patterns of

Müller, Svenja J / Pakhomov, Evgeny A / Urso, Ilenia / Sales, Gabriele / Pittà, Cristiano De / Michael, Katharina / Meyer, Bettina

Biology letters

2023 Volume 19, Issue 12, Page(s) 20230274

Abstract: ... Salpa ... ...

Abstract	Salpa thompsoni
MeSH term(s)	Antarctic Regions ; Water ; Reproduction ; Gene Expression
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2023-12-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2135022-X
ISSN	1744-957X ; 1744-9561
ISSN (online)	1744-957X
ISSN	1744-9561
DOI	10.1098/rsbl.2023.0274
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Zs.A 1364 -Letters-: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 6024: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Multidrug-resistant pathogens and ventilator-associated pneumonia in critically ill COVID-19 and non-COVID-19 patients: a prospective observational monocentric comparative study.

Montrucchio, Giorgia / Balzani, Eleonora / Sales, Gabriele / Vaninetti, Anna / Grillo, Francesca / Trompeo, Anna Chiara / Zanierato, Marinella / Fanelli, Vito / Corcione, Silvia / De Rosa, Francesco Giuseppe / Curtoni, Antonio / Costa, Cristina / Brazzi, Luca

Respiratory research

2024 Volume 25, Issue 1, Page(s) 168

Abstract: Background: The COVID-19 pandemic has increased the incidence of ventilator-associated pneumonia (VAP) among critically ill patients. However, a comparison of VAP incidence in COVID-19 and non-COVID-19 cohorts, particularly in a context with a high ... ...

Abstract	Background: The COVID-19 pandemic has increased the incidence of ventilator-associated pneumonia (VAP) among critically ill patients. However, a comparison of VAP incidence in COVID-19 and non-COVID-19 cohorts, particularly in a context with a high prevalence of multidrug-resistant (MDR) organisms, is lacking. Material and methods: We conducted a single-center, mixed prospective and retrospective cohort study comparing COVID-19 patients admitted to the intensive care unit (ICU) of the "Città della Salute e della Scienza" University Hospital in Turin, Italy, between March 2020 and December 2021 (COVID-19 group), with a historical cohort of ICU patients admitted between June 2016 and March 2018 (NON-COVID-19 group). The primary objective was to define the incidence of VAP in both cohorts. Secondary objectives were to evaluate the microbial cause, resistance patters, risk factors and impact on 28 days, ICU and in-hospital mortality, duration of ICU stay, and duration of hospitalization). Results: We found a significantly higher incidence of VAP (51.9% - n = 125) among the 241 COVID-19 patients compared to that observed (31.2% - n = 78) among the 252 NON-COVID-19 patients. The median SOFA score was significantly lower in the COVID-19 group (9, Interquartile range, IQR: 7-11 vs. 10, IQR: 8-13, p < 0.001). The COVID-19 group had a higher prevalence of Gram-positive bacteria-related VAP (30% vs. 9%, p < 0.001), but no significant difference was observed in the prevalence of difficult-to-treat (DTR) or MDR bacteria. ICU and in-hospital mortality in the COVID-19 and NON-COVID-19 groups were 71% and 74%, vs. 33% and 43%, respectively. The presence of COVID-19 was significantly associated with an increased risk of 28-day all-cause hospital mortality (Hazard ratio, HR: 7.95, 95% Confidence Intervals, 95% CI: 3.10-20.36, p < 0.001). Tracheostomy and a shorter duration of mechanical ventilation were protective against 28-day mortality, while dialysis and a high SOFA score were associated with a higher risk of 28-day mortality. Conclusion: COVID-19 patients with VAP appear to have a significantly higher ICU and in-hospital mortality risk regardless of the presence of MDR and DTR pathogens. Tracheostomy and a shorter duration of mechanical ventilation appear to be associated with better outcomes.
MeSH term(s)	Humans ; Pneumonia, Ventilator-Associated/diagnosis ; Pneumonia, Ventilator-Associated/epidemiology ; Pneumonia, Ventilator-Associated/microbiology ; Prospective Studies ; Retrospective Studies ; Critical Illness/epidemiology ; Pandemics ; COVID-19/epidemiology
Language	English
Publishing date	2024-04-18
Publishing country	England
Document type	Observational Study ; Journal Article
ZDB-ID	2041675-1
ISSN	1465-993X ; 1465-993X
ISSN (online)	1465-993X
ISSN	1465-993X
DOI	10.1186/s12931-024-02779-1
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Article ; Online: metaGraphite–a new layer of pathway annotation to get metabolite networks

Sales, Gabriele / Calura, Enrica / Romualdi, Chiara

Bioinformatics. 2019 Apr. 01, v. 35, no. 7, p. 1258-1260

2019 , Page(s) 1258–1260

Abstract: Metabolomics is an emerging ‘omics’ science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the ... ...

Abstract	Metabolomics is an emerging ‘omics’ science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements. We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks. The new graphite version (1.24) is available on Bioconductor. Supplementary data are available at Bioinformatics online.
Keywords	bioinformatics ; databases ; genes ; graphene ; metabolism ; metabolites ; metabolomics
Language	English
Dates of publication	2019-0401
Size	p. 1258-1260
Publishing place	Oxford University Press
Document type	Article ; Online
ZDB-ID	1468345-3
ISSN	1367-4811 ; 1460-2059
ISSN	1367-4811 ; 1460-2059
DOI	10.1093/bioinformatics/bty719
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Are other effects of dexmedetomidine playing a role in explaining norepinephrine requirements decrease in septic shock patients?

Montrucchio, Giorgia / Sales, Gabriele / Scanu, Martina / Bosso, Stefano / Brazzi, Luca

Minerva anestesiologica

2020 Volume 87, Issue 1, Page(s) 107–108

MeSH term(s)	Dexmedetomidine/therapeutic use ; Humans ; Hypnotics and Sedatives ; Norepinephrine ; Shock, Septic/drug therapy ; Vasoconstrictor Agents/therapeutic use
Chemical Substances	Hypnotics and Sedatives ; Vasoconstrictor Agents ; Dexmedetomidine (67VB76HONO) ; Norepinephrine (X4W3ENH1CV)
Language	English
Publishing date	2020-05-28
Publishing country	Italy
Document type	Journal Article ; Comment
ZDB-ID	123584-9
ISSN	1827-1596 ; 0026-4717 ; 0375-9393
ISSN (online)	1827-1596
ISSN	0026-4717 ; 0375-9393
DOI	10.23736/S0375-9393.20.14725-4
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Article ; Online: metaGraphite-a new layer of pathway annotation to get metabolite networks.

Sales, Gabriele / Calura, Enrica / Romualdi, Chiara

Bioinformatics (Oxford, England)

2018 Volume 35, Issue 7, Page(s) 1258–1260

Abstract: Motivation: Metabolomics is an emerging 'omics' science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data ... ...

Abstract	Motivation: Metabolomics is an emerging 'omics' science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements. Results: We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks. Availability and implementation: The new graphite version (1.24) is available on Bioconductor. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Databases, Factual ; Metabolic Networks and Pathways ; Metabolomics ; Software
Language	English
Publishing date	2018-09-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty719
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Article ; Online: BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes.

Martini, Paolo / Sales, Gabriele / Diamante, Linda / Perrera, Valentina / Colantuono, Chiara / Riccardo, Sara / Cacchiarelli, Davide / Romualdi, Chiara / Martello, Graziano

Communications biology

2022 Volume 5, Issue 1, Page(s) 146

Abstract: Genomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed mono-allelically in order to fine-tune their expression levels. Defects in genomic imprinting have been observed in ... ...

Abstract	Genomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed mono-allelically in order to fine-tune their expression levels. Defects in genomic imprinting have been observed in several neurodevelopmental disorders, in a wide range of tumours and in induced pluripotent stem cells (iPSCs). Single Nucleotide Variants (SNVs) are readily detectable by RNA-sequencing allowing the determination of whether imprinted or X-linked genes are aberrantly expressed from both alleles, although standardised analysis methods are still missing. We have developed a tool, named BrewerIX, that provides comprehensive information about the allelic expression of a large, manually-curated set of imprinted and X-linked genes. BrewerIX does not require programming skills, runs on a standard personal computer, and can analyze both bulk and single-cell transcriptomes of human and mouse cells directly from raw sequencing data. BrewerIX confirmed previous observations regarding the bi-allelic expression of some imprinted genes in naive pluripotent cells and extended them to preimplantation embryos. BrewerIX also identified misregulated imprinted genes in breast cancer cells and in human organoids and identified genes escaping XCI in human somatic cells. We believe BrewerIX will be useful for the study of genomic imprinting and XCI during development and reprogramming, and for detecting aberrations in cancer, iPSCs and organoids. Due to its ease of use to non-computational biologists, its implementation could become standard practice during sample assessment, thus raising the robustness and reproducibility of future studies.
MeSH term(s)	Alleles ; Animals ; Breast Neoplasms ; Gene Expression Regulation ; Genes, X-Linked/genetics ; Humans ; Mice ; Single-Cell Analysis ; Software ; Transcriptome/genetics
Language	English
Publishing date	2022-02-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03087-4
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Article ; Online: A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes.

Urso, Ilenia / Biscontin, Alberto / Corso, Davide / Bertolucci, Cristiano / Romualdi, Chiara / De Pittà, Cristiano / Meyer, Bettina / Sales, Gabriele

Scientific reports

2022 Volume 12, Issue 1, Page(s) 11415

Abstract: The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of ... ...

Abstract	The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB
MeSH term(s)	Animals ; Ecosystem ; Euphausiacea/physiology ; Opsins/metabolism ; Seafood ; Transcriptome
Chemical Substances	Opsins
Language	English
Publishing date	2022-07-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-15320-5
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