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List of works by Duccio Cavalieri

A Metagenomics Study on Hirschsprung's Disease Associated Enterocolitis: Biodiversity and Gut Microbial Homeostasis Depend on Resection Length and Patient's Clinical History

scientific article published on 09 August 2019

A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains

scientific article published on 20 January 2012

A guide to microarray experiments-an open letter to the scientific journals

scientific article published in The Lancet

A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma

scientific article

A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of saccharomyces cerevisiae mutants

scientific article

A systems biology approach to the mutual interaction between yeast and the immune system

scientific article published on 9 June 2010

Active microbial ecosystem in Iron-Age tombs of the Etruscan civilization

scientific article published on 16 November 2020

Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans.

scientific article published on July 2017

Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract

scientific article

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status

scientific article (publication date: 2016)

Altered feeding behavior and immune competence in paper wasps: A case of parasite manipulation?

scientific article published on 16 December 2020

Altered gut microbiota in Rett syndrome

scientific article published on 30 July 2016

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

scientific article

An integrated analysis of the effects of Esculentin 1–21 on Saccharomyces cerevisiae

article

Analysis of gene expression profiles reveals novel correlations with the clinical course of colorectal cancer

scientific article

Applications of Wild Isolates of Saccharomyces Yeast for Industrial Fermentation: The Gut of Social Insects as Niche for Yeast Hybrids' Production

scientific article published on 29 October 2020

Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections.

scientific article published on 21 February 2011

BIOKIS: A Model Payload for Multidisciplinary Experiments in Microgravity

article

Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator).

scientific article

Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates.

scientific article

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

scientific article

Bioinformatic methods for integrating whole-genome expression results into cellular networks.

scientific article

Carbon nanotube scaffolds instruct human dendritic cells: modulating immune responses by contacts at the nanoscale.

scientific article

Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae

scientific article published on 18 April 2008

Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov

scientific article published on 23 September 2019

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection

scientific article published on 31 August 2017

Chemical genetics approach to drug discovery by diversity-oriented synthesis (DOS) of peptidomimetics

article

Chemical genetics approach to identify new small molecule modulators of cell growth by phenotypic screening of Saccharomyces cerevisiae strains with a library of morpholine-derived compounds.

scientific article

Comparative analysis of gene expression: uncovering expression conservation and divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S.

scientific article published in January 2015

Comparative immunophenotyping of Saccharomyces cerevisiae and Candida spp. strains from Crohn's disease patients and their interactions with the gut microbiome

scientific article published on 26 January 2020

Constraints for monocyte-derived dendritic cell functions under inflammatory conditions

Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts.

scientific article published on 21 March 2017

Corrigendum to Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of Bifidobacterium vespertilionis sp. nov. and Bifidobacterium rousetti sp. nov. [Syst. Appl. Microbiol. 42 (2019) 126017]

scientific article published on 03 December 2020

Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids

scientific article published in January 2002

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells

scientific article published on 19 November 2010

DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism is useful for yeast typing

scientific article published on 01 September 1995

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle.

scientific article published on 13 April 2018

Denileukin diftitox (ONTAK) induces a tolerogenic phenotype in dendritic cells and stimulates survival of resting Treg.

scientific article published on 19 August 2013

Diet and the Gut Microbiota – How the Gut

article

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy.

scientific article published on 13 October 2017

Differential IL-17 Production and Mannan Recognition Contribute to Fungal Pathogenicity and Commensalism

article

Disruption and phenotypic analysis of six novel genes from chromosome IV of Saccharomyces cerevisiae reveal YDL060w as an essential gene for vegetative growth

scientific article published in November 1999

Disruption and phenotypic analysis of six novel genes from chromosome IV ofSaccharomyces cerevisiae reveal YDL060w as an essential gene for vegetative growth

article

Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level

scientific article published in April 2010

Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation.

scientific article published on 18 January 2016

ERNICA guidelines for the management of rectosigmoid Hirschsprung's disease

scientific article published on 25 June 2020

Ecological and evolutionary genomics of Saccharomyces cerevisiae

scientific article

Effects of near-infrared laser radiation on the survival and inflammatory potential of Candida spp. involved in the pathogenesis of chemotherapy-induced oral mucositis

scientific article published on 15 July 2015

Electroporated Antigen-Encoding mRNA Is Not a Danger Signal to Human Mature Monocyte-Derived Dendritic Cells.

scientific article published on 28 December 2015

Emerging treatments and gene expression profiling in high-risk medulloblastoma

scientific article published on January 2007

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles

scientific article published on 11 August 2019

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases

scientific article

Evidence for S. cerevisiae fermentation in ancient wine

scientific article (publication date: 2003)

Evolution of transcriptional regulatory networks in yeast populations ⬇️

scientific article published on May 1, 2010

Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting

scientific article

Extremely Low-Frequency Electromagnetic Fields do not Affect DNA Damage and Gene Expression Profiles of Yeast and Human Lymphocytes

article

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

scientific article

Friend or foe: using systems biology to elucidate interactions between fungi and their hosts.

scientific article published on 24 August 2011

Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease

scholarly article by Lidia Nicola et al published May 2017 in Applied Soil Ecology

Fundamentals of cDNA microarray data analysis

scientific article

Fungal Chitin Induces Trained Immunity in Human Monocytes during Cross-talk of the Host with Saccharomyces cerevisiae.

scientific article published on 17 February 2016

Gene expression profiling in evolutionary genetics

article

Genetic and biochemical characterization of Saccharomyces cerevisiae mutants resistant to trifluoroleucine

scientific article

Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes

article

Genomic and Phenotypic Variation in Morphogenetic Networks of Two Candida albicans Isolates Subtends Their Different Pathogenic Potential.

scientific article published in January 2017

Genomics approach to the analysis of bacterial communities dynamics in Hirschsprung's disease-associated enterocolitis: a pilot study.

scientific article published on 20 March 2010

Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion

scientific article

Guidelines and recommendations on yeast cell death nomenclature.

scientific article published in January 2018

Gut Microbiota Profiles Differ among Individuals Depending on Their Region of Origin: An Italian Pilot Study

scientific article published on 23 October 2019

Gut microbial composition in different castes and developmental stages of the invasive hornet Vespa velutina nigrithorax

scientific article published on 15 July 2020

Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients

scientific article published on 10 April 2021

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation

scientific article

Hsp12p and PAU genes are involved in ecological interactions between natural yeast strains

scientific article published on 16 June 2015

IL-13 mRNA Tissue Content Identifies Two Subsets of Adult Ulcerative Colitis Patients With Different Clinical and Mucosa-Associated Microbiota Profiles

scientific article published on 01 March 2020

IL-4-induced gene 1 maintains high Tob1 expression that contributes to TCR unresponsiveness in human T helper 17 cells.

scientific article

Identification by functional analysis of the gene encoding alpha-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae

scientific article

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

scientific article

Indel arrays: an affordable alternative for genotyping

scientific article

Inhibition of immune synapse by altered dendritic cell actin distribution: a new pathway of mesenchymal stem cell immune regulation

scientific article published on October 2010

Integrating whole-genome expression results into metabolic networks with Pathway Processor

scientific article

Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent traits and capacity to persist within the host.

scientific article published on 2 May 2018

Isolation, Identification and Characterization of Yeasts from Fermented Goat Milk of the Yaghnob Valley in Tajikistan

scientific article (publication date: 2016)

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory

scientific article (publication date: November 2011)

Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains

scientific article

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms ⬇️

scientific article

Letter in response to article in Journal of Infection: Impact of Routine Infant BCG Vaccination on COVID-19

scientific article published on 25 November 2020

Linking genomics and ecology to investigate the complex evolution of an invasive Drosophila pest ⬇️

scientific article (publication date: 2013)

Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization

scientific article published on 10 July 2019

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

scientific article

Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis

scientific article

Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties.

scientific article

MiRNA landscape in stage I epithelial ovarian cancer defines the histotype specificities.

scientific article published on 13 June 2013

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams.

scientific article

New evidences on the altered gut microbiota in autism spectrum disorders

scientific article published on 22 February 2017

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells

scientific article published in Scientific Reports

Non-invasive real time monitoring of yeast volatilome by PTR-ToF-MS

scientific article published on 31 August 2017

Novel insights into phenotype and mitochondrial proteome of yeast mutants lacking proteins Sco1p or Sco2p.

scientific article

ONS: an ontology for a standardized description of interventions and observational studies in nutrition.

scientific article

Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes.

scientific article

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.

scientific article

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data

scientific article

Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks

scientific article published on July 2002

Pathway-based analysis of microarray and RNAseq data using Pathway Processor 2.0.

scientific article

Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line

scientific article

Plant microRNAs as novel immunomodulatory agents

scientific article published on 11 May 2016

Population genetic variation in genome-wide gene expression

scientific article

Population genomics ofSaccharomyces cerevisiaehuman isolates: passengers, colonizers, invaders

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut

scientific article published on 21 November 2018

Propolis hosts a diversemicrobial community

scientific article published on 10 March 2020

Rarity of Human T Helper 17 Cells Is due to Retinoic Acid Orphan Receptor-Dependent Mechanisms that Limit Their Expansion

scientific article published on 09 February 2012

Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System Saccharomyces cerevisiae

scientific article

Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer

article

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification

scientific article published on 17 June 2013

Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease.

scientific article

Role of social wasps in Saccharomyces cerevisiae ecology and evolution

scientific article

SCD – Stem Cell Differentiation Toward Osteoblast Onboard the International Space Station

scientific article published in 2018

Saccharomyces cerevisiae - Insects Association: Impacts, Biogeography, and Extent

scientific article published on 14 July 2020

Saccharomyces cerevisiae Induces Immune Enhancing and Shapes Gut Microbiota in Social Wasps

scientific article published on 15 October 2019

SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns

scientific article

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains

scientific article published on 11 May 2016

Social wasps are a Saccharomyces mating nest

scientific article

Stand on the Same Side Against Covid – 19, the Future Strategies Against an Unknown Enemy

scholarly article published on Substantia in 2020

Stand on the Same Side Against Covid – 19: Scientific Evidence on Vaccine for Covid-19

scholarly article published on Substantia in 2021

Standards for microarray data

scientific article

Strain dependent variation of immune responses to A. fumigatus: definition of pathogenic species

scientific article published on 18 February 2013

Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1/Raf kinase inhibitory protein

scientific article published on 27 June 2017

Systems Level Dissection of Candida Recognition by Dectins: A Matter of Fungal Morphology and Site of Infection

scientific article

Systems biology of host-fungus interactions: turning complexity into simplicity

scientific article published on 19 June 2012

Systems biology of host-mycobiota interactions: dissecting Dectin-1 and Dectin-2 signalling in immune cells with DC-ATLAS.

scientific article published on 13 July 2013

Systems biology of infectious diseases: a focus on fungal infections

scientific article published on 16 August 2011

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

scientific article

The Root of Flowering Plants and Total Evidence

scientific article

The dectin-1/inflammasome pathway is responsible for the induction of protective T-helper 17 responses that discriminate between yeasts and hyphae of Candida albicans

scientific article published on 29 April 2011

The modular nature of dendritic cell responses to commensal and pathogenic fungi

scientific article

The orphan nuclear receptor COUP-TFII coordinates hypoxia-independent proangiogenic responses in hepatic stellate cells.

scientific article published on 17 November 2016

The underlying principles of scientific publication.

scientific article published in November 2002

To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization

scientific article published on 07 October 2020

Trifluoroleucine resistance and regulation of alpha-isopropyl malate synthase in Saccharomyces cerevisiae

scientific article

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing

scientific article

Using pathway signatures as means of identifying similarities among microarray experiments

scientific article

Yeast adapt to near-freezing temperatures by STRE/Msn2,4-dependent induction of trehalose synthesis and certain molecular chaperones

scientific article

Yeast as a model to investigate the mitochondrial role in adaptation to dietary fat and calorie surplus

scientific article published on 27 November 2008

graphite - a Bioconductor package to convert pathway topology to gene network.

scientific article

riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics

scientific article

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