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

Baets 10 Guy De Tré 9 Mariona Pinart 4 Katharina Nimptsch 4 Tobias Pischon 4 Jildau Bouwman 11 Duccio Cavalieri 2 8 the ENPADASI consortium 0 Equal contributors 1 The Microsoft Research - University of

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

Introduction Producing a wide range of volatile secondary metabolites Saccharomyces cerevisiae influences wine, beer, and bread sensory quality and hence selection of strains based on their volatilome becomes pivotal. A rapid on-line method for volatilome assessing of strains growing on standard solid media is still missing. Objectives Methodologically, the aim of this study was...

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting

Metagenomics is revolutionizing our understanding of microbial communities, showing that their structure and composition have profound effects on the ecosystem and in a variety of health and disease conditions. Despite the flourishing of new analysis methods, current approaches based on statistical comparisons between high-level taxonomic classes often fail to identify the...

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

 Sandra Höfflin,1,2 Tanushree Jaitly,1 Luca Beltrame,3 Duccio Cavalieri,4 Gerold Schuler,1 Julio Vera,1 Niels Schaft,1 and Jan Dörrie1 1Department of Dermatology, Universitätsklinikum Erlangen, Erlangen

Phylogenetic Analysis of 47 Chloroplast Genomes Clarifies the Contribution of Wild Species to the Domesticated Apple Maternal Line

Both the origin of domesticated apple and the overall phylogeny of the genus Malus are still not completely resolved. Having this as a target, we built a 134,553-position-long alignment including two previously published chloroplast DNAs (cpDNAs) and 45 de novo sequenced, fully colinear chloroplast genomes from cultivated apple varieties and wild apple species. The data produced...

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

Summary: Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher’s test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway...

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. The development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins. Biochemical and regulatory pathways have...

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

The quest for genes representing genetic relationships of strains or individuals within populations and their evolutionary history is acquiring a novel dimension of complexity with the advancement of next-generation sequencing (NGS) technologies. In fact, sequencing an entire genome uncovers genetic variation in coding and non-coding regions and offers the possibility of studying...

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

Background Gene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities such as protein complexes, gene family members and chemical compounds. The conversion of pathway topology to a gene/protein networks (where nodes are a simple element like a gene/protein) is a critical and challenging task that enables topology...

Strain Dependent Variation of Immune Responses to A. fumigatus: Definition of Pathogenic Species

For over a century microbiologists and immunologist have categorized microorganisms as pathogenic or non-pathogenic species or genera. This definition, clearly relevant at the strain and species level for most bacteria, where differences in virulence between strains of a particular species are well known, has never been probed at the strain level in fungal species. Here, we...

The Modular Nature of Dendritic Cell Responses to Commensal and Pathogenic Fungi

The type of adaptive immune response following host-fungi interaction is largely determined at the level of the antigen-presenting cells, and in particular by dendritic cells (DCs). The extent to which transcriptional regulatory events determine the decision making process in DCs is still an open question. By applying the highly structured DC-ATLAS pathways to analyze DC...

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

BMC Genomics Marco Ferrarini Marco Moretto Judson A Ward Nada urbanovski Vladimir Stevanovi Lara Giongo Roberto Viola Duccio Cavalieri Riccardo Velasco Alessandro Cestaro Daniel J Sargent Ferrarini

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

Andrea Splendiani Michaela Gu ndel Jonathan M. Austyn Duccio Cavalieri Ciro Scognamiglio Marco Brandizi Biomedical research relies increasingly on large collections of data sets and knowledge whose ... . Tel.: 44 (0) 1223 853544; Fax 39 02 42108159; E-mail: and Duccio Cavalieri, Dipartimento di Farmacologia, Universita` di Firenze, Viale Pieraccini 6, 50139, Firenze, Italia Tel: 39.055.4271327; Fax

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

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to...

A Systems Biology Approach to Characterize the Regulatory Networks Leading to Trabectedin Resistance in an In Vitro Model of Myxoid Liposarcoma

Trabectedin, a new antitumor compound originally derived from a marine tunicate, is clinically effective in soft tissue sarcoma. The drug has shown a high selectivity for myxoid liposarcoma, characterized by the translocation t(12;16)(q13; p11) leading to the expression of FUS-CHOP fusion gene. Trabectedin appears to act interfering with mechanisms of transcription regulation. In...

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis

Background The application of high-throughput genomic tools in nutrition research is a widespread practice. However, it is becoming increasingly clear that the outcome of individual expression studies is insufficient for the comprehensive understanding of such a complex field. Currently, the availability of the large amounts of expression data in public repositories has opened up...

Linking Genomics and Ecology to Investigate the Complex Evolution of an Invasive Drosophila Pest

Drosophilid fruit flies have provided science with striking cases of behavioral adaptation and genetic innovation. A recent example is the invasive pest Drosophila suzukii, which, unlike most other Drosophila, lays eggs and feeds on undamaged, ripening fruits. This not only poses a serious threat for fruit cultivation but also offers an interesting model to study evolution of...

Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments

Widespread use of microarrays has generated large amounts of data, the interrogation of the public microarray repositories, identifying similarities between microarray experiments is now one of the major challenges. Approaches using defined group of genes, such as pathways and cellular networks (pathway analysis), have been proposed to improve the interpretation of microarray...

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

Motivation: Eu.Gene Analyzer is an easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Eu.Gene supports a variety of array platforms, organisms and pathway ontologies, transparently deals with...

Population Genetic Variation in Genome-Wide Gene Expression

Evolutionary biologists seek to understand which traits display variation, are heritable, and influence differential reproduction, because such traits respond to natural selection and underlie organic evolution. Selection acts upon individual differences within a population. Whether individual differences within a natural population include variation in gene expression levels has...