RADIANT

Rapid development and distribution of statistical tools for high-throughput sequencing data

 Coordinatore THE UNIVERSITY OF MANCHESTER 

 Organization address address: OXFORD ROAD
city: MANCHESTER
postcode: M13 9PL

contact info
Titolo: Dr.
Nome: Katherine
Cognome: Boylan
Email: send email
Telefono: +44 161 2758796
Fax: +44 161 2752445

 Nazionalità Coordinatore United Kingdom [UK]
 Totale costo 4˙675˙174 €
 EC contributo 3˙672˙249 €
 Programma FP7-HEALTH
Specific Programme "Cooperation": Health
 Code Call FP7-HEALTH-2012-INNOVATION-1
 Funding Scheme CP-FP
 Anno di inizio 2012
 Periodo (anno-mese-giorno) 2012-12-01   -   2015-11-30

 Partecipanti

# participant  country  role  EC contrib. [€] 
1    THE UNIVERSITY OF MANCHESTER

 Organization address address: OXFORD ROAD
city: MANCHESTER
postcode: M13 9PL

contact info
Titolo: Dr.
Nome: Katherine
Cognome: Boylan
Email: send email
Telefono: +44 161 2758796
Fax: +44 161 2752445

UK (MANCHESTER) coordinator 635˙452.00
2    EUROPEAN MOLECULAR BIOLOGY LABORATORY

 Organization address address: Meyerhofstrasse 1
city: HEIDELBERG
postcode: 69117

contact info
Titolo: Ms.
Nome: Virginia
Cognome: Otón García
Email: send email
Telefono: 4962210000000
Fax: 4962210000000

DE (HEIDELBERG) participant 531˙472.20
3    Genomatix Software GmbH

 Organization address address: Bayerstrasse 85a
city: Muenchen
postcode: 80335

contact info
Titolo: Dr.
Nome: Korbinian
Cognome: Grote
Email: send email
Telefono: +49 599766 61
Fax: +49 599766 55

DE (Muenchen) participant 439˙000.00
4    THE UNIVERSITY OF SHEFFIELD

 Organization address address: FIRTH COURT WESTERN BANK
city: SHEFFIELD
postcode: S10 2TN

contact info
Titolo: Ms.
Nome: Joanne
Cognome: Watson
Email: send email
Telefono: +44 114 2224754
Fax: +44 114 2221452

UK (SHEFFIELD) participant 374˙941.20
5    UNIVERSITAET ZUERICH

 Organization address address: Raemistrasse 71
city: ZURICH
postcode: 8006

contact info
Titolo: Prof.
Nome: Mark
Cognome: Robinson
Email: send email
Telefono: +41 635 48 48

CH (ZURICH) participant 356˙758.00
6    ASSOCIATION POUR LA RECHERCHE ET LE DEVELOPPEMENT DES METHODES ET PROCESSUS INDUSTRIELS - ARMINES

 Organization address address: Boulevard Saint-Michel 60
city: PARIS
postcode: 75272

contact info
Titolo: Mrs.
Nome: Florence
Cognome: Thépenier
Email: send email
Telefono: +33 1 40 51 93 85
Fax: +33 1 40 51 00 94

FR (PARIS) participant 315˙428.00
7    GENOMNIA SRL

 Organization address address: CORSO MAGENTA 56
city: MILANO
postcode: 20123

contact info
Titolo: Mrs.
Nome: Cinzia
Cognome: Ferraro
Email: send email
Telefono: +39 02 93305700
Fax: +39 02 93305777

IT (MILANO) participant 306˙059.60
8    THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE

 Organization address address: The Old Schools, Trinity Lane
city: CAMBRIDGE
postcode: CB2 1TN

contact info
Titolo: Ms.
Nome: Renata
Cognome: Shaeffer
Email: send email
Telefono: +44 1223 333543
Fax: +44 1223 332988

UK (CAMBRIDGE) participant 268˙776.00
9    FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA

 Organization address address: VIA MOREGO 30
city: GENOVA
postcode: 16163

contact info
Titolo: Ms.
Nome: Alessandra
Cognome: Gastaldi
Email: send email
Telefono: +39 010 71781770

IT (GENOVA) participant 256˙862.40
10    FONDAZIONE TELETHON

 Organization address address: VIA VARESE 16/B
city: ROMA
postcode: 185

contact info
Titolo: Mrs.
Nome: Irene
Cognome: Mearelli
Email: send email
Telefono: +39 06 44015308

IT (ROMA) participant 187˙500.00

Mappa


 Word cloud

Esplora la "nuvola delle parole (Word Cloud) per avere un'idea di massima del progetto.

visualisation    series    disease    genes    software    experiments    extract    throughput    single    pre    technologies    rapid    radiant    expression    statistical    integrate    efficient    hts    data    biological    bayesian    computational    training    genome    quality    epigenome    dna    powerful    transcriptome    framework    signals    sequencing    gene    rna    tools   

 Obiettivo del progetto (Objective)

'High-throughput sequencing (HTS) is a powerful and rapidly evolving family of technologies with a multitude of applications. They include genetics of rare and common diseases, understanding of disease mechanism and progression through transcriptome and epigenome profiling, cancer stratification, personalised medicine and molecular systems biology of gene regulation. The genome, epigenome, transcriptome and interactome are all intricately connected, and modern HTS technology can probe all of these -omic levels. Statistical analysis is a crucial component of many experiments and studies, and the quality and efficiency of the analysis often determines the success of a project.

In this collaborative project we will develop a range of new statistical analysis tools to solve open problems in HTS data analysis, ranging from low-level processing of sequence reads up to systems-level modelling of disease associated and cellular processes. We will provide to a wide audience an integrated computational framework for HTS data analysis and interpretation that is robust, efficient and user-friendly. We will establish improved procedures for the publishing of statistical software as an integral part of the scientific publication process, within the framework of the Bioconductor project. We will provide tools to benchmark experimental protocols and statistical methods, and we will provide training materials and a extensive training programme to rapidly disseminate these new tools to the broader biomedical community.

SME partners will integrate these new tools within their analysis pipelines with associated user-friendly commercial software providing access to their additional proprietary tools. SMEs will benefit from basic methodology development done in a public, pre-competitive arena and will be able to use these technologies to enhance their products and services.'

Introduzione (Teaser)

High-throughput sequencing (HTS) has transformed the way scientists extract genetic information from biological systems. For the analysis of hundreds of gigabytes of data produced in a single sequencing run, EU-funded researchers are developing a series of statistical tools.

Descrizione progetto (Article)

In HTS, fragments of DNA are sequentially identified from signals emitted as each fragment is re-synthesised from a template DNA strand. This technology allows rapid sequencing of large stretches of base pairs spanning entire genomes. However, to extract meaningful biological signals, HTS experiments require powerful and computationally efficient statistical tools.

The EU-funded project 'Rapid development and distribution of statistical tools for high-throughput sequencing data' (http://radiant-project.eu/ (RADIANT)) supports improvements of the most popular statistical tools. Its ultimate objective is to integrate software packages developed by researchers in France, Germany, Italy, Switzerland and the United Kingdom into a single computational framework.

Among them is the Python library HTSeq that pre-processes RNA sequencing data for differential expression genes' analysis. The package DESeq2 provides methods to detect differentially expressed genes by means of generalised linear models. On the other hand, the BitSeq package implements a Bayesian approach to inferring the concentration of messenger RNA transcripts.

Research within the RADIANT project covers all aspects of HTS data analysis, from quality control to data visualisation. For gene expression time series, a hierarchical Bayesian modelling was proposed that can impute data missing both systematically and randomly. The RADIANT genome browser is the first visualisation application to be developed for DNA methylation data.

Thanks to its ability to reveal limitless insight into the human genome, HTS has permeated virtually all branches of biological research. With the newly developed RADIANT platform for HTS data analysis, it will become firmly entrenched as an indispensable tool. The applications hosted can transform genomic studies, surpassing boundaries and unlocking information never before imaginable.

Altri progetti dello stesso programma (FP7-HEALTH)

IMPACTT (2011)

Immunoglobulin IgY pseudomonas A clinical trial for cystic fibrosis treatment

Read More  

HIT HIDDEN HIV (2012)

Paving the way towards HIV eradication/control

Read More  

MARK-AGE (2008)

European Study to Establish Biomarkers of Human Ageing

Read More