Opendata, web and dolomites

ZENCODE-ITN SIGNED

Computational and functional annotation of genomic elements during development of the model vertebrate zebrafish

Total Cost €

0

EC-Contrib. €

0

Partnership

0

Views

0

 ZENCODE-ITN project word cloud

Explore the words cloud of the ZENCODE-ITN project. It provides you a very rough idea of what is the project "ZENCODE-ITN" about.

unprepared    hypotheses    attractive    skilled    disease    critical    young    postgenomic    fantom    urgent    months    computational    gene    science    cohort    skills    outcome    ngs    lab    biology    health    era    landmark    trained    secondments    genome    transferable    laboratory    courses    solid    sequencing    scope    experimental    private    world    pervasive    genetic    eminent    generation    functional    interdisciplinary    developmental    public    caught    decipher    vertebrate    disciplinary    19    explosion    outside    training    medicine    central    expertise    intersectoral    congenital    career    annotation    totalling    academic    transcription    academia    genomics    workshops    encode    comprehensively    personalised    vivo    foundation    ideal    highlighted    15    led    active    genomic    biologists    model    anomalies    scientists    wet    ready    members    class    annotate    codes    laboratories    shortage    coding    basic    beneficiaries    experts    ontogeny    network    data    throughput    esrs    zebrafish    conferences    function   

Project "ZENCODE-ITN" data sheet

The following table provides information about the project.

Coordinator
THE UNIVERSITY OF BIRMINGHAM 

Organization address
address: Edgbaston
city: BIRMINGHAM
postcode: B15 2TT
website: www.bham.ac.uk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Project website http://www.birmingham.ac.uk/zencode-itn
 Total cost 3˙724˙035 €
 EC max contribution 3˙724˙035 € (100%)
 Programme 1. H2020-EU.1.3.1. (Fostering new skills by means of excellent initial training of researchers)
 Code Call H2020-MSCA-ITN-2014
 Funding Scheme MSCA-ITN-ETN
 Starting year 2015
 Duration (year-month-day) from 2015-01-01   to  2018-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    THE UNIVERSITY OF BIRMINGHAM UK (BIRMINGHAM) coordinator 546˙575.00
2    KAROLINSKA INSTITUTET SE (STOCKHOLM) participant 769˙006.00
3    UNIVERSITE DE LIEGE BE (LIEGE) participant 501˙120.00
4    KARLSRUHER INSTITUT FUER TECHNOLOGIE DE (KARLSRUHE) participant 498˙432.00
5    KING'S COLLEGE LONDON UK (LONDON) participant 447˙888.00
6    MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV DE (MUENCHEN) participant 387˙670.00
7    IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE UK (LONDON) participant 273˙287.00
8    CONSORCI INSTITUT D'INVESTIGACIONS BIOMEDIQUES AUGUST PI I SUNYER ES (BARCELONA) participant 247˙872.00
9    RIKEN THE INSTITUTE OF PHYSICAL ANDCHEMICAL RESEARCH JP (WAKO SHI SAITAMA) participant 52˙181.00
10    BGI EUROPE INSTITUTE FOND DK (KOBENHAVN N) participant 0.00
11    GENOME RESEARCH LIMITED UK (LONDON) participant 0.00
12    D Young & Co LLP UK (London) partner 0.00
13    MicroDiscovery GmbH DE (BERLIN) partner 0.00
14    Skillstudio Limited UK (Chislehurst) partner 0.00
15    Zebrafish Model Organism Database US (Eugene) partner 0.00

Map

 Project objective

The recent explosion of next generation sequencing (NGS) data has caught Europe unprepared and led to a critical shortage of computational biology expertise. As NGS methods are expected to become pervasive from basic science to personalised medicine there is an urgent need for highly skilled young scientists trained in both computational biology and experimental wet lab biology. Our network addresses this important problem of the postgenomic era. We aim to provide multi-disciplinary skills for a solid foundation in computational biology and developmental genomics. Developmental genomics is central to understanding of ontogeny and many genetic and congenital anomalies, but was outside the scope of the landmark ENCODE and FANTOM projects. ENCODE highlighted the need for an in vivo vertebrate model that enables high throughput in vivo functional testing of hypotheses generated from genome scale annotation. Zebrafish is an ideal model for extending the scope of genomics to vertebrate development. We aim to comprehensively annotate functional elements, decipher genomic codes of transcription, as well as coding and non-coding gene function during development and enhance zebrafish as an attractive developmental, comparative and disease model. The participants include 7 non-academic members (2 of which are beneficiaries), major zebrafish genomics laboratories, eminent computational biologists and world class genomics technology experts active in FANTOM and ENCODE. The training program involves 15 ESRs, more than 40 intersectoral and interdisciplinary secondments totalling 19 months, 7 training courses and 2 workshops/conferences. The main outcome of this programme is a cohort of researchers with computational, experimental laboratory and transferable skills ready to further their career in academia, public health and the private sector.

 Deliverables

List of deliverables.
Gene expression datasets Documents, reports 2019-06-19 13:01:03
Manuscript preparation Documents, reports 2019-06-19 13:01:03
Verification of sequence variants Documents, reports 2019-06-19 13:01:03
Analysis of transcriptome datasets, including non-coding elements Documents, reports 2019-06-19 13:01:03
Public Engage Other 2019-06-19 13:01:03
Software packages Demonstrators, pilots, prototypes 2019-06-19 13:01:03
ChIP-seq datasets Documents, reports 2019-06-19 13:01:03
Low cell number and single cell protocols Documents, reports 2019-06-19 13:01:04
Establishment of curated high quality zebrafish sequence data repository. Documents, reports 2019-06-19 13:01:04
Website Websites, patent fillings, videos etc. 2019-06-19 13:01:02

Take a look to the deliverables list in detail:  detailed list of ZENCODE-ITN deliverables.

 Publications

year authors and title journal last update
List of publications.
2018 Swarnima Joshi, Sanamjeet Virdi, Christelle Etard, Robert Geisler, Uwe Strähle
Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
published pages: e0207747, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0207747
PLOS ONE 13/11 2019-06-19
2018 Clemens B. Hug, Juan M. Vaquerizas
The Birth of the 3D Genome during Early Embryonic Development
published pages: 903-914, ISSN: 0168-9525, DOI: 10.1016/j.tig.2018.09.002
Trends in Genetics 34/12 2019-06-19
2017 Hyun-Woo Jeong, Benjamín Hernández-Rodríguez, JungMo Kim, Kee-Pyo Kim, Rocio Enriquez-Gasca, Juyong Yoon, Susanne Adams, Hans R. Schöler, Juan M. Vaquerizas, Ralf H. Adams
Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-00738-7
Nature Communications 8/1 2019-06-19
2016 Kai Kruse, Clemens B. Hug, Benjamín Hernández-Rodríguez, Juan M. Vaquerizas
TADtool: visual parameter identification for TAD-calling algorithms
published pages: 3190-3192, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btw368
Bioinformatics 32/20 2019-06-19

Are you the coordinator (or a participant) of this project? Plaese send me more information about the "ZENCODE-ITN" project.

For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.

Send me an  email (fabio@fabiodisconzi.com) and I put them in your project's page as son as possible.

Thanks. And then put a link of this page into your project's website.

The information about "ZENCODE-ITN" are provided by the European Opendata Portal: CORDIS opendata.

More projects from the same programme (H2020-EU.1.3.1.)

synBIOcarb (2018)

Synthetic biology of carbohydrate-binding proteins: engineering protein-carbohydrate interactions for diagnostics and cell targeting

Read More  

TReSPAsS-ETN (2020)

TRaining in Secure and PrivAcy-preserving biometricS

Read More  

SuperCol (2020)

SuperCol: Rational design of super-selective and responsive colloidal particles for biomedical applications

Read More