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ZENCODE-ITN SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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 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.

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

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

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

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