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MoDATS SIGNED

Model-based Data Analysis of Transcription and Splicing

Total Cost €

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EC-Contrib. €

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Partnership

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 MoDATS project word cloud

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

machinery    acute    fundamental    noisy    integrating    stochastic    genomic    molecular    mechanisms    gigabytes    eukaryotic    previously    regulates    splicing    experimentalists    messenger    model    polymerase    underlying    unknown    observations    coding    simultaneously    rna    template    labeling    biological    cross    paradigm    generation    effect    sequencing    interrogate    shows    partial    framework    coupled    spliced    scientists    distributions    constitutive    time    removal    struggle    dna    nascent    ways    modern    models    biology    statistical    produces    genome    decades    multiple    proposes    intermediate    transcription    yielded    kinetics    encoding    resolved    genes    elongation    talk    complicates    cells    mechanism    expression    ing    ngs    polymerization    analyze    data    mrnas    gene    give    transcripts    regions    completion    biologists    functional    collect    molecules    types    transcribed    formulated    probability    interactions    components    interplay    mrna    thousands    protein    phenomenon    estimate    quantify   

Project "MoDATS" data sheet

The following table provides information about the project.

Coordinator
THE UNIVERSITY OF EDINBURGH 

Organization address
address: OLD COLLEGE, SOUTH BRIDGE
city: EDINBURGH
postcode: EH8 9YL
website: www.ed.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 https://ewallace.github.io/
 Total cost 195˙454 €
 EC max contribution 195˙454 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2014
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2016
 Duration (year-month-day) from 2016-01-05   to  2018-01-19

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    THE UNIVERSITY OF EDINBURGH UK (EDINBURGH) coordinator 195˙454.00

Map

 Project objective

Gene expression is the fundamental process that in all cells produces functional protein from a genomic DNA template using a messenger RNA (mRNA) intermediate. Eukaryotic gene expression involves transcription--the polymerization of mRNA--and splicing--the removal of non-coding regions from the mRNA. Recent evidence shows that nascent mRNAs are spliced while still being transcribed, not after completion of transcription, and that splicing machinery regulates transcription. This cross-talk complicates understanding of gene expression, as its mechanism and consequences are not understood. This project proposes using model-based data analysis, applied to multiple types of data, to study the kinetics of coupled transcription and splicing.

Model-based data analysis is a statistical framework in which models are formulated as probability distributions encoding the stochastic interactions between components, including observed data. Knowledge of the underlying mechanism--here, biological--is used to quantify both the phenomenon, and the uncertainty resulting from partial knowledge and noisy observations. The need for such analysis is acute in modern biology: decades of molecular biology have yielded detailed information on specific molecules and pathways, and now next-generation sequencing (NGS) allows scientists to collect gigabytes of data on thousands of distinct molecules simultaneously. Yet, integrating these approaches is challenging: biologists struggle to analyze NGS data in ways that give insight into known--and previously unknown--biological mechanisms.

Here, the model-based data analysis paradigm will be used to interrogate the interplay of transcription and splicing, using state-of the art data including time-resolved NGS measurements of RNA processing. Working with experimentalists, we will quantify the kinetics of splicing in constitutive genes by labeling nascent transcripts, and estimate the effect of splicing on polymerase elongation genome-wide.

 Publications

year authors and title journal last update
List of publications.
2017 Edward W.J. Wallace, Jean D. Beggs
Extremely fast and incredibly close: cotranscriptional splicing in budding yeast
published pages: 601-610, ISSN: 1355-8382, DOI: 10.1261/rna.060830.117
RNA 23/5 2019-06-18
2017 Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin, Premal Shah
riboviz: analysis and visualization of ribosome profiling datasets
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-017-1873-8
BMC Bioinformatics 18/1 2019-06-18

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