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The Microme Project: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics

Obiettivo

The exponential increase in microbial genome and metagenome sequencing throughput has widened the gap between sequence and functional understanding. A clear picture of metabolic processes across the spectrum of bacterial species is essential to enable the exploitation of microbial genomics for the purposes of environmental biotechnology. The Microme project endeavors to extend the scope of microbial genome annotation from functional assignment at the gene level to the systematic generation of pathway assemblies and genome-scale metabolic models. A few key ideas and design principles will enable the Microme reconstruction pipeline to achieve this ambitious goal.A clear definition of a metabolic pathway as a collection of reaction sets, each of which convert the same defined inputs into the same outputs, will allow species-specific pathway variants to be identified, assembled into networks, compared across species, and used for downstream computations. A unique pathways projection, curation and assembly cycle, feeding directly into the flow of newly sequenced genomes, will allow a qualitative increase in the speed and reliability of the pathway generation process. Pathways and models produced the pipeline will be accessible to the scientific community as an integrated resource via the Microme portal. Finally, taking advantage of the availability of pathway assemblies from a large sample of genomes, methods for comparative and phylogenetic analyses and novel metabolic engineering strategies for environmental biotechnology goals will be developed, applied to proof-of-concept studies, and integrated to the resource as an analytical tool layer. Microme will be supported by a robust bioinformatics infrastructure, developed by integrating a set of established European databases and tools, integrated with reference protein annotation, metabolites and reactions databases, and interfaced with the annotation pipelines of the two main European sequencing centers.

Invito a presentare proposte

FP7-KBBE-2007-2A
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Coordinatore

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Indirizzo
Meyerhofstrasse 1
69117 Heidelberg
Germania

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Research Organisations
Contatto amministrativo
Tom Ratcliff (Mr.)
Contributo UE
€ 876 000

Partecipanti (15)

COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES
Francia
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€ 567 000
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Rue Leblanc 25
75015 Paris 15

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Contatto amministrativo
Régis Copin (Mr.)
ETHNIKO KENTRO EREVNAS KAI TECHNOLOGIKIS ANAPTYXIS
Grecia
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€ 375 978
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Charilaou Thermi Road 6 Km
57001 Thermi Thessaloniki

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Contatto amministrativo
Costas Kiparissides (Prof.)
AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spagna
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€ 375 979
Indirizzo
Calle Serrano 117
28006 Madrid

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Carlos Manuel Abad Ruiz (Mr.)
FUNDACION SECTOR PUBLICO ESTATAL CENTRO NACIONAL INVESTIGACIONES ONCOLOGICAS CARLOS III
Spagna
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€ 250 481
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C Melchor Fernandez Almagro 3
28029 Madrid

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Contatto amministrativo
Ralf Dahm (Dr.)
LEIBNIZ-INSTITUT DSMZ-DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH
Germania
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€ 321 999
Indirizzo
Inhoffenstrasse 7b
38124 Braunschweig

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Contatto amministrativo
Heike Bauer (Dr.)
HELMHOLTZ-ZENTRUM FUR INFEKTIONSFORSCHUNG GMBH

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Germania
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Inhoffenstrasse 7
38124 Braunschweig

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Michael Stratz (Dr.)
Isthmus
Francia
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€ 242 480
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Rue Saint Amand 31
75015 Paris

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Private for-profit entities (excluding Higher or Secondary Education Establishments)
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Philippe Marlière (Dr.)
MOLECULAR NETWORKS GMBH COMPUTERCHEMIE
Germania
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Neumeyerstr 28-34
90411 Nurnberg

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Christof H. Schwab (Dr.)
SIB SWISS INSTITUTE OF BIOINFORMATICS
Svizzera
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Rue Michel Servet 1 Cmu
1206 Geneve

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Jocelyne Bocquet (Ms.)
UNIVERSITE LIBRE DE BRUXELLES
Belgio
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Avenue Franklin Roosevelt 50
1050 Bruxelles

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Higher or Secondary Education Establishments
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Jacques Van Helden (Prof.)
GENOME RESEARCH LIMITED
United Kingdom
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€ 321 756
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The Gibbs Building, Euston Road 215
NW1 2BE London

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David Davison (Mr.)
TEL AVIV UNIVERSITY
Israele
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€ 417 152
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Ramat Aviv
69978 Tel Aviv

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Lea Pais (Ms.)
Ceprodi Compagnie Europeenne de Produits Diabetiques

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Francia
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€ 124 091,24
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Bd De Courcelles 67
75008 Paris

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David Dieumegard (Mr.)
WAGENINGEN UNIVERSITY
Paesi Bassi
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Droevendaalsesteeg 4
6708 PB Wageningen

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Tom Bessems (Mr.)
AMABIOTICS SAS
Francia
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€ 159 496,76
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Rue Gaston Cremieux 2
91000 Evry

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Chantal Rougier (Ms.)