A5102011944- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Insect Resistance and Genetics
- Machine Learning in Bioinformatics
- Transgenic Plants and Applications
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Bacterial Genetics and Biotechnology
- Speech Recognition and Synthesis
- Amino Acid Enzymes and Metabolism
- Enzyme Structure and Function
- Speech and Audio Processing
- Genetics, Bioinformatics, and Biomedical Research
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
- Speech and dialogue systems
- Protein Structure and Dynamics
- Plant biochemistry and biosynthesis
- Gene expression and cancer classification
- Plant tissue culture and regeneration
- Glycosylation and Glycoproteins Research
- Enzyme Catalysis and Immobilization
- Ubiquitin and proteasome pathways
- Hemoglobin structure and function
Laboratoire de Biométrie et Biologie Evolutive
2004-2017
Département Mathématiques et Informatique Appliquées
2017
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2017
Université Claude Bernard Lyon 1
2004-2016
Centre National de la Recherche Scientifique
1993-2011
Institut national de recherche en informatique et en automatique
2007-2011
Wellcome Sanger Institute
2011
European Bioinformatics Institute
2011
University College London
2011
Georgetown University
2011
The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and predict the presence of important domains sites. Central are predictive models, known as signatures, from range different family databases have biological focuses use methodological approaches domains. integrates these capitalizing on respective strengths individual databases, produce powerful classification resource. Here, we report status it...
InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, makes it freely available to the public via Web-based interfaces services. Central are diagnostic models, known as signatures, against which sequences can be searched determine their potential function. has utility in large-scale analysis of whole genomes meta-genomes, well characterizing individual sequences. Herein we give an overview new...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D PANTHER. The latter two new member databases have been since last publication in this journal. There several developments InterPro, including additional reading field, database links, extensions to web interface match XML files. has always provided matches UniProtKB proteins on...
Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most these have not yet been elucidated. To engineer improve metabolic traits, we need comprehensive accurate knowledge organization regulation plant at genome scale. Here, present a computational pipeline identify enzymes, pathways, gene clusters from sequenced genome. Using this pipeline, generated pathway...
Abstract Peroxisome proliferator activated receptors (PPARs) are ligand-activated transcription factors with diverse actions including adipocyte differentiation and lipid metabolism. Recent studies have revealed anti-inflammatory activities, but the majority of these been performed in monocyte/macrophages. In studies, we investigate effects PPAR ligands murine mitogen-activated splenocytes. Ciglitazone, a PPARγ ligand, consistently decreased IFN-γ IL-2 production by splenocytes had modest on...
The structure of many proteins consists a combination discrete modules that have been shuffled during evolution. Such can frequently be recognized from the analysis homology. Here we present systematic modular organization all sequenced proteins. To achieve this developed an automatic method to identify protein domains sequence comparisons. Homologous then clustered into consistent families. was applied 21,098 nonfragment sequences in SWISS-PROT 21.0, which automatically reorganized...
The understanding of selective constraints affecting genes is a major issue in biology. It well established that gene expression level determinant the rate protein evolution, but reasons for this relationship remain highly debated. Here we demonstrate also evolution dosage: losses after whole genome duplications Paramecium lineage negatively correlated to expression, and not byproduct other factors known affect fate duplicates. This indicates changes dosage are generally more deleterious...
The consortium members are situated at different research centres around the world.
The ProDom database contains protein domain families generated from the SWISS-PROT by automated sequence comparisons. current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. can be searched World Wide Web to study arrangements within either known or proteins, help of user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements server include: queries under SRS Sequence Retrieval System; links PredictProtein...
Gene regulatory networks consist of direct interactions but also include indirect mediated by metabolites and signaling molecules. We describe how these can be derived from a model the underlying biochemical reaction network, using weak time-scale assumptions in combination with sensitivity criteria metabolic control analysis. apply this approach to carbon assimilation network Escherichia coli. Our results show that gene is densely connected, contrary what usually assumed. Moreover, largely...
A speaker-dependent speech recognition system is described for recognizing isolated word utterances using reference templates created by concatenating demisyllable (half-syllable) prototypes. Each in a vocabulary specified one or more entries user-supplied lexicon containing sequence of demisyllables drawn from corpus some 1000 units. Experiments were carried out with two talkers 1109-word "Basic English" to assess the overall effectiveness representations words. Also, effects on performance...
Classical studies in Metabolic Control Theory have shown that metabolic fluxes usually exhibit little sensitivity to changes individual enzyme activity, yet remain sensitive global of all enzymes a pathway. Therefore, selective pressure is expected on the dosage or expression genes, entire pathways should still be constrained. However, direct estimate this had not been evaluated. Whole-genome duplications (WGDs) offer good opportunity address question by analyzing fates genes during massive...
Abstract Motivation: Proteins can be naturally classified into families of homologous sequences that derive from a common ancestor. The comparison and the analysis their phylogenetic relationships provide useful information regarding function evolution genes. One important difficulty clustering methods is to distinguish highly divergent only share partial homology due by protein domain rearrangements. Existing require parameters have set priori. Given variability in pattern among proteins,...
A large‐scale purification procedure of methionyl‐tRNA transformylase (10‐formyltetrahydro‐folate: l ‐methionyl‐tRNA N ‐formyltransferase) from Escherichia coli is described. The (10000‐fold) produces 22 mg homogeneous enzyme 5 kg wet cells with a yield 45%. specific activity the in reaction formylation Met f 30‐fold higher than that reported by others [Dickerman, H. W., Steers, E., Jr, Redfield, B. G. and Weissbach, (1967) Biol. Chem. 242 , 1522‐1525]. monomer molecular weight 32000, based...
Abstract Motivation: High-throughput measurement techniques for metabolism and gene expression provide a wealth of information the identification metabolic network models. Yet, missing observations scattered over dataset restrict number effectively available datapoints make classical regression inaccurate or inapplicable. Thorough exploitation data by that explicitly cope with is therefore major importance. Results: We develop maximum-likelihood approach estimation unknown parameters models...
go name type number of genes retention rate average other pval retentions Average expression in the rest genome expr quartile #1 #2 #3
Albumin 1b peptides (A1b) are small disulfide-knotted insecticidal produced by Fabaceae (also called Leguminosae). To date, their diversity among this plant family has been essentially investigated through biochemical and PCR-based approaches. The availability of high-quality genomic resources for several fabaceae species, which the model species Medicago truncatula (Mtr), allowed a analysis protein aimed at i) deciphering evolutionary history A1b proteins links with A1b-nodulins that short...
The metabolic networks of different species show a large variety in their structural design. In this work, the evolution functional properties metabolism relation with network structure is investigated. ancestral inferred from contemporary using Bayesian model for evolution. Subsequently, these are analysed recently developed method expansion. This allows analysis as well quantification functions terms synthesising capacities when they provided certain external resources. evolutionary...
To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural functional analysis.This paper presents an algorithm graphical interface called XDOM which performs systematic analysis any sequences. The automatic method to identify putative domains sequence comparisons. tool displays proteins as linked boxes, corresponding domains. has been tested on family bacterial whole...