The authors wish it to be known that, in their opinion, the first two authors should be regarded ... more The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity e... more Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contamina...
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity e... more Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contamina...
Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In ... more Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial ‘black-box’, the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. Results: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called ‘PhylArray’, designs a combination of degenerate and nondegenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of sho...
The human GI tract is inhabited by an incredibly complex and abundant microbiota, whose compositi... more The human GI tract is inhabited by an incredibly complex and abundant microbiota, whose composition is dependent on a variety of factors. The gut microbiota has an influence in the morphological, immunological and nutritional functions of the digestive tract and may be involved in many diseases. This article proposes the rationale behind conducting in vitro diagnostics (IVDs) of the human microbiota, as well as outlining the conceptual and technical difficulties involved in IVD testing. The molecular methods that can be used according to whether the IVD tools are employed to study one individual constituent species or to determine the microbiota as a whole will also be described. In the latter case, these technologies include high-throughput sequencing for metagenomics and DNA microarrays, which can now be efficiently used to study gut ecology and are believed to represent the future of standardized diagnostics.
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity e... more Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contamina...
Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial ... more Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way. POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning. However, the selection of probes remains a very difficult task. The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design. Consequently, the use of high performance computing facilities is mandatory. In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids. We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI). We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous de...
ABSTRACT Détermination de sondes oligonucléotidiques pour biopuces phylogénétiques en environneme... more ABSTRACT Détermination de sondes oligonucléotidiques pour biopuces phylogénétiques en environnement grille de calcul
2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007
When studying complex environments where the composing microorganisms are unknown, exploratory to... more When studying complex environments where the composing microorganisms are unknown, exploratory tools able to tackle with the biological diversity have to be proposed. DNA microarrays can be a good answer if we are in a position to propose all the probes that could target a specific enzyme. In addition, in the context of new metabolic pathways discovery, it appears that
International Journal of Computational Biology and Drug Design, 2008
In the context of new metabolic pathways discovery, a full backtranslation of oligopeptides can b... more In the context of new metabolic pathways discovery, a full backtranslation of oligopeptides can be a promising approach. When studying complex environments where the composing microorganisms are unknown it is also preferable to have all the complete nucleic sequences corresponding to an enzyme of interest. In this paper, we revisit the existing bioinformatics applications, which bring partial reverse translation solutions, and we compare two algorithms based on oligopeptide degeneracy able to efficiently compute a complete backtranslation of oligopeptides. Such algorithms are precious for the discovery of new organisms and we show their performances on simulated and real biological data sets.
The authors wish it to be known that, in their opinion, the first two authors should be regarded ... more The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity e... more Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contamina...
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity e... more Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contamina...
Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In ... more Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial ‘black-box’, the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. Results: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called ‘PhylArray’, designs a combination of degenerate and nondegenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of sho...
The human GI tract is inhabited by an incredibly complex and abundant microbiota, whose compositi... more The human GI tract is inhabited by an incredibly complex and abundant microbiota, whose composition is dependent on a variety of factors. The gut microbiota has an influence in the morphological, immunological and nutritional functions of the digestive tract and may be involved in many diseases. This article proposes the rationale behind conducting in vitro diagnostics (IVDs) of the human microbiota, as well as outlining the conceptual and technical difficulties involved in IVD testing. The molecular methods that can be used according to whether the IVD tools are employed to study one individual constituent species or to determine the microbiota as a whole will also be described. In the latter case, these technologies include high-throughput sequencing for metagenomics and DNA microarrays, which can now be efficiently used to study gut ecology and are believed to represent the future of standardized diagnostics.
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity e... more Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contamina...
Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial ... more Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way. POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning. However, the selection of probes remains a very difficult task. The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design. Consequently, the use of high performance computing facilities is mandatory. In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids. We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI). We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous de...
ABSTRACT Détermination de sondes oligonucléotidiques pour biopuces phylogénétiques en environneme... more ABSTRACT Détermination de sondes oligonucléotidiques pour biopuces phylogénétiques en environnement grille de calcul
2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007
When studying complex environments where the composing microorganisms are unknown, exploratory to... more When studying complex environments where the composing microorganisms are unknown, exploratory tools able to tackle with the biological diversity have to be proposed. DNA microarrays can be a good answer if we are in a position to propose all the probes that could target a specific enzyme. In addition, in the context of new metabolic pathways discovery, it appears that
International Journal of Computational Biology and Drug Design, 2008
In the context of new metabolic pathways discovery, a full backtranslation of oligopeptides can b... more In the context of new metabolic pathways discovery, a full backtranslation of oligopeptides can be a promising approach. When studying complex environments where the composing microorganisms are unknown it is also preferable to have all the complete nucleic sequences corresponding to an enzyme of interest. In this paper, we revisit the existing bioinformatics applications, which bring partial reverse translation solutions, and we compare two algorithms based on oligopeptide degeneracy able to efficiently compute a complete backtranslation of oligopeptides. Such algorithms are precious for the discovery of new organisms and we show their performances on simulated and real biological data sets.
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Papers by Mohieddine Missaoui