Search results for "genomic"
showing 10 items of 1737 documents
Fast comparison of DNA sequences by oligonucleotide profiling
2008
Provisional abstact and full-text PDF files correspond to the article as it appeared upon acceptance. Fully formatted PDF and final abstract will be made available soon.
TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens…
2019
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 ofShewanella putrefaciensand genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed …
Detection of condition-specific marker genes from RNA-seq data with MGFR
2019
The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups s…
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
2013
Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…
Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts
2023
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The an…
Protein Interaction Networks and Disease: Highlights of the 3rd Challenges in Computational Biology Meeting
2017
Cellular functions are managed by a complex network of protein interactions, the malfunction of which may derive in disease phenotypes. In spite of the incompleteness and noise present in our current protein interaction maps, computational biologists are making strenuous efforts to extract knowledge from these intricate networks and, through their integration with other types of biological data, expedite the development of novel and more effective treatments against human disorders. The 3rd Challenges in Computational Biology meeting revolved around the Protein Interaction Networks and Disease subject, bringing expert network biologists to the city of Mainz, Germany to debate the current st…
A summary of genomic databases: overview and discussion
2009
In the last few years both the amount of electronically stored biological data and the number of biological data repositories grew up significantly (today, more than eight hundred can be counted thereof). In spite of the enormous amount of available resources, a user may be disoriented when he/she searches for specific data. Thus, the accurate analysis of biological data and repositories turn out to be useful to obtain a systematic view of biological database structures, tools and contents and, eventually, to facilitate the access and recovery of such data. In this chapter, we propose an analysis of genomic databases, which are databases of fundamental importance for the research in bioinfo…
Reproducing kernel hilbert spaces regression methods for genomic assisted prediction of quantitative traits.
2008
Abstract Reproducing kernel Hilbert spaces regression procedures for prediction of total genetic value for quantitative traits, which make use of phenotypic and genomic data simultaneously, are discussed from a theoretical perspective. It is argued that a nonparametric treatment may be needed for capturing the multiple and complex interactions potentially arising in whole-genome models, i.e., those based on thousands of single-nucleotide polymorphism (SNP) markers. After a review of reproducing kernel Hilbert spaces regression, it is shown that the statistical specification admits a standard mixed-effects linear model representation, with smoothing parameters treated as variance components.…
Array CGH defined interstitial deletion on chromosome 14: a new case
2009
Interstitial deletions of the long arm of chromosome 14 are relatively rare. We report a 8.5-year-old girl with dysmorphic facial features and mental retardation associated with a de novo interstitial deletion of chromosome 14. The comparison between our patient and all published patients is reviewed. The genetic investigations have allowed us to define the critical chromosomal region and to start an accurate follow-up.
Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent Pseudomonads
2003
ABSTRACT The diversity of the membrane-bound nitrate reductase ( narG ) and nitrous oxide reductase ( nosZ ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overa…