Computational Bioscience Research Center

Saudi Arabia

Computational Bioscience Research Center

Saudi Arabia
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News Article | February 19, 2017
Site: www.eurekalert.org

Advances in genomic research are helping scientists to reveal how corals and algae cooperate to combat environmental stresses. KAUST researchers have sequenced and compared the genomes of three strains of Symbiodinium, a member of the dinoflagellate algae family, to show their genomes have several features that promote a prosperous symbiotic relationship with corals1. Dinoflagellates are among the most prolific organisms on the planet, forming the basis of the oceanic food chain, and their close symbiotic relationships with corals help maintain healthy reefs. However, because dinoflagellates have unusually large genomes, very few species have been sequenced, leaving the exact nature of their symbiosis with corals elusive. "We had access to two Symbiodinium genomes, S.minutum and S.kawagutii, and we decided to sequence a third, S. microadriaticum," said Assistant Professor of Marine Science Manuel Aranda at the University's Red Sea Research Center, who led the project with his Center colleague Associate Professor of Marine Science Christian Voolstra and colleagues from the University's Computational Bioscience Research Center and Environmental Epigenetics Program. "This allowed us to compare the three genomes for common and disparate features and functions and hopefully to show how the species evolved to become symbionts to specific corals." The unusual makeup of the three Symbiodinium genomes meant that the team had to adjust their software to read the genomes correctly. Ultimately, their research revealed that Symbiodinium has evolved a rich array of bicarbonate and ammonium transporters. These proteins are used to harvest two important nutrients involved in coral-dinoflagellate symbiosis: carbon, which is needed for photosynthesis, and nitrogen, which is essential for growth and proliferation. Symbiodinium either evolved these transporters in response to symbiosis or the presence of these transporters allowed Symbiodinium to become a symbiont in the first place, noted Aranda.


Naveed H.,Computer | Naveed H.,Computational Bioscience Research Center | Hameed U.S.,King Abdullah University of Science and Technology | Harrus D.,French Institute of Health and Medical Research | And 7 more authors.
Bioinformatics | Year: 2015

Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug. Results: Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called 'drugs'). For a given drug, our method uses sequence order-independent structure alignment, hierarchical clustering and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drug's PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of 11 drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs - two that are of high pharmacological interest, the peroxisome proliferator-activated receptor gamma and the oncogene B-cell lymphoma 2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development. © The Author 2015. Published by Oxford University Press. All rights reserved.


Juneja P.,University of Cambridge | Osei-Poku J.,University of Cambridge | Ho Y.S.,Computational Bioscience Research Center | Ariani C.V.,University of Cambridge | And 3 more authors.
PLoS Neglected Tropical Diseases | Year: 2014

The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled - there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait. © 2014 Juneja et al.


Kodzius R.,Computational Bioscience Research Center | Kodzius R.,King Abdullah University of Science and Technology | Gojobori T.,Computational Bioscience Research Center | Gojobori T.,King Abdullah University of Science and Technology
Marine Genomics | Year: 2015

This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals. © 2015.


Juneja P.,University of Cambridge | Osei-Poku J.,University of Cambridge | Ho Y.S.,Computational Bioscience Research Center | Ariani C.V.,University of Cambridge | And 3 more authors.
PLoS neglected tropical diseases | Year: 2014

The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled - there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait.


PubMed | Computational Bioscience Research Center, French Institute of Health and Medical Research and King Abdullah University of Science and Technology
Type: Journal Article | Journal: Bioinformatics (Oxford, England) | Year: 2015

The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug.Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called drugs). For a given drug, our method uses sequence order-independent structure alignment, hierarchical clustering and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drugs PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of 11 drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs-two that are of high pharmacological interest, the peroxisome proliferator-activated receptor gamma and the oncogene B-cell lymphoma 2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development.The program, datasets and results are freely available to academic users at http://sfb.kaust.edu.sa/Pages/Software.aspx.


PubMed | Computational Bioscience Research Center and King Abdullah University of Science and Technology
Type: | Journal: Database : the journal of biological databases and curation | Year: 2015

Enhancers are cis-acting DNA regulatory regions that play a key role in distal control of transcriptional activities. Identification of enhancers, coupled with a comprehensive functional analysis of their properties, could improve our understanding of complex gene transcription mechanisms and gene regulation processes in general. We developed DENdb, a centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods generating an enriched catalogue of putative enhancers for each of the analysed cell-lines. DENdb provides information about the overlap of enhancers with DNase I hypersensitive regions, ChIP-seq regions of a number of transcription factors and transcription factor binding motifs, means to explore enhancer interactions with DNA using several chromatin interaction assays and enhancer neighbouring genes. DENdb is designed as a relational database that facilitates fast and efficient searching, browsing and visualization of information. Database URL: http://www.cbrc.kaust.edu.sa/dendb/.


PubMed | Computational Bioscience Research Center and University of Cambridge
Type: Journal Article | Journal: PLoS neglected tropical diseases | Year: 2014

The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled - there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait.

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