The Experts below are selected from a list of 3366 Experts worldwide ranked by ideXlab platform
Marek Sergot - One of the best experts on this subject based on the ideXlab platform.
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distributed and paged suffix trees for large Genetic Databases
Combinatorial Pattern Matching, 2003Co-Authors: Raphael Clifford, Marek SergotAbstract:We present two new variants of the suffix tree which allow much larger genome sequence Databases to be handled efficiently. The method is based on a new linear time construction algorithm for "sparse" suffix trees, which are subtrees of the whole suffix tree. The new data structures are called the paged suffix tree (PST) and the distributed suffix tree (DST). Both tackle the memory bottleneck by constructing subtrees of the full suffix tree independently and are designed for single processor and distributed memory parallel computing environments (e.g. Beowulf clusters), respectively. The standard operations on suffix trees of biological importance are shown to be easily translatable to these new data structures. While none of these operations on the DST require interprocess communication, many have optimal expected parallel running times.
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CPM - Distributed and paged suffix trees for large Genetic Databases
Combinatorial Pattern Matching, 2003Co-Authors: Raphael Clifford, Marek SergotAbstract:We present two new variants of the suffix tree which allow much larger genome sequence Databases to be handled efficiently. The method is based on a new linear time construction algorithm for "sparse" suffix trees, which are subtrees of the whole suffix tree. The new data structures are called the paged suffix tree (PST) and the distributed suffix tree (DST). Both tackle the memory bottleneck by constructing subtrees of the full suffix tree independently and are designed for single processor and distributed memory parallel computing environments (e.g. Beowulf clusters), respectively. The standard operations on suffix trees of biological importance are shown to be easily translatable to these new data structures. While none of these operations on the DST require interprocess communication, many have optimal expected parallel running times.
George P Patrinos - One of the best experts on this subject based on the ideXlab platform.
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Genetic Databases in Pharmacogenomics: The Frequency of Inherited Disorders Database (FINDbase)
Methods of Molecular Biology, 2013Co-Authors: Marianthi Georgitsi, George P PatrinosAbstract:: Pharmacogenomics studies how the variations of the individuals' Genetic makeup are correlated with a person's response to certain drugs in relation to the therapeutic efficiency, clinical outcome, or even survival, and how they affect drug metabolism, transport, or clearance. Yet, since the incidence of these polymorphisms, being either single-point variations or small insertions/deletions, varies among different populations, a systematic collection and documentation of these variations is warranted, in order to facilitate implementation of pharmacogenomics in different populations. Here we review the existing electronic Databases related to pharmacogenomics and pay particular attention in the description of the pharmacogenomics module Frequency of Inherited Disorders database (FINDbase), which documents curated allelic frequency data pertaining to 144 pharmacogenomics markers across 14 genes, representing approximately 87,000 individuals from 150 populations and ethnic groups worldwide. Long-term sustainability of these resources aims to contribute to the design, development, and implementation of pharmacogenomics testing towards the application of personalized approaches in medical treatment.
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Genetic Databases and their potential in pharmacogenomics
Current Pharmaceutical Design, 2010Co-Authors: George Lagoumintzis, Konstantinos Poulas, George P PatrinosAbstract:The completion of the human genome sequencing project and the establishment of new methods for the detection of point mutations have lead to a remarkable increase of sequence variants identification in a growing number of genes. As a result of this, a new field of research has emerged, pharmacogenomics, which deals with the influence of Genetic variation on drug response by correlating gene expression or single-nucleotide polymorphisms with a drugs efficacy or toxicity. Genetic Databases are continuously updated online repositories of mutation data, described for a single or more genes or specifically for a population or ethnic group. Genetic Databases can also fulfil the mission of pharmacogenomics by helping elucidate gene function, estimate the prevalence of genes in populations, differentiate among subtypes of diseases, trace how genes may predispose to or protect against illnesses, and improve medical intervention. Therefore, it is expected that Genetic Databases will gradually assume an increasing importance in all aspects of genome medicine. This article aims to provide an update of the current and emerging types of Genetic Databases relevant to the field of pharmacogenomics. Moreover, the key elements that are holding back the field as well as the challenges that should be addressed in the near future are also commented.
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ETHNOS: A versatile electronic tool for the development and curation of national Genetic Databases
Human Genomics, 2010Co-Authors: Sjozef Van Baal, George Lagoumintzis, Konstantinos Poulas, Joël Zlotogora, Vassiliki Gkantouna, Ioannis Tzimas, Athanassios Tsakalidis, Giovanni Romeo, George P PatrinosAbstract:National and ethnic mutation Databases (NEMDBs) are emerging online repositories, recording extensive information about the described Genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of Genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various Genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in Genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific Databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.
Raphael Clifford - One of the best experts on this subject based on the ideXlab platform.
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distributed and paged suffix trees for large Genetic Databases
Combinatorial Pattern Matching, 2003Co-Authors: Raphael Clifford, Marek SergotAbstract:We present two new variants of the suffix tree which allow much larger genome sequence Databases to be handled efficiently. The method is based on a new linear time construction algorithm for "sparse" suffix trees, which are subtrees of the whole suffix tree. The new data structures are called the paged suffix tree (PST) and the distributed suffix tree (DST). Both tackle the memory bottleneck by constructing subtrees of the full suffix tree independently and are designed for single processor and distributed memory parallel computing environments (e.g. Beowulf clusters), respectively. The standard operations on suffix trees of biological importance are shown to be easily translatable to these new data structures. While none of these operations on the DST require interprocess communication, many have optimal expected parallel running times.
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CPM - Distributed and paged suffix trees for large Genetic Databases
Combinatorial Pattern Matching, 2003Co-Authors: Raphael Clifford, Marek SergotAbstract:We present two new variants of the suffix tree which allow much larger genome sequence Databases to be handled efficiently. The method is based on a new linear time construction algorithm for "sparse" suffix trees, which are subtrees of the whole suffix tree. The new data structures are called the paged suffix tree (PST) and the distributed suffix tree (DST). Both tackle the memory bottleneck by constructing subtrees of the full suffix tree independently and are designed for single processor and distributed memory parallel computing environments (e.g. Beowulf clusters), respectively. The standard operations on suffix trees of biological importance are shown to be easily translatable to these new data structures. While none of these operations on the DST require interprocess communication, many have optimal expected parallel running times.
Susan M C Gibbons - One of the best experts on this subject based on the ideXlab platform.
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From Principles to Practice: Implementing Genetic Database Governance:
Medical Law International, 2008Co-Authors: Susan M C GibbonsAbstract:This paper provides a short introduction to four articles published as a special collection under the title, ‘Implementing Genetic Database Governance’. It describes the background context and the need for Genetic Databases and biobanks to be governed appropriately and effectively. It notes the current lack of any coordinated governance frameworks, whether at the national, regional or international levels. It identifies certain core guiding principles and key issues relevant to governing Genetic Databases. It then draws out and reflects on five cross-cutting themes that emerge from the articles.
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Mapping the Regulatory Framework for Human Genetic Databases in England and Wales
Medical Law International, 2008Co-Authors: Jane Kaye, Susan M C GibbonsAbstract:The ‘regulatory space’ metaphor articulated by Rancher and Moran offers a useful framing device for mapping and understanding the complex dynamics and patterns of interaction between the actors who populate existing regulatory regimes. This paper applies the ‘regulatory space’ analytical approach to map out and, thereby, gain a deeper understanding of, the current governance of Genetic Databases and biobanks in England and Wales. The paper draws on legal research undertaken for an ongoing socio-legal project into Genetic database governance. It demonstrates some benefits of using the regulatory space approach as a precursor to applying normative theories and principles to formulate specific recommendations for regulatory reform. It also identifies potential pitfalls. The findings and conclusions should assist in designing policy recommendations for regulating Genetic Databases and biobanks better in the future.
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Certainty is Absurd: Meeting Information Security Requirements in Laws on Population Genetic Databases
Medical Law International, 2008Co-Authors: Helgaso Hörđur Helgi, Susan M C GibbonsAbstract:This paper describes the problem of determining whether plans for a population Genetic database in Iceland met statutory information security requirements. It discusses the approach taken by the relevant governmental authority, which involved employing technical standards to solve the problem. By examining the background to the project, and the main challenges it faced, the paper aims to draw out insights and lessons to inform the way in which future projects are designed and governed. It reflects critically on the results of trying to meet legal requirements for information security by using technical information security standards. Particular attention is given to the founding legislation of the project, and the court case that eventually found that legislation to be unconstitutional.
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governing human Genetic Databases biobanks and research tissue banks
Research Ethics Review, 2007Co-Authors: Susan M C GibbonsAbstract:This paper reports on a recent symposium seminar series entitled ‘Governing Genetic Databases – collection, storage and use’ hosted by the Ethox Centre at the University of Oxford. It outlines the inadequacy of the current UK framework for governing Genetic Databases and biobanks and some of the implications of this. It then briefly describes and reflects on each of the five symposium papers.
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are uk Genetic Databases governed adequately a comparative legal analysis
Legal Studies, 2007Co-Authors: Susan M C GibbonsAbstract:Given the burgeoning of Genetic research and proliferation of human Genetic Databases, especially in the biomedical sphere, this paper explores whether the existing laws and regulatory structures for governing Genetic Databases in England and Wales are adequate. Through a critical survey of relevant rules, bodies and practices, it argues that the current UK framework is far from ideal in at least five major areas: (1) forms and styles of law used, especially the separate legislative regimes for physical biomaterial and data; (2) core definitions; (3) formal regulatory bodies, licensing and notification requirements; (4) ethics committees and other advisory panels; and (5) enforcement powers and sanctions. Such shortcomings could have major implications for stakeholders, hamper efforts to achieve European or international harmonisation of Genetic database principles and practices, and undermine the UK’s standing as a world leader in Genetics and biotechnology. Drawing on comparative analysis of governance strategies adopted in Estonia, Iceland and Sweden, the paper identifies alternative options and lessons from experiences abroad, suggesting possible avenues for reform that may warrant serious consideration in the UK.
George Lagoumintzis - One of the best experts on this subject based on the ideXlab platform.
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Genetic Databases and their potential in pharmacogenomics
Current Pharmaceutical Design, 2010Co-Authors: George Lagoumintzis, Konstantinos Poulas, George P PatrinosAbstract:The completion of the human genome sequencing project and the establishment of new methods for the detection of point mutations have lead to a remarkable increase of sequence variants identification in a growing number of genes. As a result of this, a new field of research has emerged, pharmacogenomics, which deals with the influence of Genetic variation on drug response by correlating gene expression or single-nucleotide polymorphisms with a drugs efficacy or toxicity. Genetic Databases are continuously updated online repositories of mutation data, described for a single or more genes or specifically for a population or ethnic group. Genetic Databases can also fulfil the mission of pharmacogenomics by helping elucidate gene function, estimate the prevalence of genes in populations, differentiate among subtypes of diseases, trace how genes may predispose to or protect against illnesses, and improve medical intervention. Therefore, it is expected that Genetic Databases will gradually assume an increasing importance in all aspects of genome medicine. This article aims to provide an update of the current and emerging types of Genetic Databases relevant to the field of pharmacogenomics. Moreover, the key elements that are holding back the field as well as the challenges that should be addressed in the near future are also commented.
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ETHNOS: A versatile electronic tool for the development and curation of national Genetic Databases
Human Genomics, 2010Co-Authors: Sjozef Van Baal, George Lagoumintzis, Konstantinos Poulas, Joël Zlotogora, Vassiliki Gkantouna, Ioannis Tzimas, Athanassios Tsakalidis, Giovanni Romeo, George P PatrinosAbstract:National and ethnic mutation Databases (NEMDBs) are emerging online repositories, recording extensive information about the described Genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of Genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various Genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in Genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific Databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.