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Search Results: 1 - 10 of 225 matches for " Vasilis Vasiliou "
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Editorial
Vasilis Vasiliou
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-3-137
Abstract: Our submission rate has increased and our publication rate is constant to the point that our Impact Factor will be provided by ISI by the summer of 2011.We have a new addition to our Editorial Board. I therefore welcome and introduce to you, Samir Zakhari, who is Director of the Division of Metabolism and Health Effects of the National Institute on Alcohol Abuse and Alcoholism at the National Institutes of Health, USA.In this issue, we start with the Research Highlights. Webb, Smith and Cotton then describe the difficulties associated with finding SNPs and related phenotypic data in world wide web resources using simple, uncomplicated search terms and they also provide a suggested solution. This is followed by the Filocamo and Morrone Review of the molecular basis and laboratory testing of lysosomal storage disorders, a group of more than 50 different inherited metabolic diseases. In the Update on Gene Completions and Annotations section, Smathers and Petersen review the human fatty acid-binding protein (FABP) family, a member to the superfamily of intracellular lipid-binding proteins. In this paper, the evolutionary divergences and functions of the FABPs are discussed. In Issue 5.2, Wright and Bruford provided an excellent Review on the nomenclature of non-coding RNAs (pp. 90-98). In the Software Review section of the current issue, Agirre and Eyras discuss databases and resources available for non-coding RNAs (sRNAs). They look at the main issues related to the integration and annotation of sRNA datasets. In the Genome Databases section, Valerio discusses toxicology models and databases as Critical Path toolkits for predicting toxicities early in drug development. Finally, Cassiman reviews the second edition of a book entitled 'Molecular Diagnostics' published by Elsevier (Academic Press) in 2010 and edited by George Patrinos and Wilhelm Ansorge.
Editorial
Vasilis Vasiliou
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-4-215
Abstract: Ikediobi and colleagues have characterised the population frequencies of clinically relevant phar-macogenetic traits in two distinct South African population groups residing in the Western Cape (the Xhosa and Cape Mixed Ancestry). Their data indicate diverse allele frequencies of key pharmaco-genetic genes within the African population. In the Update on Gene Completions and Annotations section, Jackson et al. provide an update on aldehyde dehydrogenase (ALDH) genes in several vertebrates and clarify the annotation found in the National Center for Biotechnology Information (NCBI) gene database. They also discuss gene-duplication and gene-loss events that may have occurred in the ALDH gene superfamily. In the Software Review section of the current issue, Lamy and colleagues discuss software for the genotyping of microarray single nucleotide polymorphisms, in particular software for Affymetrix and Illumina arrays. In Genome Databases, Jassal reviews the new version of the Reactome database and uses it to analyse the solute carrier (SLC) class of transporters. His study and the Reactome provide a basis for a number of analyses, which includes interactions, expression data, over-representation analysis and species comparison. Such analyses may provide the basis for further investigations using systems biology.Finally, Dan Nebert reviews the book, Designer Genes: A New Era in the Evolution of Man by Stephen Potter (Random House; 2010).
Editorial
Vasilis Vasiliou
Human Genomics , 2009, DOI: 10.1186/1479-7364-3-2-101
Abstract: Mutations in another aldehyde dehydrogenase gene (ALDH5A1) are the molecular basis for succinate semialdehyde dehydrogenase (SSADH) deficiency, which is a neurological disorder associated with developmental delay, prominent language deficits, hypotonia, ataxia, hyporeflexia and seizures. Malaspina and colleagues report on the comparative genomics of ALDH5A1 and the accumulation of gamma-hydroxybutyrate associated with its deficiency. In another paper in this issue, Gherman et al. report on how the spatial configuration of neighbouring genes affects their regulation and function. Their systematic survey of the distribution and orientation of genes and the properties of intergenic intervals reveals previously unknown properties of the genome which will be the basis for further studies.Shukla et al. have used the whole-genome approach with molecular experiments to identify factors involved in conferring cellular resistance to carboplatin, a chemotherapeutic agent used in the management of many cancers, but with treatment limited by resistance and toxicity. They have identified and validated the CD44 gene as a major factor contributing to carboplatin resistance in tumour cell lines.Garenc et al. report on the effects of the LIPE C-60G polymorphism on body fat, plasma lipid and lipoprotein concentrations, and its interaction with physical activity. Their results suggest that the associations between physical activity and body fat and plasma lipoprotein/lipid concentrations in men are dependent on the LIPE C-60G polymorphism. The study highlights the importance of taking into account the role of gene-physical activity interactions in candidate gene studies of obesity and obesity-related traits.Matimba et al. describe novel SNPs of CYP2C9, CYP2C19, CYP2D6 and NAT2 genes in African populations. While confirming African-specific variants, they found only modest variation between different African ethnicities, indicating similar metabolic profiles for most drugs, yet stressin
Human Genomics begins ePub ahead of print and a discussion forum Aiming to Bridge Academia with the Pharmaceutical Industry
Vasilis Vasiliou
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-5-419
Abstract: The open access, in combination with the ePub ahead of print, discussed below, will permit immediate public access to both the preliminary accepted version and the copyedited, typeset version published in the online journal. This option is in addition to the open access already provided through the National Institutes of Health's PubMed Central repository; all primary research published in Human Genomics is freely available through PubMed Central six months after publication.Starting in Volume 6, Human Genomics will have available the e-Pub ahead of print option for all publications. These are citations that publishers submit to PubMed for articles that appear on the publisher's website in advance of the journal release. The reason for the ePub ahead of print approach is to publish accepted, checked and proofread articles online prior to their appearance in the print version of a journal. Such an article is assigned a digital object identifier (DOI; a character string that serves as a unique identifier for an article and stays with the article even after it has been assigned volume, issue and page numbers), and is indexed by PubMed and other indexing services. As with many other journals, we believe that this is very important, simply because it allows an accepted paper (ePub article) to be cited immediately by its DOI and then associated with its traditional citation after it is published in print. The online access to 'ahead of print' articles will be limited to individual subscribers and to libraries with paid subscriptions.One of the unique features of Human Genomics is its role as the interface between the pharmaceutical industry and academic research. Our aim is to publish original research papers and review articles relevant to both. To support this feature further, we are introducing a forum, Aiming to Bridge Academia with the Pharmaceutical Industry.
Changes in Human Genomics
Vasilis Vasiliou
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-2-75
Abstract: First and foremost, I am delighted to confirm that the Journal is now accepting submissions for open-access papers. We recognise the importance of open access to experts in the field - and the necessary speed with which work needs to be published - but also that the cost to authors is of course significant. In recognition of this we are offering all authors the opportunity to publish papers on an open-access basis, with full indexing in PubMed, Medline and Chemical Abstracts, at a fee of only US$750/£500 to cover production costs. We would be delighted if you would like to submit an open-access paper and would welcome any queries you might have. This opportunity is open to individuals as well as genetics associations, research institutions and universities wishing to publish collections of research papers, review articles and proceedings of meetings in a special issue of the Journal. For further details of the Journal and how to submit open-access papers, please contact me directly at: http://Vasilis.Vasiliou@ucdenver.edu webcite. You can also find further details at: http://www.henrystewart.com/hg.aspx webcite.It is with great pleasure that we welcome Mirella Filocamo, (G. Gaslini Institute, Italy), Tadashi Imanishi (Biomedicinal Information Research Center, Japan), Hidetoshi Inoko (Tokai University School of Medicine, Japan), Poh-San Lai (National University of Singapore, Singapore), George P. Patrinos (University of Patras, Greece) and Sumio Sugano (University of Tokyo, Japan) to our Editorial Board. We also welcome Thomas Schlitt, (King's College London, UK) who is replacing Mike Weale, (King's College London, UK) as the Software Review Editor. Mike remains on the Editorial Board of the Journal and we thank him for all the support he has given to this regular feature.Finally, this issue sees the first installment of the new regular feature for Human Genomics entitled 'Research Highlights', which collates and reviews some of the most cutting-edge research papers
Editorial
Vasilis Vasiliou
Human Genomics , 2009, DOI: 10.1186/1479-7364-3-3-211
Abstract: In this issue of Human Genomics, a number of topics are covered, including the existence of ALDH2*2 in the Indian population, novel prediction methods for transcription factor binding sites, molecular technologies and bioinformatic tools, as well as Hox gene expression.Published in this issue is a very interesting study by Vaswani et al., exploring genes involved in alcohol metabolism that may be linked with alcoholism in the Indian population. Ethanol is metabolised to acetaldehyde mainly by alcohol dehydrogenase enzymes, and acetaldehyde is then metabolised to acetic acid by aldehyde dehydrogen-ases (ALDH). The ALDH2 gene product is a mito-chondrial protein responsible for acetaldehyde clearance. The ALDH2*2 allele (E487K) protects against alcoholism and is a determinant of alcohol avoidance in some East Asian populations. This is the first report of the existence of ALDH2*2 in the Indian population, and of a high frequency of ALDH2*2/*2 in Indian alcoholics.Wang et al. have developed a novel prediction method that employs genomic features related to the presence of regulatory elements to enable more accurate and efficient prediction of transcription factor binding sites (TFBSs). In their study, they used the transcription factor upstream stimulatory factor 1 (USF1) to evaluate the performance of this novel TFBS prediction method because of its known genetic association with coronary artery disease and the recent availability of USF1 chromatin immunoprecipitation microarray (ChIP-chip) results. This method can be also used for other transcription factors involved in human disease studies to help further our understanding of the biology of complex disease.An increased number of (TG/CA) repeats, especially in the first intron, have been suggestively associated with the regulation of the transcription of several cancer- and disease-related genes, including the genes encoding the epidermal growth factor receptor (EGFR), hydroxysteroid (11-beta) dehydrogenase 2 (HSD11B
Editorial
Vasilis Vasiliou
Human Genomics , 2008, DOI: 10.1186/1479-7364-3-1-1
Abstract: I would like to welcome David Ross, the new Associate Editor, and David Cooper, Larry Hunter and Carsten Wiuf as new members of the Editorial Board.The field of human genomics is rapidly evolving. Given this protean nature, we continue to be inclusive in coverage and not to provide a strict description of what the Journal will cover. We certainly do not feel in a position to predict which directions are likely to be the most promising in the coming years. It is therefore easier to recognise the kind of work that should be included rather than to define it.Obvious examples include the following:? Linkage disequilibrium association mapping of complex and multifactorial diseases and traits, and relevant methods? Comparative, functional and structural genomics? Assessment of the functional consequences of gene variations associated with disease and drug response? Biology of repetitive elements? Origin and divergence of human genes? Protein structure and human variation? Quantitative genetics and development? Epigenetics/epigenomics? Human variation and disease? Genomic redundancy? Human gene families? Statistical analyses of comparative genomics data? Regular updates on human genome completion and annotations? Human proteomicsIn this issue, the first of the re-launched Human Genomics, we are publishing one guest editorial, one review and five research papers, which are accompanied by a gene annotation update, a book review and a software review; the latter three will be regular features of the Journal.One of the most important challenges in human genomics is to localise and identify the genetic variation associated with disease phenotypes. Collins and colleagues open this issue with a guest editorial on candidate gene and genome-wide association studies of lung cancer.Mitochondria play a central role in critical metabolic pathways, apoptosis and ageing-related neurodegenerative diseases. Mancuso et al. present an impressive review on mitochondrial DNA sequence variation
Editorial
Vasilis Vasiliou
Human Genomics , 2009, DOI: 10.1186/1479-7364-4-1-1
Abstract: The reason why we have decided to proceed with six issues per year instead of the four that we had in Volume 3 is because of an increase in the number of submissions, as well as in the time and efforts of the members of the Editorial Board, which have been invaluable.We would like to welcome Richard G.H. Cotton (Genomic Disorders Research Centre, Howard Florey Institute; Human Variome Project, Australia) and Takashi Gojobori (National Institute of Genetics, Centre for Information Biology; DNA Data Bank of Japan National Institute of Genetics, Japan) to our Editorial Board. In addition, we have Tzu Lip Phang (Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Denver, CO, USA) as a Software Review Editor and Panagiotis A. Tsonis (Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, OH, USA) as a Book Review Editor.Starting with this issue, we have a new section that will include descriptions and/or reviews of Genome Databases; the first paper of this new feature is the description of the Cytochrome P450 Homepage, by David Nelson. This issue also includes an original research paper describing a regression-based approach to simultaneously use families and individuals combined to established association between a genetic marker and quantitative or binary trait. Also in this issue is a review of the use of pathway information in molecular epidemiology; Software Review Editor, Mike Weale, comments on how we can keep up to date in the rapidly changing world of genomic software; there is a review of Joram Piatigorsky's book Gene Sharing and, finally, in the Genome Review section, Brocker and colleagues explore the evolutionary divergence and functions of the ADAM and ADAMTS gene families.
The Aldehyde Dehydrogenase Gene Superfamily Resource Center
William Black, Vasilis Vasiliou
Human Genomics , 2009, DOI: 10.1186/1479-7364-4-2-136
Abstract: The completion of various genome projects and the growing trend towards high-throughput data production have created a significant knowledge base of molecular sequence data across a broad spectrum of species. This increase in available sequence information has led to a widening gap between the available raw sequence data and their functional analyses by molecular biological methods or other genetic approaches. As a consequence, the field of bioinformatics has rapidly developed as an essential aid for data analysis. A number of large-scale, gene-specific databases, including the National Center for Biotechnology Information (NCBI)'s Entrez Gene[1] and the European Bioinformatics Institute/Wellcome Trust Sanger Institute's Ensembl databases,[2] have developed to report and catalogue molecular sequence data. The intrinsic format of these databases in attempting to cover all genes for all species or to cover all genes for a given species (eg the mouse genome database[3]), however, has significant limitations. These include errors in sequence alignments due to a reliance on automated algorithms, poorly defined reference sequences and improper gene nomenclature. Other issues include lack of identification and/or categorisation of alternatively spliced transcriptional variants, as well as erroneous functional characterisations because generalised gene ontology entries do not distinguish the individual gene from other members of its gene superfamily. To address these limitations, we have developed a gene-specific database architecture and web-based scripting system which is tailored to report both the molecular sequence and functional data for all members of an individual gene superfamily across all species (Black and Vasiliou, manuscript in preparation). Using this software and relational database architecture, we have developed http://www.aldh.org webcite, a publicly available informational resource system for all members of the aldehyde dehydrogenase (ALDH) gene superfam
Human ATP-binding cassette (ABC) transporter family
Vasilis Vasiliou, Konstandinos Vasiliou, Daniel W Nebert
Human Genomics , 2009, DOI: 10.1186/1479-7364-3-3-281
Abstract: Membrane transport proteins can be divided into four types: ion channels; transporters; aquaporins; and ATP-powered pumps http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.figgrp.4031 webcite. Genes from all four categories are ancient -- with members present in most, if not all, prokaryotes, as well as in virtually all cell types of all eukaryotes. Transporters in eukaryotic cells move ions, sugars, amino acids and other molecules across all cellular and organelle membranes (cell surface, mitochondrial, endoplasmic reticulum, Golgi apparatus and other vesicles) -- with the possible exception of nuclear membranes (which have pores). The portion of the cell exposed to the lumen is called the apical surface; the rest of the cell (ie sides and base) makes up the basolateral surface. Movement of ions or other molecules into the cell is called influx; movement of ions or other molecules out of the cell is termed efflux.Membrane transport proteins can be either passive or active. Passive transporters (also called uni-porters or facilitative transporters) transport substrates down a concentration gradient. By contrast, active transporters (or cotransporters) couple the movement of one type of ion or molecule against its concentration gradient, to the movement of another ion or molecule down its concentration gradient. Like ATP pumps, cotransporters mediate coupled reactions in which an energetically unfavourable reaction is coupled to an energetically favourable reaction. When the transported molecule and cotransported ion move in the same direction across a membrane, the transporter is called a symporter; when they move in opposite directions, the transporter is called an antiporter (or exchanger). If the intracellular net charge following transport becomes more negative, the process is termed electronegative; if the intracellular net charge becomes more positive, the process is called electropositive; if the resulting intracellular net charge remains unchanged, the proce
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