Volume 5
Volume 4
GUEST EDITORIAL: VISIONARY GENOMICS: J. Mark Petrash, Philip A. Ruzycki, Gregory J. Zablocki, Department of Ophthalmology, University of Colorado School of Medicine
RESEARCH PAPER:
Role of CYP2E1 genotypes in susceptibility to colorectal cancer in the Kashmiri population
A. Syed Sameer, Saniya Nissar, Qurteeba Qadri, Shafia Alam, Shahid Mudasir Baba, Mushtaq A. Siddiqi, Department of Immunology and Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences
RESEARCH PAPER: Systems biology-based analysis implicates a novel role for vitamin D metabolism in the pathogenesis of age-related macular degeneration
Margaux A. Morrison, Alexandra C. Silveira, Nancy Huynh, Sato, Stephanie Loomis, Michael T. Andreoli, Scott M. Adams, Margaret M. DeAngelis, Ocular Molecular Genetics Institute, Harvard Medical School, Gyungah Jun, Departments of Medicine (Section of Biomedical Genetics), Ophthalmology and Biostatistics, Boston University Schools of Medicine and Public Health, Silvia E. Smith, Gregory S. Hageman, Department of Ophthalmology and Visual Sciences, University of Utah, Fani Zacharaki, Aristoteles N. Tsiloulis, Dimitrios Z. Chatzoulis, Maria G. Kotoula, Evangelia E. Tsironi, Department of Ophthalmology, University of Thessaly School of Medicine, Hajime Monte J. Radeke, Center for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Austin S. Jelcick, Yang Yuan, Neena B. Haider, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Giuliana Silvestri, Centre for Vision and Vascular Science, Queen's University, Belfast, Bruce W. Hollis, Pediatric Nutritional Sciences, Medical University of South Carolina, Rui Chen, Department of Molecular and Human Genetics, Baylor College of Medicine, Joan W. Miller, Ivana K. Kim, Retina Service, Harvard Medical School, Lindsay A. Farrer, Departments of Medicine (Section of Biomedical Genetics), Ophthalmology and Biostatistics, Neurology, Epidemiology, Boston University Schools of Medicine and Public Health, Debra A. Schaumberg, Division of Preventive Medicine, Brigham and Women's Hospital and the Department of Ophthalmology, Harvard Medical School
RESEARCH PAPER: The role of ALDH2 and ADH1B polymorphism in alcohol consumption and stroke in Han Chinese
Chung-Tay Yao, Department of Surgery, Cathay General Hospital, Chun-An Cheng, Giia-Sheun Peng, Department of Neurology, Tri-Service General Hospital, Taipei, Hsu-Kun Wang, Department of Biochemistry and Molecular Genetics, University of Alabama, Shao-Wen Chiu, Healthcare Business Division, InfoExplorer Co, Yi-Chyan Chen, Department of Psychiatry, Tri-Service General Hospital, Taipei, Ming-Fang Wang, Shih-Jiun Yin, Department of Biochemistry, National Defense Medical Center, Taipei
REVIEW ARTICLE: Human genetics and genomics a decade after the release of the draft sequence of the human genome
Nasheen Naidoo, Chee-Seng Ku, Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Yudi Pawitan, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Richie Soong, Cancer Science Institute of Singapore, National University of Singapore, David N. Cooper, Institute of Medical Genetics, School of Medicine, Cardiff University
REVIEW ARTICLE: Neurofibromatosis type 1-associated tumours: Their somatic mutational spectrum and pathogenesis
Sebastian Laycock-van Spyk, Nick Thomas, David N. Cooper, Meena Upadhyaya, Institute of Medical Genetics, School of Medicine, Cardiff University
GENOME UPDATE: Update of the human secretoglobin (SCGB) gene superfamily and an example of ‘evolutionary bloom’ of androgen-binding protein genes within the mouse Scgb gene superfamily
Brian C. Jackson, Vasilis Vasiliou, Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, David C. Thompson, Department of Clinical Pharmacy, University of Colorado Anschutz Medical Center, Mathew W. Wright, HUGO Gene Nomenclature Committee (HGNC), EMBL-EBI, Monica McAndrews, The Jackson Laboratory, Mouse Genome Informatics, Alfred Bernard, Unit of Toxicology and Applied Pharmacology, Catholic University of Louvain, Daniel W. Nebert, Department of Environmental Health and Center for Environmental Genetics (CEG), University of Cincinnati Medical Center
SOFTWARE REVIEW: Overview of biological database mapping services for interoperation between different ‘omics’ datasets
Shweta S. Chavan, University of Arkansas Little Rock (UALR)/University of Arkansas Medical Sciences (UAMS) Joint Bioinformatics Program, John D. Shaughnessy, Ricky D. Edmondson, Myeloma Institute for Research and Therapy, UAMS
GENOME DATABASE: In-silico human genomics with GeneCards
G
il Stelzer, Irina Dalah, Tsippi Iny Stein, Yigeal Satanower, Naomi Rosen, Noam Nativ, Danit Oz-Levi, Tsviya Olender, Frida Belinky, Iris Bahir, Hagit Krug, Doron Lancet Marilyn Safran, Department of Molecular Genetics, Weizmann Institute of Science, Paul Perco, Emergentec Biodevelopment, Bernd Mayer, Institute for Theoretical Chemistry, University of Vienna, Eugene Kolker Seattle Children's Research Institute, Seattle Children's Hospital, and Informatics Department, School of Medicine, University of Washington
RESEARCH HIGHLIGHTS: Robert Scheinman, University of Colorado Anschutz Medical Campus
EDITORIAL: Human Genomics begins ePub ahead of print and a discussion forum Aiming to Bridge Academia with the Pharmaceutical Industry: Vasilis Vasiliou, University of Colorado Denver
RESEARCH PAPER: Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration
Gregory S. Hageman, Margaret M. DeAngelis, Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Karen Gehrs, The Center for Macula and Retinal Disease Serguei Lejnine, Bioguidance Consultants, Aruna T. Bansal, Acclarogen, Robyn H. Guymer, Paul N. Baird, Centre for Eye Research Australia, Royal Victorian Eye & Ear Hospital, University of Melbourne, Rando Allikmets, Departments of Ophthalmology and Pathology and Cell Biology, Columbia University, Cosmin Deciu, Paul Oeth, Sequenom Center for Molecular Medicine, Lorah T. Perlee, Sequenom
RESEARCH PAPER: Analysis of molecular aberrations of Wnt pathway gladiators in colorectal cancer in the Kashmiri population
A. Syed Sameer, Zaffar A. Shah, Safiya Abdullah, Mushtaq A. Siddiqi, Department of Immunology and Molecular Medicine, Nissar A. Chowdri, Department of General Surgery, Sher-I-Kashmir Institute of Medical Sciences
RESEARCH PAPER: Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations
Guojie Zhang, Zhang Pei, Bioinformatics Department, Beijing Genomics Institute at Shenzhen, Edward V. Ball, Matthew Mort, David N. Cooper, Institute of Medical Genetics, School of Medicine, Cardiff University, Hildegard Kehrer-Sawatzki, Institute of Human Genetics, University of Ulm
GENOME UPDATE: The human sirtuin family: Evolutionary divergences and functions
Athanassios Vassilopoulos, Department of Radiation Oncology, David Gius, Departments of Cancer Biology, Pediatric and Radiation Oncology, Vanderbilt University Medical Center, Kristofer S. Fritz, Dennis R. Petersen, Department of Pharmaceutical Sciences, University of Colorado Denver
SOFTWARE REVIEW: Survey of public domain software for docking simulations and virtual screening
Jacek Biesiada, Prakash Velayutham, Michal Kouril, Biomedical Informatics, Children's Hospital Research Foundation, Aleksey Porollo, Department of Environmental Health, University of Cincinnati College of Medicine, Jaroslaw Meller, Department of Informatics, Nicholas Copernicus University
GENOME DATABASE: e-PKGene: A knowledge-based research tool for analysing the impact of genetics on drug exposure
Houda Hachad, Sophie Argon, Catherine K. Yeung, Isabelle Ragueneau-Majlessi, René H. Levy, Department of Pharmaceutics, University of Washington, Casey Lynnette Overby, Department of Medical Education and Biomedical Informatics, University of Washington
RESEARCH HIGHLIGHTS: Robert Scheinman, University of Colorado Anschutz Medical Campus
BOOK REVIEW: "Outsmart Your Genes: How Understanding Your DNA Will Empower You to Protect Yourself Against Cancer, Alzheimer's, Heart Disease, Obesity, and Many Other Conditions”
Reviewed by Jean-Jacques Cassiman, Center for Human Genetics, KULeuven
EDITORIAL: Vasilis Vasiliou, University of Colorado Denver
RESEARCH PAPER: Inter-chromosomal variation in the pattern of human population genetic structure
Tesfaye M. Baye, Department of Pediatrics, Cincinnati Children's Hospital Medical Center
RESEARCH PAPER: A meta-analysis of single base-pair substitutions in translational termination codons (‘nonstop’ mutations) that cause human inherited disease
Stephen E. Hamby, Nadia Chuzhanova, School of Science and Technology, Nottingham Trent University, Nick S. T. Thomas and David N. Cooper, Institute of Medical Genetics, School of Medicine, Cardiff University
RESEARCH PAPER: Analysis of pharmacogenetic traits in two distinct South African populations
Ogechi Ikediobi, School of Pharmacy, Department of Clinical Pharmacy, Bradley Aouizerat, Institute for Human Genetics, Yuanyuan Xiao, Center for Bioinformatics and Molecular Biostatistics, Monica Gandhi, School of Medicine, University of California, San Francisco, Stefan Gebhardt, Department of Obstetrics and Gynaecology and Louise Warnich, Department of Genetics, Stellenbosch University
GENOME UPDATE: Update on the aldehyde dehydrogenase gene (ALDH) superfamily
Brian Jackson, Chad Brocker, William Black, Konstandinos Vasiliou, Vasilis Vasiliou, Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Center, David C. Thompson, Department of Clinical Pharmacy, University of Colorado Anschutz Medical Center and Daniel W. Nebert, Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati
SOFTWARE REVIEW: A review of software for microarray genotyping
Philippe Lamy, Bioinformatics Research Centre and Department of Molecular Medicine, Aarhus University Hospital, Jakob Grove Department of Human Genetics, Aarhus University and Carsten Wiuf, Bioinformatics Research Centre
GENOME DATABASE: Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters
Bijay Jassal, European Bioinformatics Institute
RESEARCH HIGHLIGHTS: Robert Scheinman, University of Colorado Anschutz Medical Campus
BOOK REVIEW: Designer Genes: A New Era in the Evolution of Man by Steven Potter
Daniel W. Nebert, Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati
EDITORIAL: Vasilis Vasiliou, University of Colorado Denver
RESEARCH PAPER: Difficulties in finding DNA mutations and associated phenotypic data in World Wide Web resources using simple, uncomplicated search terms and a suggested solution
Elizabeth A. Webb, Timothy D. Smith, Richard G.H. Cotton, Genomic Disorders Research Centre
REVIEW ARTICLE: Lysosomal disorders: Molecular basis and laboratory testing
Mirella Filocamo, S.S.D. Lab. Diagnosi Pre-Postnatale Malattie Metaboliche, Dipartimento di Neuroscienze, IRCCS G. Gaslini and Amelia Morrone, Clinic of Pediatric Neurology, Department of Sciences for Woman and Child's Health, University of Florence
GENOME UPDATE: The human fatty acid-binding protein family: Evolutionary divergences and functions
Rebecca L. Smathers and Dennis R. Petersen, Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver
SOFTWARE REVIEW: Databases and resources for human small non-coding RNAs
Eneritz Agirre Universitat Pompeu Fabra, Eduardo Eyras, Institució Catalana de Recerca i Estudis Avançats (ICREA)
GENOME DATABASE: In silico toxicology models and databases as critical path toolkits
Luis G. Valerio, Office of Pharmaceutical Science, Center for Drug Evaluation and Research, U.S. Food and Drug Administration
RESEARCH HIGHLIGHTS: Robert Scheinman, University of Colorado Anschutz Medical Campus
BOOK REVIEW: "Molecular diagnostics” edited by George P. Patrinos and Wilhelm J. Ansorge
Reviewed by Jean-Jacques Cassiman, Center for Human Genetics, KULeuven
EDITORIAL: Changes in Human Genomics
Vasilis Vasiliou, University of Colorado Denver
RESEARCH PAPER: Ancestry-informative markers on chromosomes 2, 8 and 15 are associated with the insulin-related traits in a racially diverse sample of children
Yann C. Klimentidis, T. Mark Beasley, Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Jasmin Divers, Department of Biostatistical Sciences, Wake Forest University Health Sciences, Krista Casazza, David B. Allison and Jose R. Fernandez, Department of Nutrition Sciences, University of Alabama at Birmingham
REVIEW ARTICLE: Naming 'junk': Human non-protein coding RNA (ncRNA) gene nomenclature
Matthew Wright and Elspeth A. Bruford, HUGO Gene Nomenclature Committee
REVIEW ARTICLE: Exploring the potential relevance of human-specific genes to complex disease
David N. Cooper, Institute of Medical Genetics, School of Medicine, Cardiff University and Hildegard Kehrer-Sawatzki, Institute of Human Genetics, University of Ulm
GENOME UPDATE: Transient receptor potential (TRP) gene superfamily encoding cation channels
Zan Pan, Margaret Dyson Vision Institute, Weill Cornell Medical College, Hua Yang and Peter S. Reinach, Department of Biological Science, State University of New York
SOFTWARE REVIEW: A short survey of computational analysis methods in analysing ChIP-seq data
Hyunmin Kim, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Jihye Kim, Heather Selby, Aik Choon Tan, Division of Medical Oncology, University of Colorado School of Medicine, Dexiang Gao, Department of Biostatistics and Informatics, University of Colorado School of Public Health, Tiejun Tong, Department of Applied Mathematics, University of Colorado and Tzu Lip Phang, Division of Critical Care and Pulmonary, Department of Medicine, University of Colorado School of Medicine
GENOME DATABASE: RGD: A comparative genomics platform
Mary Shimoyama, Jennifer R. Smith, Howard Jacob, Melinda Dwinell, Tom Hayman, Stan Laulederkind, Tim Lowry, Victoria Petri, Rajni Nigam and Shur-Jen Wang, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin
RESEARCH HIGHLIGHTS: Robert Scheinman, University of Colorado Anschutz Medical Campus
BOOK REVIEW: "Evidence and Evolution: The Logic Behind the Science" by Elliott Sobert
Reviewed by Christian P. Robert
GUEST EDITORIAL: Prospects for the automated extraction of mutation data from the scientific literature
Peter D. Stenson and David N. Cooper, Institute of Medical Genetics, School of Medicine, Cardiff University
RESEARCH PAPER: Analysing breast cancer microarrays of African-Americans using shrinkage-based discriminant analysis
Herbert Pang, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Keita Ebisu, School of Forestry & Environmental Studies, Yale University,Emi Watanabe, Department of Epidemiology and Public Health, Yale University School of Medicine, Laura Y. Sue, Division of Cancer Epidemiology and Genetics, National Cancer Institute and Tiejun Tong, Department of Applied Mathematics, University of Colorado at Boulder
REVIEW ARTICLE: What the papers say: Text mining for genomics and systems biology
Nathan Harmston, Wendy Filsell, Michael P.H. Stumpf, Division of Molecular Biosciences, Centre for Bioinformatics, Imperial College London
GENOME UPDATE: Update on gene completions and annotations: Evolutionary divergence and functions of the human interleukin (IL) gene family
Chad Brocker, Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, David Thompson, Department of Clinical Practice, Vasilis Vasiliou, Professor & Director of Toxicology Graduate Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Daniel W. Nebert, Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center
SOFTWARE REVIEW: A survey of statistical software for analyzing RNA-seq data
Dexiang Gao, Department of Pediatrics, Jihye Kim, Heather Selby, Aik Choon Tan, Division of Medical Oncology, Hyunmin Kim, Department of Biochemistry and Molecular Genetics, Tzu L. Phang, Division of Critical Care and Pulmonary, Department of Medicine and Tiejun Tong, Department of Applied Mathematics, University of Colorado, Boulder
GENOME DATABASE: A useful tool for drug interaction evaluation: The University of Washington Metabolism & Transport Drug Interaction Database
Houda Hachad, Metabolism and Transport Drug Interaction Database, Isabelle Ragueneau-Majlessi, Drug Interaction Database Program and René H. Levy, Department of Pharmaceutics, University of Washington
BOOK REVIEW: Vogel and Motulsky's Human Genetics: Problems and Approaches
Madhuri Kango-Singh, Department of Biology, University of Dayton