Articles

Molecular Diagnostics: George P. Patrinos and Wilhelm J. Ansorge (eds) Elsevier (Academic Press); 2nd edn; 2010

Authors: Jean-Jacques Cassiman

In silicotoxicology models and databases as FDA Critical Path Initiative toolkits

In silico toxicology methods are practical, evidence-based and high throughput, with varying accuracy. In silico approaches are of keen interest, not only to scientists in the private sector and to academic resea...

Authors: Luis G Valerio Jr

Databases and resources for human small non-coding RNAs

Recent advances in high-throughput sequencing have facilitated the genome-wide studies of small non-coding RNAs (sRNAs). Numerous studies have highlighted the role of various classes of sRNAs at different leve...

Authors: Eneritz Agirre and Eduardo Eyras

The human fatty acid-binding protein family: Evolutionary divergences and functions

Fatty acid-binding proteins (FABPs) are members of the intracellular lipid-binding protein (iLBP) family and are involved in reversibly binding intracellular hydrophobic ligands and trafficking them throughout...

Authors: Rebecca L Smathers and Dennis R Petersen

Lysosomal storage disorders: Molecular basis and laboratory testing

Lysosomal storage disorders (LSDs) are a large group of more than 50 different inherited metabolic diseases which, in the great majority of cases, result from the defective function of specific lysosomal enzym...

Authors: Mirella Filocamo and Amelia Morrone

Difficulties in finding DNA mutations and associated phenotypic data in web resources using simple, uncomplicated search terms, and a suggested solution

DNA mutation data currently reside in many online databases, which differ markedly in the terminology used to describe or define the mutation and also in completeness of content, potentially making it difficul...

Authors: Elizabeth A Webb, Timothy D Smith and Richard GH Cotton

Editorial

Authors: Vasilis Vasiliou

Evidence and Evolution: The logic behind the science: Elliott Sober Cambridge University Press, Cambridge, UK; 2008;

Authors: Christian P. Robert

RGD: A comparative genomics platform

The Rat Genome Database (RGD) (http://​rgd.​mcw.​edu) provides a comprehensive platform for comparative genomics and genetics research. RGD houses gene, QTL and...

Authors: Mary Shimoyama, Jennifer R. Smith, Tom Hayman, Stan Laulederkind, Tim Lowry, Rajni Nigam, Victoria Petri, Shur-Jen Wang, Melinda Dwinell and Howard Jacob

A short survey of computational analysis methods in analysing ChIP-seq data

Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computati...

Authors: Hyunmin Kim, Jihye Kim, Heather Selby, Dexiang Gao, Tiejun Tong, Tzu Lip Phang and Aik Choon Tan

Transient receptor potential (TRP) gene superfamily encoding cation channels

Transient receptor potential (TRP) non-selective cation channels constitute a superfamily, which contains 28 different genes. In mammals, this superfamily is divided into six subfamilies based on differences i...

Authors: Zan Pan, Hua Yang and Peter S Reinach

Exploring the potential relevance of human-specific genes to complex disease

Although human disease genes generally tend to be evolutionarily more ancient than non-disease genes, complex disease genes appear to be represented more frequently than Mendelian disease genes among genes of ...

Authors: David N Cooper and Hildegard Kehrer-Sawatzki

Naming 'junk': Human non-protein coding RNA (ncRNA) gene nomenclature

Previously, the majority of the human genome was thought to be 'junk' DNA with no functional purpose. Over the past decade, the field of RNA research has rapidly expanded, with a concomitant increase in the nu...

Authors: Mathew W. Wright and Elspeth A. Bruford

Ancestry-informative markers on chromosomes 2, 8 and 15 are associated with insulin-related traits in a racially diverse sample of children

Type 2 diabetes represents an increasing health burden. Its prevalence is rising among younger age groups and differs among racial/ethnic groups. Little is known about its genetic basis, including whether ther...

Authors: Yann C. Klimentidis, Jasmin Divers, Krista Casazza, T. Mark Beasley, David B. Allison and Jose R. Fernandez

Research Highlights

Authors: Robert I Scheinman

Changes in Human Genomics

Authors: Vasilis Vasiliou

Vogel and Motulsky's human genetics-problems and approaches: Michael Speicher, Stylianos E. Antonarakis, Arno G. Motulsky (eds)

Authors: Madhuri Kango-Singh

A useful tool for drug interaction evaluation: The University of Washington Metabolism and Transport Drug Interaction Database

The Metabolism and Transport Drug Interaction Database (http://​www.​druginteractioni​nfo.​org) is a web-based research and analysis tool developed in the Depart...

Authors: Houda Hachad, Isabelle Ragueneau-Majlessi and René H Levy

A survey of statistical software for analysing RNA-seq data

High-throughput RNA sequencing is rapidly emerging as a favourite method for gene expression studies. We review three software packages -- edgeR, DEGseq and baySeq -- from Bioconductor

Authors: Dexiang Gao, Jihye Kim, Hyunmin Kim, Tzu L Phang, Heather Selby, Aik Choon Tan and Tiejun Tong

Evolutionary divergence and functions of the human interleukin (IL) gene family

Cytokines play a very important role in nearly all aspects of inflammation and immunity. The term 'interleukin' (IL) has been used to describe a group of cytokines with complex immunomodulatory functions -- in...

Authors: Chad Brocker, David Thompson, Akiko Matsumoto, Daniel W Nebert and Vasilis Vasiliou

What the papers say: Text mining for genomics and systems biology

Keeping up with the rapidly growing literature has become virtually impossible for most scientists. This can have dire consequences. First, we may waste research time and resources on reinventing the wheel sim...

Authors: Nathan Harmston, Wendy Filsell and Michael PH Stumpf

Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis

Breast cancer tumours among African Americans are usually more aggressive than those found in Caucasian populations. African-American patients with breast cancer also have higher mortality rates than Caucasian...

Authors: Herbert Pang, Keita Ebisu, Emi Watanabe, Laura Y Sue and Tiejun Tong

Prospects for the automated extraction of mutation data from the scientific literature

Authors: Peter D Stenson and David N Cooper

KinSNP software for homozygosity mapping of disease genes using SNP microarrays

Consanguineous families affected with a recessive genetic disease caused by homozygotisation of a mutation offer a unique advantage for positional cloning of rare diseases. Homozygosity mapping of patient geno...

Authors: El-Ad David Amir, Ofer Bartal, Efrat Morad, Tal Nagar, Jony Sheynin, Ruti Parvari and Vered Chalifa-Caspi

A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation

Copy number variants (CNVs) create a major source of variation among individuals and populations. Array-based comparative genomic hybridisation (aCGH) is a powerful method used to detect and compare the copy n...

Authors: Anis Karimpour-Fard, Laura Dumas, Tzulip Phang, James M Sikela and Lawrence E Hunter

Color Atlas of Pharmacology: Heinz Lüllmann, Klaus Mohr, Lutz Hein and Detlef Bieger

Authors: Maria Konstandi

ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research -- an update

ArrayTrack™is a Food and Drug Administration (FDA) bioinformatics tool that has been widely adopted by the research community for genomics studies. It provides an integrated environment for microarray data man...

Authors: Joshua Xu, Reagan Kelly, Hong Fang and Weida Tong

Evolutionary divergence and functions of the human acyl-CoA thioesterase gene (ACOT) family

The acyl-CoA thioesterase gene (ACOT) family encodes enzymes that catalyse the hydrolysis of acyl-CoA thioester compounds, also known as activated fatty acids, to their corresponding non-esterified (free) fatty a...

Authors: Chad Brocker, Christopher Carpenter, Daniel W Nebert and Vasilis Vasiliou

Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides

The cytosine-guanine (CpG) dinucleotide has long been known to be a hotspot for pathological mutation in the human genome. This hypermutability is related to its role as the major site of cytosine methylation ...

Authors: David N Cooper, Matthew Mort, Peter D Stenson, Edward V Ball and Nadia A Chuzhanova

Intronic polymorphisms of cytochromes P450

The cytochrome P450 enzymes active in drug metabolism are highly polymorphic. Most allelic variants have been described for enzymes encoded by the cytochrome P450 family 2 (CYP2) gene family, which has 252 dif...

Authors: Magnus Ingelman-Sundberg and Sarah C Sim

An isolated case of lissencephaly caused by the insertion of a mitochondrial genome-derived DNA sequence into the 5' untranslated region of the PAFAH1B1(LIS1) gene

A 130 base pair (bp) insertion (g.-8delCins130) into the 5' untranslated region of the PAFAH1B1 (LIS1) gene, seven nucleotides upstream of the translational initiation site, was detected in an isolated case of li...

Authors: David S Millar, Carolyn Tysoe, Lazarus P Lazarou, Daniela T Pilz, Shehla Mohammed, Katharine Anderson, Nadia Chuzhanova, David N Cooper and Rachel Butler

Endothelial nitric oxide synthase gene polymorphisms -786T >C and 894G >Tin coronary artery bypass graft surgery patients

Polymorphisms in the endothelial nitric oxide synthase (eNOS) gene (-786T >C and 894G >T) enhance endo-thelial dysfunction and have been studied in relation to coronary artery disease (CAD). In the present study,...

Authors: Georgia Ragia, Eleftherios Nikolaidis, Anna Tavridou, Kostas I Arvanitidis, Stavroula Kanoni, George V Dedoussis, George Bougioukas and Vangelis G Manolopoulos

General considerations for integrating pharmacogenomics into mainstream medical practice

Authors: George P Patrinos

The Machinery of Life: David S. Goodsell 2nd edn., 2009 Springer-Verlag, London

Authors: Tina Toni

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

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 fac...

Authors: Sjozef van Baal, Joël Zlotogora, George Lagoumintzis, Vassiliki Gkantouna, Ioannis Tzimas, Konstantinos Poulas, Athanassios Tsakalidis, Giovanni Romeo and George P Patrinos

A survey of current software for network analysis in molecular biology

Software for network motifs and modules is briefly reviewed, along with programs for network comparison. The three major software packages for network analysis, CYTOSCAPE, INGENUITY and PATHWAY STUDIO, and the...

Authors: Sterling Thomas and Danail Bonchev

Update of human and mouse forkhead box (FOX) gene families

The forkhead box (FOX) proteins are transcription factors that play complex and important roles in processes from development and organogenesis to regulation of metabolism and the immune system. There are 50 FOX ...

Authors: Brian C. Jackson, Christopher Carpenter, Daniel W. Nebert and Vasilis Vasiliou

The other lives of ribosomal proteins

Despite the fact that ribosomal proteins are the constituents of an organelle that is present in every cell, they show a surprising level of regulation, and several of them have also been shown to have other e...

Authors: Rital B. Bhavsar, Leah N. Makley and Panagiotis A. Tsonis

Gene-environment interaction tests for family studies with quantitative phenotypes: A review and extension to longitudinal measures

Longitudinal studies are an important tool for analysing traits that change over time, depending on individual characteristics and environmental exposures. Complex quantitative traits, such as lung function, m...

Authors: Hortensia Moreno-Macias, Isabelle Romieu, Stephanie J London and Nan M Laird

Characterisation of a functional intronic polymorphism in the human growth hormone (GHI) gene

The +1169A allele of the A/T single nucleotide polymorphism (SNP; rs2665802), located within intron 4 of the human growth hormone I (GHI) gene, has been associated with reduced levels of circulating GH and insuli...

Authors: David S. Millar, Martin Horan, Nadia A. Chuzhanova and David N. Cooper

Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes

Authors: David N. Cooper

From DNA to proteins via the ribosome: Structural insights into the workings of the translation machinery

Understanding protein synthesis in bacteria and humans is important for understanding the origin of many human diseases and devising treatments for them. Over the past decade, the field of structural biology h...

Authors: Xabier Agirrezabala and Joachim Frank

Metagenomics: Theory, Methods, and Applications: Edited by Diana Marco Caister Academic Press, Norfolk, UK; 2010

Authors: Zissis C. Chroneos

The Human Cytochrome P450 (CYP) Allele Nomenclature website: a peer-reviewed database of CYP variants and their associated effects

Pharmacogenetics affects both pharmacokinetics and pharmacodynamics, thereby influencing an individual's response to drugs, both in terms of response and adverse reactions. Within the area of pharmacogenetics,...

Authors: Sarah C Sim and Magnus Ingelman-Sundberg

State of the art de novoassembly of human genomes from massively parallel sequencing data

Recent studies in human genomes have demonstrated the use of de novo assemblies to identify genetic variations that are difficult for mapping-based approaches. Construction of multiple human genome assemblies is ...

Authors: Yingrui Li, Yujie Hu, Lars Bolund and Jun Wang

Krüppel-like factors: Three fingers in control

Krüppel-like factors (KLFs), members of the zinc-finger family of transcription factors capable of binding GC-rich sequences, have emerged as critical regulators of important functions all over the body. They ...

Authors: Shivalingappa K Swamynathan

Hyperferritinaemia-cataract syndrome: Worldwide mutations and phenotype of an increasingly diagnosed genetic disorder

The hereditary hyperferritinaemia-cataract syndrome (HHCS) is characterised by an autosomal dominant cataract and high levels of serum ferritin without iron overload. The cataract develops due to L-ferritin de...

Authors: Gunda Millonig, Martina U Muckenthaler and Sebastian Mueller

The clinical application of UGT1A1pharmacogenetic testing: Gene-environment interactions

Over the past decade, the number of pharmacogenetic tests has increased considerably, allowing for the development of our knowledge of their clinical application. The uridine diphosphate glucuronosyltransferas...

Authors: Sara Correia Marques and Ogechi N Ikediobi

The clinical pharmacogeneticist: An emerging regulatory scientist at the US Food and Drug Administration

Authors: Issam Zineh and Janet Woodcock

Highlights of the 'Gene Nomenclature Across Species' Meeting

The first 'Gene Nomenclature Across Species' meeting was held on 12th and 13th October 2009, at the Møller Centre in Cambridge, UK. This meeting, organised and hosted by the HUGO Gene Nomenclature Committee (H...

Authors: Elspeth A Bruford