Articles
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Citation: Human Genomics 2010 5:73
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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...
Citation: Human Genomics 2010 5:61 -
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
Citation: Human Genomics 2010 5:56 -
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...
Citation: Human Genomics 2010 5:30 -
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...
Citation: Human Genomics 2010 5:17 -
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...
Citation: Human Genomics 2010 5:5 -
Prospects for the automated extraction of mutation data from the scientific literature
Citation: Human Genomics 2010 5:1 -
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...
Citation: Human Genomics 2010 4:394 -
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...
Citation: Human Genomics 2010 4:421 -
Color Atlas of Pharmacology: Heinz Lüllmann, Klaus Mohr, Lutz Hein and Detlef Bieger
Citation: Human Genomics 2010 4:435 -
ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research -- an update
ArrayTrackâ„¢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...
Citation: Human Genomics 2010 4:428 -
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...
Citation: Human Genomics 2010 4:411 -
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 ...
Citation: Human Genomics 2010 4:406 -
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...
Citation: Human Genomics 2010 4:402 -
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...
Citation: Human Genomics 2010 4:384 -
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,...
Citation: Human Genomics 2010 4:375 -
General considerations for integrating pharmacogenomics into mainstream medical practice
Citation: Human Genomics 2010 4:371 -
The Machinery of Life: David S. Goodsell 2nd edn., 2009 Springer-Verlag, London
Citation: Human Genomics 2010 4:369 -
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...
Citation: Human Genomics 2010 4:361 -
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...
Citation: Human Genomics 2010 4:353 -
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 ...
Citation: Human Genomics 2010 4:345 -
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...
Citation: Human Genomics 2010 4:327 -
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...
Citation: Human Genomics 2010 4:302 -
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...
Citation: Human Genomics 2010 4:289 -
Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes
Citation: Human Genomics 2010 4:284 -
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...
Citation: Human Genomics 2010 4:226 -
Metagenomics: Theory, Methods, and Applications: Edited by Diana Marco Caister Academic Press, Norfolk, UK; 2010
Citation: Human Genomics 2010 4:282 -
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,...
Citation: Human Genomics 2010 4:278 -
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 ...
Citation: Human Genomics 2010 4:271 -
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 ...
Citation: Human Genomics 2010 4:263 -
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...
Citation: Human Genomics 2010 4:250 -
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...
Citation: Human Genomics 2010 4:238 -
The clinical pharmacogeneticist: An emerging regulatory scientist at the US Food and Drug Administration
Citation: Human Genomics 2010 4:221 -
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...
Citation: Human Genomics 2010 4:213 -
Pharmaceutical biotechnology - concepts and applications: Walsh Gary Wiley, Chichester, West Sussex, UK
Citation: Human Genomics 2010 4:218 -
The CATH database
The CATH database provides hierarchical classification of protein domains based on their folding patterns. Domains are obtained from protein structures deposited in the Protein Data Bank and both domain identi...
Citation: Human Genomics 2010 4:207 -
An introduction to effective use of enrichment analysis software
In recent years, there has been an explosion in the range of software available for annotation enrichment analysis. Three classes of enrichment algorithms and their associated software implementations are intr...
Citation: Human Genomics 2010 4:202 -
Update of human and mouse matrix metalloproteinase families
Matrix metalloproteinases (MMPs) are a family of zinc proteases that degrade most of the components of the extracellular matrix (ECM). MMPs also have a number of non-traditional roles in processing factors rel...
Citation: Human Genomics 2010 4:194 -
Maternal transmission of Alzheimer's disease: Prodromal metabolic phenotype and the search for genes
After advanced age, having a parent affected with Alzheimer's disease (AD) is the most significant risk factor for developing AD among cognitively normal (NL) individuals. Although rare genetic mutations have ...
Citation: Human Genomics 2010 4:170 -
Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients
Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial...
Citation: Human Genomics 2010 4:147 -
Response to Stenson et al. in Human GenomicsVol. 4, No. 2, pp. 69-72: 'The Human Gene Mutation Database: Providing a comprehensive central mutation database for molecular diagnostics and personalised genomics'
Citation: Human Genomics 2010 4:145 -
Neuroscience of birdsong: Cambridge University Press, Cambridge, H Philip Zeigler and Peter Marler
Citation: Human Genomics 2009 4:143 -
The Aldehyde Dehydrogenase Gene Superfamily Resource Center
The website http://​www.​aldh.​org is a publicly available database for nomenclature and functional and molecular sequence information for members of the aldehy...
Citation: Human Genomics 2009 4:136 -
R and Bioconductor solutions for alternative splicing detection
The detection of alternative splicing using microarray technology involves multiple computational steps: normalisation, filtering, detection and visualisation. In this review, these analyses are approached usi...
Citation: Human Genomics 2009 4:131 -
The mammalian aldehyde oxidase gene family
Aldehyde oxidases (EC 1.2.3.1) are a small group of structurally conserved cytosolic proteins represented in both the animal and plant kingdoms. In vertebrates, aldehyde oxidases constitute the small sub-famil...
Citation: Human Genomics 2009 4:119 -
Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents
Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs), which form the largest multigene family in vertebrates. Identificatio...
Citation: Human Genomics 2009 4:107 -
Cholinesterase inhibitors in Alzheimer's disease and Lewy body spectrum disorders: the emerging pharmacogenetic story
This review provides an update on the current state of pharmacogenetic research in the treatment of Alzheimer's disease (AD) and Lewy body disease (LBD) as it pertains to the use of cholinesterase inhibitors (...
Citation: Human Genomics 2009 4:91 -
Identifying positive selection candidate loci for high-altitude adaptation in Andean populations
High-altitude environments (>2,500 m) provide scientists with a natural laboratory to study the physiological and genetic effects of low ambient oxygen tension on human populations. One approach to understandi...
Citation: Human Genomics 2009 4:79 -
Detecting genes contributing to longevity using twin data
Searching for genes contributing to longevity is a typical task in association analysis. A number of methods can be used for finding this association -- from the simplest method based on the technique of conti...
Citation: Human Genomics 2009 4:73 -
The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalised genomics
Citation: Human Genomics 2009 4:69
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