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We present a set of statistical methods for the analysis of DNA methylation microarray data, which account for tumor purity. These methods are an extension of our previously developed method for purity estimat...
Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenoty...
Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the i...
Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is dif...
Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. Th...
The director of the Montreal Neurological Institute (MNI), Guy Rouleau, discusses the recent announcement that the MNI will be completely committed to open science.
Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illnes...
The Correction to this article has been published in Genome Biology 2018 19:49
In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatme...
The original article was published in Genome Biology 2016 17:192
The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet...
The original article was published in Genome Biology 2013 14:3097
Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different co...
The Erratum to this article has been published in Genome Biology 2017 18:154
We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele freque...
A report on the Genome Informatics conference, held at the Wellcome Genome Campus Conference Centre, Hinxton, United Kingdom, 19–22 September 2016.
Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive d...
Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosi...
Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects l...
Alternative splice isoforms are common and important and have been shown to impact many human diseases. A new study by Nellore et al. offers a comprehensive study of splice junctions in humans by re-analyzing ...
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on ...
The Erratum to this article has been published in Genome Biology 2017 18:41
The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticate...
Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuin...
The original article was published in Genome Biology 2015 16:126
The original article was published in Genome Biology 2016 17:238
In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration...
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated an...
A new study of disorders of sex development presents an improved targeted next-generation sequencing approach for their diagnosis.
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective con...
The original article was published in Genome Biology 2016 17:239
The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated ...
Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inf...
The 10th anniversary ‘Genomics of Common Diseases’ meeting was held in Baltimore, September 25-28, 2016. Professor Chris Haley reports from the meeting on progress and challenges in the field.
Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. Th...
A report on the Wellcome Trust Conference on Computational RNA Biology, held in Hinxton, UK, on 17–19 October 2016.
Understanding the link between non-coding sequence variants, identified in genome-wide association studies, and the pathophysiology of complex diseases remains challenging due to a lack of annotations in non-c...
The original article was published in Genome Biology 2016 17:218
Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, a...
Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate ...
The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; ye...
A new study on sex chromosome evolution in papaya helps to illuminate sex chromosome biology, including deviations from expected trajectories.
Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients recei...
Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge...
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing st...
The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were u...
The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying differe...
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize k...
The Erratum to this article has been published in Genome Biology 2016 17:256
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely...
The Erratum to this article has been published in Genome Biology 2016 17:262
Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene–environment interactions. Whole genome sequence analysis of amino acid levels may ...
Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some rib...
The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign “disease mutations” are difficult to analyze due to their rarity. The Saudi Ara...
Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their eff...
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