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DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins...
The use of transposons as insertional mutagens to identify cancer genes in mice has generated a wealth of information over the past decade. Here, we discuss recent major advances in transposon-mediated inserti...
The original article was published in Genome Biology 2014 15:R65
The original article was published in Genome Biology 2015 16:134
Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impe...
A response to ‘Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data’ by Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND and Betel D in Genome B...
During the asexual replication cycle of the malaria parasite Plasmodium falciparum, the RNA-binding protein PfAlba1 binds and stabilizes a subset of transcripts for translation at a later time point.
Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, w...
The Erratum to this article has been published in Genome Biology 2015 16:233
X-chromosome inactivation is a striking example of epigenetic silencing in which expression of the long non-coding RNA XIST initiates the heterochromatinization and silencing of one of the pair of X chromosome...
Artificial selection provides a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions where allele-frequencies have diverged during se...
A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome asse...
A mutation in the WDR4 gene, coding for a tRNA-modifying enzyme, leads to reduced levels of guanosine methylation in tRNA in patients with primordial dwarfism.
The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. Th...
DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited.
Short-read high-throughput RNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maxim...
Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, chan...
Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatu...
Transcriptome-wide ribosome occupancy studies have suggested that during the intra-erythrocytic lifecycle of Plasmodium falciparum, select mRNAs are post-transcriptionally regulated. A subset of these encodes par...
Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity.
Previously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte DNA methylome by whole genome approaches revealed t...
The Erratum to this article has been published in Genome Biology 2015 16:271
The dispensable genome of a species, consisting of the dispensable sequences present only in a subset of individuals, is believed to play important roles in phenotypic variation and genome evolution. However, ...
Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present ...
The spatiotemporal behavior of chromatin is an important control mechanism of genomic function. Studies in Saccharomyces cerevisiae have broadly contributed to demonstrate the functional importance of nuclear org...
Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a ...
Comparative analyses of the control of mammalian microbiomes by host genetic architecture reveal striking conserved features that have implications for the evolution of host–microbiome interactions.
Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. The core spliceosome component PRPF8 is essential for spliceosome assembly through its partici...
Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have s...
Cell-cycle fluctuations drive significant transcriptomic heterogeneity in murine hematopoietic stem cells. Additionally, deletion of Bcl11a alters the regulation of hematopoietic stem cell quiescence, self-renewa...
Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulator...
Hematopoietic stem cells (HSCs) are a rare cell type with the ability of long-term self-renewal and multipotency to reconstitute all blood lineages. HSCs are typically purified from the bone marrow using cell ...
SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insert...
The detailed analysis of leaf growth dynamics, when coupled with transcriptomic research, can facilitate the discovery of genes required for leaf elongation.
Allelic expression analysis has become important for integrating genome and transcriptome data to characterize various biological phenomena such as cis-regulatory variation and nonsense-mediated decay. We analyze...
Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. Here, we perform methylome analysis of...
The Author Correction to this article has been published in Genome Biology 2024 25:150
Genome wide-association studies have successfully identified several hundred independent loci harboring common cancer susceptibility alleles that are distinct from the more than 110 cancer predisposition genes...
Plants commit to flowering based on endogenous and exogenous information that they can remember across mitotic cell divisions. Here, we review how signal perception and epigenetic memory converge at key integr...
The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental...
Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cros...
Millions of small open reading frames exist in eukaryotes. We do not know how many, or which are translated, but bioinformatics is getting us closer to the answer.
There is increasing evidence that transcripts or transcript regions annotated as non-coding can harbor functional short open reading frames (sORFs). Loss-of-function experiments have identified essential devel...
To sustain the global requirements for food and renewable resources, unraveling the molecular networks underlying plant growth is becoming pivotal. Although several approaches to identify genes and networks in...
Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to guide predictive crop b...
A multiparent advanced-generation intercross population of maize has been developed to help plant geneticists identify sequence variants affecting important agricultural traits.
Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced...
Serious and underappreciated sources of bias mean that extreme caution should be applied when using or interpreting functional enrichment analysis to validate findings from global RNA- or protein-expression an...
Diagnostics of the human ageing process may help predict future healthcare needs or guide preventative measures for tackling diseases of older age. We take a transcriptomics approach to build the first reprodu...
The Correspondence to this article has been published in Genome Biology 2019 20:152
The Correspondence to this article has been published in Genome Biology 2018 19:97
RNA-Seq has emerged as the standard for measuring gene expression and is an important technique often used in studies of human disease. Gene expression quantification involves comparison of the sequenced reads...
We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model v...
The rapidly increasing quantity of genome-wide chromosome conformation capture data presents great opportunities and challenges in the computational modeling and interpretation of the three-dimensional genome....
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