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To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed fo...
The phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with...
The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the divers...
Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed.
Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domes...
The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in d...
Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish nove...
The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...
Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression b...
Hybridization is an important evolutionary process that results in increased plant diversity....Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characterist...
The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the...
Numerous completely sequenced bacterial genomes harbor prophage elements. These elements have been implicated in increasing the virulence of the host and in phage immunity. The e14 element is a defective lambd...
To coincide with International Women's Day, Genome Biology asked several female scientists about their experience of an academic career, how they managed to balance an active research career with family life, and...
Epigenomic data from ENCODE can be used to associate specific combinations of chromatin marks with regulatory elements in the human genome. Hidden Markov models and the expectation-maximization (EM) algorithm ...
How predictable is evolution at the molecular level? An example of repeated evolution in rice and Brassica illustrates how selection might preferentially target certain genes and mutations.
A recent report reveals widespread mis-splicing of RNA transcripts in eukaryotes, with mis-spliced RNA destroyed by nonsense-mediated mRNA decay. This striking inefficiency deepens the mystery of the prolifera...
An intriguing study shows that, in epidermal progenitor cells, circadian genes are expressed in successive waves that modulate responses to differentiation signals.
A report of the 2nd Wellcome Trust Conference on Genomic Epidemiology of Malaria, Hinxton, UK, 14-17 June 2009.
Genome-wide measures of DNA strand composition have been used to find archaeal DNA replication origins. Archaea seem to replicate using a single origin (as do eubacteria) even though archaeal replication facto...
The first draft of human genome sequencing is complete. A large amount of DNA sequences are already available in the database but these are not ordered and assembled. In many cases, these sequences are shorter...
A report on the joint second Plant Genomics European Meeting (Plant GEMs) and fourth Genomic Arabidopsis Resource Network (GARNet) meeting, York, UK, 3-6 September 2003.
How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans eff...
A report on the 16th International Caenorhabditis elegans Meeting, Los Angeles, USA, 27 June-1 July 2007.
A report on the 12th International Conference on the Cell and Molecular Biology of Chlamydomonas, Portland, USA, 9-14 May 2006.
A report on the Plant and Animal Genome XIV Conference, San Diego, USA, 14-18 January 2006.
A report of the meeting 'Gene Expression and Signaling in the Immune System', Cold Spring Harbor, USA, 22-26 April 2008.
High-dimensional -omics profiling predicts responses to therapeutic agents in breast cancer cell lines that can be effectively applied to patient selection in clinical trials.
Proteins of the Rab and SNARE families target vesicles to their intracellular destinations. A comparison of these families from the budding yeast, fission yeast, nematode and fruitfly genomes has implications ...
A report on the European Molecular Biology Laboratory (EMBL) 'Oncogenes and Growth Control' meeting, Heidelberg, Germany, 17-20 April 2004.
A report of the 24th Fungal Genetics Conference, Asilomar, USA, 20-25 March 2007.
A report on the Advances in Genome Biology and Technology meeting held in Marco Island, Florida, USA, on February 12–15, 2014.
A response to Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions by AJ Enright, CA Ouzounis. Genome Biology 2000, 2:research0034.1-0034.7
A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs).
The ubiquitin system (Ub-system) can be defined as the ensemble of components including Ub/ubiquitin-like proteins, their conjugation and deconjugation apparatus, binding partners and the proteasomal system. W...
DNA sequences that are shared between closely related organisms while being absent from their common ancestor and from sister lineages of that ancestor are likely to have been acquired by horizontal gene trans...
The original article was published in Genome Biology 2023 24:113
Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsis...
Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, esp...
Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, ...
Characterization of the innate immune repertoire of extant cnidarians is of both fundamental and applied interest - it not only provides insights into the basic immunological 'tool kit' of the common ancestor ...
Gene duplications have been hypothesized to be a major factor in enabling the evolution of tissue differentiation. Analyses of the expression profiles of duplicate genes in mammalian tissues have indicated tha...
Recent studies in comparative genomics demonstrate that interspecies comparison represents a powerful tool for identifying both conserved and specialized biologic processes across large evolutionary distances....
The lamins are the major architectural proteins of the animal cell nucleus. Lamins line the inside of the nuclear membrane, where they provide a platform for the binding of proteins and chromatin and confer me...
Embryonic development is coordinated by sets of cis-regulatory elements that are collectively responsible for the precise spatio-temporal organization of regulatory gene networks. There is little information on h...
The heterogeneity of cancer genomes in terms of acquired mutations complicates the identification of genes whose modification may exert a driver role in tumorigenesis. In this study, we present a novel method ...
Genes in populations are in constant flux, being gained through duplication and occasionally retained or, more frequently, lost from the genome. In this study we compare pairs of identifiable gene duplicates g...
Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can p...
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