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Numerous studies over the past decade have elucidated a large set of long intergenic noncoding RNAs (lincRNAs) in the human genome. Research since has shown that lincRNAs constitute an important layer of genom...
Ebolaviruses cause a severe and often fatal haemorrhagic fever in humans, with some species such as Ebola virus having case fatality rates approaching 90%. Currently, the worst Ebola virus outbreak since the d...
In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA...
Superfamily and family analyses provide an effective tool for the functional classification of proteins, but must be automated for use on large datasets. We describe a 'gold standard' set of enzyme superfamili...
Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbion...
Next-generation sequencing is set to transform the discovery of genes underlying neurodevelopmental disorders, and so offer important insights into the biological bases of spoken language. Success will depend ...
Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain ...
Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are gover...
Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,49...
The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations...
Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown.
We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, ...
Riboswitches are vital components of many genomes. The additional riboswitch variants and updated aptamer structure models reported here will improve future efforts to annotate these widespread regulatory RNAs in...
Filamentous fungi synthesize many secondary metabolites and are rich in genes encoding proteins involved in their biosynthesis. Genes from the same pathway are often clustered and co-expressed in particular co...
Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somat...
Transcriptional regulation plays an important role in the control of many biological processes. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity an...
The duck-billed platypus (Ornithorhynchus anatinus) belongs to the mammalian subclass Prototheria, which diverged from the Theria line early in mammalian evolution. The platypus genome sequence provides a unique ...
Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi a...
Potassium channels are the largest and most diverse type of ion channel found in nature. The completion of the sequencing of the genomes of Drosophila melanogaster and Anopheles gambiae, which belong to the same ...
Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small ...
Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable...
Apoptosis, one of the main types of programmed cell death, is regulated and performed by a complex protein network. Studies in model organisms, mostly in the nematode Caenorhabditis elegans, identified a relative...
Cyclin-dependent kinases (CDKs) are protein kinases characterized by needing a separate subunit - a cyclin - that provides domains essential for enzymatic activity. CDKs play important roles in the control of ...
We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long (2 to 10-mers) in microbial complete genomes with corresponding distributions obtained from random sequences and...
The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. Although the protein repertoires of distantly related spec...
Alignment-free methods, more time and memory efficient than alignment-based methods, have been widely used for comparing genome sequences or raw sequencing samples without assembly. However, in this study, we ...
What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of geno...
Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building meth...
Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play m...
The Erratum to this article has been published in Genome Biology 2016 17:179
The Data Descriptor to this article has been published in Scientific Data 2020 7:217
Evidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; however, the evolutionary ...
Molecular characterization of cattle breeds is important for the prevention of germplasm erosion by cross breeding. The present study was carried out to characterize two Indian cattle breeds, Ongole and Deoni ...
Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. ...
Analysis of the human MASP-1/3 gene, which encodes two proteases of the lectin-triggered complement cascade, has revealed alternatively used serine-protease-encoding regions for the gene's two protein products. P...
Having a working draft of the human genome sequence is proving invaluable to mouse genetic and genomic studies, providing a useful stepping-stone towards the finished sequence of the mouse genome.
Under starvation conditions, the soil bacterium Sinorhizobium meliloti divides into two types of daughter cell: one suited to short-term and the other to long-term starvation.
Recent studies of the nematode dauer state provide new insights into epigenetic processes that underlie cellular memory.
A report of the meeting Comparative Genomics of Eukaryotic Microorganisms, 17-22 October 2009, San Feliu de Guixols, Spain.
The recent completion and assembly of the first draft of the human genome, which combines samples from several ethnically diverse males and females, provides preliminary data on the extent of human genetic var...
Koalas are currently undergoing a wave of germline infections by the retrovirus KoRV. Study of this phenomenon not only provides an opportunity for understanding the processes regulating retrovirus endogenizat...
A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012.
A report of the Biochemical Society meeting 'The Molecular Biology of Archaea', St Andrews, UK, 19-21 August 2008.
A report on the Mouse Initiatives V meeting 'Genomics of Complex Systems in Biomedical Research', The Jackson Laboratory, Bar Harbor, USA, 30 July-2 August 2003.
A report on the 15th Annual Center for Advanced Biotechnology and Medicine Symposium on structural genomics in pharmaceutical design, Princeton, USA, 24-25 October 2001.
A report on the talks presented at the Cold Spring Harbor 2000 Meeting on Arabidopsis Genomics, New York, 7-10 December, 2000.
Function is an onerous concept, as the recent study by Steven Salzberg and colleagues demonstrates. We should be careful and always specific in using the ‘F-word’.
The original article was published in Genome Biology 2018 19:208
N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability...
Defensins, small endogenous peptides with antimicrobial activity, are pivotal components of the innate immune response. A large cluster of defensin genes is located on human chromosome 8p; among them the beta ...
An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies ...
The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental dup...
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