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Archaeal and bacterial genomes contain a number of genes of foreign origin that arose from recent horizontal gene transfer, but the role of integrative elements (IEs), such as viruses, plasmids, and transposab...
Advances in sequencing technology and genome-wide association studies are now revealing the complex interactions between hosts and pathogen through genomic variation signatures, which arise from evolutionary c...
We describe here the sequencing, annotation and comparative analysis of an 8 Mb region of pig chromosome 17, which provides a useful test region to assess coverage and quality for the pig genome sequencing pro...
The basic/helix-loop-helix (bHLH) proteins are important components of the transcriptional regulatory network, controlling a variety of biological processes, especially the development of the central nervous s...
The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic analysis (AMPHORA) tha...
Transcription initiation is a key component in the regulation of gene expression. mRNA 5' full-length sequencing techniques have enhanced our understanding of mammalian transcription start sites (TSSs), reveal...
A report on work presented at the 39th Annual Meeting of the American Society for Cell Bilogy, Washington DC, December 11-15, 1999
We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein m...
Bioinformatic analysis has been used to identify gene-fusion events in complete genomes and thus infer protein interactions on the basis of sequence analysis alone.
Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron evolution, including age, mechanisms o...
The original article was published in Genome Biology 2013 14:402
By comparing two fully sequenced genomes of Chlamydia trachomatis using competitive hybridization on DNA microarrays, a logarithmic correlation was demonstrated between the signal ratio of the arrays and the 75-9...
The particular interest of David Ussery and his group is in creating 'structural atlases' of genomes from a detailed analysis of variations in DNA structure.
Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression. The deposition of H3 lysine 27 tri-methylation (H3K27me3) by PRC2 is known to be required for tran...
Myb proteins contain a conserved DNA-binding domain composed of one to four repeat motifs (referred to as R0R1R2R3); each repeat is approximately 50 amino acids in length, with regularly spaced tryptophan resi...
Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one opt...
We have developed a global strategy based on the Bayesian network framework to prioritize the functional modules mediating genetic perturbations and their phenotypic effects among a set of overlapping candidat...
It is widely acknowledged that synonymous codons are used unevenly among genes in a genome. In organisms under translational selection, genes encoding highly expressed proteins are enriched with specific codon...
Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development con...
The Software to this article has been published in Genome Biology 2020 21:260
RNA interference (RNAi) screens have enabled the systematic analysis of many biological processes in cultured cells and whole organisms. The success of such screens and the interpretation of the data depend on...
This article is part of a Supplement: Volume 12 Supplement 1
The Homer family of adaptor proteins consists of three members in mammals, and homologs are also known in other animals but not elsewhere. They are predominantly localized at the postsynaptic density in mammal...
The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods.
A selection of evaluations from Faculty of 1000 covering gene expression in Salmonella, artificial endonucleases, the draft genome of Ciona intestinalis, the use of image informatics to analyze C. elegansbehavior...
Understanding the relationships between the structure (topology) andfunction of biological networks is a central question of systems biology. The idea thattopology is a major determinant of systems function ha...
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is...
A great site for anyone interested in breast cancer or mammary gland development - beginners and experienced researchers alike.
Differences in responses to bacterial surface lipopolysaccharides (LPSs) are apparent between and within mammalian species. It has been shown in mice that resistance to LPS is caused by defects in the Toll-lik...
Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely...
Metazoans contain multiple complex microbial ecosystems in which the balance between host and microbe can be tipped from commensalism to pathogenicity. This transition is likely to depend both on the prevailin...
MicroRNAs (miRNAs), which originate from precursor transcripts with stem-loop structures, are essential gene expression regulators in eukaryotes.
Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project ha...
This article is part of a Supplement: Volume 11 Supplement 1
Transcriptional analysis has been used to probe the biology of mycobacterial responses to antibiotics and to suggest new drug targets.
Subcellular messenger RNA localization is important in most eukaryotic cells, even in unicellular organisms like yeast for which this process has been underestimated. Microarrays are rarely used to study subce...
As an antioxidant and cofactor to numerous metabolic enzymes, ascorbate has an essential role in plants and animals. Cytochromes b561 constitute a class of intrinsic membrane proteins involved in ascorbate regene...
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