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Using cDNA copies of transcripts and corresponding genomic sequences from the Berkeley Drosophila Genome Project, a set of 24,753 donor and acceptor splice sites were computed with a scanning algorithm that te...
Genes of advanced organisms undergo alternative splicing, which can be mutually exclusive, in the sense that only one exon is included in the mature mRNA out of a cluster of alternative choices, often arranged...
The three consensus elements at the 3' end of human introns - the branch point sequence, the polypyrimidine tract, and the 3' splice site AG dinucleotide - are usually closely spaced within the final 40 nucleo...
The original article was published in Genome Biology 2003 4:R83
A report on a Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on 'Prion Biology', Hinxton, UK, 7-11 September 2005.
A report on the European Science Foundation Conference 'Functional Genomics and Disease', Oslo, Norway, 6-10 September 2005.
The mechanisms of signal transduction and vesicular transport have traditionally been studied in isolation, but recent studies make it clear that the two processes are inextricably linked. A new genome-wide an...
Recent work has identified the topology of almost all the inner membrane proteins in Escherichia coli, and advances in nuclear magnetic resonance spectroscopy now allow the determination of α-helical membrane pro...
Translational efficiencies in Saccharomyces cerevisiae vary from transcript to transcript by approximately two orders of magnitude. Many of the poorly translated transcripts were found to respond to the appropria...
We have developed an application, iVici, to analyze cellular networks represented as addressable symmetric or asymmetric two-dimensional matrices. iVici was designed to permit simultaneous visualization and co...
Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applying phylogenetic foo...
Numerous studies have employed microarray techniques to study changes in gene expression in connection with human disease, aging and evolution. The vast majority of human samples available for research are obt...
Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulator...
The AP-2 family of transcription factors consists of five different proteins in humans and mice: AP-2α, AP-2β, AP-2γ, AP-2δ and AP-2ε. Frogs and fish have known orthologs of some but not all of these proteins,...
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...
A report on the 15th International Society of Developmental Biologists Congress, Sydney, Australia, 3-7 September 2005.
Recent work shows that the inhibition of the SOS stress response in Escherichia coli reduces the development of resistance to the antibiotics ciprofloxacin and rifampicin. This finding may help in the battle agai...
We have developed a general probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data. This framework was validated by accurately recovering kn...
Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene pr...
MicroRNAs are non-coding small RNAs of ~22 nucleotides that regulate the gene expression by base-paring with target mRNAs, leading to mRNA cleavage or translational repression. It is currently estimated that m...
The biological mechanisms that underlie aging have not yet been fully identified. Senescence, a phenomenon occurring in vitro, limits the number of cell divisions in mammalian cell cultures and has been suggested...
Down syndrome, caused by trisomic chromosome 21, is the leading genetic cause of mental retardation. Recent studies demonstrated that dosage-dependent increases in chromosome 21 gene expression occur in trisom...
A selection of evaluations from Faculty of 1000 Biology: yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism.
A report on the Third Annual International Conference on Transposition and Animal Biotechnology, Minneapolis, USA, 23-24 June 2005, and the FASEB Summer Research Conference 'Mammalian Mobile Elements', Tuscon,...
Transplantation of human breast cancer cells into immunodeficient mice together with gene-expression microarray studies has recently identified genes implicated in the tissue tropism of breast-cancer metastasi...
We developed Ulysses as a user-oriented system that uses a process called Interolog Analysis for the parallel analysis and display of protein interactions detected in various species. Ulysses was designed to p...
Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of in...
We have developed several new methods to investigate transcriptional motifs in vertebrates. We developed a specific alignment tool appropriate for regions involved in transcription control, and exhaustively en...
Transcription factors regulate gene expression by binding to specific cis-regulatory elements in gene promoters. Although DNA sequences that serve as transcription-factor binding sites have been characterized and...
The male-specific region of the mouse Y chromosome long arm (MSYq) is comprised largely of repeated DNA, including multiple copies of the spermatid-expressed Ssty gene family. Large deletions of MSYq are associat...
The Correction to this article has been published in Genome Biology 2019 20:160
Plants growing in their natural habitat represent a valuable resource for elucidating mechanisms of acclimation to environmental constraints. Populus euphratica is a salt-tolerant tree species growing in saline s...
A report on the Fourth Annual HUPO World Congress (HUPO2005) 'From Defining the Proteome to Understanding Function', Munich, Germany, 28 August-1 September 2005.
Silencing of splicing regulators by RNA interference, combined with splicing-specific microarrays, has revealed a complex network of distinct alternative splicing events in Drosophila, while a high-throughput scr...
Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has...
The expansin superfamily of plant proteins is made up of four families, designated α-expansin, β-expansin, expansin-like A and expansin-like B. α-Expansin and β-expansin proteins are known to have cell-wall lo...
Alternative polyadenylation is one of the mechanisms in human cells that give rise to a variety of transcripts from a single gene. More than half of the human genes have multiple polyadenylation sites (poly(A)...
A report on the 64th Annual Meeting of the Society for Developmental Biology, San Francisco, USA, 27 July-1 August 2005.
A selection of evaluations from Faculty of 1000 Biology Genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversit...
The steroid hormone 20-hydroxyecdysone (20E) triggers the major developmental transitions in Drosophila, including molting and metamorphosis, and provides a model system for defining the developmental and molecul...
Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other...
Glycosylation, the attachment of carbohydrates to proteins and lipids, influences many biological processes. Despite detailed characterization of the cellular components that carry out glycosylation, a complet...
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