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Comprehensive mapping of transcription factor binding sites is essential in postgenomic biology. For this, we propose a mining approach combining noisy data from ChIP (chromatin immunoprecipitation)-chip exper...
A report of the meeting 'From Proteomics to Lipidomics - Basics, Advances and Applications', Bonn, Germany, 30 June-1 July 2006.
A report on the EMBO/SNF symposium 'The Genomics of Development', Arolla, Switzerland, 21-27 August 2006.
A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer.
Biologists can now prepare and image thousands of samples per day using automation, enabling chemical screens and functional genomics (for example, using RNA interference). Here we describe the first free, ope...
The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the r...
Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determin...
Although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with nucleoli or ribosomes is still incom...
Deciphering gene regulatory networks requires the systematic identification of functional cis-acting regulatory elements. We present a suite of web-based bioinformatics tools, called GeneACT
To identify divergent seven-transmembrane receptor (7TMR) candidates from the Arabidopsis thaliana genome, multiple protein classification methods were combined, including both alignment-based and alignment-free ...
A Melanesian variant of the genetic disease α-thalassemia has recently been shown to be due to a single-nucleotide polymorphism located between the adult α-globin genes and their enhancers. The finding that th...
A 'better' Escherichia coli K-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. Comparison with related bacterial genomes that have undergone a natural...
Alcoholism presents widespread social and human health problems. Alcohol sensitivity, the development of tolerance to alcohol and susceptibility to addiction vary in the population. Genetic factors that predis...
Selenocysteine (Sec) is co-translationally inserted into protein in response to UGA codons. It occurs in oxidoreductase active sites and often is catalytically superior to cysteine (Cys). However, Sec is used ...
Interpretation of lists of genes or proteins with altered expression is a critical and time-consuming part of microarray and proteomics research, but relatively little attention has been paid to methods for ex...
Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense pa...
Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chr...
Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isol...
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...
In vertebrates, the arrestins are a family of four proteins that regulate the signaling and trafficking of hundreds of different G-protein-coupled receptors (GPCRs). Arrestin homologs are also found in insects...
Mammalian olfactory receptor (OR) genes reside in numerous genomic clusters of up to several dozen genes. Whole-genome sequence alignment nets of five mammals allow their comprehensive comparison, aimed at rec...
Whether or not bacteria have species is a perennially vexatious question. Given what we now know about variation among bacterial genomes, we argue that there is no intrinsic reason why the processes driving di...
Polygalacturonases (PGs) belong to a large gene family in plants and are believed to be responsible for various cell separation processes. PG activities have been shown to be associated with a wide range of pl...
A report of the meeting 'Regulatory RNAs', the 71st Cold Spring Harbor Symposium on Quantitative Biology, Cold Spring Harbor, USA, 31 May-5 July 2006.
The circadian clock determines the rhythmic expression of many different genes throughout a 24-hour period. A recent study investigating the circadian regulation of liver proteins reveals multiple levels of re...
Endogenous retroviruses (ERVs) and solitary long terminal repeats (LTRs) have a significant antisense bias when located in gene introns, suggesting strong negative selective pressure on such elements oriented ...
Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CRE...
Neuroblastoma tumor cells are assumed to originate from primitive neuroblasts giving rise to the sympathetic nervous system. Because these precursor cells are not detectable in postnatal life, their transcript...
The Erratum to this article has been published in Genome Biology 2007 8:401
The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and ev...
A report on the 12th International Conference on the Cell and Molecular Biology of Chlamydomonas, Portland, USA, 9-14 May 2006.
Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specifici...
High-throughput approaches are beginning to have an impact on many areas of yeast biology. Two recent studies, using different experimental platforms, provide insight into new pathways involved in the response...
The respiratory pathogen Bordetella parapertussis is a valuable model in which to study the complex phenotype of host specificity because of its unique two-species host range. One subset of strains, including the...
A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16.
Urine is a desirable material for the diagnosis and classification of diseases because of the convenience of its collection in large amounts; however, all of the urinary proteome catalogs currently being gener...
Embryonic stem cells (ES cells) are powerful tools for genetic engineering and hold significant potential for regenerative medicine. Recent work provides new insights into ES cell pluripotency and delineates s...
Efforts to manipulate living organisms have raised the question of whether engineering principles of hierarchy, abstraction and design can be applied to biological systems. Here, we consider the practical chal...
Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findin...
Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic co...
A report on 'The Biology of Genomes' meeting, Cold Spring Harbor, USA, 10-14 May 2006.
A report on the Human Genome Organisation (HUGO) 11th Human Genome Meeting, Helsinki, Finland, 31 May-3 June 2006.
A report of the annual meeting of the European Society of Human Genetics, Amsterdam, 6-9 May 2006.
The original article was published in Genome Biology 2006 7:R9
Peptidoglycan recognition proteins (PGRPs) are innate immunity molecules present in insects, mollusks, echinoderms, and vertebrates, but not in nematodes or plants. PGRPs have at least one carboxy-terminal PGR...
The TATA box, one of the most well studied core promoter elements, is associated with induced, context-specific expression. The lack of precise transcription start site (TSS) locations linked with expression i...
Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these large datasets requires...
Genome-wide transcript profiling and analyses of enzyme activities from central carbon and nitrogen metabolism show that transcript levels undergo marked and rapid changes during diurnal cycles and after trans...
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...
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