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Details of functional speciation within gene families can be difficult to identify using standard multiple sequence alignment (MSA) methods. The evolutionary trace (ET) was developed as a visualization tool to...
In the rhizobia, a group of symbiotic Gram-negative soil bacteria, RpoN (σ54, σN, NtrA) is best known as the sigma factor enabling transcription of the nitrogen fixation genes. Recent reports, however, demonstrat...
Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Frequent cytogenetic abnormalities that occur in HCC suggest that tumor-modifying genes (oncogenes or tumor suppressors) may be driving sel...
Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. We carried out a comprehensive analysis o...
One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes ...
We focus on microarray data where experiments monitor gene expression in different tissues and where each experiment is equipped with an additional response variable such as a cancer type. Although the number ...
Bioinformatics and classical genetics reveal a positive correlation between recombination rate and GC content at silent sites in coding regions of Saccharomyces cerevisiae
The more data compiled from serial analysis of gene expression experiments, the more novel genes are likely to be found, in contrast to the situation with expressed sequence tags.
A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes...
The association-rules discovery (ARD) technique has yet to be applied to gene-expression data analysis. Even in the absence of previous biological knowledge, it should identify sets of genes whose expression i...
We have developed a relational database, called the General Repository for Interaction Datasets (The GRID; http://​biodata.​mshri.​on.​ca/​grid) to archive and di...
We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function ...
Methods of microarray analysis that suit experimentalists using the technology are vital. Many methodologies discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly appli...
Two recent papers illustrate contrasting approaches to studying gene expression during development of the xylem, the tissue that transports water and solutes around higher plants. The two methods used, studyin...
Multiple A- and B-type cyclins have been identified in animals, but their study is complicated by varying degrees of functional redundancy. A non-essential phenotype may reflect redundancy with a known or as y...
Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by se...
MRD is a database system to access the microsatellite repeats information of genomes such as archea, eubacteria, and other eukaryotic genomes whose sequence information is available in public domains. MRD stor...
Membrane-associated progesterone receptors (MAPRs) are thought to mediate a number of rapid cellular effects not involving changes in gene expression. They do not show sequence similarity to any of the classic...
Whereas genome sequencing has given us high-resolution pictures of many different species of bacteria, microarrays provide a means of obtaining information on genome composition for many strains of a given spe...
Experimental analysis of the proteomes of virulent and non-virulent strains of Brucella melitensis reveals differences in the proteins involved in iron metabolism
Comparative genomics using the pufferfish genome will help with identifying and characterizing human genes
The apoptosis signaling molecule caspase 3 is also required for differentiation in myoblasts
Structural data are critical for the elucidation of how peptides are synthesized and how they function. Two recent studies have used nanoscale chromatography together with mass spectrometry to determine the st...
The human malaria parasite Plasmodium falciparum, one of the world's most devastating pathogens, has an astonishing array of sequences and genes that play key roles in pathogenesis and immune evasion. We must und...
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