Andrej Bugrim

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BACKGROUND In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed ('housekeeping') genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological(More)
BACKGROUND The identification of key target nodes within complex molecular networks remains a common objective in scientific research. The results of pathway analyses are usually sets of fairly complex networks or functional processes that are deemed relevant to the condition represented by the molecular profile. To be useful in a research or clinical(More)
We have measured the initial propagation velocity of the sperm-induced Ca(2+) wave in the egg of Xenopus laevis and have compared it with the initial propagation velocities of the inositol triphosphate (IP(3))-induced and Ca(2+)-induced Ca(2+) waves. The initial mean propagation velocity of the sperm-induced wave (13 microm/s) is very similar to that of the(More)
Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological(More)
BACKGROUND The problem of prostate cancer progression to androgen independence has been extensively studied. Several studies systematically analyzed gene expression profiles in the context of biological networks and pathways, uncovering novel aspects of prostate cancer. Despite significant research efforts, the mechanisms underlying tumor progression are(More)
The challenge of predicting the metabolism or toxicity of a drug in humans has been approached using in vivo animal models, in vitro systems, high throughput genomics and proteomics methods, and, more recently, computational approaches. Understanding the complexity of biological systems requires a broader perspective rather than focusing on just one method(More)
We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were found on multiple microarray platforms and in studies with different end-points and patient cohorts. Bimodal genes tend to cluster into small groups of four to six genes(More)
OBJECTIVE This study aimed to discover "signature pathways" that characterize biologic processes, based on genes differentially expressed in the uterine cervix before and after spontaneous labor. STUDY DESIGN The cervical transcriptome was characterized previously from biopsy specimens taken before and after term labor. Pathway analysis was used to study(More)
The challenge of predicting the metabolism or toxicity of a drug in humans has been approached using in vivo animal models, in vitro systems, high throughput genomics and proteomics methods, and, more recently, computational approaches. Understanding the complexity of biological systems requires a broader perspective rather than focusing on just one method(More)
Over the past several years there has been a paradigm shift in life science research as a result of the unprecedented advances in several laboratory techniques , such as automated DNA sequencing, global gene expression measurements, and proteomics and metabonomics techniques. The high throughput data collectively referred to as 'OMICs' data are ubiquitous(More)