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Results for “Computational approach”

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At least 145 records · Page 8Linked to original sources
PubMed2006

A computational approach for identifying pseudogenes in the ENCODE regions.

BACKGROUND: Pseudogenes are inheritable genetic elements showing sequence similarity to functional genes but with deleterious mutations. We describe a computational pipeline for identifying them, which in contrast to previous work explicitly uses intron-exon structure in parent genes to classify pseudogenes. We require alignments between duplicated pseudogenes and their parents to span intron-exon junctions, and this can be used to distinguish between true duplicated and processed pseudogenes (with insertions). RESULTS: Applying our approach to the ENCODE regions, we identify about 160 pseudogenes, 10% of which have clear 'intron-exon' structure and are thus likely generated from recent duplications. CONCLUSION: Detailed examination of our results and comparison of our annotation with the GENCODE reference annotation demonstrate that our computation pipeline provides a good balance between identifying all pseudogenes and delineating the precise structure of duplicated genes.

Computational Biology↗
PubMed2006

Computational approaches for modeling human intestinal absorption and permeability.

Human intestinal absorption (HIA) is an important roadblock in the formulation of new drug substances. Computational models are needed for the rapid estimation of this property. The measurements are determined via in vivo experiments or in vitro permeability studies. We present several computational models that are able to predict the absorption of drugs by the human intestine and the permeability through human Caco-2 cells. The training and prediction sets were derived from literature sources and carefully examined to eliminate compounds that are actively transported. We compare our results to models derived by other methods and find that the statistical quality is similar. We believe that models derived from both sources of experimental data would provide greater consistency in predictions. The performance of several QSPR models that we investigated to predict outside the training set for either experimental property clearly indicates that caution should be exercised while applying any of the models for quantitative predictions. However, we are able to show that the qualitative predictions can be obtained with close to a 70% success rate.

Caco-2 Cells↗
PubMed2000

Computational approaches to sensorimotor transformations.

Behaviors such as sensing an object and then moving your eyes or your hand toward it require that sensory information be used to help generate a motor command, a process known as a sensorimotor transformation. Here we review models of sensorimotor transformations that use a flexible intermediate representation that relies on basis functions. The use of basis functions as an intermediate is borrowed from the theory of nonlinear function approximation. We show that this approach provides a unifying insight into the neural basis of three crucial aspects of sensorimotor transformations, namely, computation, learning and short-term memory. This mathematical formalism is consistent with the responses of cortical neurons and provides a fresh perspective on the issue of frames of reference in spatial representations.

Animals↗
PubMed2006

Computational approaches to model ligand selectivity in drug design.

To be effective, a designed drug must discriminate successfully the macromolecular target from alternative structures present in the organism. The last few years have witnessed the emergence of different computational tools aimed to the understanding and modeling of this process at molecular level. Although still rudimentary, these methods are shaping a coherent approach to help in the design of molecules with high affinity and specificity, both in lead discovery and in lead optimization. It is the purpose of this review to illustrate the array of computational tools available to consider selectivity in the design process, to summarize the most relevant applications, and to sketch the challenges ahead.

Amino Acid Sequence↗
PubMed2004

Computational approaches to unveiling ancient genome duplications.

Recent analyses of complete genome sequences have revealed that many genomes have been duplicated in their evolutionary past. Such events have been associated with important biological transitions, major leaps in evolution and adaptive radiations of species. Here, we consider recently developed computational methods to detect such ancient large-scale gene duplication events. Several new approaches have been used to show that large-scale gene duplications are more common than previously thought.

Computational Biology↗
PubMed2005

Defining electrical communication in skeletal muscle resistance arteries: a computational approach.

Vascular cells communicate electrically to coordinate their activity and control tissue blood flow. To foster a quantitative understanding of this fundamental process, we developed a computational model that was structured to mimic a skeletal muscle resistance artery. Each endothelial cell and smooth muscle cell in our virtual artery was treated as the electrical equivalent of a capacitor coupled in parallel with a non-linear resistor representing ionic conductance; intercellular gap junctions were represented by ohmic resistors. Simulations revealed that the vessel wall is not a syncytium in which electrical stimuli spread equally to all constitutive cells. Indeed, electrical signals spread in a differential manner among and between endothelial cells and smooth muscle cells according to the initial stimulus. The predictions of our model agree with physiological data from the feed artery of the hamster retractor muscle. Cell orientation and coupling resistance were the principal factors that enable electrical signals to spread differentially along and between the two cell types. Our computational observations also illustrated how gap junctional coupling enables the vessel wall to filter and transform transient electrical events into sustained voltage responses. Functionally, differential electrical communication would permit discrete regions of smooth muscle activity to locally regulate blood flow and the endothelium to coordinate regional changes in tissue perfusion.

Animals↗