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At least 127 records · Page 7Linked to original sources
PubMed2004

A novel computational approach for the prediction of networked transcription factors of aryl hydrocarbon-receptor-regulated genes.

A novel computational method based on a genetic algorithm was developed to study composite structure of promoters of coexpressed genes. Our method enabled an identification of combinations of multiple transcription factor binding sites regulating the concerted expression of genes. In this article, we study genes whose expression is regulated by a ligand-activated transcription factor, aryl hydrocarbon receptor (AhR), that mediates responses to a variety of toxins. AhR-mediated change in expression of AhR target genes was measured by oligonucleotide microarrays and by reverse transcription-polymerase chain reaction in human and rat hepatocytes. Promoters and long-distance regulatory regions (>10 kb) of AhR-responsive genes were analyzed by the genetic algorithm and a variety of other computational methods. Rules were established on the local oligonucleotide context in the flanks of the AhR binding sites, on the occurrence of clusters of AhR recognition elements, and on the presence in the promoters of specific combinations of multiple binding sites for the transcription factors cooperating in the AhR regulatory network. Our rules were applied to search for yet unknown Ah-receptor target genes. Experimental evidence is presented to demonstrate high fidelity of this novel in silico approach.

Algorithms↗
PubMed2002

New computational approaches for analysis of cis-regulatory networks.

The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.

Chromosomes, Artificial, Bacterial↗
PubMed2005

Oligomerization states of Bowman-Birk inhibitor by atomic force microscopy and computational approaches.

Several methods have been applied to study protein-protein interaction from structural and thermodynamic point of view. The present study reveals that atomic force microscopy (AFM), molecular modeling, and docking approaches represent alternative methods offering new strategy to investigate structural aspects in oligomerization process of proteinase inhibitors. The topography of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) was recorded by AFM and compared with computational rigid-bodies docking approaches. Multimeric states of BTCI identified from AFM analysis showed globular-ellipsoidal shapes. Monomers, dimers, trimers, and hexamers were the most prominent molecular arrays observed in AFM images as evaluated by molecular volume calculations and corroborated by in silico docking and theoretical approaches. We therefore propose that BTCI adopts stable and well-packed self-assembled states in monomer-dimer-trimer-hexamer equilibrium. Although there are no correlation between specificity and packing efficiency among proteinases and proteinase inhibitors, the AFM and docked BTCI analyses suggest that these assemblies may exist in situ to play their potential function in oligomerization process.

Computational Biology↗
PubMed1988

A simple computational approach to irregular field dosimetry.

Treatment of certain malignant tumors requires very large and irregular fields. The dose computations in such field configurations are quite complicated and tedious and hence accessible to computer methods only. This paper describes an easy method for estimating dose to any point in such irregular fields except those which are in the shielded region. For radiotherapy centres which do not have access to a computer, this paper presents an algorithm that can be used with a desk calculator for dose computation at any point. The dose values calculated using this algorithm at different points and at different depths in the mantle and inverted Y-fields agree within +/- 3% with the values computed using detailed sector integration method of Clarkson.

Algorithms↗
PubMed1994

Computational approaches to human pattern recognition.

This paper consolidates recent findings on how humans detect and recognize patterns and considers computational procedures which reflect observed performance. A multi-level correlation model for spatial information processing is proposed and used to interpret past results on human psychophysical performance.

Computer Graphics↗
PubMed2004

Recent developments in computational approaches for uncovering genomic homology.

Identifying genomic homology within and between genomes is essential when studying genome evolution. In the past years, different computational techniques have been developed to detect homology even when the actual similarity between homologous segments is low. Depending on the strategy used, these methods search for pairs of chromosomal segments between which either both gene content and order are conserved or gene content only. However, due to fact that, after their divergence, homologous segments can lose a different set of genes, these methods still often fail to detect genomic homology. Recently, more advanced approaches have been developed that can combine gene order and content information of multiple genomic segments.

Animals↗
PubMed1991

Steps in the implementation of a micro-computer approach to the management of animal disease information.

The stages in the design, procurement and implementation of a micro-computer-based animal health information system are described. The scenario presented is that of a national Director of Veterinary Services taking his first steps in the computerisation of an epidemiology unit, but sub-national and international issues are also discussed. The administrative and management aspects are considered and the need to incorporate computers into a carefully designed and appropriate information system is emphasised. The principles of the specification of initial systems and their subsequent development are described; suggestions are made for the procurement and continuing support of both hardware and software.

Animal Diseases↗
PubMed1983

A computer approach to measuring shuttle box activity and conditioned place preference.

A procedure is described for measuring locomotor activity and place preference using an Apple II + computer. The interface consists of a single integrated circuit connected by a 16 pin jumper cable to the Apple's game I/O connector. This approach can be easily adapted to provide sequential reading of one to seven input lines from up to 16 different test boxes. The software is written in basic and doesn't require any knowledge of memory addressing or machine language programming.

Animals↗
PubMed2002

Computational approaches to the prediction of the blood-brain distribution.

This review attempts to summarise present knowledge related to the theoretical modelling of drug transport across the blood-brain barrier. Several computational protocols are described ranging from quantum mechanics-based approaches through molecular mechanics-related techniques to simple and fast procedures based on only the 2-D graph of the investigated structures. Amazingly, few descriptors have been shown to influence the derived relationships in a significant manner and a cornerstone in most of the described models are terms describing hydrogen bonding. A very quick quantitative assessment of the brain partitioning of a compound has also been devised using the following two rules: If N+O (the number of nitrogen and oxygen atoms) in a molecule is less than or equal to five, it has a high chance of entering the brain. The second rule predicts that if log P-(N+O) is positive then log BB is positive.

Algorithms↗
PubMed2006

Progress in computational approach to drug development against SARS.

Since the outbreak of SARS (severe acute respiratory syndrome) in November 2002 in Southern China's Guangdong Province, considerable progress has been made in the development of drugs for SARS therapy. The present mini review is focused on the area of computer-aided drug discovery, i.e., the advances achieved mainly from the approaches of structural bioinformatics, pharmacophore modeling, molecular docking, peptide-cleavage site prediction, and other computational means. It is highlighted that the compounds C(28)H(34)O(4)N(7)Cl, C(21)H(36(O)5)N(6) and C(21)H(36)O(5)N(6) (Wei et al., Amino Acids, 2006, 31: 73-80), as well as KZ7088 (Chou et al. Biochem. Biophys. Res. Commun., 2003, 308: 148-151), a derivative of AG7088, might be the promising candidates for further investigation, and that the octapeptides ATLQAIAS and ATLQAENV, as well as AVLQSGFR, might be converted to effective inhibitors against the SARS enzyme. Meanwhile, how to modify these octapeptides based on the "distorted key" theory to make them become potent inhibitors is explicitly elucidated. Finally, a brief introduction is given for how to use computer-generated graphs to rapidly diagnose SARS coronavirus.

Diagnosis, Computer-Assisted↗
PubMed2001

Computational approaches to the architecture and operations of the prefrontal cortical circuit for working memory.

1. This article reviews recent progress in the computational studies towards the architecture and operations of the prefrontal cortical circuit, which are keys to understand the mechanisms of working memory processing. 2. The recurrent excitatory connections form closed-loop circuits, which contribute to the sustainment of delay-period activity. These connections subserve the cortical amplification of the activity. 3. Recent experimental studies (Wilson et al. 1994; Rao et al. 1999, 2000) suggested that at least two architectonically distinct types of intracortical inhibition, isodirectional and cross-directional inhibition, play significant roles in the formation of memory fields. 4. Computer simulations of a prefrontal cortical circuit model (Tanaka 1999, 2000a) showed that the isodirectional inhibition in the model regulated the amplitude of memory fields (i.e., the maximum firing rate) while the cross-directional inhibition contributed to the sharpening of the memory fields or the tuning curves. 5. The above characteristics enable the prefrontal cortical circuit to control memory fields, which would be necessary to general working memory processing. It would also be interesting to know whether different subtypes of the interneurons have distinct roles. 6. Another important issue is how neuromodulators contribute to working memory processing. Recent computer simulations by Durstewitz et al. (1999, 2000) showed that stronger dopamine action required stronger intervening input to destroy working memory, suggesting that dopamine contributes to the stabilization of working memory representation. 7. Further elucidation of these issues based on more detailed anatomical data of the cortical circuitry would make the architecture and operations of the prefrontal cortical circuit be more clearly described.

Animals↗