Miranda is a high order hydrodynamics code for computing fluid instabilities and turbulent mixing. It employs FFTs and band-diagonal matrix solvers for computing spectrally-accurate derivatives, combined with high-order integration methods for time advanc...

BackgroundGene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting ...

DEVELOPING GENETIC MAPS We can determine s for pairs of genes or loci. Next question is how. #12;Developing Genetic Maps 2 MAPMAKER (Lander et al., 1987) is a computer program for multipoint analysis of any number of loci necessary for the development of an accurate genetic map. It computes the maximum

One of the difficulties in using gene expression profiles to predict cancer is how to effectively select a few informative genes to construct accurate prediction models from thousands or ten thousands of genes. We screen highly discriminative genes and gene pairs to create ...

Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious ...

Much important evolutionary activity occurs in gene clusters, where a copy of a gene may be free to evolve new functions. Computational methods to extract evolutionary information from sequence data for such clusters are currently imperfect, in part because accurate sequence data are often lacking in these genomic ...

AbstractMuch important evolutionary activity occurs in gene clusters, where a copy of a gene may be free to acquire new functions. Current computational methods to extract evolutionary information from sequence data for such clusters are suboptimal, in part because accurate sequence data are often lacking in these ...

Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved ...

Page 1. EFFICIENT AND ACCURATE COMPUTATION OF NON-NEGATIVE ANISOTROPIC SCATTERING CROSS SECTIONS ...

Correct classification of genes into gene families is important for understanding gene function and evolution. Although gene families of many species have been resolved both computationally and experimentally with high accuracy, gene family classification in most newly ...

The number of completely sequenced bacterial genomes has been growing fast. There are computer methods available for finding genes but yet there is a need for more accurate algorithms. The GeneMark.hmm algorithm presented here was designed to improve the gene prediction quality in terms of ...

Imprinted genes are essential in embryonic development, and imprinting dysregulation contributes to human disease. We report two new human imprinted genes: KCNK9 is predominantly expressed in the brain, is a known oncogene, and may be involved in bipolar disorder and epilepsy, while DLGAP2 is a candidate bladder cancer tumor suppressor. Both ...

Accurate computation of sensitivity derivatives is becoming an important item in Computational Fluid

With the overwhelming volume of genomic and molecular information available on many databases nowadays, researchers need from bioinformaticians more than encouragement to refine their searches. We present here GeneRanker, an online system that allows researchers to obtain a ranked list of genes potentially related to a specific disease or biological ...

Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated ...

A two-stage computational procedure is presented for the accurate determination of transverse normal

BackgroundMulticlass classification of microarray data samples with a reduced number of genes is a rich and challenging problem in Bioinformatics research. The problem gets harder as the number of classes is increased. In addition, the performance of most classifiers is tightly linked to the effectiveness of mandatory gene selection methods. Critical to ...

The rapid accumulation of genetic information and advancement of experimental techniques have opened a new frontier in biomedical engineering. With the availability of well-characterized components from natural gene networks, the stage has been set for the engineering of artificial gene regulatory networks with sophisticated ...

Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such clusters can confound both accurate sequence assembly and downstream computational analysis, yet they represent a hotbed of functional innovation, ...

BackgroundDifficulties associated with implementing gene therapy are caused by the complexity of the underlying regulatory networks. The forms of interactions between the hundreds of genes, proteins, and metabolites in these networks are not known very accurately. An alternative approach is to limit consideration to ...

... Title : Time-Accurate Computations of Free-Flight Aerodynamics of a Spinning Projectile With and Without Flow Control. ...

Jul 25, 2006 ... PROPOSAL TITLE: Efficient and Accurate Computational Framework for ... to real fluid thermodynamics, as well as turbulent mixing effects. ...

... Accurate Computation of Non-Negative Anisotropic Group Scattering Cross Sections for Discrete Ordinates and Monte Carlo Radiation Transport. ...

... Accession Number : ADD419324. Title : An Accurate, Economical, Solar Insolation Computer Model for the United States,. Corporate Author : ...

BackgroundTightly regulated gene networks, precisely controlling the expression of protein molecules, have received considerable interest by the biomedical community due to their promising applications. Among the most well studied inducible transcription systems are the tetracycline regulatory expression systems based on the tetracycline resistance operon of Escherichia coli, ...

Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of ...

The availability of expression quantitative trait loci (eQTL) data can help understanding the genetic basis of variation in gene expression. However, it has proven difficult to accurately predict functional genetic changes due to low statistical power. To address this challenge, we developed a novel computational approach for combining ...

The computation of the multinomial distribution function is of interest to many researchers and practicers who are working in the areas of engineering and in the related disciplines of computing sciences. The accurate computation of probabilities is very ...

We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to ...

BackgroundProtein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have problems with small genes (either over-predicting or under-predicting). Therefore the question arises as to whether ...

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using Fgenes (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new ...