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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

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An efficient algorithm for perfect phylogeny haplotyping

An efficient algorithm for perfect phylogeny haplotyping

引用

Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： R. VijayaSatya A. Mukherjee School of Computer Science University of Central Florida USA

The Perfect Phylogeny Haplotyping (PPH) problem is one of the many computational approaches to the Haplotype Inference (HI) problem. Though there are many O(nm/sup 2/) solutions to the PPH problem, the complexity of the PPH problem itself has remained an open question. In this paper, we introduce the FlexTree data structure that represents all the solutions for a PPH instance. We also introduce row ordering that arranges the genotypes in a more manageable fashion. The column ordering, the FlexTree data structure and the row ordering together make the O(nm) OPPH algorithm possible. We also present some results on simulated data, which demonstrate that the OPPH algorithm performs quiet impressively when compared to the earlier O(nm/sup 2/) algorithms.

关键词： Phylogeny Humans Genomics bioinformatics Biological cells Inference algorithms Data structures History Computer science Diseases

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TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree

TreeRefiner: a tool for refining a multiple alignment on a p...

引用

Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： A. Manohar S. Batzoglou Department of Computer Science University of Stanford Stanford CA USA

We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefiner optimizes the sum-of-pairs function in a restricted three-dimensional space around the alignment. At each internal node of the unrooted tree, the multiple alignment is projected to the sub-alignments corresponding to the three neighboring nodes, and three-dimensional dynamic programming is performed within a user-specified radius r around the original alignment. We test TreeRefiner on simulated sequences aligned by several popular tools, and demonstrate substantial improvements in the percentage of correctly aligned positions.

关键词： Phylogeny bioinformatics Genomics Proteins Iterative methods Testing Computer science Biology Dynamic programming Biological system modeling

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Islands of tractability for parsimony haplotyping

Islands of tractability for parsimony haplotyping

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： R. Sharan B.V. Halldorsson S. Istrail School of Computer Science Tel-Aviv University Tel-Aviv Israel DeCode Genetics Reykjavik Iceland Division of Biology California Institute of Technology Pasadena CA USA

We study the parsimony approach to haplotype inference, which calls for finding a set ofhaplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.

关键词： bioinformatics Genomics Sequences Biological cells Genetics Inference algorithms Computer science Decoding Biology Polynomials

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Sequential classification for microarray and clinical data

Sequential classification for microarray and clinical data

引用

ieee computational systems bioinformatics conference, CSB Workshops and Poster Abstracts

作者： G. Tusch Grand Rapids Medical Education and Research Center for Health Professions (MERC) Grand Rapids MI USA Grand Valley State University Allendale MI USA

Sequential classification uses in a stepwise process only part of the data (evidence) for partial classification, i.e., classifying only objects with sufficient evidence and leaving the rest unclassified. In the following steps the procedure is repeated using additional data until all objects are classified. This is especially useful when data become available only at certain points in time, as in surgical decision making, i.e., clinical patient data, lab data, or cDNA microarray expression data from tissue samples become available before, during and after the operation. Surgeons are interested in classifying patients into low or high risk groups, which might need special measures, e.g., prolonged intensive care.

关键词： Surgery Error analysis Decision making Neoplasms Costs Statistical analysis Clinical trials Neurons Artificial neural networks bioinformatics

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The synthetic gene designer: a flexible Web platform to explore sequence space of synthetic genes for heterologous expression

The synthetic gene designer: a flexible Web platform to expl...

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ieee computational systems bioinformatics conference, CSB Workshops and Poster Abstracts

作者： G. Wu N. Bashir-Bello S. Freeland Department of Biological Sciences University of Maryland Baltimore MD USA

"Codon optimization" is a general approach that seeks to improve heterologous expression when a gene is moved into a foreign genome that exhibits different codon usage from its native genome. However, it is still unclear exactly what it means to optimize codons for protein expression: diverse interpretations exist, and exploratory research continues. Thus, to facilitate flexible redesign of genes for heterologous expression, we have developed a bona fide web application: the "synthetic gene designer". Compared with existing codon optimization software, the synthetic gene designer provides greater flexibility in several key features of codon optimization strategy. The software, together with online tutorials and help, is available at http://***. net/codon/***.

关键词： Space exploration Sequences bioinformatics Application software Design optimization Genomics Genetics Organisms Proteins Biology

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Operon prediction in cyanobacteria using comparative genomics

Operon prediction in cyanobacteria using comparative genomic...

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ieee computational systems bioinformatics conference, CSB Workshops and Poster Abstracts

作者： N. Khuri N.S. Rao Carnegie Institution Wa Dpb Stanford CA USA College of Engineering San Jose State University Foundation San Jose CA USA

In this work, we performed a comprehensive analysis of the genome organization of eight publicly available cyanobacterial genomes and of the extensively studied Escherichia coli K12. Our comparison revealed striking similarities in organization of different microbial genomes. We examined the orientation of putative CDS, and distance distribution patterns between adjacent putative CDS in the whole genome as well as between genes within operons and across operon borders. Our results enabled us to calculate distance log-likeihoods for gene pairs to be part of the same operon and to apply this metric to predict operons in two newly sequenced cyanobacterial genomes, Synechococcus OS-A and OS-B'.

关键词： Genomics bioinformatics Educational institutions Performance analysis Proteins Prediction methods Organisms Predictive models DNA conferences

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computational method for temporal pattern discovery in biomedical genomic databases

Computational method for temporal pattern discovery in biome...

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： M.I. Rafiq M.J. O'Connor A.K. Das Stanford Medical Informatics Stanford CA USA

With the rapid growth of biomedical research databases, opportunities for scientific inquiry have expanded quickly and led to a demand for computational methods that can extract biologically relevant patterns among vast amounts of data. A significant challenge is identifying temporal relationships among genotypic and clinical (phenotypic) data. Few software tools are available for such pattern matching, and they are not interoperable with existing databases. We are developing and validating a novel software method for temporal pattern discovery in biomedical genomics. In this paper, we present an efficient and flexible query algorithm (called TEMF) to extract statistical patterns from time-oriented relational databases. We show that TEMF-as an extension to our modular temporal querying application (Chronus II)-can express a wide range of complex temporal aggregations without the need for data processing in a statistical software package. We show the expressivity of TEMF using example queries from the Stanford HIV Database.

关键词： Biomedical computing Genomics bioinformatics Relational databases Biology computing Data mining Software tools Pattern matching Application software Data processing

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An approach to generating and verifying complex scripts and procedures

An approach to generating and verifying complex scripts and ...

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ieee computational systems bioinformatics conference, CSB Workshops and Poster Abstracts

作者： J.L. Rash M.G. Hinchey D. Gracanin C.A. Rouff Information Systems Division NASA Goddard Space Flight Center Greenbelt MD USA Department of Computer Science Virginia Polytechnic Institute and State University Blacksburg VA USA Advanced Concepts Business Unit SAIC McLean VA USA

Currently available tools and methods for system development that start with a formal model of a system and mechanically produce a provably equivalent implementation are valuable but not sufficient. The "gap" that such tools and methods leave unfilled is that the formal models cannot be proven to be equivalent to the system requirements as originated by the customer. For the classes of complex systems whose behavior can be described as a finite (but significant) set of scenarios, we offer a method for mechanically transforming requirements expressed in restricted natural language, or appropriate graphical notations, into a provably equivalent formal model that can be used as the basis for code generation and other transformations. The same approach may be applied to address computer science aspects of bioinformatics problems. Many software tools for bioinformatics have been developed using scripting languages such as Perl and Python. Scripts are developed based on a set of requirements that can be expressed using English-like statements. Using our approach, these may be used to automatically generate and validate scripts rather than write them from scratch.

关键词： bioinformatics Software tools Computer science Databases Software performance Hardware Software quality NASA Information systems Natural languages

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ssahaSNP - a polymorphism detection tool on a whole genome scale

ssahaSNP - a polymorphism detection tool on a whole genome s...

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ieee computational systems bioinformatics conference, CSB Workshops and Poster Abstracts

作者： Z. Ning M. Caccamo J.C. Mullikin Wellcome Trust Genome Campus Cambridge UK Genome Technology Branch/NHGRI Bethesda MD USA

We present a software package which can detect homozygous SNPs and indels on a eukaryotic genome scale from millions of shotgun reads. Matching seeds of a few kmer words are found to locate the position of the read on the genome. Full sequence alignment is performed to detect base variations. Quality values of both variation bases and neighbouring bases are checked to exclude possible sequence base errors. To analyze polymorphism level in the genome, we used the package to detect indels from 20 million WGS reads against the draft WGS assembly. From the dataset, we detected a total number of 663,660 indels, giving an estimated average indel density at about one indel every 2.48 kilobases. Distribution of indels length and variation of indel mapped times are also analyzed.

关键词： Genomics bioinformatics Packaging Assembly Software packages Error analysis Cancer detection Diseases Databases Data structures

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Visualization of logic analysis of phylogenetic profiles (LAPP)

Visualization of logic analysis of phylogenetic profiles (LA...

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ieee computational systems bioinformatics conference, CSB Workshops and Poster Abstracts

作者： K.A. Robbins L. Zhao Department of Computer Science Cajal Neuroscience Research Institute University of Technology San Antonio USA Department of Computer Science University of Technology San Antonio USA

Recently Bowers et al analyzed triplet logic relationships among 4873 clusters of orthologous groups (COGS) from 67 fully sequenced organisms by calculating how well logic relationships between proteins a and b predicted the presence or absence of protein c (the uncertainty). The log of the normalized uncertainty distribution follows an approximately linear relationship for uncertainties in the interval [0.1, 0.9]. Using fitted parameters of this relationship as a characterization, we develop four types of visual analysis for LAPP data: distributions of uncertainty over logical relation type, distributions of uncertainty over functional categories, relationships of uncertainty of the overall population to known network relationships of a particular organism, and relationships of uncertainty distributions to groups obtained by standard clustering techniques. The purpose of this study is two-fold: to better understand the implications of uncertainty predictions for automatic protein network generation and to create new visualization tools for looking at this type of data.

关键词： Visualization Logic Phylogeny Uncertainty Proteins bioinformatics Organisms Genomics Computer science Databases

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