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Search Results: 1 - 10 of 8344 matches for " Victor Olman "
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Barcodes for genomes and applications
Fengfeng Zhou, Victor Olman, Ying Xu
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-546
Abstract: We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness.These and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.The challenges being faced in sorting out short genomic fragments generated by metagenome sequencing projects [1] pose a fundamental question: "does each genome have a unique signature imprinted on its short sequence fragments so that fragments from the same genomes in a metagenome can be identified accurately?" A positive answer to this question could have significant implications to many important genome and metagenome analysis problems such as identification of genetic material transferred from other organisms [2] or through virus invasions [3,4], separation of short sequence fragments generated by metagenome sequencing into individual genomes [5] and phylogenetic analyses of genomes [6].Understanding the intrinsic properties of genome sequences, either general to all or specific to some classes of genomes, has been the focus of many studies in the past two decades. Earlier work includes the discovery of the periodicity property of DNA sequences across bot
Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea
Fengfeng Zhou, Victor Olman, Ying Xu
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-36
Abstract: In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures.This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.Mobile genetic elements (MGEs) can move themselves within a genome and between genomes. They play key roles in modification of gene expression patterns by generating insertion mutations [1-3] and in genome rearrangement and evolution through homologous recombination [4-6]. Some of them, such as Tn5 in E. coli [7] and Salmonella typhimirium [7,8], have been extensively used to mediate insertional mutagenesis to perform genetic studies. The simplest form of MGE is the insertion sequence (IS) element, which usually encodes only a transposase [9]. IS elements are widely distributed in eubacterial and archaeal domains [9-11] and more than 1,500 different IS elements have been identified as of now [12].IS elements are usually organized compactly, most of which span 700 to 3,500 b
Computational prediction of Pho regulons in cyanobacteria
Zhengchang Su, Victor Olman, Ying Xu
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-156
Abstract: We have predicted and analyzed the Pho regulons in 19 sequenced cyanobacterial genomes using a highly effective scanning algorithm that we have previously developed. Our results show that different cyanobacterial species/ecotypes may encode diverse sets of genes responsible for the utilization of various sources of phosphorus, ranging from inorganic phosphate, phosphodiester, to phosphonates. Unlike in E. coli, some cyanobacterial genes that are directly involved in phosphorus assimilation seem to not be under the regulation of the regulator SphR (orthologue of PhoB in E coli.) in some species/ecotypes. On the other hand, SphR binding sites are found for genes known to play important roles in other biological processes. These genes might serve as bridging points to coordinate the phosphorus assimilation and other biological processes. More interestingly, in three cyanobacterial genomes where no sphR gene is encoded, our results show that there is virtually no functional SphR binding site, suggesting that transcription regulators probably play an important role in retaining their binding sites.The Pho regulons in cyanobacteria are highly diversified to accommodate to their respective living environments. The phosphorus assimilation pathways in cyanobacteria are probably tightly coupled to a number of other important biological processes. The loss of a regulator may lead to the rapid loss of its binding sites in a genome.Cyanobacteria are among the oldest life form on Earth. These organisms inhabit a broad range of ecological environments from fresh water, soil to diverse open oceanographic areas [1]. It is estimated that several cyanobacteria living in the open oceans contribute a significant fraction of Earth's primary production [2]. These bacteria also play important roles in the global cycling of nitrogen and phosphorus [3,4]. Therefore their activities have significant impacts on global environmental changes.Phosphorus is one of the essential elements for all li
Genomic Arrangement of Regulons in Bacterial Genomes
Han Zhang, Yanbin Yin, Victor Olman, Ying Xu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029496
Abstract: Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF's genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles.
Barcode Server: A Visualization-Based Genome Analysis System
Fenglou Mao, Victor Olman, Yan Wang, Ying Xu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056726
Abstract: We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a) identification of horizontally transferred genes, (b) identification of genomic islands with special properties and (c) binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculation of the k-mer based barcode image for a provided DNA sequence; (b) detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c) clustering of provided DNA sequences into groups having similar barcodes; and (d) homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode.
A Comparative Analysis of Gene-Expression Data of Multiple Cancer Types
Kun Xu,Juan Cui,Victor Olman,Qing Yang,David Puett,Ying Xu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013696
Abstract: A comparative study of public gene-expression data of seven types of cancers (breast, colon, kidney, lung, pancreatic, prostate and stomach cancers) was conducted with the aim of deriving marker genes, along with associated pathways, that are either common to multiple types of cancers or specific to individual cancers. The analysis results indicate that (a) each of the seven cancer types can be distinguished from its corresponding control tissue based on the expression patterns of a small number of genes, e.g., 2, 3 or 4; (b) the expression patterns of some genes can distinguish multiple cancer types from their corresponding control tissues, potentially serving as general markers for all or some groups of cancers; (c) the proteins encoded by some of these genes are predicted to be blood secretory, thus providing potential cancer markers in blood; (d) the numbers of differentially expressed genes across different cancer types in comparison with their control tissues correlate well with the five-year survival rates associated with the individual cancers; and (e) some metabolic and signaling pathways are abnormally activated or deactivated across all cancer types, while other pathways are more specific to certain cancers or groups of cancers. The novel findings of this study offer considerable insight into these seven cancer types and have the potential to provide exciting new directions for diagnostic and therapeutic development.
Computational prediction of the osmoregulation network in Synechococcus sp. WH8102
Xizeng Mao, Victor Olman, Rhona Stuart, Ian T Paulsen, Brian Palenik, Ying Xu
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-291
Abstract: We present here a computational study of the osmoregulation network in response to hyperosmotic stress of Synechococcus sp strain WH8102 using comparative genome analyses and computational prediction. In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress.From the predicted network model, we have made a number of interesting observations about WH8102. Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) σ38, one of the seven types of σ factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.Osmotic stress refers to the stress on a cell induced by sudden changes in impermeable solute concentrations around a cell that affect the equilibrium with the solution inside the cell. When this happens, water molecules will move in and out of cells by diffusion via the lipid bilayer or the aquaporin channels to regain the equilibrium. The induced water flow across the cell membrane will tend to cause changes in the cell volume, specifically in the cytoplasmic volume, and will induce a number of cellular responses to maintain the homeostasis of the cell's water content [1]. When the solute concentration inside a cell is higher than around the cell, i.e., when under hypoosmotic stress, water molecules will flow inwards, potentially causing animal cells to swell and increasing the turgor pressure in plant and bacterial cells. Alternatively when the impermeable solute concentration inside a cell is lower, i.e., when under hyperosmotic stress, water will flow outwards, hence shocking the cell
Genotype by environment interaction and genetic gain on unbalanced Pinus oocarpa provenances trials!
Olman Murillo
Agronomía Costarricense , 2001,
Abstract:
Indices de calidad para la reforestacion en Costa Rica
Olman Murillo
Agronomía Costarricense , 2000,
Abstract: Se propone 5 indices de calidad que penni- ten estimar certerarnentel nivel de calidad y po- tencial productivo de una plantaci6n forestal. £1 primer indice es el de calidad general y debe uti- lizarse preferiblemente en plantaciones no ralea- das. £ste indiceproducira valores de 1.0-4.0. Valo- res cercanos a 1 serlin de plantaciones de la mas al- ta calidad. £1 segundo es el de calidad de cosecha y se basa en la cantidad de individuos presentes por ha de calidad 1 y 2. Una plantaci6n con 400 indi- viduos de calidad 1 +2 seria excelente y con menos de 200 individuos seria de mala calidad. £1 tercero es el de calidad maxima, que busca reflejar en que proporci6n la plantaci6n se aproxima al maximo numero posible de individuos de calidad 1 y de 40 cm de dap que puede contener una plantaci6n fo- festal ala cosecha; es basado en N 1=250 Y genera harvalores porcentuales, donde una plantaci6n con >90% seria excelente y <50% de muy baja calidad. Sin embargo, para la industria forestal es de mayor valor practico basar los criterios de calidad en ter- infonnaminos de productos 0 trozas comerciales. Por tan- to, se puede utilizar el indice de calidad de trozas de 2.5 m de largo. Aquellas plantaciones con >1600 trozas/ha de calidad 1+2 son excelentes y aquellas <800 trozas son inaceptables. Por ultimo se incluye el indice de calidad de productividad, que permite valorar la calidad de una plantaci6n en
PRIME: A Mass Spectrum Data Mining Tool for De Novo Sequencing and PTMs Identification
Bo Yan,You-Xing Qu,Feng-Lou Mao,Victor N Olman,Ying XU,
Bo Yan
,You-Xing Qu,Feng-Lou Mao,Victor N. Olman,and Ying Xu

计算机科学技术学报 , 2005,
Abstract: sequencing is one of the most promising proteomics techniques for identification of protein post-translation modifications (PTMs) in studying protein regulations and functions. We have developed a computer tool PRIME for identification of b and y ions in tandem mass spectra, a key challenging problem in de novo sequencing. PRIME utilizes a feature that ions of the same and different types follow different mass-difference distributions to separate b from y ions correctly. We have formulated the problem as a graph partition problem. A linear integer-programming algorithm has been implemented to solve the graph partition problem rigorously and efficiently. The performance of PRIME has been demonstrated on a large amount of simulated tandem mass spectra derived from Yeast genome and its power of detecting PTMs has been tested on 216 simulated phosphopeptides. This research was supported in part by the National Science Foundation of U.S.A (Grant Nos.NSF/DBI-0354771 and #NSF/ITR-IIS-0407204). It was also funded in part by the U.S. Department of Energy's Genomes to Life program (http://doegenomestolife.org/) under project, “Carbon Sequestration in Synechococcus sp.: From Molecular Machines to Hierarchical Modeling” (www.genomes2life.org). Bo Yan received his Ph.D. degree in chemistry from Peking University. He is now working in the Computational Systems Biology Lab at University of Georgia, USA. His research interests include Monte Carlo simulations, graph theory, computational biology/chemistry and bioinformatics. You-Xing Qu received his Ph.D. degree in biophysics from Peking University, China. Currently he is working in the Computational Systems Biology Lab at the University of Georgia, USA. His research interests include computational biology, protein folding, structural biology, and biophysics. Feng-Lou Mao received his Ph.D. degree in computational chemistry from Peking University in 2001. He is now a postdoc researcher at University of Georgia, USA. His current research interests include bioinformatics, systems biology and computational biology. Victor N. Olman is a Senior Research Scientist in Biochemistry and Molecular Biology Department of UGA. He got the Ph.D. degree in mathematics from S. Petersburg University, Russia. Right now his main interests are in the field of mathematical applications in bioinformatics that include methods of mathematical statistics, graph theory, simulation and modeling of dynamic systems. He is a member of American Statistical Association. Ying Xu is a chair professor of bioinformatics and computational biology in the Biochemistry and Molecular Biology Department, and the director of the Institute of Bioinformatics, University of Georgia, USA. Before joining UGA in Sept 2003, he was a senior staff scientist and group leader at Oak Ridge National Laboratory, USA, where he still holds a joint position. He also holds guest or research professor positions at the University of Tennessee at Knoxville of USA, Jilin Univer
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