genome scale metabolic models reconstruction and analysis

... elementary mode and extreme pathway analysis [13] cannot be scaled up to analyze genome- scale metabolic networks, and to circumvent these problems, Schuster and colleagues have recently developed ... can be applied to genome- scale networks Design features of metabolic networks The reconstruction of metabolic networks for several organisms spread across the tree of life and that thrive in ... networks using elementary flux patterns Genome Res 2009, 19:1872-1883 Ebenhoh O, Handorf T, Heinrich R: Structural analysis of expanding metabolic networks Genome Inform 2004, 15:35-45 Matthaus...

Ngày tải lên: 12/08/2014, 17:20

... Computational mathematics : models, methods, and analysis with MATLAB and MPI / Robert E White p cm Includes bibliographical references and index ISBN 1-58488-364-2 (alk paper) Numerical analysis MATLAB ... Computers and Matrix Products 6.2 Vector Computations for Heat Di usion 6.3 Multiprocessors and Mass Transfer 6.4 MPI and the IBM/SP 6.5 MPI and Matrix Products 6.6 MPI and 2D Models ... numerical analysis, matrix algebra and partial di erential equations It does develop topics in these areas as is needed and also includes modeling and computation, and so there is more breadth and...

Ngày tải lên: 08/04/2014, 10:01

... segmentation and reconstruction run in well under one minute (about 15 seconds for segmentation and about 30 seconds for reconstruction) Analysis Results To determine the composition and volumes ... segmentation, reconstruction, and analysis of 3D thrombi in 2-photon microscopic images Our method and platform have been applied to study the structural differences between thrombi formed in wildtype and ... surface reconstruction strategies Section shows the experimental results Section provides quantitative analysis of various clot structures and properties Section summarizes our work and gives...

Ngày tải lên: 21/06/2014, 19:20

... database of metabolic pathways and enzymes,” Nucleic Acids Research, vol 32, database issue, pp D438–D442, 2004 [4] J L Reed, T D Vo, C H Schilling, and B O Palsson, “An expanded genome- scale of ... h, T Handorf, and R Heinrich, “A cross species o comparison of metabolic network functions,” Genome Informatics, vol 16, no 1, pp 203–213, 2005 13 [8] T Handorf, N Christian, O Ebenh¨ h, and D ... h, T Handorf, and D Kahn, “Evolutionary changes o of metabolic networks and their biosynthetic capacities,” IEE Proceedings: Systems Biology, vol 153, no 5, pp 354–358, 2006 [23] T Handorf and...

Ngày tải lên: 22/06/2014, 00:20

... genome- scale experimental datasets begin to emerge for B subtilis, genome- scale models of B subtilis are required for the analysis and interpretation of these datasets Genomescale metabolic models ... BO: Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome- scale metabolic model Genome Res 2004, 14:1298-1309 Becker SA, Palsson BO: Genome- scale reconstruction ... (Additional data file 4), and mappings of model compound and reaction IDs to IDs in the KEGG and other genome- scale models (Tables S1 and S2 in Additional data files and 2) The reactions included...

Ngày tải lên: 14/08/2014, 21:20

... interpretation of metabolic changes through metabolic flux analysis Metab Eng 2000, 2:277-292 128 Sheikh K, Forster J, Nielsen LK: Modeling hybridoma cell metabolism using a generic genome- scale metabolic ... optima in lp models for metabolic networks Comp Chem Eng 2000, 2:711-716 135 Mahadevan R, Schilling CH: The effects of alternate optimal solutions in constraint-based genome- scale metabolic models ... level, and its potential to analyze cellular metabolic behaviour in silico Preliminary analysis of some other common metabolic diseases such as hyperammonaemia, maple syrup urine disease and phenylketonuria...

Ngày tải lên: 13/08/2014, 16:21

... multi-way analysis, and as such he is the reason for this thesis Many e-mails, meetings, beers, and letters from and with Age Smilde have enabled me to grasp, refine and develop my ideas and those ... analysis of the data, and the goal of the analysis Several decomposition and calibration methods will be explained in the following Most of the models will be described using three-way data and ... improving the models and algorithms now available Hence, two other important aspects are the development of new models aimed at handling problems typical of today's scientific work, and better algorithms...

Ngày tải lên: 31/03/2014, 22:20

... www.it-ebooks.info 12 Models and Analysis in Distributed Systems Models and Analysis for Distributed Systems Nets (CPN) so their behavioral symmetries allow us to use quotient state graphs and compact ... transitions and incompatible elementary actions As modern distributed systems and consequently their models become very large and complex it is important to express their structure Architecture and Analysis ... of real-time systems being theoretically well www.it-ebooks.info 14 Models and Analysis in Distributed Systems Models and Analysis for Distributed Systems founded, tools have been developed for...

Ngày tải lên: 24/04/2014, 15:35

... conditions and models It is meant to be self contained Thermal effects, which often accompany friction are presented Recent models for wear and adhesion are described fully, and so are models for ... temperature, and QA and R are additional parameters More elaborate expressions can be found in [101], and we refer the reader there and the references therein, and also to [60] and the references ... control and of system parameter identification can be addressed These are of considerable theoretical and applied interest Moreover, optimal M Shillor, M Sofonea, J.J Telega: Models and Analysis...

Ngày tải lên: 24/04/2014, 16:49

... Computing System Reliability Models and Analysis This page intentionally left blank Computing System Reliability Models and Analysis Min Xie Yuan-Shun Dai and Kim-Leng Poh National University ... hardware and integrated software/hardware systems It also introduces typical models in the reliability analysis of the distributed/networked systems, and then further develops some new models and ... processes and Nonhomogeneous Poisson processes (NHPP) are also introduced, which are essential tools used in this book Chapters and present important models for the reliability analysis of hardware and...

Ngày tải lên: 01/06/2014, 00:08

... Watson and Venter), one Chinese, two Koreans, and three Africans (only the Bantu genome from [16] was included as, unlike the Khoisan genome, SNP Tong et al Genome Biology 2010, 11:R91 http://genomebiology.com/2010/11/9/R91 ... Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al: Initial sequencing and analysis of the human genome Nature 2001, 409:860-921 Genome. gov | ENCODE and ... density STRUCTURE [54,55] and principle components analyses of the Irish cohort both in comparison to similar cohorts from the UK, Netherlands, Denmark, Sweden and Finland [15], and in separate analyses...

Ngày tải lên: 09/08/2014, 22:23

... poplar genome, two commercial oligonucleotide genome- scale microarrays were designed One was produced by NimbleGen and another by Affymetrix In STM-homolog over-expressing poplars, 102 and 173 ... transcriptome analysis using the Affymetrix Poplar Genome GeneChip It monitors more than 56,000 transcripts based on poplar genome and EST sequences In this report, we describe the identities and biological ... poplar and Arabidopsis, and the low level of conservation between poplar and rice, are not surprising given the considerably larger phylogenetic distance between rice, a monocot, and poplar and...

Ngày tải lên: 12/08/2014, 03:21

... error and statistical criteria in the design and analysis of experiments for discrimination between rival kinetic models Metods Enzymol 1982, 87:370-390 Gurevich KG: Definition of equilibrium, and ... measurements of ligandreceptor complex concentration, [RL] are determined The investigator has to solve two basic interrelated problems [6]: discrimination among the ligand-receptor binding models (1–3 ... http://www.tbiomed.com/content/1/1/11 among receptor binding models or to analyse the parameters by traditional analytical methods Materials and methods Let us write the law of mass action for each ligand-receptor interaction scheme...

Ngày tải lên: 13/08/2014, 22:22

... compartmentalized genome- scale metabolic model Genome Res 2004, 14:1298-1309 Heinemann M, Kummel A, Ruinatscha R, Panke S: In silico genomescale reconstruction and validation of the Staphylococcus aureus metabolic ... undertaken to construct and describe the properties of metabolic networks at the genome scale It is timely, therefore, to integrate both efforts and move towards a genome- scale analysis of cell metabolism ... lactis using a genome- scale flux model BMC Microbiol 2005, 5:39 Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genomescale model of Escherichia coli K-12 (iJR904 GSM/GPR) Genome Biol 2003,...

Ngày tải lên: 14/08/2014, 07:21

... contributions AB and TFS contributed to the design and implementation of the algorithm, the analysis and interpretation of the data, and to drafting and revising the manuscript WMG contributed to the analysis ... and 5) Conclusion This approach has been shown to outperform existing techniques with its speed and ability to handle genome- scale datasets far exceeding current limitations The ability to handle ... number of genomes and number of genes BPAnalysis works for gene orders on uni-chromosomal genomes and trees of eight or fewer leaves [23] GRAPPA is an optimized re-implementation of the BPAnalysis...

Ngày tải lên: 14/08/2014, 08:20

... of the three mammalian genomes Human, mouse and rat genes and orthologous gene sets By aligning all known and predicted transcripts to the latest human, mouse and rat genomes we obtained 34,949, ... CpG-islands (see Materials and methods), we found that most RefSeq genes are CpG-island related In total, 68%, 54% and 56% promoters obtained above for human, mouse and rat are CpG-island related ... RefSeq and GenBank (mRNA), and transcripts predicted by Ensembl, TWINSCAN and GenomeScan (RefSeq XM) in the annotation of UCSC genome assemblies were obtained They were aligned to the genomes...

Ngày tải lên: 14/08/2014, 14:22

... R44.2 Genome Biology 2006, Volume 7, Issue 5, Article R44 Mau et al development of whole -genome comparison tools [15-17], initially focused LGT discovery on genome- wide scans for islands of ... allelic substitution Results As seen in Figure 1, the Mauve genome aligner takes the four E coli and two Shigella flexneri genome sequences and returns 34 local alignments spanning 3.4 Mb of homologous ... Mbp Mbp Mbp E coli K−12 genome coordinates Figure MG1655 as reference KO, and Three excursions (KS ,genome KC) spanning the alignment with K-12 Three excursions (KS, KO, and KC) spanning the alignment...

Ngày tải lên: 14/08/2014, 16:21

... extensibility and procedural stability Analysis procedures and results are made transparent to users, allowing them to formulate their own opinion of results and providing a means to reproduce and maintain ... used in the analysis of genome annotation, gene structure determination, alternative splicing, and gene copy distribution [13-17] Developing ad hoc methods for such analyses is expensive and time ... cognate cDNA and EST alignments (Figure items 11 and 12) Also, displayed are the alignments of homologous Oryza sativa protein annotations (Figure item 10), Genome Biology 2006, 7:R111 http://genomebiology.com/2006/7/11/R111...

Ngày tải lên: 14/08/2014, 17:22

... mimics human diseases and offers the ability to quickly and inexpensively test the efficacy and safety of compound libraries (Amatruda and Patton, 2008; Liu and Leach, 2011; Zon and Peterson, 2005) ... transgenesis and microinjection, further strengthen the use of zebrafish Recently, there is increased generation and analysis of zebrafish models of human diseases (Amatruda and Patton, 2008; Liu and ... as its entirely sequenced genome and the genetic and biological similarities to human (Fausto and Campbell, 2010) Furthermore, the mouse together with other mammalian models including rats has...

Ngày tải lên: 10/09/2015, 15:48

... sensitivity analysis Local sensitivity analysis is a particular form of sensitivity analysis similar to metabolic control analysis (Salter et al., 1994) It has been widely applied on models of ... A+B v1 v2 AB (2.1) where A and B are substrates, AB denotes the formed complex, and v1 and v2 represents CHAPTER BACKGROUND AND RELATED WORK 20 the association rate and dissociation rate respectively ... friendly, and fun My time at NUS has been wonderful because of all of them Finally, I want to thank my family I thank my cousins, Liu Mei and Cai Xiaoming, and my uncle and auntie, Liu Yingzhu and...

Ngày tải lên: 10/09/2015, 15:48