Data Integration, Metabolic Networks and Systems Biology

[1]  Søren Bak,et al.  Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  S. Kanaya,et al.  Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. , 2001, Gene.

[3]  M. Hirai,et al.  Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Makoto Kobayashi,et al.  Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana , 2007, BMC Systems Biology.

[5]  R. Dixon,et al.  Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. , 2005, Journal of experimental botany.

[6]  F. Hynne,et al.  Full-scale model of glycolysis in Saccharomyces cerevisiae. , 2001, Biophysical chemistry.

[7]  P. May,et al.  Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii , 2008, Genetics.

[8]  Gianluca Bontempi,et al.  minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information , 2008, BMC Bioinformatics.

[9]  Kazuki Saito,et al.  Rice-Arabidopsis FOX line screening with FT-NIR-based fingerprinting for GC-TOF/MS-based metabolite profiling , 2010, Metabolomics.

[10]  Joachim Kopka,et al.  Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration. , 2007, The Plant journal : for cell and molecular biology.

[11]  F. Carrari,et al.  Metabolic regulation underlying tomato fruit development. , 2006, Journal of experimental botany.

[12]  Jacques van Helden,et al.  RSAT: regulatory sequence analysis tools , 2008, Nucleic Acids Res..

[13]  M. Sjöström,et al.  Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. , 2004, Analytical biochemistry.

[14]  Rongchen Wang,et al.  Genomic Analysis of a Nutrient Response in Arabidopsis Reveals Diverse Expression Patterns and Novel Metabolic and Potential Regulatory Genes Induced by Nitrate , 2000, Plant Cell.

[15]  P. Mendes,et al.  The origin of correlations in metabolomics data , 2005, Metabolomics.

[16]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[17]  Age K. Smilde,et al.  Metabolic network discovery through reverse engineering of metabolome data , 2009, Metabolomics.

[18]  Joost T. van Dongen,et al.  Combined Transcript and Metabolite Profiling of Arabidopsis Leaves Reveals Fundamental Effects of the Thiol-Disulfide Status on Plant Metabolism1[W][OA] , 2006, Plant Physiology.

[19]  Stefan R. Henz,et al.  A gene expression map of Arabidopsis thaliana development , 2005, Nature Genetics.

[20]  An-Ping Zeng,et al.  The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks , 2003, Bioinform..

[21]  Ramana V. Davuluri,et al.  AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors , 2003, BMC Bioinformatics.

[22]  P. May,et al.  ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii , 2009, BMC Genomics.

[23]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[24]  A. Marshall,et al.  Trends in biotech literature 2006 , 2007, Nature Biotechnology.

[25]  Sara L. Zimmer,et al.  The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions , 2007, Science.

[26]  Antônio de Pádua Braga,et al.  Constructive and pruning methods for neural network design , 2002, VII Brazilian Symposium on Neural Networks, 2002. SBRN 2002. Proceedings..

[27]  B O Palsson,et al.  Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. , 2001, American journal of physiology. Regulatory, integrative and comparative physiology.

[28]  Kazuki Saito,et al.  Identification of a Flavonol 7-O-Rhamnosyltransferase Gene Determining Flavonoid Pattern in Arabidopsis by Transcriptome Coexpression Analysis and Reverse Genetics*♦ , 2007, Journal of Biological Chemistry.

[29]  Lothar Willmitzer,et al.  Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. , 2005, Journal of experimental botany.

[30]  Tetsuya Sakurai,et al.  PRIMe: A Web Site That Assembles Tools for Metabolomics and Transcriptomics , 2008, Silico Biol..

[31]  Björn H. Junker,et al.  Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central Metabolism1[W] , 2008, Plant Physiology.

[32]  J. Macgregor,et al.  Analysis of multiblock and hierarchical PCA and PLS models , 1998 .

[33]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[34]  D. Deforce,et al.  Joint GC-MS and LC-MS platforms for comprehensive plant metabolomics: repeatability and sample pre-treatment. , 2009, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[35]  D. Fell,et al.  Is maximization of molar yield in metabolic networks favoured by evolution? , 2008, Journal of theoretical biology.

[36]  L. Quek,et al.  AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis1[W] , 2009, Plant Physiology.

[37]  Joachim Selbig,et al.  Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1 , 2005, Plant Physiology.

[38]  Dong-Liang Lin,et al.  Peer Reviewed: Isotopically Labeled Analogues for Drug Quantitation , 2002 .

[39]  Peter J. F. Lucas,et al.  Constraint-based probabilistic learning of metabolic pathways from tomato volatiles , 2009, Metabolomics.

[40]  Thomas Hankemeier,et al.  Microbial metabolomics: toward a platform with full metabolome coverage. , 2007, Analytical biochemistry.

[41]  Alisdair R Fernie,et al.  Dynamic Plastid Redox Signals Integrate Gene Expression and Metabolism to Induce Distinct Metabolic States in Photosynthetic Acclimation in Arabidopsis[W] , 2009, The Plant Cell Online.

[42]  Andreas Hoppe,et al.  Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks , 2007, BMC Systems Biology.

[43]  R. Díaz-Sierra,et al.  Deduction of Chemical Mechanisms from the Linear Response around Steady State , 1999 .

[44]  Bartolomeu Acioli-Santos,et al.  Transcriptional and metabolic profiling of grape (Vitis vinifera L.) leaves unravel possible innate resistance against pathogenic fungi. , 2008, Journal of experimental botany.

[45]  Artem Cherkasov,et al.  Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length , 2010, J. Comput. Biol..

[46]  Shoshi Kikuchi,et al.  Development of a novel data mining tool to find cis-elements in rice gene promoter regions , 2008, BMC Plant Biology.

[47]  Tommy S. Jørstad,et al.  Towards global understanding of plant defence against aphids--timing and dynamics of early Arabidopsis defence responses to cabbage aphid (Brevicoryne brassicae) attack. , 2008, Plant, cell & environment.

[48]  Nick James,et al.  NASCArrays: a repository for microarray data generated by NASC's transcriptomics service , 2004, Nucleic Acids Res..

[49]  U. Sauer,et al.  Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. , 2009, Analytical chemistry.

[50]  Marc-Thorsten Hütt,et al.  Consistency analysis of metabolic correlation networks , 2007, BMC Systems Biology.

[51]  Masanori Arita,et al.  Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis , 2010, BMC Bioinformatics.

[52]  Jie Luo,et al.  A Novel Polyamine Acyltransferase Responsible for the Accumulation of Spermidine Conjugates in Arabidopsis Seed[W][OA] , 2009, The Plant Cell Online.

[53]  D. Fell,et al.  A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties1[C][W] , 2009, Plant Physiology.

[54]  Peter D. Karp,et al.  MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research1[w] , 2005, Plant Physiology.

[55]  R. Steuer,et al.  Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation. , 2006, Bio Systems.

[56]  P. Zimmermann,et al.  GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w] , 2004, Plant Physiology.

[57]  M. Hirai,et al.  Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'. , 2008, Trends in plant science.

[58]  A. Burgard,et al.  Optimization-based framework for inferring and testing hypothesized metabolic objective functions. , 2003, Biotechnology and bioengineering.

[59]  J. Roger,et al.  Fusion of aroma, FT-IR and UV sensor data based on the Bayesian inference. Application to the discrimination of white grape varieties , 2003 .

[60]  A. Smilde,et al.  Fusion of mass spectrometry-based metabolomics data. , 2005, Analytical chemistry.

[61]  J. Bowman,et al.  Genetic interactions among floral homeotic genes of Arabidopsis. , 1991, Development.

[62]  Hideyuki Suzuki,et al.  KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps1[w] , 2005, Plant Physiology.

[63]  Yuji Sawada,et al.  Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis. , 2009, Plant & cell physiology.

[64]  Joachim Selbig,et al.  Stability of Metabolic Correlations under Changing Environmental Conditions in Escherichia coli – A Systems Approach , 2009, PloS one.

[65]  Kiana Toufighi,et al.  The Botany Array Resource: E-northerns, Expression Angling, and Promoter Analyses , 2022 .

[66]  Yuji Sawada,et al.  Omics-based approaches to methionine side chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase. , 2009, Plant & cell physiology.

[67]  O. Fiehn,et al.  Differential metabolic networks unravel the effects of silent plant phenotypes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Sven P. Jacobsson,et al.  Evaluation of different techniques for data fusion of LC/MS and 1H-NMR , 2007 .

[69]  Kim Sneppen,et al.  Pathway identification by network pruning in the metabolic network of Escherichia coli , 2009, Bioinform..

[70]  Ilya Venger,et al.  Gene Expression and Metabolism in Tomato Fruit Surface Tissues1[C][W] , 2008, Plant Physiology.

[71]  Bjarne Gram Hansen,et al.  Biochemical Networks and Epistasis Shape the Arabidopsis thaliana Metabolome[W] , 2008, The Plant Cell Online.

[72]  Kengo Kinoshita,et al.  COXPRESdb: a database of coexpressed gene networks in mammals , 2007, Nucleic Acids Res..

[73]  C. Ouzounis,et al.  Expansion of the BioCyc collection of pathway/genome databases to 160 genomes , 2005, Nucleic acids research.

[74]  S. Schuster,et al.  Metabolic network structure determines key aspects of functionality and regulation , 2002, Nature.

[75]  W. Scheible,et al.  AtMyb41 Regulates Transcriptional and Metabolic Responses to Osmotic Stress in Arabidopsis[W][OA] , 2009, Plant Physiology.

[76]  Kengo Kinoshita,et al.  ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis , 2006, Nucleic Acids Res..

[77]  M. Hirai,et al.  Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks in Arabidopsis by Integration of Metabolomics and Transcriptomics* , 2005, Journal of Biological Chemistry.

[78]  A. Burgard,et al.  Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.

[79]  Erwin P. Gianchandani,et al.  Predicting biological system objectives de novo from internal state measurements , 2008, BMC Bioinformatics.

[80]  Urs von Stockar,et al.  Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways , 2009, Biotechnology and bioengineering.

[81]  J. Collins,et al.  Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.

[82]  Bernard Henrissat,et al.  Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. , 2006, The Plant journal : for cell and molecular biology.

[83]  Je-Gun Joung,et al.  Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology1[W][OA] , 2009, Plant Physiology.

[84]  David Heckerman,et al.  Learning With Bayesian Networks (Abstract) , 1995, ICML.

[85]  Alberto de la Fuente,et al.  Discovery of meaningful associations in genomic data using partial correlation coefficients , 2004, Bioinform..

[86]  Matej Oresic,et al.  Normalization method for metabolomics data using optimal selection of multiple internal standards , 2007, BMC Bioinformatics.

[87]  Richard A. Dixon,et al.  Activation Tagging Identifies a Conserved MYB Regulator of Phenylpropanoid Biosynthesis , 2000, Plant Cell.

[88]  Erwin P. Gianchandani,et al.  Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks , 2008, PLoS Comput. Biol..

[89]  Yan Ni,et al.  Metabolic profiling using combined GC–MS and LC–MS provides a systems understanding of aristolochic acid‐induced nephrotoxicity in rat , 2007, FEBS letters.

[90]  R. Bino,et al.  Intra- and inter-metabolite correlation spectroscopy of tomato metabolomics data obtained by liquid chromatography-mass spectrometry and nuclear magnetic resonance , 2008, Metabolomics.

[91]  Kazuki Saito,et al.  Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. , 2009, Analytical chemistry.

[92]  G. Weiller,et al.  Global Changes in the Transcript and Metabolic Profiles during Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants1[W][OA] , 2009, Plant Physiology.

[93]  D. Inzé,et al.  A functional genomics approach toward the understanding of secondary metabolism in plant cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[94]  Stephen J. Roberts,et al.  Probabilistic Modeling in Bioinformatics and Medical Informatics , 2010 .

[95]  Kevin Murphy,et al.  Modelling Gene Expression Data using Dynamic Bayesian Networks , 2006 .

[96]  Steffen Klamt,et al.  Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. , 2002, Biotechnology and bioengineering.

[97]  C. Shelton,et al.  Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis1[W][OA] , 2008, Plant Physiology.

[98]  M. Hirai,et al.  Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. , 2005, The Plant journal : for cell and molecular biology.

[99]  J. W. Allwood,et al.  1H NMR, GC-EI-TOFMS, and data set correlation for fruit metabolomics: application to spatial metabolite analysis in melon. , 2009, Analytical chemistry.

[100]  Oliver Fiehn,et al.  A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[101]  Oliver Fiehn,et al.  Metabolic networks of Cucurbita maxima phloem. , 2003, Phytochemistry.

[102]  H. Qian,et al.  Energy balance for analysis of complex metabolic networks. , 2002, Biophysical journal.

[103]  Daniel Eriksson,et al.  Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. , 2007, The Plant journal : for cell and molecular biology.

[104]  Jesper Tegnér,et al.  Reverse engineering gene networks using singular value decomposition and robust regression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[105]  Shigehiko Kanaya,et al.  Informatics for unveiling hidden genome signatures. , 2003, Genome research.

[106]  Suzanne M. Paley,et al.  The Pathway Tools cellular overview diagram and Omics Viewer , 2006, Nucleic acids research.

[107]  John A. Morgan,et al.  BMC Systems Biology BioMed Central Research article , 2009 .

[108]  Douglas E Lake.  Nonparametric entropy estimation using kernel densities. , 2009, Methods in enzymology.

[109]  Daniel J. Kliebenstein,et al.  Linking Metabolic QTLs with Network and cis-eQTLs Controlling Biosynthetic Pathways , 2007, PLoS genetics.

[110]  Masami Y. Hirai,et al.  Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model , 2007, BMC Bioinformatics.

[111]  M. Hirai,et al.  Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis , 2007, Proceedings of the National Academy of Sciences.

[112]  Eytan Ruppin,et al.  Network-based prediction of metabolic enzymes' subcellular localization , 2009, Bioinform..

[113]  Anthony Hall,et al.  Plant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage , 2005, Science.

[114]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[115]  Wei Sha,et al.  A Systems Biology Study of Two Distinct Growth Phases of Saccharomyces cerevisiae Cultures , 2004 .

[116]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[117]  O. Fiehn,et al.  Metabolite profiling for plant functional genomics , 2000, Nature Biotechnology.

[118]  Rithy K. Roth,et al.  Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays , 2000, Nature Biotechnology.

[119]  Claudio Altafini,et al.  Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data , 2007, Bioinform..

[120]  J. Pech,et al.  Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling[W] , 2009, The Plant Cell Online.

[121]  Kazuo Shinozaki,et al.  Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. , 2009, The Plant journal : for cell and molecular biology.

[122]  Carsten O. Daub,et al.  Estimating mutual information using B-spline functions – an improved similarity measure for analysing gene expression data , 2004, BMC Bioinformatics.

[123]  Ute Roessner,et al.  Metabolic Profiling Allows Comprehensive Phenotyping of Genetically or Environmentally Modified Plant Systems , 2001, Plant Cell.

[124]  W. Weckwerth.  Metabolomics in systems biology. , 2003, Annual review of plant biology.

[125]  Korbinian Strimmer,et al.  An empirical Bayes approach to inferring large-scale gene association networks , 2005, Bioinform..

[126]  Johan Trygg,et al.  Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. , 2007, The Plant journal : for cell and molecular biology.

[127]  R. A. van den Berg,et al.  Centering, scaling, and transformations: improving the biological information content of metabolomics data , 2006, BMC Genomics.

[128]  Johan Trygg,et al.  Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen. , 2009, Journal of proteome research.

[129]  Martin Müller,et al.  ADP-Glucose Pyrophosphorylase-Deficient Pea Embryos Reveal Specific Transcriptional and Metabolic Changes of Carbon-Nitrogen Metabolism and Stress Responses1[W] , 2008, Plant Physiology.

[130]  M. Mann,et al.  Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system , 2006, Genome Biology.

[131]  Arun Rawat,et al.  Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data , 2008, BMC Bioinformatics.

[132]  Ian D Wilson,et al.  Analytical strategies in metabonomics. , 2007, Journal of proteome research.

[133]  Erwin P. Gianchandani,et al.  Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks , 2008, PLoS Computational Biology.

[134]  B. Hammock,et al.  Mass spectrometry-based metabolomics. , 2007, Mass spectrometry reviews.

[135]  Kazuki Saito,et al.  Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene–Metabolite Correlations in Arabidopsis[W][OA] , 2008, The Plant Cell Online.

[136]  Björn Usadel,et al.  Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process1[W][OA] , 2008, Plant Physiology.

[137]  U. Sauer,et al.  Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli , 2007, Molecular systems biology.

[138]  Carsten O. Daub,et al.  The mutual information: Detecting and evaluating dependencies between variables , 2002, ECCB.

[139]  D. Kell.  Metabolomics and systems biology: making sense of the soup. , 2004, Current opinion in microbiology.

[140]  Holger Puchta,et al.  Biochemical characterization of RecQ helicases from Arabidopsis thaliana , 2007 .

[141]  J. Selbig,et al.  Parallel analysis of transcript and metabolic profiles: a new approach in systems biology , 2003, EMBO reports.

[142]  C. Chassagnole,et al.  Dynamic modeling of the central carbon metabolism of Escherichia coli. , 2002, Biotechnology and bioengineering.

[143]  A. Fernie,et al.  Deciphering Transcriptional and Metabolic Networks Associated with Lysine Metabolism during Arabidopsis Seed Development1[C][W][OA] , 2009, Plant Physiology.

[144]  Chris Wiggins,et al.  ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.

[145]  Kazuo Shinozaki,et al.  The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. , 2008 .

[146]  B. Palsson,et al.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli Covert , 2002 .

[147]  Xiaodong Wang,et al.  Gene Regulatory Network Reconstruction Using Conditional Mutual Information , 2008, EURASIP J. Bioinform. Syst. Biol..

[148]  Jürgen Kurths,et al.  Observing and Interpreting Correlations in Metabolic Networks , 2003, Bioinform..

[149]  Achille Messac,et al.  Integrated Energy and Flux Balance Based Multiobjective Framework for Large-Scale Metabolic Networks , 2007, Annals of Biomedical Engineering.

[150]  S. Wold,et al.  Orthogonal projections to latent structures (O‐PLS) , 2002 .

[151]  V. Steinmetz,et al.  A Methodology for Sensor Fusion Design: Application to Fruit Quality Assessment , 1999 .

[152]  Daniel Eriksson,et al.  Orthogonal projections to latent structures as a strategy for microarray data normalization , 2007, BMC Bioinformatics.

[153]  E. Bornberg-Bauer,et al.  The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. , 2007, The Plant journal : for cell and molecular biology.

[154]  I. Wilson,et al.  A multi-analytical platform approach to the metabonomic analysis of plasma from normal and Zucker (fa/fa) obese rats. , 2006, Molecular bioSystems.

[155]  Kengo Kinoshita,et al.  ATTED-II provides coexpressed gene networks for Arabidopsis , 2008, Nucleic Acids Res..

[156]  Kenji Akiyama,et al.  AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development[W][OA] , 2009, Plant Physiology.

[157]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[158]  Stacy Lawrence,et al.  Trends in biotech literature 2005 , 2006, Nature Biotechnology.

[159]  Joachim Kopka,et al.  Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling. , 2005, Trends in biotechnology.

[160]  Lijun Luo,et al.  Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis , 2009, Proceedings of the National Academy of Sciences.

[161]  Choon Nam Ong,et al.  A multi-analytical approach for metabolomic profiling of zebrafish (Danio rerio) livers. , 2009, Molecular bioSystems.

[162]  A. Barsch,et al.  Antisense Repression of the Medicago truncatula Nodule-Enhanced Sucrose Synthase Leads to a Handicapped Nitrogen Fixation Mirrored by Specific Alterations in the Symbiotic Transcriptome and Metabolome1[W] , 2007, Plant Physiology.

[163]  S. Rhee,et al.  MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. , 2004, The Plant journal : for cell and molecular biology.

[164]  Adam M. Feist,et al.  Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.

[165]  Barbara M. Bakker,et al.  Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. , 2000, European journal of biochemistry.

[166]  Mark P. Styczynski,et al.  Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery. , 2007, Analytical chemistry.

[167]  Catherine Deborde,et al.  Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development1[C][W][OA] , 2009, Plant Physiology.