Systems medicine and metabolic modelling

Mardinoglu A, Nielsen J (University of Technology, Gothenburg, Sweden). Systems medicine and metabolic modelling (Key Symposium). J Intern Med 2012; 271:142–154.

[1]  E. Lundberg,et al.  Towards a knowledge-based Human Protein Atlas , 2010, Nature Biotechnology.

[2]  Yanli Wang,et al.  PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..

[3]  E. Ruppin,et al.  Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism , 2010, Molecular systems biology.

[4]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[5]  J. Nielsen,et al.  Uncovering transcriptional regulation of metabolism by using metabolic network topology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  E. Lundberg,et al.  Creation of an antibody‐based subcellular protein atlas , 2010, Proteomics.

[7]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[8]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[9]  F. Bruggeman,et al.  Introduction to systems biology. , 2007, EXS.

[10]  John T. Wei,et al.  Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression , 2009, Nature.

[11]  Erik K. Malm,et al.  A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics* , 2005, Molecular & Cellular Proteomics.

[12]  O. Demin,et al.  The Edinburgh human metabolic network reconstruction and its functional analysis , 2007, Molecular systems biology.

[13]  Daniel Rios,et al.  Ensembl 2011 , 2010, Nucleic Acids Res..

[14]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[15]  F. Bruggeman,et al.  The nature of systems biology. , 2007, Trends in microbiology.

[16]  Jens Nielsen,et al.  Systems biology of lipid metabolism: From yeast to human , 2009, FEBS letters.

[17]  T. Welborn,et al.  The metabolic syndrome as a tool for predicting future diabetes: the AusDiab study , 2008, Journal of Internal Medicine.

[18]  Vinay Satish Kumar,et al.  GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions , 2009, PLoS Comput. Biol..

[19]  I. Nookaew,et al.  Identifying Molecular Effects of Diet through Systems Biology: Influence of Herring Diet on Sterol Metabolism and Protein Turnover in Mice , 2010, PloS one.

[20]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[21]  J. Nielsen,et al.  Integration of metabolome data with metabolic networks reveals reporter reactions , 2006, Molecular systems biology.

[22]  Antje Chang,et al.  BRENDA, the enzyme information system in 2011 , 2010, Nucleic Acids Res..

[23]  B. Palsson,et al.  Systems approach to refining genome annotation , 2006, Proceedings of the National Academy of Sciences.

[24]  Jeffrey D. Orth,et al.  Systematizing the generation of missing metabolic knowledge , 2010, Biotechnology and bioengineering.

[25]  L. Hood,et al.  Systems medicine: the future of medical genomics and healthcare , 2009, Genome Medicine.

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

[27]  E. Lundberg,et al.  A global view of protein expression in human cells, tissues, and organs , 2009, Molecular systems biology.

[28]  Dennis B. Troup,et al.  NCBI GEO: archive for functional genomics data sets—10 years on , 2010, Nucleic Acids Res..

[29]  P. Zimmet,et al.  Genotype, obesity and cardiovascular disease – has technical and social advancement outstripped evolution? , 2003, Journal of internal medicine.

[30]  Jens Nielsen,et al.  Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes , 2010, PLoS Comput. Biol..

[31]  P. Karp,et al.  Computational prediction of human metabolic pathways from the complete human genome , 2004, Genome Biology.

[32]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[33]  C. Bouchard,et al.  Obesity – is it a genetic disorder? , 2003, Journal of internal medicine.

[34]  Harvey J. Greenberg,et al.  Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data* , 2004, Journal of Biological Chemistry.

[35]  B. Palsson,et al.  Large-scale in silico modeling of metabolic interactions between cell types in the human brain , 2010, Nature Biotechnology.

[36]  Igor Goryanin,et al.  Compartmentalization of the Edinburgh Human Metabolic Network , 2010, BMC Bioinformatics.

[37]  Bernhard O. Palsson,et al.  Metabolic systems biology , 2009, Encyclopedia of Complexity and Systems Science.

[38]  H. Parkinson,et al.  Large scale comparison of global gene expression patterns in human and mouse , 2010, Genome Biology.

[39]  L. Groop,et al.  The dysmetabolic syndrome , 2001, Journal of internal medicine.

[40]  Carol A. Bocchini,et al.  A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) , 2011, Human mutation.

[41]  Edward A Dennis,et al.  Applications of mass spectrometry to lipids and membranes. , 2011, Annual review of biochemistry.

[42]  C. Fenselau.  Applications of Mass Spectrometry , 1978 .

[43]  Keith Tyo,et al.  Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism. , 2010, FEMS yeast research.

[44]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2006, Nucleic Acids Res..

[45]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[46]  J Bruce German,et al.  Genomics and metabolomics as markers for the interaction of diet and health: lessons from lipids. , 2003, The Journal of nutrition.

[47]  Rolf Apweiler,et al.  Evidence standards in experimental and inferential INSDC Third Party Annotation data. , 2006, Omics : a journal of integrative biology.

[48]  Michael J. Lush,et al.  genenames.org: the HGNC resources in 2011 , 2010, Nucleic Acids Res..

[49]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[50]  Kiran Raosaheb Patil,et al.  Use of genome-scale microbial models for metabolic engineering. , 2004, Current opinion in biotechnology.

[51]  J. Nielsen,et al.  Integration of gene expression data into genome-scale metabolic models. , 2004, Metabolic engineering.

[52]  Sangdun Choi,et al.  Introduction To Systems Biology , 2010 .

[53]  Bernhard O. Palsson,et al.  Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems , 2006, PLoS Comput. Biol..

[54]  Markus J. Herrgård,et al.  Network-based prediction of human tissue-specific metabolism , 2008, Nature Biotechnology.

[55]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[56]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[57]  Markus Perola,et al.  Metabonomic, transcriptomic, and genomic variation of a population cohort , 2010, Molecular systems biology.

[58]  J. Nicholson.  Global systems biology, personalized medicine and molecular epidemiology , 2006, Molecular systems biology.

[59]  E. Webb.  Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. , 1992 .

[60]  Piero Carninci,et al.  Whole transcriptome analysis: what are we still missing? , 2011, Wiley interdisciplinary reviews. Systems biology and medicine.

[61]  Andrew G. McDonald,et al.  ExplorEnz: the primary source of the IUBMB enzyme list , 2008, Nucleic Acids Res..

[62]  David S. Wishart,et al.  HMDB: a knowledgebase for the human metabolome , 2008, Nucleic Acids Res..

[63]  Chunhui Li,et al.  Exploring the diversity of complex metabolic networks , 2005, Bioinform..

[64]  María Martín,et al.  Ongoing and future developments at the Universal Protein Resource , 2010, Nucleic Acids Res..

[65]  F. Milagro,et al.  Individuality and epigenetics in obesity , 2009, Obesity reviews : an official journal of the International Association for the Study of Obesity.

[66]  C. Gille,et al.  HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology , 2010, Molecular systems biology.

[67]  Markus J. Herrgård,et al.  Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.

[68]  Intawat Nookaew,et al.  Prospects for systems biology and modeling of the gut microbiome. , 2011, Trends in biotechnology.

[69]  B. Palsson,et al.  Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions , 2010, Molecular systems biology.

[70]  G. Hon,et al.  Next-generation genomics: an integrative approach , 2010, Nature Reviews Genetics.

[71]  Aleksander S Popel,et al.  Systems Biology and Physiome Projects , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.

[72]  F. Pontén,et al.  The Human Protein Atlas—a tool for pathology , 2008, The Journal of pathology.

[73]  G. Stephanopoulos,et al.  Exploiting biological complexity for strain improvement through systems biology , 2004, Nature Biotechnology.

[74]  J. Stelling,et al.  Genome‐scale metabolic networks , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.

[75]  A. Bairoch,et al.  The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. , 2004, Plant physiology and biochemistry : PPB.

[76]  A. Barabasi,et al.  Drug—target network , 2007, Nature Biotechnology.

[77]  Fredrik H. Karlsson,et al.  A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut , 2011, Microbial Ecology.

[78]  Jens Nielsen,et al.  Can yeast systems biology contribute to the understanding of human disease? , 2008, Trends in biotechnology.

[79]  I. Goryanin,et al.  Human metabolic network reconstruction and its impact on drug discovery and development. , 2008, Drug discovery today.

[80]  Tudor I. Oprea,et al.  Computational systems chemical biology. , 2011, Methods in molecular biology.

[81]  Bernhard Ø Palsson,et al.  Understanding human metabolic physiology: a genome-to-systems approach. , 2009, Trends in biotechnology.

[82]  L. Magni,et al.  Diabetes: Models, Signals, and Control , 2010, IEEE Reviews in Biomedical Engineering.

[83]  Thomas S Deisboeck,et al.  Personalizing medicine: a systems biology perspective , 2009, Molecular systems biology.

[84]  Jens Nielsen,et al.  MEMOSys: Bioinformatics platform for genome-scale metabolic models , 2011, BMC Systems Biology.

[85]  D. Kell.  Systems biology, metabolic modelling and metabolomics in drug discovery and development. , 2006, Drug discovery today.

[86]  M. Tewari,et al.  The Clinical Applications of a Systems Approach , 2006, PLoS medicine.

[87]  Ted G. Lewis,et al.  Network Science: Theory and Practice , 2009 .

[88]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[89]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences: current status, policy and new initiatives , 2008, Nucleic Acids Res..