systems biology

Summary

Summary: Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.

Top Publications

  1. pmc KEGG for representation and analysis of molecular networks involving diseases and drugs
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 38:D355-60. 2010
  2. pmc EcoCyc: fusing model organism databases with systems biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 41:D605-12. 2013
  3. ncbi The ERBB network: at last, cancer therapy meets systems biology
    Yosef Yarden
    Department of Biological Regulation, Weizmann Institute of Science, 1 Hertzl Street, Candiotty Building, Room 312, Rehovot 76100, Israel
    Nat Rev Cancer 12:553-63. 2012
  4. pmc A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011
    Jeffrey D Orth
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Mol Syst Biol 7:535. 2011
  5. pmc Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans
    Troy D Querec
    Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, Georgia 30329, USA
    Nat Immunol 10:116-25. 2009
  6. ncbi Network pharmacology: the next paradigm in drug discovery
    Andrew L Hopkins
    Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Dundee, UK
    Nat Chem Biol 4:682-90. 2008
  7. pmc Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
    Peter D Karp
    Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA
    Brief Bioinform 11:40-79. 2010
  8. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
  9. pmc A methodology for performing global uncertainty and sensitivity analysis in systems biology
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 254:178-96. 2008
  10. pmc Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
    Sharon Greenblum
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 109:594-9. 2012

Research Grants

  1. Mapping the Human Binary Interactome Network
    MARC contact VIDAL; Fiscal Year: 2010
  2. Conference on Systems & Biology
    Marc Vidal; Fiscal Year: 2005
  3. Integrated interactome mapping
    Marc Vidal; Fiscal Year: 2006
  4. A C. elegans localization-of-expression mapping project
    Marc Vidal; Fiscal Year: 2005
  5. Rewiring Pathways and Networks by Environmental Perturbations
    Marc Vidal; Fiscal Year: 2010
  6. Intelligent Information Systems for Systems Biology
    Leroy Hood; Fiscal Year: 2003
  7. Correlative Multimodal Imaging of Cardiac Electrophysiology and Metabolism
    JOHN PETER contact WIKSWO; Fiscal Year: 2010
  8. Mathematical Modeling of Anthrax Infection
    Yoram Vodovotz; Fiscal Year: 2002
  9. GPx-3, Vascular Oxidant Stress, and Thrombosis
    Joseph Loscalzo; Fiscal Year: 2006
  10. HOMOCYST(E)INE, OXIDATIVE STRESS, AND NITRIC OXIDE
    Joseph Loscalzo; Fiscal Year: 2004

Detail Information

Publications303 found, 100 shown here

  1. pmc KEGG for representation and analysis of molecular networks involving diseases and drugs
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 38:D355-60. 2010
    ..The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets...
  2. pmc EcoCyc: fusing model organism databases with systems biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 41:D605-12. 2013
    ..coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc...
  3. ncbi The ERBB network: at last, cancer therapy meets systems biology
    Yosef Yarden
    Department of Biological Regulation, Weizmann Institute of Science, 1 Hertzl Street, Candiotty Building, Room 312, Rehovot 76100, Israel
    Nat Rev Cancer 12:553-63. 2012
    ....
  4. pmc A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011
    Jeffrey D Orth
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Mol Syst Biol 7:535. 2011
    ..Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.
  5. pmc Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans
    Troy D Querec
    Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, Georgia 30329, USA
    Nat Immunol 10:116-25. 2009
    A major challenge in vaccinology is to prospectively determine vaccine efficacy. Here we have used a systems biology approach to identify early gene 'signatures' that predicted immune responses in humans vaccinated with yellow fever ..
  6. ncbi Network pharmacology: the next paradigm in drug discovery
    Andrew L Hopkins
    Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Dundee, UK
    Nat Chem Biol 4:682-90. 2008
    ..Advances in systems biology are revealing a phenotypic robustness and a network structure that strongly suggests that exquisitely ..
  7. pmc Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
    Peter D Karp
    Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA
    Brief Bioinform 11:40-79. 2010
    ..The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of ..
  8. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
    ..In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification...
  9. pmc A methodology for performing global uncertainty and sensitivity analysis in systems biology
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 254:178-96. 2008
    ....
  10. pmc Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
    Sharon Greenblum
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 109:594-9. 2012
    ..Here, we introduce a metagenomic systems biology computational framework, integrating metagenomic data with an in silico systems-level analysis of metabolic ..
  11. pmc The biomass objective function
    Adam M Feist
    GT Life Sciences, Inc, 10520 Wateridge Circle, San Diego, CA 92122, USA
    Curr Opin Microbiol 13:344-9. 2010
    ..Here we review fundamental issues associated with its formulation and use to compute optimal growth states...
  12. ncbi Gene regulatory network inference: data integration in dynamic models-a review
    Michael Hecker
    Leibniz Institute for Natural Product Research and Infection Biology Hans Knoell Institute, Jena, Germany
    Biosystems 96:86-103. 2009
    b>Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques...
  13. doi Systems biology: Metabonomics
    Jeremy K Nicholson
    Nature 455:1054-6. 2008
  14. pmc Towards a rigorous assessment of systems biology models: the DREAM3 challenges
    Robert J Prill
    IBM T J Watson Research Center, Yorktown Heights, New York, United States of America
    PLoS ONE 5:e9202. 2010
    b>Systems biology has embraced computational modeling in response to the quantitative nature and increasing scale of contemporary data sets. The onslaught of data is accelerating as molecular profiling technology evolves...
  15. pmc Connecting extracellular metabolomic measurements to intracellular flux states in yeast
    Monica L Mo
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    BMC Syst Biol 3:37. 2009
    ..Extracellular metabolome or metabolic profiling data, in particular, can provide an insightful view of intracellular physiological states in a noninvasive manner...
  16. pmc Effects of abiotic stress on plants: a systems biology perspective
    Grant R Cramer
    Department of Biochemistry and Molecular Biology, Mail Stop 330, University of Nevada, Reno, Nevada 89557, USA
    BMC Plant Biol 11:163. 2011
    ..Plant responses to these stresses are equally complex. Systems biology approaches facilitate a multi-targeted approach by allowing one to identify regulatory hubs in complex ..
  17. pmc Systems biology of vaccination for seasonal influenza in humans
    Helder I Nakaya
    Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
    Nat Immunol 12:786-95. 2011
    Here we have used a systems biology approach to study innate and adaptive responses to vaccination against influenza in humans during three consecutive influenza seasons...
  18. ncbi Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology
    T S Keshava Prasad
    Institute of Bioinformatics, Bangalore, India
    Methods Mol Biol 577:67-79. 2009
    ....
  19. pmc InnateDB: facilitating systems-level analyses of the mammalian innate immune response
    David J Lynn
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    Mol Syst Biol 4:218. 2008
    ....
  20. ncbi Boolean modeling in systems biology: an overview of methodology and applications
    Rui Sheng Wang
    Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
    Phys Biol 9:055001. 2012
    ..In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as ..
  21. ncbi Event extraction for systems biology by text mining the literature
    Sophia Ananiadou
    University of Manchester, Manchester M13 9PL, UK
    Trends Biotechnol 28:381-90. 2010
    b>Systems biology recognizes in particular the importance of interactions between biological components and the consequences of these interactions. Such interactions and their downstream effects are known as events...
  22. pmc Single-cell systems biology by super-resolution imaging and combinatorial labeling
    Eric Lubeck
    Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, USA
    Nat Methods 9:743-8. 2012
    ..These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells is a natural approach to bring systems biology into single cells.
  23. pmc Systems biology of stem cell fate and cellular reprogramming
    Ben D MacArthur
    Department of Gene and Cell Medicine and Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
    Nat Rev Mol Cell Biol 10:672-81. 2009
    ....
  24. pmc Global reconstruction of the human metabolic network based on genomic and bibliomic data
    Natalie C Duarte
    Bioengineering Department, University of California at San Diego, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 104:1777-82. 2007
    ..These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.
  25. ncbi Towards environmental systems biology of Shewanella
    James K Fredrickson
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Nat Rev Microbiol 6:592-603. 2008
    ....
  26. ncbi Quantitative, high-resolution proteomics for data-driven systems biology
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D 82152, Germany
    Annu Rev Biochem 80:273-99. 2011
    b>Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins...
  27. ncbi Systems biology and combination therapy in the quest for clinical efficacy
    Jonathan B Fitzgerald
    Merrimack Pharmaceuticals, One Kendall Square, Building 700 2nd floor, Cambridge, Massachusetts 02139, USA
    Nat Chem Biol 2:458-66. 2006
    ....
  28. pmc Controlled vocabularies and semantics in systems biology
    Melanie Courtot
    Terry Fox Laboratory, Vancouver, Canada
    Mol Syst Biol 7:543. 2011
    The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an ..
  29. pmc InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation
    Karin Breuer
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A1S6, Canada
    Nucleic Acids Res 41:D1228-33. 2013
    ..Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism...
  30. pmc A systems biology approach for pathway level analysis
    Sorin Draghici
    Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48202, USA
    Genome Res 17:1537-45. 2007
    ..By using a systems biology approach, we developed an impact analysis that includes the classical statistics but also considers other ..
  31. ncbi The heat shock response: systems biology of proteotoxic stress in aging and disease
    Richard I Morimoto
    Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
    Cold Spring Harb Symp Quant Biol 76:91-9. 2011
    ..This complex, systems-wide interdependence ensures cellular health span and organismal life span...
  32. ncbi Impact of genome reduction on bacterial metabolism and its regulation
    Eva Yus
    Centre for Genomic Regulation CRG and Universitat Pompeu Fabra, Avenida Dr Aiguader 88, 08003 Barcelona, Spain
    Science 326:1263-8. 2009
    ....
  33. ncbi Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
    Henning Schmidt
    Fraunhofer Chalmers Research Centre for Industrial Mathematics, Chalmers Science Park, SE 41288 Göteborg, Sweden
    Bioinformatics 22:514-5. 2006
    We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB...
  34. pmc Maximizing the information content of experiments in systems biology
    Juliane Liepe
    Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
    PLoS Comput Biol 9:e1002888. 2013
    ..Constructing and inferring global mathematical models from experimental data is, however, central to systems biology. Different experimental setups provide different insights into such systems...
  35. pmc The ciliopathies: a transitional model into systems biology of human genetic disease
    Erica E Davis
    Center for Human Disease Modeling, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
    Curr Opin Genet Dev 22:290-303. 2012
    ....
  36. pmc Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir
    Li Xie
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 7:e1002037. 2011
    ..This finding provides a molecular basis to explain the broad-spectrum anti-cancer effect of Nelfinavir and presents opportunities to optimize the drug as a targeted polypharmacology agent...
  37. ncbi Systems biology: parameter estimation for biochemical models
    Maksat Ashyraliyev
    Centrum voor Wiskunde en Informatica, Amsterdam, The Netherlands
    FEBS J 276:886-902. 2009
    ..In this minireview, we discuss the identifiability of models, both intrinsic to the model and taking into account the available data. Furthermore, we give an overview of the most frequently used approaches to search the parameter space...
  38. ncbi Physicochemical modelling of cell signalling pathways
    Bree B Aldridge
    Center for Cell Decision Processes, Department Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Nat Cell Biol 8:1195-203. 2006
    ....
  39. pmc A decade of systems biology
    Han Yu Chuang
    Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
    Annu Rev Cell Dev Biol 26:721-44. 2010
    b>Systems biology provides a framework for assembling models of biological systems from systematic measurements...
  40. pmc Eigengene networks for studying the relationships between co-expression modules
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 1:54. 2007
    ..Ample literature exists on how to detect biologically meaningful modules in networks but there is a need for methods that allow one to study the relationships between modules...
  41. pmc A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
    Kartik M Mani
    Department of Biomedical Informatics DBMI, Columbia University, New York, NY 10032, USA
    Mol Syst Biol 4:169. 2008
    ..In this paper, we introduce a systems biology approach, based on the analysis of molecular interactions that become dysregulated in specific tumor ..
  42. pmc Geometric interpretation of gene coexpression network analysis
    Steve Horvath
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
    PLoS Comput Biol 4:e1000117. 2008
    ..The unification of coexpression network methods with traditional data mining methods can inform the application and development of systems biologic methods...
  43. pmc Structural identifiability of systems biology models: a critical comparison of methods
    Oana Teodora Chis
    Bioprocess Engineering Group, IIM CSIC, Vigo, Spain
    PLoS ONE 6:e27755. 2011
    ..The results reveal that the generating series approach, in combination with identifiability tableaus, offers the most advantageous compromise among range of applicability, computational complexity and information provided...
  44. pmc How to infer gene networks from expression profiles
    Mukesh Bansal
    Telethon Institute of Genetics and Medicine, Via P Castellino, Naples, Italy
    Mol Syst Biol 3:78. 2007
    ....
  45. ncbi Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
    Mark Gilchrist
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Nature 441:173-8. 2006
    ..Because ATF3 is itself induced by lipopolysaccharide, it seems to regulate TLR-stimulated inflammatory responses as part of a negative-feedback loop...
  46. pmc Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
    Sarah L Kinnings
    Department of Biology, University of York, York, UK
    PLoS Comput Biol 5:e1000423. 2009
    ..Previously we developed a chemical systems biology approach to identify off-targets of major pharmaceuticals on a proteome-wide scale...
  47. pmc A systems biology approach reveals that tissue tropism to West Nile virus is regulated by antiviral genes and innate immune cellular processes
    Mehul S Suthar
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
    PLoS Pathog 9:e1003168. 2013
    ..Using a systems biology approach, we defined the host innate immune response signature and actions that restrict WNV tissue tropism...
  48. pmc Boolean network model predicts cell cycle sequence of fission yeast
    Maria I Davidich
    Institut fur Theoretische Physik, Universitat Bremen, Bremen, Germany
    PLoS ONE 3:e1672. 2008
    ..While the latter operates in a strongly damped mode, driven by external excitation, the S. pombe network represents an auto-excited system with external damping...
  49. pmc Network analyses in systems pharmacology
    Seth I Berger
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
    Bioinformatics 25:2466-72. 2009
    ..Taken together, these types of analyses can lead to new therapeutic options while improving the safety and efficacy of existing medications...
  50. pmc Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
    Nathan E Lewis
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    Mol Syst Biol 6:390. 2010
    ..Thus, differential gene and protein expression from wild-type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM-computed optimal growth states...
  51. pmc Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples
    Douglas B Kell
    School of Chemistry and The Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK
    Arch Toxicol 84:825-89. 2010
    ..g. of iron chelators plus antioxidants) are likely to prove most effective. A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the ..
  52. ncbi The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
    Neil Swainston
    Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom
    J Integr Bioinform 8:186. 2011
    ..The individual modules manipulate reconstructions encoded in Systems Biology Markup Language (SBML), and can be chained to generate a reconstruction pipeline, or used individually during ..
  53. ncbi Visualization of omics data for systems biology
    Nils Gehlenborg
    European Bioinformatics Institute, Cambridge, UK
    Nat Methods 7:S56-68. 2010
    ..In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions...
  54. pmc Structure-based systems biology for analyzing off-target binding
    Lei Xie
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, MC9743, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Curr Opin Struct Biol 21:189-99. 2011
    ..While a very ambitious goal, some progress is being made...
  55. pmc A data integration methodology for systems biology
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17296-301. 2005
    ..In an accompanying companion paper, we demonstrate the applicability of our approach to biological data. We have integrated our methodology into a free open source software package named POINTILLIST...
  56. pmc Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling
    Benjamin Volkmer
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    PLoS ONE 6:e23126. 2011
    b>Systems biology modeling typically requires quantitative experimental data such as intracellular concentrations or copy numbers per cell...
  57. pmc Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
    Jacek Puchałka
    Synthetic and Systems Biology Group, Helmholtz Center for Infection Research HZI, Braunschweig, Germany
    PLoS Comput Biol 4:e1000210. 2008
    ..The solidly validated model yields valuable insights into genotype-phenotype relationships and provides a sound framework to explore this versatile bacterium and to capitalize on its vast biotechnological potential...
  58. pmc Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions
    Sonia Osorio
    Max Planck Institut fur Molekulare Pflanzenphysiologie, 14476 Potsdam Golm, Germany
    Plant Physiol 157:405-25. 2011
    ..These results further revealed multiple ethylene-associated events during tomato ripening, providing new insights into the molecular biology of ethylene-mediated ripening regulatory networks...
  59. pmc Environments that induce synthetic microbial ecosystems
    Niels Klitgord
    Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 6:e1001002. 2010
    ....
  60. ncbi Software for systems biology: from tools to integrated platforms
    Samik Ghosh
    The Systems Biology Institute, Minato, Tokyo, Japan
    Nat Rev Genet 12:821-32. 2011
    ..Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, ..
  61. pmc A systems approach to prion disease
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 5:252. 2009
    ..Our systems analysis provides a comprehensive basis for developing models for prion replication and disease, and suggests some possible therapeutic approaches...
  62. pmc Genome-scale gene/reaction essentiality and synthetic lethality analysis
    Patrick F Suthers
    Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Syst Biol 5:301. 2009
    ..By analyzing the functional classifications of the genes involved in synthetic lethals, we reveal surprising connections within and across clusters of orthologous group functional classifications...
  63. pmc Nonequilibrium thermodynamics of thiol/disulfide redox systems: a perspective on redox systems biology
    Melissa Kemp
    The Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
    Free Radic Biol Med 44:921-37. 2008
    ..b>Systems biology provides approaches to address the complexity of these responses...
  64. ncbi Functional integration of a metabolic network model and expression data without arbitrary thresholding
    Paul A Jensen
    Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
    Bioinformatics 27:541-7. 2011
    ..This procedure requires selecting relatively subjective expression thresholds, often requiring several iterations and refinements to capture the expression dynamics and retain model functionality...
  65. ncbi Metabolomics for functional genomics, systems biology, and biotechnology
    Kazuki Saito
    RIKEN Plant Science Center, Tsurumi ku, Yokohama, Japan
    Annu Rev Plant Biol 61:463-89. 2010
    ..b>Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to ..
  66. pmc VirtualPlant: a software platform to support systems biology research
    Manpreet S Katari
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
    Plant Physiol 152:500-15. 2010
    ..VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective...
  67. ncbi Systems biology: experimental design
    Clemens Kreutz
    Physics Department, University of Freiburg, Germany
    FEBS J 276:923-42. 2009
    ..Furthermore, the relevant classical aspects of experimental design, such as randomization, replication and confounding, are reviewed...
  68. pmc Functional cis-regulatory genomics for systems biology
    Jongmin Nam
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 107:3930-5. 2010
    ..This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology...
  69. pmc The genetic control of growth rate: a systems biology study in yeast
    Pinar Pir
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Syst Biol 6:4. 2012
    ..It has not been determined whether the set of HFC genes is the same at all growth rates or whether it is the same in conditions of nutrient limitation or excess...
  70. ncbi Network systems biology for drug discovery
    D K Arrell
    Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
    Clin Pharmacol Ther 88:120-5. 2010
    b>Systems biology provides a platform for integrating multiple components and interactions underlying cell, organ, and organism processes in health and disease...
  71. pmc Precise generation of systems biology models from KEGG pathways
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    BMC Syst Biol 7:15. 2013
    ..Thus, a direct conversion into systems biology models would produce incomplete and erroneous models.
  72. pmc VANTED v2: a framework for systems biology applications
    Hendrik Rohn
    Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Corrensstr 3, 06466 Gatersleben, Germany
    BMC Syst Biol 6:139. 2012
    ..Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets...
  73. pmc Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range
    Ty M Thomson
    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 108:20265-70. 2011
    ..Additional analysis and experiment suggest that scaffold abundance sets a tradeoff between maximum system output and system dynamic range, a prediction supported by recent experiments...
  74. ncbi Computational systems biology and in silico modeling of the human microbiome
    Elhanan Borenstein
    University of Washington, Seattle, 98195 5065, USA
    Brief Bioinform 13:769-80. 2012
    ..I also discuss possible future applications and research avenues that such metagenomic systems biology and predictive system-level models may facilitate.
  75. ncbi A unifying view of 21st century systems biology
    Marc Vidal
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    FEBS Lett 583:3891-4. 2009
    ....
  76. pmc Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
    Juan Nogales
    Center for Systems Biology, University of Iceland, 101 Reykjavik, Iceland
    Proc Natl Acad Sci U S A 109:2678-83. 2012
    ..The results and modeling approach presented here may promote a better understanding of the photosynthetic process. They can also guide bioengineering projects toward optimal biofuel production in photosynthetic organisms...
  77. ncbi Systems pharmacology: bridging systems biology and pharmacokinetics-pharmacodynamics (PKPD) in drug discovery and development
    Piet H van der Graaf
    Pfizer, Department of Pharmacometrics, Global Clinical Pharmacology, IPC 096, Sandwich, CT13 9NJ, UK
    Pharm Res 28:1460-4. 2011
    ..realisation that innovation could be dramatically catalysed by creating synergy at the interface between Systems Biology and PKPD, two disciplines which until now have largely existed in 'parallel universes' with a limited track ..
  78. pmc Dynamical modeling and multi-experiment fitting with PottersWheel
    Thomas Maiwald
    Freiburg Center for Data Analysis and Modeling, Freiburg University, Freiburg, Germany
    Bioinformatics 24:2037-43. 2008
    Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously...
  79. pmc Molecular links between cellular senescence, longevity and age-related diseases - a systems biology perspective
    Robi Tacutu
    The Shraga Segal Department of Microbiology and Immunology, Center for Multidisciplinary Research on Aging, Ben Gurion University of the Negev, Beer Sheva, Israel
    Aging (Albany NY) 3:1178-91. 2011
    ..Our comprehensive data mining revealed over 250 genes tightly associated with CS. Using systems biology tools, we found that CS is closely interconnected with aging, longevity and ARDs, either by sharing common ..
  80. pmc When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases
    Vincent Navratil
    Universite de Lyon, IFR128 Biosciences Lyon Gerland, Lyon 69007, France
    BMC Syst Biol 5:13. 2011
    ..New advances in the field are expected from systems-level modelling and integration of the incessant torrent of high-throughput "-omics" data...
  81. pmc Comparative systems biology across an evolutionary gradient within the Shewanella genus
    Konstantinos T Konstantinidis
    School of Civil and Environmental Engineering and School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Proc Natl Acad Sci U S A 106:15909-14. 2009
    ..Collectively, our results provide important new information toward beginning a systems-level understanding of bacterial species and genera...
  82. ncbi Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network
    Tao Ma
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua National Laboratory of Information Science and Technology Department of Automation, Tsinghua University, Beijing 100084, China
    Mol Biosyst 6:613-9. 2010
    b>Systems biology is a general trend of contemporary scientific development...
  83. pmc Boolean network models of cellular regulation: prospects and limitations
    Stefan Bornholdt
    Institute for Theoretical Physics, University of Bremen, Bremen, Germany
    J R Soc Interface 5:S85-94. 2008
    ..Finally, prospects of Boolean models in exploratory dynamical models for biological circuits and their mutants will be discussed...
  84. pmc Modular cell biology: retroactivity and insulation
    Domitilla Del Vecchio
    Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Syst Biol 4:161. 2008
    ..We introduce, in particular, a mechanism based on a phosphorylation-dephosphorylation cycle. This mechanism enjoys a remarkable insulation property, due to the fast timescales of the phosphorylation and dephosphorylation reactions...
  85. ncbi Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models
    Kamil Erguler
    Centre for Bioinformatics, Imperial College London, UK
    Mol Biosyst 7:1593-602. 2011
    ..Here we present a comprehensive analysis of 180 systems biology models, which allows us to classify the parameters with respect to their contribution to the overall ..
  86. ncbi Drug-target network
    Muhammed A Yildirim
    Center for Cancer Systems Biology CCSB, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Biotechnol 25:1119-26. 2007
    ..Significant differences in distance were found between etiological and palliative drugs. A recent trend toward more rational drug design was observed...
  87. ncbi Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference
    Minh Quach
    IBISC FRE CNRS 2873, University of Evry and Genopole 523, place des terrasses 91025 Evry, France
    Bioinformatics 23:3209-16. 2007
    ..However, biological systems considered as dynamical, non-linear and generally partially observed processes may be difficult to estimate even if the structure of interactions is given...
  88. pmc Transcript length bias in RNA-seq data confounds systems biology
    Alicia Oshlack
    Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia
    Biol Direct 4:14. 2009
    ..As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data...
  89. ncbi The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    Edgar Wingender
    Department of Bioinformatics, Medical School, University of Gottingen, Goldschmidtstr 1, D 37077 Gottingen, Germany
    Brief Bioinform 9:326-32. 2008
    ..In the following, I describe what the original concepts were, what their present status is and how they may be expected to contribute to future system biology approaches...
  90. pmc Identifying disease-specific genes based on their topological significance in protein networks
    Zoltan Dezso
    GeneGo Inc, Renaissance Drive, Saint Joseph, Michigan 49085, USA
    BMC Syst Biol 3:36. 2009
    ..To be useful in a research or clinical laboratory, the results need to be translated to the level of testable hypotheses about individual genes and proteins within the condition of interest...
  91. ncbi Networks for systems biology: conceptual connection of data and function
    F Emmert-Streib
    Queen s University Belfast, Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
    IET Syst Biol 5:185-207. 2011
    The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks...
  92. pmc Metabolic syndrome: from epidemiology to systems biology
    Aldons J Lusis
    Department of Medicine and Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Nat Rev Genet 9:819-30. 2008
    ..Systems-based approaches that integrate genomic, molecular and physiological data are complementing traditional genetic and biochemical approaches to more fully address the complexity of MetSyn...
  93. ncbi Pathway analysis of coronary atherosclerosis
    Jennifer Y King
    Donald W Reynolds Cardiovascular Research Center, Division of Cardiovascular Medicine, Falk Cardiovascular Research Center, Stanford University, Stanford, California 94305, USA
    Physiol Genomics 23:103-18. 2005
    ..A systems biology approach that accounts for gene interactions, incorporates nontranscriptionally regulated genes, and ..
  94. ncbi Reverse engineering the genotype-phenotype map with natural genetic variation
    Matthew V Rockman
    Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, New York, New York 10003, USA
    Nature 456:738-44. 2008
    ..It is then possible to use this information about causes and effects to build models of probabilistic 'causal networks'. These networks are beginning to define the outlines of the 'genotype-phenotype map'...
  95. ncbi Stochastic modelling for quantitative description of heterogeneous biological systems
    Darren J Wilkinson
    School of Mathematics and Statistics and the Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
    Nat Rev Genet 10:122-33. 2009
    Two related developments are currently changing traditional approaches to computational systems biology modelling...
  96. ncbi Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    Scott A Becker
    Department of Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093 0412, USA
    Nat Protoc 2:727-38. 2007
    ..are included in the toolbox, allowing a user to input a genome-scale metabolic model distributed in Systems Biology Markup Language format and perform these calculations with just a few lines of code...
  97. pmc A systems biology perspective on sVEGFR1: its biological function, pathogenic role and therapeutic use
    Florence T H Wu
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Cell Mol Med 14:528-52. 2010
    ..physiological and pathological roles of sVEGFR1 is then given, with emphasis on the utility of computational systems biology models in deciphering the molecular mechanisms by which sVEGFR1's purported biological functions occur...
  98. ncbi Systems biology approaches and pathway tools for investigating cardiovascular disease
    Craig E Wheelock
    Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
    Mol Biosyst 5:588-602. 2009
    b>Systems biology aims to understand the nonlinear interactions of multiple biomolecular components that characterize a living organism...
  99. pmc Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
    Caroline B Milne
    Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
    Biotechnol J 4:1653-70. 2009
    ..Going forward, genome-scale in silico models promise to extend their application and analysis scope to become a trans-formative tool in biotechnology...
  100. pmc Cancer systems biology: a network modeling perspective
    Pamela K Kreeger
    Department of Biomedical Engineering, University of Wisconsin Madison, Madison, WI 53706, USA
    Carcinogenesis 31:2-8. 2010
    ....
  101. ncbi GPU computing for systems biology
    Lorenzo Dematté
    CoSBi Centre, Italy
    Brief Bioinform 11:323-33. 2010
    ..In this paper, we review some recent efforts in exploiting the processing power of GPUs for the simulation of biological systems...

Research Grants77

  1. Mapping the Human Binary Interactome Network
    MARC contact VIDAL; Fiscal Year: 2010
    ..Our modified specific aims are to: i) Provide an expanded high-confidence/high-coverage version of the human binary interactome map ii) Validate human binary interaction data iii) Analyze the expanded human interactome model ..
  2. Conference on Systems & Biology
    Marc Vidal; Fiscal Year: 2005
    ..One of the current limitations in the field of Systems Biology relates to the relative lack of students and post-docs who can both think in terms of systems and formulate ..
  3. Integrated interactome mapping
    Marc Vidal; Fiscal Year: 2006
    ..abstract_text> ..
  4. A C. elegans localization-of-expression mapping project
    Marc Vidal; Fiscal Year: 2005
    ..Using a complete set of worm promoters, we then propose to develop high-throughput methods to localize gene expression in vivo and initiate a protein-DNA interaction mapping project (R33). ..
  5. Rewiring Pathways and Networks by Environmental Perturbations
    Marc Vidal; Fiscal Year: 2010
    ..The Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute, together with a growing number of laboratories, is mapping and ..
  6. Intelligent Information Systems for Systems Biology
    Leroy Hood; Fiscal Year: 2003
    ..Finally, we propose some novel educational programs designed to put graduate students together into interdisciplinary teams for problem solving. ..
  7. Correlative Multimodal Imaging of Cardiac Electrophysiology and Metabolism
    JOHN PETER contact WIKSWO; Fiscal Year: 2010
    ..This work will be a key step towards developing improved metabolic therapies. ..
  8. Mathematical Modeling of Anthrax Infection
    Yoram Vodovotz; Fiscal Year: 2002
    ..The results of the research proposed herein will not only impact the treatment of victims of anthrax infection, but will also yield a valuable tool for the treatment of sepsis in general. ..
  9. GPx-3, Vascular Oxidant Stress, and Thrombosis
    Joseph Loscalzo; Fiscal Year: 2006
    ..abstract_text> ..
  10. HOMOCYST(E)INE, OXIDATIVE STRESS, AND NITRIC OXIDE
    Joseph Loscalzo; Fiscal Year: 2004
    ..With these studies, we hope to gain insight into the molecular mechanisms of homocyst(e)ine-induced endothelial dysfunction and potential therapies for this common metabolic abnormality. ..
  11. Transport and Complexity in Biological Systems
    ARTHUR LANDER; Fiscal Year: 2004
    ..abstract_text> ..
  12. NAPS2 Continuation - Genome-Wide Association Study of Pancreatitis
    David C Whitcomb; Fiscal Year: 2010
    ..Knowledge of the genetic basis of pancreatitis will lead to new treatments, and help remove the stigma that chronic pancreatitis is only a disease of drunkards. ..
  13. MOLECULAR GENETICS OF HEREDITARY PANCREATITIS
    David Whitcomb; Fiscal Year: 2008
    ..The HP and familial pancreatitis studies are especially important because of the statistical power of family studies and the ability to detect modifier genes in a uniform background of susceptibility factors. ..
  14. TRAINING PROGRAM IN CELLULAR AND MOLECULAR NEUROSCIENCE
    ARTHUR LANDER; Fiscal Year: 2007
    ..Following completion of this program, trainees will be qualified for careers in Neuroscience research and/or teaching in basic science departments and medical schools, or for research careers in non-academic research laboratories. ..
  15. 14th Internatinal Symposium on Inherited Diseases
    David Whitcomb; Fiscal Year: 2004
    ..The format, venue, and content are designed to maximize participation, education, translation and implementation of the key elements of the many new findings in the genetics of the pancreas. ..
  16. PROTEOGLYCANS AND BRAIN DEVELOPMENT
    ARTHUR LANDER; Fiscal Year: 2004
    ..These studies should provide insights into how an important and poorly understood class of molecules regulates basic developmental processes, particularly in the nervous system. ..
  17. GORDON RESEARCH CONFERENCE ON PROTEOGLYCANS
    ARTHUR LANDER; Fiscal Year: 2002
    ....
  18. SIGNALING PATHWAYS INTERACTIONS AND MAMMARY TUMOR
    SRINIVAS RAVI IYENGAR; Fiscal Year: 2004
    ..abstract_text> ..
  19. STRUCTURE AND FUNCTION OF SIGNAL TRANSDUCING COMPONENTS
    SRINIVAS RAVI IYENGAR; Fiscal Year: 2008
    ..abstract_text> ..
  20. Blood Systems Biology
    Scott Diamond; Fiscal Year: 2008
    ..Lay Statement: Blood is ideal for Systems Biology research since it is easily obtained from donors or patients, amenable to high throughput liquid handling ..
  21. Multiplexed HTS of Serine and Cysteine Proteases (RMI)
    Scott Diamond; Fiscal Year: 2005
    ..The use of multiplexed assay on microarrays allows the generation of critical data for the chemical protease interactome. ..
  22. The Penn Center For Molecular Discovery
    Scott Diamond; Fiscal Year: 2008
    ..This project is responsive to the NIH Roadmap objectives to apply both establish HTS/Synthetic methods and emerging next generation technologies developed at the University of Pennsylvania. ..
  23. Connecting the Genome to the Cytoplasm
    Pamela A Silver; Fiscal Year: 2010
    ..The experiments proposed in this grant will not only lead to new basic insights but also to new ways to analyze on a genome-wide level the situation in genetically defective cells and certain cancers. ..
  24. Mitochondria and Cardiac Cell Death
    James Weiss; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  25. PROPERTIES OF INWARD RECTIFIER K CHANNELS
    James Weiss; Fiscal Year: 2007
    ..abstract_text> ..
  26. MECHANOSENSITIVE MODULATION OF AIRWAY CONTRACTION
    Chi Ming Hai; Fiscal Year: 2008
    ..Understanding the basic science of this cellular mechanism may lead to new methods for the treatment of airway diseases such as asthma. ..
  27. Towards Quantitative Study of Systems Biology
    Ping Ao; Fiscal Year: 2007
    ..at the associate professorship level to complete my transition from theoretical physics into quantitative systems biology. My immediate goal is to deepen my understanding of biology and the related chemistry...
  28. Gordon Conference on Glycolipid & Sphingolipid Biology
    ALFRED MERRILL; Fiscal Year: 2002
    ....
  29. TM4: Software for High-Dimensional Data Analysis
    John Quackenbush; Fiscal Year: 2009
    ....
  30. Reaction and Transport Dynamics in Human Blood
    Scott Diamond; Fiscal Year: 2009
    ..Overall, these studies seek to provide fundamental insight into cell-cell interacitions and coagulation biochemistry that occur under flow. ..
  31. Intracellular mycobacterial proteome
    Qingbo Li; Fiscal Year: 2008
    ..They may be important for understanding the physiology of intracellular persistence of mycobacteria within different macrophages. ..
  32. Metabolic Oscillations in Heart
    JAMES N contact WEISS; Fiscal Year: 2010
    ..These insights may suggest novel therapies to protect the heart from injury during metabolic stresses such as heart attacks. ..
  33. EXPRESSION PROFILING OF RODENT MODELS OF HUMAN DISEASE
    John Quackenbush; Fiscal Year: 2004
    ..abstract_text> ..
  34. STRUCTURE/FUNCTION STUDIES OF LONG-CHAIN BASES
    ALFRED MERRILL; Fiscal Year: 2003
    ....
  35. ERBB 2 ERBB 3 HETERODIMERIC RECEPTOR OF CARCINOMAS
    Yosef Yarden; Fiscal Year: 2004
    ..This model will be examined by using mutant receptors, and the recycling machinery characterized in details. The suspected cancer-inhibitory activity of drugs interfering with ErbB routing will be tested in vivo. ..
  36. Activity-Dependent Gene Expression in Human Epilepsy
    Jeffrey A Loeb; Fiscal Year: 2010
    ..abstract_text> ..
  37. NO AND EXERCISE VASODILATION IN HUMAN HYPERLIPIDEMIA
    Michael Joyner; Fiscal Year: 2004
    ..Data from these patient- oriented studies have implications related to understanding the contribution of endothelial function in a variety of common diseases. ..
  38. Afterdepolarizations and Cardiac Arrhythmias
    James N Weiss; Fiscal Year: 2010
    ..S. citizens each year. The goal is to use this information to develop novel therapies to prevent this deadly manifestation of heart disease. ..
  39. Integrated approaches to deriving predictive networks from public data sources
    John Quackenbush; Fiscal Year: 2010
    ..The end goals will not only be to create the framework for creating such predictive models, but to develop software and tools to allow others in the community to create models for their own systems of interest. ..
  40. MODULATION BY GROWTH FACTORS AND SIGNAL TRANSDUCTION
    ALFRED MERRILL; Fiscal Year: 2003
    ..abstract_text> ..
  41. Modeling of chemotactic sensing in Dictyostelium
    Pablo Iglesias; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  42. Role of Small GTPases in Muscarinic Receptor Trafficking
    ALFRED MERRILL; Fiscal Year: 2005
    ..abstract_text> ..
  43. Renal 11b-Hydroxysteroid Dehydrogenases and Hypertension
    Mingyu Liang; Fiscal Year: 2008
    ..The results are expected to elucidate a novel aspect of the pathophysiology of salt- sensitive hypertension and to provide potential new targets for prevention and treatment of hypertension. ..
  44. 2006 Glycolipid & Sphingolipid Gordon Conference
    ALFRED MERRILL; Fiscal Year: 2007
    ..abstract_text> ..
  45. GORDON RESEARCH CONFERENCE ON MAMMARY GLAND BIOLOGY
    MARY BARCELLOS HOFF; Fiscal Year: 2003
    ..abstract_text> ..
  46. Metabolomic and Toxicogenetic Study of Ethanol Toxicity
    Ivan Rusyn; Fiscal Year: 2009
    ..Here, the investigators are proposing to use metabolomics and mouse models in a new systems biology approach for molecular dissection and discovery of biological pathways underlying the susceptibility to ..
  47. Genes Influencing Social Behaviors
    DONALD WELLS PFAFF; Fiscal Year: 2010
    ..Impact: OT may be involved in postpartum depression. OT systems certainly facilitate social recognition, disorders of which are prominent in autism and in schizophrenia. ..
  48. Quantifying Protein Predictors of Macrophage Responses
    Jared Roach; Fiscal Year: 2007
    ..This model will be a starting point for the development of a comprehensive network model of macrophage signaling. This approach will ultimately be applicable to a broad array of biological systems. ..
  49. Hierarchical Methods for Large BioMolecular Complexes
    Chandrajit L Bajaj; Fiscal Year: 2010
    ..AIM 4: To implement, test, package and freely distribute our structural feature determination and fast search/fitting techniques. ..
  50. Molecular Fingerprinting of Breast Cancer Development
    Vladimir Shulaev; Fiscal Year: 2009
    ..At the same time they point to the molecular mechanisms of breast cancer origin and will increase our knowledge about the etiology of breast cancer. ..
  51. Functionality and Fracture Susceptibility of Corticocancellous Structures
    Karl J Jepsen; Fiscal Year: 2010
    ..This systems analysis, which examines the relationship among traits in the context of functionality, will provide new insight into the genetic basis of fracture susceptibility. ..
  52. Metabolomics of the Virus-host Cell Interaction
    Joshua D Rabinowitz; Fiscal Year: 2010
    ..Such pathways, once identified, will be attractive new targets for antiviral therapy. ..
  53. International Conference on Molecular Systems Biology
    Michael Savageau; Fiscal Year: 2004
    This application is a request for partial support of the International Conference on Molecular Systems Biology: Gene Circuitry, Dynamical Control in Biology and Medicine, and Biomedical Software Development and Integration (ICMSB'04), ..
  54. INTERACTIONS OF CALCIUM CHANNELS WITH ADAPTOR PROTEINS
    Ilya Bezprozvanny; Fiscal Year: 2003
    ....
  55. A signal transduction pathway database/modeling system
    Eric Mjolsness; Fiscal Year: 2006
    ..3) Ingest and store results from computational simulations and provide tools for comparing, visualizing and mining simulation results. ..
  56. SLEEP, AGING, AND THE HYPOCRETIN/OREXIN SYSTEM
    THOMAS KILDUFF; Fiscal Year: 2007
    ..To address these questions, we will use a combination of in vivo physiological, neuroanatomical, molecular, and receptor pharmacological methods. ..
  57. DIFFERENTIAL FUNCTION AND REGULATION OF RUNX2 ISOFORMS
    L Quarles; Fiscal Year: 2007
    ..These studies will define the unique functions of the N-terminal domains, and determine if translational regulation contributes to the tissue-specific expression of Runx2-I and Runx2-II isoforms. ..
  58. Computational Methods for Proteins
    Hagai Meirovitch; Fiscal Year: 2003
    ..Our unique tools are applicable to a wide range of problems in structural biology, such as protein engineering, docking, and threading. ..
  59. DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASE
    Peter Karp; Fiscal Year: 2003
    ....
  60. Vitamin D Status and Prostate Cancer
    JAMES FLEET; Fiscal Year: 2008
    ..These data will provide us with the mechanistic basis for dietary recommendations to prevent prostate cancer and optimize bone health. ..
  61. GIVEN BUILDING ANIMAL FACILITY UPGRADE
    Russell Tracy; Fiscal Year: 2004
    ....
  62. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2005
    ..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
  63. Biomarkers of Formaldehyde Exposure and Toxicity
    Luoping Zhang; Fiscal Year: 2010
    ..The data produced from these studies will be useful to public health agencies in their evaluation of the leukemia risk presented by formaldehyde. ..
  64. ENDOTHELIAL GENE REGULATION BY BIOMECHANICAL FORCES
    MICHAEL GIMBRONE; Fiscal Year: 2003
    ....
  65. Role of Erythrocytes in Circulatory Control
    Randy Sprague; Fiscal Year: 2004
    ..abstract_text> ..
  66. Probabilistic Modeling of Information from Images and Text in Online Journals
    Robert Murphy; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  67. Genetic and Immunological Impact of the HRES-1/Rab4 Locus in SLE
    Andras Perl; Fiscal Year: 2008
    ..Under Specific Aim 3, we will test the hypothesis that the HindIIIG653C allele, alone or in combination with other genetic factors of lupus-associated haplotypes, enhances the expression of HRES-1/Rab4. ..
  68. PHOSPHOLIPASE ACTIVATION BY G-PROTEIN-LINKED RECEPTORS
    Alex Brown; Fiscal Year: 2004
    ..These studies will utilize both intact cells and cell-free preparations that retain purinergic receptor-stimulated activation of PLD1. ..
  69. Exhaled Air Biomarkers in COPD
    Norbert Voelkel; Fiscal Year: 2005
    ..abstract_text> ..
  70. ENDOTHELIAL CELL OUTGROWTH FROM BLOOD
    Robert Hebbel; Fiscal Year: 2001
    ..abstract_text> ..
  71. Myocardial Stiffness in Aging Associated Diastolic Heart Failure
    Kenneth Campbell; Fiscal Year: 2007
    ..The experimental results will provide new information about the underlying causes of DHF and should help scientists develop better treatments for diastolic dysfunction in elderly populations. [unreadable] [unreadable] [unreadable]..
  72. PROSTATE CELL PROLIFERATION IN CANCER AND AGING
    ANA SOTO; Fiscal Year: 2005
    ..We expect that this research will lead to the development of markers to identify this phenotype, and to the development of specific therapeutic strategies. ..
  73. Perinatal xenoestrogen exposure: epigenesis and neoplasia
    ANA SOTO; Fiscal Year: 2007
    ..This will also have a great impact on the way we study risk factors and conduct epidemiological studies; it may even influence public policy about breast cancer prevention. [unreadable] [unreadable] [unreadable] [unreadable]..
  74. GORDON CONFERENCE ON ENVIRONMENTAL ENDOCRINE DISRUPTORS
    ANA SOTO; Fiscal Year: 2002
    ..abstract_text> ..
  75. Sex Differences in Dopamine Systems
    Arthur Arnold; Fiscal Year: 2006
    ..e.g., Multiple Sclerosis). Understanding sex differences in brain function will help develop sex-specific strategies for treatment of brain diseases. ..