Bernhard O Palsson

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
    Scott A Becker
    Department of Bioengineering, University of California, San Diego, La Jolla, USA
    BMC Microbiol 5:8. 2005
  2. pmc Metabolite coupling in genome-scale metabolic networks
    Scott A Becker
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    BMC Bioinformatics 7:111. 2006
  3. pmc An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    Jennifer L Reed
    Department of Bioengineering, University of California, San Diego, Gilman Drive, La Jolla, CA 92092, USA
    Genome Biol 4:R54. 2003
  4. pmc The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states
    Christian L Barrett
    Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 102:19103-8. 2005
  5. pmc Systems approach to refining genome annotation
    Jennifer L Reed
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 103:17480-4. 2006
  6. ncbi request reprint In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium
    Anu Raghunathan
    Department of Bioengineering, University of California at San Diego, La Jolla, California, USA
    OMICS 8:25-41. 2004
  7. ncbi request reprint Integrating high-throughput and computational data elucidates bacterial networks
    Markus W Covert
    Bioengineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nature 429:92-6. 2004
  8. pmc Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition
    Christian L Barrett
    Bioengineering Department, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093 0412, USA
    BMC Bioinformatics 7:132. 2006
  9. ncbi request reprint In silico design and adaptive evolution of Escherichia coli for production of lactic acid
    Stephen S Fong
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Biotechnol Bioeng 91:643-8. 2005
  10. pmc k-Cone analysis: determining all candidate values for kinetic parameters on a network scale
    Iman Famili
    Department of Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0412, USA
    Biophys J 88:1616-25. 2005

Collaborators

Detail Information

Publications79

  1. pmc Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
    Scott A Becker
    Department of Bioengineering, University of California, San Diego, La Jolla, USA
    BMC Microbiol 5:8. 2005
    ..We present the first manually curated elementally and charge balanced genome-scale reconstruction and model of S. aureus' metabolic networks and compute some of its properties...
  2. pmc Metabolite coupling in genome-scale metabolic networks
    Scott A Becker
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    BMC Bioinformatics 7:111. 2006
    ..Metabolite coupling is derived from the matrix ŝŝT, whose off-diagonal elements indicate the number of reactions in which any two metabolites participate together, where ŝ is the binary form of S...
  3. pmc An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    Jennifer L Reed
    Department of Bioengineering, University of California, San Diego, Gilman Drive, La Jolla, CA 92092, USA
    Genome Biol 4:R54. 2003
    ..The most comprehensive E. coli model to date (E. coli iJE660a GSM) accounts for 660 genes and includes 627 unique biochemical reactions...
  4. pmc The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states
    Christian L Barrett
    Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 102:19103-8. 2005
    ....
  5. pmc Systems approach to refining genome annotation
    Jennifer L Reed
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 103:17480-4. 2006
    ..This study thus demonstrates the use of systems analysis to discover metabolic and transport functions and their genetic basis by a combination of experimental and computational approaches...
  6. ncbi request reprint In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium
    Anu Raghunathan
    Department of Bioengineering, University of California at San Diego, La Jolla, California, USA
    OMICS 8:25-41. 2004
    ..This study demonstrates the significance of an integrated approach to the characterization of H. influenzae metabolism...
  7. ncbi request reprint Integrating high-throughput and computational data elucidates bacterial networks
    Markus W Covert
    Bioengineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nature 429:92-6. 2004
    ..We find that a systems biology approach that combines genome-scale experimentation and computation can systematically generate hypotheses on the basis of disparate data sources...
  8. pmc Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition
    Christian L Barrett
    Bioengineering Department, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093 0412, USA
    BMC Bioinformatics 7:132. 2006
    ..Therefore an alternative approach is needed to reveal regulatory properties of steady state solution spaces of genome-scale stoichiometric matrices...
  9. ncbi request reprint In silico design and adaptive evolution of Escherichia coli for production of lactic acid
    Stephen S Fong
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Biotechnol Bioeng 91:643-8. 2005
    ..Strains grown on 2 g/L glucose at 37 degrees C showed lactate titers ranging from 0.87 to 1.75 g/L and secretion rates that were directly coupled to growth rates...
  10. pmc k-Cone analysis: determining all candidate values for kinetic parameters on a network scale
    Iman Famili
    Department of Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0412, USA
    Biophys J 88:1616-25. 2005
    ....
  11. pmc Antibacterial mechanisms identified through structural systems pharmacology
    Roger L Chang
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    BMC Syst Biol 7:102. 2013
    ..coli, structurally accounting for protein complexes. Carefully selected case studies are demonstrated to display the potential for this structural systems pharmacology framework in discovery and development of antibacterial compounds...
  12. doi request reprint Constraint-based models predict metabolic and associated cellular functions
    Aarash Bordbar
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093 0412, USA
    Nat Rev Genet 15:107-20. 2014
    ..As reviewed here, these recent successes have tangible implications in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery. ..
  13. pmc In silico method for modelling metabolism and gene product expression at genome scale
    Joshua A Lerman
    Department of Bioengineering, University of California San Diego, PFBH Room 419, 9500 Gliman Drive, La Jolla, California 92093 0412, USA
    Nat Commun 3:929. 2012
    ....
  14. pmc Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices
    Nathan D Price
    Department of Bioengineering, University of California San Diego, La Jolla, California 92093 0412, USA
    Biophys J 84:794-804. 2003
    ..Therefore, SVD of matrices of extreme pathways has proved to be a useful method for analyzing the steady-state solution space of genome-scale metabolic networks...
  15. pmc Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach
    Christian L Barrett
    Bioengineering Department, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 2:e52. 2006
    ..The algorithm is able to utilize probability estimates based on a wide range of computational and experimental sources to suggest experiments with the highest potential of discovering the greatest amount of new regulatory knowledge...
  16. ncbi request reprint Minimal metabolic pathway structure is consistent with associated biomolecular interactions
    Aarash Bordbar
    Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
    Mol Syst Biol 10:737. 2014
    ..This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated. ..
  17. pmc Context-specific metabolic networks are consistent with experiments
    Scott A Becker
    Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 4:e1000082. 2008
    ..This work represents progress towards producing constraint-based models of metabolism that are specific to the conditions where the expression profiling data is available...
  18. ncbi request reprint Microbial regulatory and metabolic networks
    Byung Kwan Cho
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Curr Opin Biotechnol 18:360-4. 2007
    ....
  19. ncbi request reprint Genome-scale microbial in silico models: the constraints-based approach
    Nathan D Price
    Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 2093 0412, USA
    Trends Biotechnol 21:162-9. 2003
    ..These results are useful as a basis for iterative model building and for several practical applications...
  20. ncbi request reprint Towards multidimensional genome annotation
    Jennifer L Reed
    Department of Bioengineering, University of California, San Diego, La Jolla, California, 92093, USA
    Nat Rev Genet 7:130-41. 2006
    ..Here we discuss all four levels of genome annotation, with specific emphasis on two-dimensional annotation methods...
  21. ncbi request reprint Comparison of network-based pathway analysis methods
    Jason A Papin
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive 0412, La Jolla, CA 92093 0412, USA
    Trends Biotechnol 22:400-5. 2004
    ..Descriptions of network properties generated by using these two approaches in the analysis of realistic metabolic networks need careful interpretation...
  22. ncbi request reprint In silico analysis of SNPs and other high-throughput data
    Neema Jamshidi
    Department of Bioengineering, University of California, San Diego, CA, USA
    Methods Mol Biol 366:267-85. 2007
    ....
  23. pmc Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis
    Christian L Barrett
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
    Nucleic Acids Res 39:1656-65. 2011
    ....
  24. 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...
  25. ncbi request reprint Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli
    Anuradha Raghunathan
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Biotechnol Lett 25:435-41. 2003
    ..Non-synonymous substitutions, Val119Gly and Gly179Trp, were also observed in each of the two strains. This procedure can be scaled to determine genome-scale sequence variations that have occurred during adaptive evolution...
  26. pmc Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes
    Neema Jamshidi
    Department of Bioengineering, 9500 Gilman Drive, University of California, San Diego, La Jolla, CA 92093 0412, USA
    BMC Syst Biol 3:44. 2009
    ..Genetic and environmental perturbations were applied to a cell-scale model of the human erythrocyte and subsequently investigated...
  27. ncbi request reprint Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data
    You Kwan Oh
    Department of Bioengineering, University of California at San Diego, La Jolla, California 92093 0412, USA
    J Biol Chem 282:28791-9. 2007
    ..Hence, the in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes...
  28. pmc Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    Iman Famili
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 100:13134-9. 2003
    ..cerevisiae allows for computation of its integrated functions, producing in silico results that were consistent with observed phenotypic functions for approximately 70-80% of the conditions considered...
  29. pmc Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant
    Nicole L Fong
    Department of Bioengineering, University of California, San Diego, CA 92093 0412, USA
    FEMS Microbiol Lett 342:62-9. 2013
    ..These results demonstrate the feasibility of our approach to drive biological discovery while simultaneously refining metabolic network reconstructions...
  30. doi request reprint Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks
    Yu Qiu
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    Nat Commun 4:1755. 2013
    ..This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria...
  31. pmc Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli
    Roger L Chang
    Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 0412, USA
    Science 340:1220-3. 2013
    ..Inclusion of structural information expanded the content and predictive capability of genome-scale metabolic networks that enable structural systems biology of metabolism...
  32. pmc Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features
    Joo Hyun Seo
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Genomics 13:679. 2012
    ..The development of next-generation sequencing technologies now permits rapid sequencing of many K. pneumoniae isolates, but sequence information alone does not provide important structural and operational information for its genome...
  33. pmc A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
    Aarash Bordbar
    GT Life Sciences, 10520 Wateridge Circle, San Diego, CA 92121, USA
    BMC Syst Biol 5:180. 2011
    ..These models have shown utility in the study of systems medicine. However, no integrated analysis between human tissues has been done...
  34. pmc Network context and selection in the evolution to enzyme specificity
    Hojung Nam
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    Science 337:1101-4. 2012
    ..Furthermore, these properties are conserved in Archaea and Eukarya. Thus, the metabolic network context and environmental conditions influence enzyme evolution toward high specificity...
  35. ncbi request reprint Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach
    Andrew R Joyce
    Bioinformatics Program, University of California, San Diego, La Jolla, California, USA
    Prog Drug Res 64:265, 267-309. 2007
    ..Finally, the chapter concludes with an assessment of future directions focusing on the efforts that will be required to utilize the constraint-based approach in generating a holistic model of a viable organism...
  36. ncbi request reprint Reconstruction of cellular signalling networks and analysis of their properties
    Jason A Papin
    Department of Bioengineering, 9500 Gilman Drive, Mail Code 0412, University of California, San Diego, La Jolla, California 92093 0412, USA
    Nat Rev Mol Cell Biol 6:99-111. 2005
    ..After careful reconstruction of signalling networks, their properties must be described within an integrative framework that accounts for the complexity of the cellular signalling network and that is amenable to quantitative modelling...
  37. ncbi request reprint Network-based analysis of metabolic regulation in the human red blood cell
    Nathan D Price
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    J Theor Biol 225:185-94. 2003
    ..This topological approach may provide candidate regulatory structures for metabolic networks with known stoichiometry but poorly characterized regulation...
  38. pmc Three factors underlying incorrect in silico predictions of essential metabolic genes
    Scott A Becker
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive 0412, La Jolla, CA 92093, USA
    BMC Syst Biol 2:14. 2008
    ..The success rate of these predictions is less than desirable, especially with regard to comprehensively locating essential genes...
  39. 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...
  40. ncbi request reprint Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices
    Iman Famili
    Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    J Theor Biol 224:87-96. 2003
    ..Thus, we can now define systemic metabolic reactions, or eigen-reactions, for the study of systems biology of metabolism and have a basis for comparing the overall properties of genome-specific metabolic networks...
  41. ncbi request reprint Metabolic pathways in the post-genome era
    Jason A Papin
    Department of Bioengineering, University of California, San Diego, La Jolla 92093 0412, USA
    Trends Biochem Sci 28:250-8. 2003
    ..Recently, these properties have also been studied in genome-scale networks. Thus, network-based pathways are emerging as an important paradigm for analysis of biological systems...
  42. pmc The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools
    Iman Famili
    Department of Bioengineering, University of California San Diego, La Jolla, California 92093 0412, USA
    Biophys J 85:16-26. 2003
    ..The analysis of the left null space of the stoichiometric matrix allows us to define the achievable states of the cell and their physiological relevance...
  43. ncbi request reprint Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?
    Markus W Covert
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Biotechnol Bioeng 84:763-72. 2003
    ..This review considers constraints in terms of environmental, physicochemical, and self-imposed regulatory and evolutionary constraints with the purpose of refining current constraints-based models of cell phenotype...
  44. ncbi request reprint Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
    Jason A Papin
    Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Trends Biochem Sci 29:641-7. 2004
    ..As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration...
  45. ncbi request reprint Isotopomer analysis of myocardial substrate metabolism: a systems biology approach
    Thuy D Vo
    Department of Bioengineering, University of California, San Diego, California 92093, USA
    Biotechnol Bioeng 95:972-83. 2006
    ..Further study of 12 commonly used (13)C glucose mixtures showed that the mixtures of 20% [U-(13)C(6)] glucose, 80% [3 (13)C] glucose and 20% [U-(13)C(6)] glucose, 80% [4 (13)C] were best for resolving fluxes in the current network...
  46. ncbi request reprint Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data
    Thuy D Vo
    Department of Bioengineering, University of California, San Diego, California 92093, USA
    J Biol Chem 279:39532-40. 2004
    ..Examinations of optimal flux distributions also identified correlated reaction sets that form functional modules in the network...
  47. ncbi request reprint Building the power house: recent advances in mitochondrial studies through proteomics and systems biology
    Thuy D Vo
    Department of Bioengineering, University of California San Diego, MC 0412, La Jolla, CA 92093, USA
    Am J Physiol Cell Physiol 292:C164-77. 2007
    ..Successes and limitations of the studies reviewed here provide opportunities and challenges that must be addressed to facilitate the application of systems biology to larger systems...
  48. pmc Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states
    Byung Kwan Cho
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Biol 12:4. 2014
    ..Although the crucial role of σ-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function...
  49. pmc Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578
    Tzu Wen Huang
    Department of Bioengineering, University of California, San Diego La Jolla, CA, 92093 0412 USA
    BMC Res Notes 7:13. 2014
    ..A defining characteristic of this pathogen is the presence of a thick, exterior capsule that has been reported to play a role in biofilm formation and to protect the organism from threats such antibiotics and host immune challenge...
  50. pmc Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    Nathan E Lewis
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nat Rev Microbiol 10:291-305. 2012
    ..These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour...
  51. pmc iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states
    Aarash Bordbar
    Department of Bioengineering, University of California San Diego, La Jolla, 92093 0412, USA
    BMC Syst Biol 5:110. 2011
    ....
  52. pmc Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies
    Nathan D Price
    Department of Bioengineering, University of California at San Diego, La Jolla, California 92093 0412, USA
    Biophys J 87:2172-86. 2004
    ....
  53. ncbi request reprint Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    Rafael U Ibarra
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nature 420:186-9. 2002
    ..These results open the possibility of using adaptive evolution of entire metabolic networks to realize metabolic states that have been determined a priori based on in silico analysis...
  54. ncbi request reprint Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome
    Thuy D Vo
    Department of Bioengineering, University of California, San Diego, CA 92093, USA
    Mol Genet Metab 91:15-22. 2007
    ....
  55. doi request reprint Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome
    Nathan E Lewis
    CHOmics, Inc, San Diego, California, USA
    Nat Biotechnol 31:759-65. 2013
    ..The details of this genetic diversity highlight the value of the hamster genome as the reference upon which CHO cells can be studied and engineered for protein production. ..
  56. pmc Multispecific drug transporter Slc22a8 (Oat3) regulates multiple metabolic and signaling pathways
    Wei Wu
    Departments of Pediatrics H C L, K T B, S K N, Medicine, Division of Nephrology and Hypertension W W, S A E, S K N, Cellular and Molecular Medicine S K N, and Bioengineering N J, B O P, S K N, University of California, San Diego, La Jolla, California
    Drug Metab Dispos 41:1825-34. 2013
    ..The data seemingly consistent with the Remote Sensing and Signaling Hypothesis (Ahn and Nigam, 2009; Wu et al., 2011), also suggests that Oat3 is essential for the handling of dietary flavonoids and antioxidants. ..
  57. pmc COBRApy: COnstraints-Based Reconstruction and Analysis for Python
    Ali Ebrahim
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC0412, La Jolla, CA 92093 0412, USA
    BMC Syst Biol 7:74. 2013
    ..The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software...
  58. pmc Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
    Aarash Bordbar
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    Mol Syst Biol 8:558. 2012
    ..Our study demonstrates metabolism's role in regulating activation may be greater than previously anticipated and elucidates underlying connections between activation and metabolic effectors...
  59. pmc Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction
    Pep Charusanti
    Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 7:e33727. 2012
    ..These results demonstrate that competition-based adaptive laboratory evolution can constitute a platform to create mutants that overproduce known antibiotics and possibly to discover new compounds as well...
  60. pmc An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
    Pep Charusanti
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    BMC Syst Biol 5:163. 2011
    ..Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas...
  61. ncbi request reprint Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk
    Jason A Papin
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412 USA
    J Theor Biol 227:283-97. 2004
    ..Due to the scalability of the stoichiometric formalism used, the results presented for the prototypic signaling network can be obtained for large signaling networks once their reconstruction is completed...
  62. ncbi request reprint PCR-based tandem epitope tagging system for Escherichia coli genome engineering
    Byung Kwan Cho
    University of California at San Diego, La Jolla, CA 92093, USA
    Biotechniques 40:67-72. 2006
    ..Furthermore, judging from the measurement of gene expression using reverse transcription PCR (RT-PCR), the epitope-fused transcription factors retained their normal function for gene regulation in vivo...
  63. doi request reprint A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent
    Douglas McCloskey
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093 0412
    Biotechnol Bioeng 111:803-15. 2014
    ..This analysis also identified enzyme promiscuity for the pykA gene, that is critical for anaerobic growth, and which has not been previously incorporated into metabolic models of E coli...
  64. pmc Genome-scale metabolic model of Helicobacter pylori 26695
    Christophe H Schilling
    Genomatica, Inc, San Diego, California 92121, USA
    J Bacteriol 184:4582-93. 2002
    ..Collectively, the results presented herein suggest an effective strategy of combining in silico modeling with experimental technologies to enhance biological discovery for less characterized organisms and their genomes...
  65. pmc The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis
    Jason A Papin
    Department of Bioengineering, University of California, San Diego, La Jolla 92093, USA
    Biophys J 87:37-46. 2004
    ..As large-scale reconstructions of signaling networks emerge, such scalable analyses will lead to a description of the fundamental systems properties of signal transduction networks...
  66. ncbi request reprint Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types
    Imran B Clark
    Cyntellect, Inc, 6620 Mesa Ridge Road, Suite 100, San Diego, California 92121 2906, USA
    J Biomed Opt 11:014034. 2006
    ..We establish the broad utility of optoinjection, and furthermore, are the first to demonstrate its implementation in an automated, high-throughput manner...
  67. ncbi request reprint Constraints-based models: regulation of gene expression reduces the steady-state solution space
    Markus W Covert
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    J Theor Biol 221:309-25. 2003
    ..5 and 97.5%. The method developed here provides a way to interpret how regulatory mechanisms are used to constrain network functions and produce a small range of physiologically meaningful behaviors from all allowable network functions...
  68. pmc Extreme pathway analysis of human red blood cell metabolism
    Sharon J Wiback
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    Biophys J 83:808-18. 2002
    ..The extreme pathways for the red blood cell thus give a concise representation of red blood cell metabolism and a way to interpret its metabolic physiology...
  69. pmc BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
    Jan Schellenberger
    Bioinformatics Program, University of California San Diego, La Jolla, California, 92093 0419, USA
    BMC Bioinformatics 11:213. 2010
    ..As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use...
  70. pmc Matrix formalism to describe functional states of transcriptional regulatory systems
    Erwin P Gianchandani
    Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
    PLoS Comput Biol 2:e101. 2006
    ....
  71. ncbi request reprint Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes
    Stephen S Fong
    Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond 28284 3028, USA
    J Biol Chem 281:8024-33. 2006
    ..coli to compensate for genetic perturbations and the utility of combining multiple high throughput data sets to differentiate between causal and noncausal mechanistic changes...
  72. ncbi request reprint Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices
    Megan J Anderson
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, MS 128 95, Pasadena, California 91125, USA
    Biochemistry 46:5722-31. 2007
    ....
  73. pmc Description and analysis of metabolic connectivity and dynamics in the human red blood cell
    Kenneth J Kauffman
    Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
    Biophys J 83:646-62. 2002
    ..In conclusion, systems science methods can decipher detailed information about individual enzymes and metabolites within metabolic networks and provide further understanding of complex biological networks...
  74. ncbi request reprint Characterizing the metabolic phenotype: a phenotype phase plane analysis
    Jeremy S Edwards
    Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
    Biotechnol Bioeng 77:27-36. 2002
    ..Supplementary information can be downloaded from our website (http://epicurus.che.udel.edu)...
  75. ncbi request reprint Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
    Jochen Forster
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
    OMICS 7:193-202. 2003
    ..A genome-scale in silico model can thus be used to systematically reconcile existing data and fill in our knowledge gaps about an organism...
  76. pmc Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
    Eugene Kolker
    BIATECH, Bothell, Washington 98011, USA
    J Bacteriol 185:4593-602. 2003
    ..The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism...
  77. ncbi request reprint The evolution of molecular biology into systems biology
    Hans V Westerhoff
    Department of Molecular Cell Physiology, BioCentrum Amsterdam, De Boelelaan 1085, NL 108, HV Amsterdam, The Netherlands
    Nat Biotechnol 22:1249-52. 2004
    ..We argue here that two distinct lines of inquiry in molecular biology have converged to form contemporary systems biology...
  78. ncbi request reprint Development of network-based pathway definitions: the need to analyze real metabolic networks
    Bernhard O Palsson
    Trends Biotechnol 21:195-8. 2003
  79. ncbi request reprint H. influenzae Consortium: integrative study of H. influenzae-human interactions
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    OMICS 6:341-8. 2002
    ..Data from the HIC will allow greater understanding of cellular behavior, pathogen-host interactions, bacterial infection, and provide future scientific endeavors with a template for studies of other pathogens...