H Steven Wiley

Summary

Affiliation: Pacific Northwest National Laboratory
Country: USA

Publications

  1. ncbi request reprint Trafficking of the ErbB receptors and its influence on signaling
    H Steven Wiley
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99353, USA
    Exp Cell Res 284:78-88. 2003
  2. pmc Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data
    Katrina M Waters
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 7:e34515. 2012
  3. pmc HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells
    Yi Zhang
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
    BMC Cell Biol 10:78. 2009
  4. pmc An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells
    Tyler H Heibeck
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Richland, Washington 99352, USA
    J Proteome Res 8:3852-61. 2009
  5. pmc Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamics
    Harish Shankaran
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MS J4 33, Richland, WA 99352, USA
    Mol Biosyst 8:2868-82. 2012
  6. pmc Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor
    Harish Shankaran
    Systems Biology Program, Pacific Northwest National Laboratory, Richland, WA, USA
    Mol Syst Biol 5:332. 2009
  7. ncbi request reprint An analysis pipeline for the inference of protein-protein interaction networks
    Ronald C Taylor
    Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory US Department of Energy, Richland, WA 99352, USA
    Int J Data Min Bioinform 3:409-30. 2009
  8. pmc Receptor downregulation and desensitization enhance the information processing ability of signalling receptors
    Harish Shankaran
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland WA 99352, USA
    BMC Syst Biol 1:48. 2007
  9. pmc Modeling the effects of HER/ErbB1-3 coexpression on receptor dimerization and biological response
    Harish Shankaran
    Pacific Northwest National Laboratory, Richland, WA, USA
    Biophys J 90:3993-4009. 2006
  10. pmc Multiple mechanisms are responsible for transactivation of the epidermal growth factor receptor in mammary epithelial cells
    Karin D Rodland
    Systems Biology Program, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Biol Chem 283:31477-87. 2008

Collaborators

Detail Information

Publications37

  1. ncbi request reprint Trafficking of the ErbB receptors and its influence on signaling
    H Steven Wiley
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99353, USA
    Exp Cell Res 284:78-88. 2003
    ..Because different ErbB receptor substrates are localized in different cellular compartments, disrupted trafficking could be an important factor in the altered signaling patterns observed as a consequence of receptor overexpression...
  2. pmc Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data
    Katrina M Waters
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 7:e34515. 2012
    ..These results demonstrate the value of integrating multiple levels of biological information to more accurately reconstruct networks of cellular response...
  3. pmc HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells
    Yi Zhang
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
    BMC Cell Biol 10:78. 2009
    ..Using our clone library, we have quantified the receptor activation patterns and systematically tested the validity of the existing hypotheses about the interaction patterns between HER1-3 receptors...
  4. pmc An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells
    Tyler H Heibeck
    Biological Sciences Division and Environmental Molecular Sciences Laboratory, Richland, Washington 99352, USA
    J Proteome Res 8:3852-61. 2009
    ....
  5. pmc Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamics
    Harish Shankaran
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MS J4 33, Richland, WA 99352, USA
    Mol Biosyst 8:2868-82. 2012
    ..This study demonstrates that an iterative cycle of experiments and modeling can be used to gain mechanistic insight regarding complex cell signaling networks...
  6. pmc Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor
    Harish Shankaran
    Systems Biology Program, Pacific Northwest National Laboratory, Richland, WA, USA
    Mol Syst Biol 5:332. 2009
    ..Our characterization of single-cell ERK dynamics provides a quantitative foundation for understanding the regulatory structure of this signaling cascade...
  7. ncbi request reprint An analysis pipeline for the inference of protein-protein interaction networks
    Ronald C Taylor
    Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory US Department of Energy, Richland, WA 99352, USA
    Int J Data Min Bioinform 3:409-30. 2009
    ..Also, the pipeline incorporates the Collective Analysis of Biological Interaction Networks (CABIN) software. We have thus created a structured workflow for protein-protein network inference and supplemental analysis...
  8. pmc Receptor downregulation and desensitization enhance the information processing ability of signalling receptors
    Harish Shankaran
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland WA 99352, USA
    BMC Syst Biol 1:48. 2007
    ....
  9. pmc Modeling the effects of HER/ErbB1-3 coexpression on receptor dimerization and biological response
    Harish Shankaran
    Pacific Northwest National Laboratory, Richland, WA, USA
    Biophys J 90:3993-4009. 2006
    ..Results indicate that coexpression of EGFR with HER2 and HER3 at low to moderate levels may enable cells to match the response of a high HER2 expresser...
  10. pmc Multiple mechanisms are responsible for transactivation of the epidermal growth factor receptor in mammary epithelial cells
    Karin D Rodland
    Systems Biology Program, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Biol Chem 283:31477-87. 2008
    ....
  11. doi request reprint Basic fibroblast growth factor regulates persistent ERK oscillations in premalignant but not malignant JB6 cells
    Thomas J Weber
    Cell Biology and Biochemistry Group, Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
    J Invest Dermatol 130:1444-56. 2010
    ..Our data suggest that bFGF regulates ERK oscillations in premalignant but not malignant JB6 cells...
  12. doi request reprint The mammary epithelial cell secretome and its regulation by signal transduction pathways
    Jon M Jacobs
    Systems Biology Program, Cell Biology and Biochemistry, Biological Separations and Mass Spectrometry, Computational Biology Groups, and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Proteome Res 7:558-69. 2008
    ..This study demonstrates a tiered strategy by which extracellular proteins can be identified and progressively assigned to classes of increasing confidence and regulatory importance...
  13. pmc Cholesterol dictates the freedom of EGF receptors and HER2 in the plane of the membrane
    Galya Orr
    Chemical and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    Biophys J 89:1362-73. 2005
    ..The association of the receptors with lipid rafts could therefore promote their rapid interactions only upon ligand stimulation...
  14. pmc Cell surface receptors for signal transduction and ligand transport: a design principles study
    Harish Shankaran
    Systems Biology Program, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS Comput Biol 3:e101. 2007
    ..Our analysis reveals that the location of a receptor system in the avidity-consumption parameter space can be used to understand both its function and its regulation...
  15. ncbi request reprint Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assays
    Julia L Sharp
    Clemson University, 237 Barre Hall, Clemson, South Carolina 29634 0313, Pacific Northwest National Laboratory, P O Box 999, Richland, Washington 99352, USA
    J Proteome Res 6:3788-95. 2007
    ..We also found that Monte Carlo simulation is a feasible tool for checking modeling assumptions, estimating parameters, and evaluating the significance of results in protein association studies...
  16. ncbi request reprint Computational modeling of the EGF-receptor system: a paradigm for systems biology
    H Steven Wiley
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Trends Cell Biol 13:43-50. 2003
    ..The success of EGFR modeling can be a guide to combining models and experiments productively to understand complex biological processes as integrated systems...
  17. ncbi request reprint Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library
    Michael J Feldhaus
    Pacific Northwest National Laboratories, Biological Sciences Division, 902 Battelle Blvd, P O Box 999, Richland, WA 99352, USA
    Nat Biotechnol 21:163-70. 2003
    ..The ability to use multiplex library screening demonstrates the usefulness of this approach for high-throughput antibody isolation for proteomics applications...
  18. ncbi request reprint Should software hold data hostage?
    H Steven Wiley
    Biomolecular Systems Initiative, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Nat Biotechnol 22:1037-8. 2004
  19. ncbi request reprint Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager
    Anuj R Shah
    Biomolecular Systems Initiative, Pacific Northwest National Laboratory, Richland, WA, USA
    Bioinformatics 23:906-9. 2007
    ..BRM is developed using Java and other open-source technologies for free distribution. AVAILABILITY: BRM, sample data sets and a user manual can be downloaded from http://www.sysbio.org/dataresources/brm.stm...
  20. doi request reprint Smad signaling dynamics: insights from a parsimonious model
    Harish Shankaran
    Systems Biology Program, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Sci Signal 1:pe41. 2008
    ..As a result, the output can faithfully track gradual changes in the input while the rapid input fluctuations that constitute signaling noise are dampened out...
  21. doi request reprint Oscillatory dynamics of the extracellular signal-regulated kinase pathway
    Harish Shankaran
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
    Curr Opin Genet Dev 20:650-5. 2010
    ..Biochemical oscillations are more enigmatic, but could provide a mechanism for encoding different types of inputs into a common signaling pathway...
  22. doi request reprint Integrating multiple types of data for signaling research: challenges and opportunities
    H Steven Wiley
    EMSL, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Sci Signal 4:pe9. 2011
    ..However, solving the fundamental issues of data sharing will enable the investigation of entirely new areas of cell signaling research...
  23. ncbi request reprint High speed method for in situ multispectral image registration
    Kenneth A Perrine
    Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Microsc Res Tech 70:382-9. 2007
    ....
  24. pmc An integrated model of epidermal growth factor receptor trafficking and signal transduction
    Haluk Resat
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Biophys J 85:730-43. 2003
    ..Importantly, the stochastic and compartmental nature of the simulation allows these models to be directly tested by high-throughput approaches, such as quantitative image analysis...
  25. ncbi request reprint Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks
    Lye Meng Markillie
    Pacific Northwest National Laboratory, 902 Battelle Blvd, P O Box 999, Richland, Washington 99354, USA
    J Proteome Res 4:268-74. 2005
    ..Our method is simple and easy to scale-up and automate, making it suitable for high-throughput mapping of protein interaction networks and functional proteomics...
  26. ncbi request reprint Induced autocrine signaling through the epidermal growth factor receptor contributes to the response of mammary epithelial cells to tumor necrosis factor alpha
    Wan Nan U Chen
    Cell Biology Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Biol Chem 279:18488-96. 2004
    ..Our results indicate a novel and important role for metalloprotease activation and EGFR transmodulation in mediating the cellular response to TNF...
  27. ncbi request reprint EGF-receptor-mediated mammary epithelial cell migration is driven by sustained ERK signaling from autocrine stimulation
    Elizabeth J Joslin
    Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
    J Cell Sci 120:3688-99. 2007
    ..Thus, in our mammary epithelial cell system, migration and proliferation are differentially sensitive to the mode of EGF ligand presentation...
  28. ncbi request reprint Coregulation of epidermal growth factor receptor/human epidermal growth factor receptor 2 (HER2) levels and locations: quantitative analysis of HER2 overexpression effects
    Bart S Hendriks
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Cancer Res 63:1130-7. 2003
    ..We anticipate that this model should ultimately be useful in parsing the relative contributions of direct effects of HER2 via signaling vis-a-vis indirect effects of HER2 via modification of EGFR signaling...
  29. ncbi request reprint Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo- and heterodimers depends on relative HER2 levels
    Bart S Hendriks
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    J Biol Chem 278:23343-51. 2003
    ....
  30. pmc HER2-mediated effects on EGFR endosomal sorting: analysis of biophysical mechanisms
    Bart S Hendriks
    Department of Chemical Engineering, Biological Engineering Division, and Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Biophys J 85:2732-45. 2003
    ..In contrast, model predictions for alternative mechanisms-blocking of EGFR/ERC coupling, or altering EGF/EGFR dissociation-were inconsistent with the qualitative trends of the experimental data...
  31. ncbi request reprint Parsing ERK activation reveals quantitatively equivalent contributions from epidermal growth factor receptor and HER2 in human mammary epithelial cells
    Bart S Hendriks
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    J Biol Chem 280:6157-69. 2005
    ....
  32. pmc Ligand accumulation in autocrine cell cultures
    Michael I Monine
    Department of Chemical Engineering and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 88:2384-90. 2005
    ..We demonstrate how the theory works by analyzing the autocrine epidermal growth factor receptor system and discuss the extension of our methods to other experiments with cultured autocrine cells...
  33. pmc The membrane-anchoring domain of epidermal growth factor receptor ligands dictates their ability to operate in juxtacrine mode
    Jianying Dong
    Department of Pathology, Division of Cell Biology and Immunology, University of Utah, Salt Lake City, UT 84133, USA
    Mol Biol Cell 16:2984-98. 2005
    ..Our data suggest that the membrane-anchoring domain of ligands selectively controls their ability to participate in juxtacrine signaling and thus, only a subclass of EGFR ligands can act in a juxtacrine mode...
  34. ncbi request reprint Affinity regulates spatial range of EGF receptor autocrine ligand binding
    Ann DeWitt
    Department of Chemical Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139, USA
    Dev Biol 250:305-16. 2002
    ..Our experimental data confirm this prediction, demonstrating that cells can use ligand/receptor binding affinity to regulate ligand spatial distribution when autocrine ligand production is limiting for receptor signaling...
  35. pmc Self-organization of polarized cell signaling via autocrine circuits: computational model analysis
    Ivan V Maly
    Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Biophys J 86:10-22. 2004
    ..We additionally offer particular suggestions for critical nodes in the EGFR signaling circuits governing this self-organization capability...
  36. doi request reprint A general system for studying protein-protein interactions in Gram-negative bacteria
    Dale A Pelletier
    Biosciences Division, Chemical Sciences Division, Computer Science and Mathematics Division, and Physical Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    J Proteome Res 7:3319-28. 2008
    ..Results compared favorably with those for both plasmid and chromosomally encoded affinity-tagged fusion proteins expressed in a model organism, Escherichia coli...
  37. ncbi request reprint The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks
    Yoshiyuki Sakaki
    Syst Biol (Stevenage) 152:53-4. 2005