Genomes and Genes
H Steven Wiley
Affiliation: Pacific Northwest National Laboratory
- Trafficking of the ErbB receptors and its influence on signalingH 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...
- Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation dataKatrina 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...
- HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cellsYi 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...
- An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cellsTyler H Heibeck
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Richland, Washington 99352, USA
J Proteome Res 8:3852-61. 2009....
- Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamicsHarish 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...
- Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factorHarish 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...
- An analysis pipeline for the inference of protein-protein interaction networksRonald 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...
- Receptor downregulation and desensitization enhance the information processing ability of signalling receptorsHarish Shankaran
Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland WA 99352, USA
BMC Syst Biol 1:48. 2007....
- Modeling the effects of HER/ErbB1-3 coexpression on receptor dimerization and biological responseHarish 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...
- Multiple mechanisms are responsible for transactivation of the epidermal growth factor receptor in mammary epithelial cellsKarin D Rodland
Systems Biology Program, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
J Biol Chem 283:31477-87. 2008....
- Basic fibroblast growth factor regulates persistent ERK oscillations in premalignant but not malignant JB6 cellsThomas 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...
- The mammary epithelial cell secretome and its regulation by signal transduction pathwaysJon 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...
- Cholesterol dictates the freedom of EGF receptors and HER2 in the plane of the membraneGalya 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...
- Cell surface receptors for signal transduction and ligand transport: a design principles studyHarish 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...
- Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assaysJulia 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...
- Computational modeling of the EGF-receptor system: a paradigm for systems biologyH 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...
- Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display libraryMichael 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...
- 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
- Enabling high-throughput data management for systems biology: the Bioinformatics Resource ManagerAnuj 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...
- Smad signaling dynamics: insights from a parsimonious modelHarish 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...
- Oscillatory dynamics of the extracellular signal-regulated kinase pathwayHarish 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...
- Integrating multiple types of data for signaling research: challenges and opportunitiesH 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...
- High speed method for in situ multispectral image registrationKenneth A Perrine
Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Microsc Res Tech 70:382-9. 2007....
- An integrated model of epidermal growth factor receptor trafficking and signal transductionHaluk 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...
- Simple protein complex purification and identification method for high-throughput mapping of protein interaction networksLye 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...
- Induced autocrine signaling through the epidermal growth factor receptor contributes to the response of mammary epithelial cells to tumor necrosis factor alphaWan 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...
- EGF-receptor-mediated mammary epithelial cell migration is driven by sustained ERK signaling from autocrine stimulationElizabeth 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...
- Coregulation of epidermal growth factor receptor/human epidermal growth factor receptor 2 (HER2) levels and locations: quantitative analysis of HER2 overexpression effectsBart 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...
- Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo- and heterodimers depends on relative HER2 levelsBart S Hendriks
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
J Biol Chem 278:23343-51. 2003....
- HER2-mediated effects on EGFR endosomal sorting: analysis of biophysical mechanismsBart 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...
- Parsing ERK activation reveals quantitatively equivalent contributions from epidermal growth factor receptor and HER2 in human mammary epithelial cellsBart S Hendriks
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
J Biol Chem 280:6157-69. 2005....
- Ligand accumulation in autocrine cell culturesMichael 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...
- The membrane-anchoring domain of epidermal growth factor receptor ligands dictates their ability to operate in juxtacrine modeJianying 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...
- Affinity regulates spatial range of EGF receptor autocrine ligand bindingAnn 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...
- Self-organization of polarized cell signaling via autocrine circuits: computational model analysisIvan 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...
- A general system for studying protein-protein interactions in Gram-negative bacteriaDale 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...
- The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory NetworksYoshiyuki Sakaki
Syst Biol (Stevenage) 152:53-4. 2005