2010-

  1. Ciaccio M.F., J.P. Wagner, C.-P. Chuu, D.A. Lauffenburger, and R.B. Jones, “Systems Analysis of EGF Receptor Signaling Dynamics with Micro-Western Arrays”, Nature Methods 7: 148-155 (2010).
  2. Kreeger, P.K., Y. Wang, K.M. Haigis, and D.A. Lauffenburger, “Integration of Multiple Signaling Pathway Activities Resolves K-Ras/N-Ras Mutation Paradox in Colon Epithelial Cell Response to Inflammatory Cytokine Stimulation”, Integrative Biology 2: 202-208 (2010).
  3. Lazzara, M.J., K. Lane, R. Chan, P.J. Jasper, M.B. Yaffe, P.K. Sorger, T. Jacks, B.G. Neel, and D.A. Lauffenburger, “Impaired SHP2-Mediated ERK Activation Contributes to Gefitinib Sensitivity of Lung Cancer Cells with EGFR-Activating Mutations”, Cancer Res. 70: 3843-3850 (2010).
  4. Das, A., D.A. Lauffenburger, H. Asada, and R.D. Kamm, “A Hybrid Continuum-Discrete Modelling Approach to Predict and Control Angiogenesis: Analysis of Combinatorial Growth Factor and Matrix Effects on Vessel-Sprouting Morphology”, Phil. Trans. Roy. Soc. A 368: 2937-2960 (2010).
  5. Prince, R.N., E.R. Schreiter, P. Zou, H.S. Wiley, A.Y. Ting, R.T. Lee, and D.A. Lauffenburger, “The Heparin-Binding Domain of HB-EGF Mediates Localization to Cell-Cell Contact Sites and Prevents HB-EGF Release”, J. Cell Sci. 123: 2308-2318 (2010).
  6. Cosgrove, B.D., L.G. Alexopoulos, T.-c. Hang, B.S. Hendriks, P.K. Sorger, L.G. Griffith, and D.A. Lauffenburger, “Cytokine-Associated Drug Toxicity in Human Hepatocytes is Associated with Signaling Network Dysregulation”, Molec. BioSyst. (in press, 2010).
  7. Joslin, E.J., H. Shankaran, L.K. Opresko, N. Bollinger, D.A. Lauffenburger, and H.S. Wiley, “Structure of the EGF Receptor Transactivation Circuit Integrates Multiple Signals with Cell Context”, Molec. BioSyst. (in press, 2010).
  8. Spangler, J.B., J.R. Neil, S. Abramovitch, Y. Yarden, F.M. White, D.A. Lauffenburger, and K.D. Wittrup, “Combination Antibody Treatment Downregulates EGF Receptor by Inhibiting Endosomal Recycling”, Proc. Natl. Acad. Sci. USA 107: 13252-13257 (2010).
  9. Alexopoulos, L.G., J. Saez-Rodriguez, B.D. Cosgrove, D.A. Lauffenburger, and P.K. Sorger, “Networks Inferred from Biochemical Data Reveal Profound Differences in TLR and Inflammatory Signaling Between Normal and Transformed Hepatocytes”, Molec. Cell. Proteomics 9: 1849-1865 (2010).
  10. Espelin, C.W., A. Goldsipe, P.K. Sorger, D.A. Lauffenburger, D. de Graaf, and B.S. Hendriks, “Elevated GM-CSF and IL-1β Levels Compromise the Ability of p38 MAPK Inhibitors to Modulate TNFα Levels in the Human Monocytic/Macrophage U937 Cell Line”,Molec. BioSyst. 6: 1956-1972 (2010).
  11. Naegle, K.M., M. Gymrek, B.A. Joughin, J.P. Wagner, R.E. Welsch, M.B. Yaffe, D.A. Lauffenburger, and F.M. White, “PTMScout: A Web Resource for Analysis of High-Throughput Post-Translational Proteomic Studies”, Molec. Cell. Proteomics 9: 2558-2570 (2010).
  12. Das, A., Lauffenburger D.A., H. Asada, and R.D. Kamm, “Determining Cell Fate Transition Probabilities to VEGF/AngI Levels: Relating Computational Modeling to Microfluidic Angiogenesis Studies”, Cell. Molec. Bioeng. 3: 345-360 (2010).
  13. Paradise, R.K., D.A. Lauffenburger, and K.J. Van Vliet, “Acidic Extracellular pH Promotes Activation of Integrin αvβ3”, PLoS One 6: e15746 (2011).
  14. Jiang, H., J.R. Pritchard, R.T. Williams, D.A. Lauffenburger, and M.T. Hemann, “A Mammalian Functional Genetic Approach to Characterizing Cancer Therapeutics”, Nature Chem. Biol. 7: 92-100 (2011).
  15. Bagheri, N., M. Shiina, D.A. Lauffenburger, and W.M. Korn, “A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK Inhibition”, PLoS Comp. Biol. 7: e1001085 (2011).
  16. Morris, M.K., J. Saez-Rodriguez, D.C. Clarke, P.K. Sorger, and D.A. Lauffenburger, “Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli”, PLoS Comp. Biol. 7: e1001099 (2011).
  17. Peyton, S.R., I. Kalcioglu, J.C. Cohen, A.P. Runkle, K.J. Van Vliet, D.A. Lauffenburger, and L.G. Griffith, “Marrow-Derived Stem Cell Motility in 3D Synthetic Scaffold is Governed by Geometry along with Adhesivity and Stiffness”, Biotech. Bioeng. 108: 1181-1193 (2011).
  18. Lau, K.S., A.M. Juchheim, K.R. Cavaliere, S.R. Philips, D.A. Lauffenburger, and K.M. Haigis, “In Vivo Systems Analysis Identifies Spatial and Temporal Aspects of MAPK Modulation of TNFa-induced Apoptosis and Proliferation”, Science Signaling 4: ra16 (2011).
  19. Miller, M.A., L. Barkal, K. Jeng, A. Herrlich, M. Moss, L.G. Griffith, and D.A. Lauffenburger, “Proteolytic Activity Matrix Analysis (PrAMA) for Simultaneous Detection of Multiple Protease Activities”, Integr. Biol. 3: 422-438 (2011).
  20. Palmer, M.J., V.S. Mahajan, J. Chen, D.J. Irvine, and D.A. Lauffenburger, “Signaling Thresholds Govern Heterogeneity in IL-7 Receptor-Mediated Responses of Naïve CD8+ T-Cells”, Immunol. Cell Biol. 89: 581-594 (2011).
  21. . Roussos, E.T., M. Balsamo, S.K. Alford, J.B. Wyckoff, B. Gligorijevic, Y. Wang, M. Pozzuto, R. Stobezki, S. Goswami, J.E. Segall, D.A. Lauffenburger, A.R. Bresnick, F.B. Gertler, and J.S. Condeelis, “MenaINV Promotes Multicellular Streaming Motility and Transendothelial Migration in a Mouse Model of Breast Cancer”, J. Cell Science 124: 2120-2131 (2011).
  22. Naegle, K.M., R.E. Welsch, M.B. Yaffe, F.M. White, and D.A. Lauffenburger, “MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets”, PLoS Comp Biol 7: e1002119 (2011).
  23. Chen, C.-H., A. Sarkar, Y.-A. Song, M. Miller, L.G. Griffith, D.A. Lauffenburger, and J. Han, “Enhancing Protease Activity Assay in Droplet-Based Microfluidics using a Biomolecule Concentrator”, J. Am. Chem. Soc. 133: 10368-10371 (2011).
  24. Wu, S., A. Wells, L.G. Griffith, and D.A. Lauffenburger, “Controlling Multi-Potent Stromal Cell Migration by Integrating ‘Course-Graining’ Materials and ‘Fine-Tuning’ Small Molecules via Decision Tree Modeling”, Biomaterials 32: 7524-7531 (2011).
  25. Saez-Rodriguez, J., L. Alexopoulos, M.-S. Zheng, M.K. Morris, D.A. Lauffenburger, and P.K. Sorger, “Comparing Signaling Networks Between Normal and Transformed Hepatocytes Using Discrete Logic Models”, Cancer Res. 71: 5400-5411 (2011).
  26. Pritchard, J.R., L.A. Gilbert, C.E. Meacham, J.L. Ricks, H. Jiang, D.A. Lauffenburger, and M.T. Hemann, “Bcl-2 Family Genetic Profiling Reveals Microenvironment-Specific Determinants of Chemotherapeutic Response”, Cancer Res. 71: 5850-5858 (2011).
  27. Kleiman, L.B., T. Maiwald, H. Conzelmann, D.A. Lauffenburger, and P.K. Sorger, “Rapid Phospho-Turnover by Receptor Tyrosine Kinases Impacts Downstream Signaling and Drug Binding”, Molec. Cell 43: 723-737 (2011).
  28. Kim, H.D., A.S. Meyer, J.P. Wagner, S.K. Alford, A. Wells, F.B. Gertler, and D.A. Lauffenburger, “Signaling Network State Predicts Twist-Mediated Effects on Breast Cell Migration Across Diverse Growth Factor Contexts”, Molec. Cell. Proteomics 10: M111.008433 (2011).
  29. Moss, M.L., G. Powell, M.A. Miller, L. Edwards, Q. Bin, Q.X. Sang, B. De Strooper, I. Tesseur, S.F. Lichtenthaler, M. Taverna, J.L. Zhang, C. Dingwall, T. Ferdous, U. Schlomann, P. Zhou, L. Griffith, D.A. Lauffenburger, R. Petrovich, and J.W. Bartsch, “ADAM9 Inhibition Increases Membrane Activity of ADAM10 and Controls α-Secretase Processing of Amyloid Precursor Protein”, J. Biol. Chem. 286: 40443-40451 (2011).
  30. Aldridge, B.B., S. Gaudet, D.A. Lauffenburger, and P.K. Sorger, “Lyapunov Exponents and Phase Diagrams Reveal Multi-Factorial Control over TRAIL-Induced Apoptosis”, Molec. Syst. Biol. 7: 553 (2011).
  31. Hang, T., D.A. Lauffenburger, L.G. Griffith, and D.B. Stolz, “Lipids Promote Survival, Proliferation, and Maintenance of Differentiation of Rat Liver Sinusoidal Endothelial Cells in Vitro”, Am. J. Physiol. Gastrointest. Liver Physiol. 302: G375-G388 (2012).
  32. Tentner AR, MJ Lee, GJ Ostheimer, LD Samson, DA Lauffenburger, MB Yaffe, “Combined Experimental and Computational Analysis of DNA Damage Signaling Reveals Context-Dependent Roles for ERK in Apoptosis and G1/S Arrest after Genotoxic Stress”, Molec. Syst. Biol. 8: 568 (2012).
  33. Han, Q., N. Bagheri, E.M. Bradshaw, D.A. Hafler, D.A. Lauffenburger, and J.C. Love, “Polyfunctional Responses by Human T Cells Result from Sequential Release of Cytokines”, Proc. Natl. Acad. Sci. USA 109: 1607-1612 (2012).
  34. Stains CI, NC Tedford, TC Walkup, E Lukovic, BN Goguen, LG Griffith, DA Lauffenburger, and B Imperiali, “Interrogating Signaling Nodes Involved in Cellular Transformations using Kinase Activity Probes”, Chem. & Biol. 19: 210-217 (2012).
  35. Morris, M.K., Z. Shriver, R. Sasisekharan, and D.A. Lauffenburger, “Querying Quantitative Logic Models to Study Intracellular Signaling Networks and Cell/Cytokine Interactions”, Biotech. J. 7: 374-386 (2012).
  36. Meyer, A.S., S.K. Hughes-Alford, J.E. Kay, A. Castillo, A. Wells, F.B. Gertler, and D.A. Lauffenburger, “2D Protrusion but not Motility Predicts Growth Factor-Induced Cancer Cell Migration in 3D Collagen”, J. Cell Biol. 197: 721-729 (2012).
  37. Lau, K.S., T. Zhang, K.R. Kendall, D.A. Lauffenburger, N.S. Gray, and K.M. Haigis, “BAY61-3606 Affects the Viability of Colon Cancer Cells in a Genotype-Directed Manner”, PLoS ONE 7: e41343 (2012).
  38. Kirouac, D.C., J. Saez-Rodriguez, J. Swantek, J.M. Burke, D.A. Lauffenburger, and P.K. Sorger, “Creating and Analyzing Pathway and Protein Interaction Compendia for Modeling Signal Transduction Networks”, BMC Syst. Biol. 6: 29 (2012).
  39. Miller, M., M. Hafner, E. Sontag, N. Davidsohn, S. Subramaniam, P.E.M. Purnick, D.A. Lauffenburger, and R. Weiss, “Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity”, PLoS Comp. Biol.8 e1002579 (2012).
  40. Joughin, B.A., C., Liu, D.A. Lauffenburger, C.W.V. Hogue, and M.B. Yaffe, “Protein Kinases Display Minimal Interpositional Dependence on Substrate Sequence: Potential Implications for the Evolution of Signalling Networks”, Phil. Trans. Roy. Soc. B 367: 2574-2583 (2012).
  41. Gupton, S.L., D. Riquelme, S.K. Hughes-Alford, J. Tadros, S.S. Rudina, R.O. Hynes, D.A. Lauffenburger, and F.B. Gertler, “Mena Binds a5 Integrin Directly and Modulates a5b1 Function”, J. Cell Biol. 198: 657-676 (2012).
  42. Naegle, K.M., F.M. White, D.A. Lauffenburger, and M.B. Yaffe, “Robust Co-Regulation of Tyrosine Phosphorylation Sites on Proteins Reveals Novel Protein Interactions”, Molec. BioSyst. 8 2771-2782 (2012).
  43. Noonan, E.M., D. Shah, M.B. Yaffe, D.A. Lauffenburger, and L.D. Samson, “O6-Methylguanine DNA Lesions Induce an Intra-S-Phase Arrest from which Cells Exit into Apoptosis Governed by Early and Late Multi-Pathway Signaling Network Activation”, Integr. Biol. 4 1237-1255 (2012).
  44. Lau, K.S., V. Cortez-Reta, S.R. Philips, M.J. Pittet, D.A. Lauffenburger, and K.M. Haigis, “Multi-Scale In Vivo Systems Analysis Reveals the Influence of Immune Cells on TNFa-Induced Apoptosis in the Intestinal Epithelium”, PLoS Biol. 10: e1001393 (2012).
  45. Terfve C.D.A., T. Cokelaer, D. Henriques, A. MacNamara, E. Goncalves, M.K. Morris, M. van Iersel, D.A. Lauffenburger, and J. Saez-Rodriguez, “CellNOptR: A Flexible Toolkit to Train Protein Signaling Networks to Data Using Multiple Logic Formalisms”, BMC Syst. Biol. 6: 133 (2012).
  46. Mitsos A., I.N. Melas, M.K. Morris, J. Saez-Rodriguez, D.A. Lauffenburger, and L.G. Alexopoulos, “Non-Linear Programming Formulation for Quantitative Modeling of Protein Signal Transduction Pathways”, PLoS One 7: e50085 (2012).
  47. Clarke D.C., M.K. Morris, and D.A. Lauffenburger, “Normalization and Statistical Analysis of Multiplexed Bead-Based Immunoassay Data using Mixed-Effects Modeling”, Molec. Cell. Proteomics 12: 245-262 (2012).
  48. Yamanaka Y.J., G.L. Szeto, T.M. Gierahn, T.L. Forcier, K.F. Benedict, M.S. Brefo, D.A. Lauffenburger, D.J. Irvine, and J.C. Love, “Cellular Barcodes for Efficiently Profiling Single-Cell Secretory Responses by Microengraving”, Anal. Chem. 84: 10531-10536 (2012).
  49. Pritchard J.P., P.M. Bruno, L.A. Gilbert, K.L. Capron, D.A. Lauffenburger, and M.T. Hemann, “Defining Principles of Combination Drug Mechanisms of Action”, Proc. Natl. Acad. Sci. USA 110: E170-179 (2013).
  50. Paradise R.K., M. Whitfield, D.A. Lauffenburger, and K.J. Van Vliet, “Directional Cell Migration in an Extracellular pH Gradient”, Expt. Cell Res. 319: 487-497 (2013).
  51. Chen C.H., M.A. Miller, A. Sarkar, M.T. Beste, K.B. Isaacson, D.A. Lauffenburger, L.G. Griffith, and J. Han, “Multiplexed Protease Activity Assay for Low-Volume Clinical Samples using Droplet-Based Microfluidics and its Application to Endometriosis”, J. Am. Chem. Soc. 135: 1645-1648 (2013).
  52. Huang S.C., D.C. Clarke, A. Labadorf, C.R. Chouinard, W. Gordon, D.A. Lauffenburger, and E. Fraenkel, “Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-Induced Signaling”, PLoS Comp. Biol. 9: e1002887 (2013).
  53. Rimchala, T., R.D. Kamm, and D.A. Lauffenburger, “Endothelial Cell Phenotypic Behaviors Cluster into Dynamic Transition Programs Modulated by Angiogenic and Angiostatic Cytokines”, Integr. Biol. 5: 510-522 (2013).
  54. Miller M.A., A.S. Meyer, M.T. Beste, Z. Lasisi, S. Reddy, K.W. Jeng, C.-H. Chen, J. Han, K. Isaacson, L.G. Griffith, and D.A. Lauffenburger, “ADAM-10 and -17 Regulate Endometriotic Cell Migration via Concerted Ligand and Receptor Shedding Feedback on Kinase Signaling”, Proc. Natl. Acad. Sci. USA 110: E2074-E2083 (2013).
  55. Dang, M., N. Armbruster, M.A. Miller, E. Cermeno-Blondet, M. Hartmann, G.W. Bell, D. Root, D.A. Lauffenburger, H. Lodish, and A. Herrlich, “Regulated ADAM17-dependent EGF Family Ligand Release by Substrate-Selecting Signaling Pathways”, Proc. Natl. Acad. Sci. USA 110: 9776-9781 (2013).
  56. Pritchard, J.R., P.M. Bruno, M.T. Hemann, and D.A. Lauffenburger, “Predicting Cancer Drug Mechanisms of Action using Molecular Signatures”, Molec. BioSyst. 9: 1604-1619 (2013).
  57. Miraldi, E.R., H. Sharfi, R.H. Friedline, H. Johnson, T. Zhang, K.S. Lau, H.J. Ko, T.G. Curran, K.M. Haigis, M.B. Yaffe, R. Bonneau, D.A. Lauffenburger, B.B. Kahn, J.K. Kim, B.G. Neel, A. Saghatelian, and F.M. White, “Molecular Network Analysis of Phosphotyrosine and Lipid Metabolism in Hepatic PTP1b-Deletion Mice”, Integrative Biol. (in press, 2013).
  58. Wagner, J.P., A. Wolf-Yadlin, M. Sevecka, J.K. Grenier, D.E. Root, D.A. Lauffenburger, and G. MacBeath, “Receptor Tyrosine Kinases Fall into Distinct Classes Based on their Inferred Signaling Networks”, Science Signaling (in press, 2013).
  59. Simmons, R.P., E.P. Scully, E.E. Groden, K.F. Benedict, J.J. Chang, K. Lane, J. Lifson, E. Rosenberg, D.A. Lauffenburger, and M. Altfeld, “HIV-1 Infection Induces Strong Production of IP-10 through TLR7/9-Dependent Pathways”, AIDS (accepted, 2013).
  60. Meyer, A.S., M.A. Miller, F.B. Gertler, and D.A. Lauffenburger, “AXL Diversifies EGFR Signaling and Mitigates Response to EGFR-Targeted Therapeutics in Triple-Negative Breast Carcinoma Cells”, Science Signaling (accepted, 2013).
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