Lauffenburger:Publications

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==Books==
==Books==
   
   
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2. Lauffenburger, D.A. and J.J. Linderman, Receptors: Models for Binding, Trafficking, and Signalling, Oxford  
2. Lauffenburger, D.A. and J.J. Linderman, Receptors: Models for Binding, Trafficking, and Signalling, Oxford  
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University Press, 365 pgs. (1993); 2nd printing (1996).  
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University Press, 365 pgs. (1993); 2nd printing (1996).
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==Invited reviews, commentaries, and book chapters==
==Invited reviews, commentaries, and book chapters==
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40. Wells, A., A. Huttenlocher, and D.A. Lauffenburger, “Calpain Proteases in Cell Adhesion and Motility”, Intl. Rev.  
40. Wells, A., A. Huttenlocher, and D.A. Lauffenburger, “Calpain Proteases in Cell Adhesion and Motility”, Intl. Rev.  
Cytology 245: 1-16 (2005).  
Cytology 245: 1-16 (2005).  
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41. Janes, K.A. and D.A. Lauffenburger, “A Biological Approach to Computational Models of Proteomic Networks”, Curr. Op. Chem. Biol. (2005, in press).
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42. Ideker, T., R. Winslow, and D.A. Lauffenburger, “Bioengineering and Systems Biology”, Annals Biomed. Eng. (2005, accepted).
   
   
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==Refereed journal articles:==
==Refereed journal articles:==
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Stability of IL-2 and GCSF”, Protein Sci. 12: 1030-1038 (2003).  
Stability of IL-2 and GCSF”, Protein Sci. 12: 1030-1038 (2003).  
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155.  Sarkar, C.A., Lowenhaupt, K., Wang, P.J., Horan, T., and D.A. Lauffenburger, “Parsing the Effects of  
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161.  Sarkar, C.A., Lowenhaupt, K., Wang, P.J., Horan, T., and D.A. Lauffenburger, “Parsing the Effects of  
Binding, Signaling, and Trafficking on the Mitogenic Potency of GCSF Analogs”, Biotech. Progr. 19:  
Binding, Signaling, and Trafficking on the Mitogenic Potency of GCSF Analogs”, Biotech. Progr. 19:  
955-964 (2003).  
955-964 (2003).  
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156.  Hendriks, B., L.K. Opresko, H.S. Wiley, and D.A. Lauffenburger, “Quantitative Analysis of HER2-Mediated  
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162.  Hendriks, B., L.K. Opresko, H.S. Wiley, and D.A. Lauffenburger, “Quantitative Analysis of HER2-Mediated  
Effects on HER2 and EGFR Endocytosis: Distribution of Homo- and Hetero-dimers Depends on Relative  
Effects on HER2 and EGFR Endocytosis: Distribution of Homo- and Hetero-dimers Depends on Relative  
HER2 Levels”, J. Biol. Chem. 278: 23343-23351 (2003).  
HER2 Levels”, J. Biol. Chem. 278: 23343-23351 (2003).  
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157.  Cheng, C., D.A. Lauffenburger, and T. Morales, “Motile Chondrocytes: Migration Properties and Synthesis  
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163.  Cheng, C., D.A. Lauffenburger, and T. Morales, “Motile Chondrocytes: Migration Properties and Synthesis  
of Collagen II”, Osteoarthr. Cart. 11: 603-612 (2003).  
of Collagen II”, Osteoarthr. Cart. 11: 603-612 (2003).  
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158.  Mamoune, A., J.-H. Luo, D.A. Lauffenburger, and A. Wells, “Calpain-2 as a Target for Limiting Prostate  
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164.  Mamoune, A., J.-H. Luo, D.A. Lauffenburger, and A. Wells, “Calpain-2 as a Target for Limiting Prostate  
Cancer Invasion”, Cancer Res. 63: 4632-4640 (2003).  
Cancer Invasion”, Cancer Res. 63: 4632-4640 (2003).  
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159.  Janes, K.A., J.G. Albeck, L.X. Peng, P.K. Sorger, D.A. Lauffenburger, and M.B. Yaffe, “High-Throughput  
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165.  Janes, K.A., J.G. Albeck, L.X. Peng, P.K. Sorger, D.A. Lauffenburger, and M.B. Yaffe, “High-Throughput  
Multiplex Kinase Assay for Monitoring Information Flow in Signaling Networks: Application to Sepsis-  
Multiplex Kinase Assay for Monitoring Information Flow in Signaling Networks: Application to Sepsis-  
Apoptosis”, Molec. Cell. Proteomics 2: 463-473 (2003).  
Apoptosis”, Molec. Cell. Proteomics 2: 463-473 (2003).  
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160. Hendriks, B., H.S. Wiley, and D.A. Lauffenburger, “HER2-Mediated Effects on EGFR Endosomal Sorting:  
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166. Hendriks, B., H.S. Wiley, and D.A. Lauffenburger, “HER2-Mediated Effects on EGFR Endosomal Sorting:  
Analysis of Biophyical Mechanisms”, Biophys. J. 85: 2732-2745 (2003).  
Analysis of Biophyical Mechanisms”, Biophys. J. 85: 2732-2745 (2003).  
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161.  Viswanathan, S., T. Benatar, M. Mileikovsky, D.A. Lauffenburger, A. Nagy, and P.W. Zandstra,  
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167.  Viswanathan, S., T. Benatar, M. Mileikovsky, D.A. Lauffenburger, A. Nagy, and P.W. Zandstra,  
“Supplementation-Dependent Differences in the Rates of Embryonic Stem Cell  Self-Renewal,  
“Supplementation-Dependent Differences in the Rates of Embryonic Stem Cell  Self-Renewal,  
Differentiation, and Apoptosis”, Biotech. Bioeng. 84: 505-517 (2003).  
Differentiation, and Apoptosis”, Biotech. Bioeng. 84: 505-517 (2003).  
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162.  Rao, B.J., A.T. Girvin, T. Ciardelli, D.A. Lauffenburger, and K.D. Wittrup, “Interleukin-2 Mutants with  
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168.  Rao, B.J., A.T. Girvin, T. Ciardelli, D.A. Lauffenburger, and K.D. Wittrup, “Interleukin-2 Mutants with  
Enhanced α-Receptor Subunit Binding Affinity”, Protein Eng. 16: 1081-10877 (2003).  
Enhanced α-Receptor Subunit Binding Affinity”, Protein Eng. 16: 1081-10877 (2003).  
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163.  Maly, I., H.S. Wiley, and D.A. Lauffenburger, “Self-Organization of Polarized Cell Signaling via Autocrine  
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169.  Maly, I., H.S. Wiley, and D.A. Lauffenburger, “Self-Organization of Polarized Cell Signaling via Autocrine  
EGFR Circuits: Computational Model Analysis”, Biophys. J. 86: 10-22 (2004).  
EGFR Circuits: Computational Model Analysis”, Biophys. J. 86: 10-22 (2004).  
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164.  Prudhomme, W., K. Duggar, G.Q. Daly, P.W. Zandstra, and D.A. Lauffenburger, “Multi-Variate Proteomic  
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170.  Prudhomme, W., K. Duggar, G.Q. Daly, P.W. Zandstra, and D.A. Lauffenburger, “Multi-Variate Proteomic  
Analysis of Murine Embryonic Stem Cell Self-Renewal vs Differentiation Behavior”, Proc. Natl. Acad.  
Analysis of Murine Embryonic Stem Cell Self-Renewal vs Differentiation Behavior”, Proc. Natl. Acad.  
Sci. USA 101: 2900-2905 (2004).  
Sci. USA 101: 2900-2905 (2004).  
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165.  Iwabu, A., K. Smith, F.D. Allen, D.A. Lauffenburger, and A. Wells, “EGF Induces Fibroblast Contractility  
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171.  Iwabu, A., K. Smith, F.D. Allen, D.A. Lauffenburger, and A. Wells, “EGF Induces Fibroblast Contractility  
and Motility via a PKCδ-Dependent Pathway”, J. Biol. Chem. 279: 14551-14560 (2004).  
and Motility via a PKCδ-Dependent Pathway”, J. Biol. Chem. 279: 14551-14560 (2004).  
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166.  Tschumperlin, D.J., G. Dai, I.V. Maly, L.H. Laiho, A.K. McVittie, P.T. So, D.A. Lauffenburger, R.D.  
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172.  Tschumperlin, D.J., G. Dai, I.V. Maly, L.H. Laiho, A.K. McVittie, P.T. So, D.A. Lauffenburger, R.D.  
Kamm, and J.M. Drazen, “Mechanotransduction via Growth Factor Shedding into a Compliant  
Kamm, and J.M. Drazen, “Mechanotransduction via Growth Factor Shedding into a Compliant  
Extracellular Space”, Nature 429: 83-86 (2004).  
Extracellular Space”, Nature 429: 83-86 (2004).  
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167.  Janes, K.A., J. R. Kelly, S. Gaudet, J.G.Albeck, P.K. Sorger, and D.A. Lauffenburger, “Cue-Signal-Response  
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173.  Janes, K.A., J. R. Kelly, S. Gaudet, J.G.Albeck, P.K. Sorger, and D.A. Lauffenburger, “Cue-Signal-Response  
Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multi-Variate  
Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multi-Variate  
Signaling Network Measurements”, J. Comp. Biol. 11: 544-561 (2004).  
Signaling Network Measurements”, J. Comp. Biol. 11: 544-561 (2004).  
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168. Lu, H., L.Y. Koo, D.A. Lauffenburger, L.G. Griffith, and K.F. Jensen, “Microfluidic Shear Devices for  
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174. Lu, H., L.Y. Koo, D.A. Lauffenburger, L.G. Griffith, and K.F. Jensen, “Microfluidic Shear Devices for  
Quantitative Analysis of Cell Adhesion”, Analyt. Chem. 76: 5257-5264 (2004).  
Quantitative Analysis of Cell Adhesion”, Analyt. Chem. 76: 5257-5264 (2004).  
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169. Rao, B.M., I. Driver, D.A. Lauffenburger, and K.D. Wittrup, “IL-2 Variants Engineered for Increased IL-2Ra  
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175. Rao, B.M., I. Driver, D.A. Lauffenburger, and K.D. Wittrup, “IL-2 Variants Engineered for Increased IL-2Ra  
Affinity Exhibit Increased Potency Arising from a Cell Surface Ligand Reservoir Effect”, Molec.  
Affinity Exhibit Increased Potency Arising from a Cell Surface Ligand Reservoir Effect”, Molec.  
Pharmacol. 66: 864-869 (2004).   
Pharmacol. 66: 864-869 (2004).   
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170. Maly, I., R.T. Lee, and D.A. Lauffenburger, “A Model for Mechanotransduction in Cardiac Muscle: Effects of  
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176. Maly, I., R.T. Lee, and D.A. Lauffenburger, “A Model for Mechanotransduction in Cardiac Muscle: Effects of  
Extracellular Matrix Deformation on Autocrine Signaling”, Ann. Biomed. Eng. 32: 1319-1335 (2004).  
Extracellular Matrix Deformation on Autocrine Signaling”, Ann. Biomed. Eng. 32: 1319-1335 (2004).  
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171. Prudhomme, W., K.H. Duggar, and D.A. Lauffenburger, “Kinetic Model for Deconvolution of Murine  
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177. Prudhomme, W., K.H. Duggar, and D.A. Lauffenburger, “Kinetic Model for Deconvolution of Murine  
Embryonic Stem Cell Self-Renewal and Differentiation Responses to Cytokines and Extracellular Matrix”,  
Embryonic Stem Cell Self-Renewal and Differentiation Responses to Cytokines and Extracellular Matrix”,  
Biotech. Bioeng. 88: 264-272 (2004).  
Biotech. Bioeng. 88: 264-272 (2004).  
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172. Lazar, C.S., C.M. Cresson, D.A. Lauffenburger, and G.N. Gill, “The Na+/H+ Exchanger Regulatory Factor  
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178. Lazar, C.S., C.M. Cresson, D.A. Lauffenburger, and G.N. Gill, “The Na+/H+ Exchanger Regulatory Factor  
Stabilizes EGFR at the Cell Surface”, Molec. Biol. Cell 15: 5470-5480 (2004).  
Stabilizes EGFR at the Cell Surface”, Molec. Biol. Cell 15: 5470-5480 (2004).  
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173. Said, M.R., T.J. Begley, A.V. Oppenheim, D.A. Lauffenburger, and L.D. Samson, “Global Network Analysis  
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179. Said, M.R., T.J. Begley, A.V. Oppenheim, D.A. Lauffenburger, and L.D. Samson, “Global Network Analysis  
of Phenotypic Effects: Protein Networks and Toxicity Modulation in S. cerevisiae”, Proc. Natl. Acad.  
of Phenotypic Effects: Protein Networks and Toxicity Modulation in S. cerevisiae”, Proc. Natl. Acad.  
Sci. USA 101: 18006-18011 (2004).  
Sci. USA 101: 18006-18011 (2004).  
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174. Hendriks, B.S., G. Orr, A. Wells, H.S. Wiley, and D.A. Lauffenburger, “Parsing ERK Activation Reveals  
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180. Hendriks, B.S., G. Orr, A. Wells, H.S. Wiley, and D.A. Lauffenburger, “Parsing ERK Activation Reveals  
Quantitatively Equivalent Contributions from EGFR and HER2 in Human Mammary Epithelial Cells”, J.  
Quantitatively Equivalent Contributions from EGFR and HER2 in Human Mammary Epithelial Cells”, J.  
Biol. Chem. 280: 6157-6169 (2005).  
Biol. Chem. 280: 6157-6169 (2005).  
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175. Harms, B.D, G.M. Bassi, A.R. Horwitz, and D.A. Lauffenburger, “Directional Persistence of EGF-induced  
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181. Harms, B.D, G.M. Bassi, A.R. Horwitz, and D.A. Lauffenburger, “Directional Persistence of EGF-induced  
Cell Migration is Associated with Stabilization of Lamellipodal Protrusions”, Biophys. J. 88: 1479-1488  
Cell Migration is Associated with Stabilization of Lamellipodal Protrusions”, Biophys. J. 88: 1479-1488  
(2005).  
(2005).  
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176. Woolf, P.J., W. Prudhomme, L. Daheron, G.Q. Daley, and D.A. Lauffenburger, “Bayesian Analysis of  
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182. Woolf, P.J., W. Prudhomme, L. Daheron, G.Q. Daley, and D.A. Lauffenburger, “Bayesian Analysis of  
Signaling Networks Governing Embryonic Stem Cell Fate Decisions”, Bioinformatics 21: 741-753  
Signaling Networks Governing Embryonic Stem Cell Fate Decisions”, Bioinformatics 21: 741-753  
(2005).  
(2005).  
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177. Shults, M.D., K.A. Janes, D.A. Lauffenburger, and B. Imperiali, “A Multiplexed Fluorescence-Based Assay  
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183. Shults, M.D., K.A. Janes, D.A. Lauffenburger, and B. Imperiali, “A Multiplexed Fluorescence-Based Assay  
for Protein Kinase Activity in Cell Lysates”, Nature Methods 2: 277-284 (2005).  
for Protein Kinase Activity in Cell Lysates”, Nature Methods 2: 277-284 (2005).  
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178. Monine, M.I., A.M. Berezhkovskii, E.J. Joslin, H.S. Wiley, D.A. Lauffenburger, and S.Y. Shvartsman,  
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184. Monine, M.I., A.M. Berezhkovskii, E.J. Joslin, H.S. Wiley, D.A. Lauffenburger, and S.Y. Shvartsman,  
“Ligand Accumulation in Autocrine Cell Cultures”, Biophys. J. 88: 2384-2390 (2005).  
“Ligand Accumulation in Autocrine Cell Cultures”, Biophys. J. 88: 2384-2390 (2005).  
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179. Sachs, K., O. Perez, D. Pe’er, D.A. Lauffenburger, and G.P. Nolan, “Causal Protein Signaling Networks  
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185. Sachs, K., O. Perez, D. Pe’er, D.A. Lauffenburger, and G.P. Nolan, “Causal Protein Signaling Networks  
Derived From Multiparameter Single-Cell Data”, Science 308: 523-529 (2005).  
Derived From Multiparameter Single-Cell Data”, Science 308: 523-529 (2005).  
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180. Hautaniemi, S., S. Kharait, A. Iwabu, A. Wells, and D.A. Lauffenburger, “Modeling of Signal-Response  
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186. Hautaniemi, S., S. Kharait, A. Iwabu, A. Wells, and D.A. Lauffenburger, “Modeling of Signal-Response  
Cascades using Decision Tree Analysis”, Bioinformatics 21: 2027-2035 (2005).  
Cascades using Decision Tree Analysis”, Bioinformatics 21: 2027-2035 (2005).  
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181. Dong, J., L.K. Opresko, W. Chrisler, G. Orr, R.D. Quesenberry, D.A. Lauffenburger, and H.S. Wiley, “The  
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187. Dong, J., L.K. Opresko, W. Chrisler, G. Orr, R.D. Quesenberry, D.A. Lauffenburger, and H.S. Wiley, “The  
Membrane-Anchoring Domain of EGF Receptor Ligands Dictates Their Ability to Operate in Juxtacrine  
Membrane-Anchoring Domain of EGF Receptor Ligands Dictates Their Ability to Operate in Juxtacrine  
Mode”, Molec. Biol. Cell 16: 2984-2998 (2005).  
Mode”, Molec. Biol. Cell 16: 2984-2998 (2005).  
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182. Varga, C.M. N.C. Tedford, M. Thomas, A.M. Klibanov, L.G. Griffith, and D.A. Lauffenburger, “Quantitative  
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188. Varga, C.M. N.C. Tedford, M. Thomas, A.M. Klibanov, L.G. Griffith, and D.A. Lauffenburger, “Quantitative  
Comparison of Polyethylenimine Formulations and Adenoviral Vectors in terms of Intracellular Gene  
Comparison of Polyethylenimine Formulations and Adenoviral Vectors in terms of Intracellular Gene  
Delivery Processes”, Gene Therapy 12: 1023-1032 (2005).  
Delivery Processes”, Gene Therapy 12: 1023-1032 (2005).  
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183. Hua, F., M.G. Cornejo, M.H. Cardone, C.L. Stokes, and D.A. Lauffenburger, “Effects of Bcl-2 Levels on Fas  
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189. Hua, F., M.G. Cornejo, M.H. Cardone, C.L. Stokes, and D.A. Lauffenburger, “Effects of Bcl-2 Levels on Fas  
Signaling-Induced Caspase-3 Activation: Molecular Genetic Tests of Computational Model Predictions”,  
Signaling-Induced Caspase-3 Activation: Molecular Genetic Tests of Computational Model Predictions”,  
J. Immunol. 175: 985-995 (2005).  
J. Immunol. 175: 985-995 (2005).  
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184. Yoshioka, J., R.N. Prince, H. Huang, S.B. Perkins, F.U. Cruz, C. MacGillivray, D.A. Lauffenburger, and R.T.  
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190. Yoshioka, J., R.N. Prince, H. Huang, S.B. Perkins, F.U. Cruz, C. MacGillivray, D.A. Lauffenburger, and R.T.  
Lee, “Cardiomyocyte Hypertrophy and Degradation of Connexin-43 through Spatially Restricted  
Lee, “Cardiomyocyte Hypertrophy and Degradation of Connexin-43 through Spatially Restricted  
Autocrine/Paracrine HB-EGF”, Proc. Natl. Acad. Sci. USA 102: 10622-10627 (2005).  
Autocrine/Paracrine HB-EGF”, Proc. Natl. Acad. Sci. USA 102: 10622-10627 (2005).  
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185. Zaman, M.H., R.D. Kamm, P.T. Matsudaira, and D.A. Lauffenburger, “Computational Model for Cell  
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191. Zaman, M.H., R.D. Kamm, P.T. Matsudaira, and D.A. Lauffenburger, “Computational Model for Cell  
Migration in Three-Dimensional Matrices”, Biophys. J. 89: 1389-1397 (2005).  
Migration in Three-Dimensional Matrices”, Biophys. J. 89: 1389-1397 (2005).  
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186. Rao, B.M., Driver I., D.A. Lauffenburger, and K.D. Wittrup, “High-Affinity CD25-Binding IL-2 Mutants  
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192. Rao, B.M., Driver I., D.A. Lauffenburger, and K.D. Wittrup, “High-Affinity CD25-Binding IL-2 Mutants  
Potently Stimulate Persistent T-Cell Growth”, Biochem. 44: 10696-10701 (2005).  
Potently Stimulate Persistent T-Cell Growth”, Biochem. 44: 10696-10701 (2005).  
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187. Zhang, Y., A. Wolf-Yadlin, D.J. Pappin, J. Rush, D.A. Lauffenburger, and F.M. White, “Time-Resolved Mass  
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193. Zhang, Y., A. Wolf-Yadlin, D.J. Pappin, J. Rush, D.A. Lauffenburger, and F.M. White, “Time-Resolved Mass  
Spectrometry of Tyrosine Phosphorylation Sites in the EGF Receptor Signaling Network Reveals  
Spectrometry of Tyrosine Phosphorylation Sites in the EGF Receptor Signaling Network Reveals  
Dynamic Modules”, Molec. Cell. Proteomics 4: 1240-1250 (2005).  
Dynamic Modules”, Molec. Cell. Proteomics 4: 1240-1250 (2005).  
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188. Gaudet, S., K.A. Janes, J.G. Albeck, E.A. Pace, D.A. Lauffenburger, and P.K. Sorger, “A Compendium of  
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194. Gaudet, S., K.A. Janes, J.G. Albeck, E.A. Pace, D.A. Lauffenburger, and P.K. Sorger, “A Compendium of  
Signals and Responses Triggered by Prodeath and Prosurvival Cytokines”, Molec. Cell. Proteomics 4:  
Signals and Responses Triggered by Prodeath and Prosurvival Cytokines”, Molec. Cell. Proteomics 4:  
1569-1590 (2005).  
1569-1590 (2005).  
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189. Viswanathan, S., D. Cheng, R.C. Raghu, D.A. Lauffenburger, and P.W. Zandstra, “Clonal Evolution of Stem  
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195. Viswanathan, S., D. Cheng, R.C. Raghu, D.A. Lauffenburger, and P.W. Zandstra, “Clonal Evolution of Stem  
and Differentiated Cells can be Predicted by Integrating Cell-Instrinsic and Extrinsic Parameters”,  
and Differentiated Cells can be Predicted by Integrating Cell-Instrinsic and Extrinsic Parameters”,  
Biotech. Appl. Biochem. 42: 119-131 (2005).  
Biotech. Appl. Biochem. 42: 119-131 (2005).  
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190. Kamei, D.T., B.J. Lao, M.S. Ricci, R. Deshpande, H. Xu, B. Tidor, and D.A. Lauffenburger, “Quantitative  
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196. Kamei, D.T., B.J. Lao, M.S. Ricci, R. Deshpande, H. Xu, B. Tidor, and D.A. Lauffenburger, “Quantitative  
Methods for Developing Fc Mutants with Extended Half-Lives”, Biotech. Bioeng. (2005, in press).  
Methods for Developing Fc Mutants with Extended Half-Lives”, Biotech. Bioeng. (2005, in press).  
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191. Hendriks, B.S., J. Cook, J.M. Burke, J.M. Beusmans, D.A. Lauffenburger, and D. deGraaf, “Computational
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197. Janes, K.A., J.G. Albeck, S. Gaudet, P.K. Sorger, D.A. Lauffenburger, and M.B. Yaffe, “A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis”, Science 310: 1646-1653 (2005).
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Modeling of ErbB Family Phosphorylation Dynamics in Response to TGFα and Heregulin Indicates
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Spatial Compartmentation of Phosphatase Activity”, IEE Systems Biol. (2005, accepted).  
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198. Semino, C.E., R.D. Kamm, and D.A. Lauffenburger, “Autocrine EGF Receptor Activation Mediates Endothelial Cell Migration and Vascular Morphogenesis Induced by VEGF Under Interstitial Flow”, Exptl. Cell Res. (2005, in press).
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192. Semino, C.E., R.D. Kamm, and D.A. Lauffenburger, “Autocrine EGF Receptor Activation Mediates
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199. Hendriks, B.S., J. Cook, J.M. Burke, J.M. Beusmans, D.A. Lauffenburger, and D. deGraaf, “Computational Modeling of ErbB Family Phosphorylation Dynamics in Response to TGFα and Heregulin Indicates Spatial Compartmentation of Phosphatase Activity”, IEE Systems Biol. (2005, accepted).
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Endothelial Cell Migration and Vascular Morphogenesis Induced by VEGF Under Interstitial Flow”,
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Exptl. Cell Res. (2005, accepted).  
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'''Other articles'''  
'''Other articles'''  
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2. Mutant Interleukin-2 Polypeptides; w/ K.D. Wittrup & B. Rao (application filed July 2003)
2. Mutant Interleukin-2 Polypeptides; w/ K.D. Wittrup & B. Rao (application filed July 2003)
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Current revision

Lauffenburger Lab

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Contents

Books

1. Linderman, J.J. and D.A. Lauffenburger, Receptor/Ligand Sorting Along the Endocytic Pathway, Lecture Notes in Biomathematics Series, vol. 78, Springer-Verlag, Heidelberg, 164 pgs. (1989).

2. Lauffenburger, D.A. and J.J. Linderman, Receptors: Models for Binding, Trafficking, and Signalling, Oxford University Press, 365 pgs. (1993); 2nd printing (1996).

Invited reviews, commentaries, and book chapters

1. Lauffenburger, D.A. and C. DeLisi, "Cell Surface Receptors: Physical Chemistry and Cellular Recognition", Int. Rev. Cytol. 84, 269-302 (1983).

2. Lauffenburger, D.A., "Measurement of Phenomenological Parameters for Leukocyte Motility and Chemotaxis", Agents and Actions Supplements 12, 34-53 (1983).

3. Lauffenburger, D.A., "Chemotaxis: Analysis for Quantitative Studies", Biotech. Prog. 1, 151-160 (1985).

4. Zigmond, S.H., R.O. Klausner, R.T. Tranquillo and D.A. Lauffenburger, "Analysis of the Requirements for Time- Averaging of Receptor Occupancy for Gradient Detection by Leukocytes", in Membrane Receptors and Cellular Regulation, ed. M. Czech and C. R. Kahn, pp. 347-356 (1985).

5. Lauffenburger, D.A., "Mathematical Analysis of the Macrophage Response to Bacterial Challenge in the Lung", in Mononuclear Phagocytes: Characteristics, Physiology and Function, ed. R. van Furth, Z. Cohn and S. Gordon, pp. 351-357 (1986).

6. Zigmond, S.H. and D.A. Lauffenburger, "Assays for Leukocyte Chemotaxis", Annu. Rev. Med. 37: 149-155 (1986).

7. Lauffenburger, D.A., D.A. Hammer, R.T. Tranquillo, H.M. Buettner and E.S. Fisher, "How Immune Cells Find Their Targets: Quantitative Studies of Cell Adhesion, Migration and Chemotaxis", in Theoretical Immunology, ed. A. Perelson, part two, pp. 3-18 (1988).

8. Lauffenburger, D.A., "Models for Receptor-Mediated Cell Phenomena: Adhesion and Migration", Annu. Rev. Biophys. Biophys. Chem. 20: 387-414 (1991).

9. Lauffenburger, D.A., "Bacterial Chemotaxis and Microbial Ecology", Microb. Ecol. 22: 175-185 (1991).

10. Ford, R.M., B. . Phillips, J.A. Quinn, and D.A. Lauffenburger, "Stopped-Flow Chamber and Image Analysis System for Quantitative Characterization of Bacterial Population Migration", Microb. Ecol. 22: 127-138 (1991).

11. Lauffenburger, D.A., "Molecules, Mechanics, and Migration of Cells", Appl. Mech. Rev., 47: S287-S290 (1994).

12. Linderman, J.J., P.A. Mahama, K.E. Forsten, and D.A. Lauffenburger, "Diffusion and Probability in Receptor Binding and Signalling", Adv. Chem. Eng. 19: 51-127 (1994).

13. Lauffenburger, D.A., "Cell Engineering", Biomedical Engineering Handbook, J. D. Bronzino, ed., CRC Press, pp. 1536-1544 (1995).

14. Lauffenburger, D.A. and A.F. Horwitz, "Cell Migration: A Physically Integrated Molecular Process", Cell 84: 359- 369 (1996).

15. Lauffenburger, D.A., “Cell Motility: Making Connections Count”, Nature 383: 390-391 (1996).

16. Grodzinsky, A.J., R.D. Kamm, and D.A. Lauffenburger, "Quantitative Aspects of Tissue Engineering: Basic Issues in Kinetics, Transport, and Mechanics", Textbook in Tissue Engineering, R. Lanza, R. Langer, and W. Chick, eds., R.G. Landes, pp. 193-207 (1997).

17. Lauffenburger, D.A., E.M. Fallon, and J.M. Haugh, “Scratching the (Cell) Surface: Cytokine Engineering for Improved Ligand/Receptor Trafficking Dynamics”, Chem. Biol. 5: R257-R263 (1998).

18. Oehrtman, G., L. Walker, B. Will, L. Opresko, H.S. Wiley, and D.A. Lauffenburger, “Methods for Quantitative Assessment of Autocrine Cell Loops”, in Tissue Engineering Methods and Protocols, J. Morgan and M. Yarmush, eds., Humana Press, Totowa NJ, pp. 143-154 (1998).

19. Maheshwari, G. and D.A. Lauffenburger, “Deconstructing (and Reconstructing) Cell Migration”, Microscopy Rev. Tech. 43: 358-368 (1998).

20. Palecek, S.P., E.A. Cox, A. Huttenlocher, D.A. Lauffenburger, and A.F. Horwitz, “Integrin Adhesion in Cell Migration”, in Adv. Molec. Cell Biol. 28: 367-388 (1999).

21. Lauffenburger, D.A. and D.V. Schaffer, “The Matrix Delivers: Gene Therapy and Tissue Engineering Team Up to Speed Bone Regeneration”, Nature Med. 5: 733-734 (1999).

22. Asthagiri, A.R. and D.A. Lauffenburger, “Bioengineering Models of Cell Signaling”, Annu. Rev. Biomed. Eng. 2: 31-53 (2000).

23. Schaffer, D.V. and D.A. Lauffenburger, “Targeted Synthetic Gene Delivery Vectors”, Curr. Op. Molec. Therapeutics 2: 155-161 (2000).

24. Lauffenburger, D.A., “Cell Signaling Pathways as Control Modules: Complexity for Simplicity?”, Proc. Natl. Acad. Sci. 97: 5031-5033 (2000).

25. Zandstra, P.W., D.A. Lauffenburger, and C.J. Eaves, “A Ligand-Receptor Signaling Threshold [LIST] Model of Stem Cell Differentiation Control: A Biologically-Conserved Mechanism Applicable to Hematopoiesis”, Blood 96: 1215-1222 (2000).

26. Varga, C.M., T.J. Wickham, and D.A. Lauffenburger, “Receptor-Mediated Targeting of Gene Delivery Vectors: Insights from Molecular Mechanisms for Improved Vehicle Design”, Biotech. Bioeng. 70: 593-605 (2000).

27. Lauffenburger, D.A. and L.G. Griffith, “Who’s Got Pull Around Here? Cell Organization in Development and Tissue Engineering”, Proc. Natl. Acad. Sci. 98: 4282-4284 (2001).

28. Kassis, J., D.A. Lauffenburger, T. Turner, and A. Wells, “Tumor Invasion as Dysregulated Cell Motility”, Sem. Cancer Biol. 11: 105-117 (2001).

29. Lauffenburger, D.A. and A. Wells, “Getting a Grip: New Insights for Cell Adhesion and Traction”, Nature Cell Biol. 3: E110-E112 (2001).

30. Orsello, C.E., D.A. Lauffenburger, and D.A. Hammer, “Molecular Perspectives in Cell Adhesion: A Physical and Engineering Perspective”, Trends Biotech. 19: 310-316 (2001).

31. Caplan, M.R. and D.A. Lauffenburger, “Nature’s Complex Copolymers: Engineering Design of Oligopeptide Materials”, Ind. Eng. Chem. Res. 41: 403-412 (2002).

32. Glading, A., D.A. Lauffenburger, and A. Wells, “Cutting to the Chase: Calpain Proteases in Cell Motility”, Trends Cell Biol. 12: 46-54 (2002).

33. Wells, A., J. Kassis, J. Solava, T. Turner, and D.A. Lauffenburger, “Induced Cell Motility in Tumor Invasion”, Acta Oncol. 41: 124-130 (2002).

34. Sachs, K., D. Gifford, T. Jaakkola, P. Sorger, and D.A. Lauffenburger, “Bayesian Network Approach to Cell Signaling Pathway Modeling”, Science STKE, www.stke.org/cgi/content/full/sigtrans; 2002/148/pe38 (2002).

35. Wiley, H.S., S.Y. Shvartsman, and D.A. Lauffenburger, “Computational Modeling of the EGF Receptor System: A Paradigm for Systems Biology”, Trends Cell Biol. 13: 43-50 (2003).

36. Lauffenburger, D.A. and A. Wells, “Quantitative Parsing of Cell Multi-tasking in Wound Repair and Tissue Morphogenesis”, Biophys. J. 84: 3499-3500 (2003).

37. Ideker, T. and D.A. Lauffenburger, “High- to Low-Level Computational Modeling of Biological Pathways”, Trends Biotech. 21: 255-262 (2003).

38. Shvartsman, S.Y., H.S. Wiley, and D.A. Lauffenburger, “Random Walks and Feedback Loops in Autocrine EGFR Signaling”, IEEE Control Systems 24: 53-61 (2004).

39. Rao, B.M., D.A. Lauffenburger, and K.D. Wittrup, “Integrating Cell-Level Kinetic Modeling into the Design of Engineered Protein Therapeutics”, Nature Biotech 23: 191-194 (2005).

40. Wells, A., A. Huttenlocher, and D.A. Lauffenburger, “Calpain Proteases in Cell Adhesion and Motility”, Intl. Rev. Cytology 245: 1-16 (2005).

41. Janes, K.A. and D.A. Lauffenburger, “A Biological Approach to Computational Models of Proteomic Networks”, Curr. Op. Chem. Biol. (2005, in press).

42. Ideker, T., R. Winslow, and D.A. Lauffenburger, “Bioengineering and Systems Biology”, Annals Biomed. Eng. (2005, accepted).


Refereed journal articles:

1. Keller, K.H. and D.A. Lauffenburger, "The Effect of Flow Channel Thickness on Surface-Induced Blood Damage", J. Bioeng. 2, 205-217 (1978).

2. Lauffenburger, D.A. and R. Aris, "Measurement of Leukocyte Motility and Chemotaxis Parameters Using a Quantitative Analysis of the Under-Agarose Migration Assay", Math Biosci. 44, 121-138 (1979).

1. Lauffenburger, D.A. and K.H. Keller, "Effects of Leukocyte Random Motility and Chemotaxis in Tissue Inflammatory Response", J. Theor. Biol. 81, 475-503 (1979).

2. Lauffenburger, D.A., "Mathematical Model for Tissue Inflammation Dynamics: Effects of Spatial Distribution, Cell Motility and Chemotaxis", Lect. Notes Biomath. 38, 397-409 (1980).

3. Lauffenburger, D.A. and S.H. Zigmond, "Chemotactic Factor Concentration Gradients in Chemotaxis Assay Systems", J. Immunol. Methods 40, 45-60 (1981).

4. Lauffenburger, D.A. and C.R. Kennedy, "Analysis of a Lumped Model for Tissue Inflammation Dynamics", Math. Biosci. 53, 189-221 (1981).

5. Lauffenburger, D.A., R. Aris and K.H. Keller, "Effects of Random Motility on Growth of Bacterial Populations", Microb. Ecol. 7, 207-227 (1981).

6. Zigmond, S.H., S.J. Sullivan and D.A. Lauffenburger, "Kinetic Analysis of Chemotactic Peptide Receptor Modulation", J. Cell Biol. 92, 34-43 (1982).

7. Lauffenburger, D.A., "Influence of External Concentration Fluctuations on Leukocyte Chemotactic Orientation", Cell Biophys. 4, 177-209 (1982)

8. Lauffenburger, D.A., R. Aris and K.H. Keller, "Effects of Cell Motility and Chemotaxis on Microbial Population Growth", Biophys. J. 40, 209-219 (1982).

9. Lauffenburger, D.A. and C.R. Kennedy, "Localized Bacterial Infection in a Distributed Model for Tissue Inflammation", J. Math. Biol. 16, 141-163 (1983).

10. Daukas, G., D.A. Lauffenburger and S.H. Zigmond, "Reversible Pinocytosis in Polymorphonuclear Leukocytes", J. Cell Biol. 96, 1642-1650 (1983).

11. Lauffenburger, D.A., C.R. Rothman and S.H. Zigmond, "Measurement of Leukocyte Motility and Chemotaxis Parameters with a Linear Under-Agarose Migration Assay", J. Immunol. 131, 940-947 (1983).

12. Lauffenburger, D.A. and B. Calcagno, "Competition Between Two Microbial Populations in a Non-Mixed Environment: Effect of Cell Random Motility", Biotech. Bioeng. 25, 2103-2125 (1983).

13. Lauffenburger, D.A., C.R. Kennedy and R. Aris, "Traveling Bands of Chemotactic Bacteria in the Context of Population Growth", Bull. Math. Biol. 46, 19-40 (1984).

14. Stickle, D.F., D.A. Lauffenburger and S.H. Zigmond, "Measurement of Chemoattractant Concentration Profiles and Diffusion Coefficient in Agarose", J. Immunol. Meth. 70, 65-74 (1984)

15. Rothman, C.R. and D.A. Lauffenburger, "Analysis of the Linear Under-Agarose Leukocyte Migration Assay", Ann. Biomed. Eng. 11, 451-477 (1984).

16. Lauffenburger, D.A., M. Grady and K.H. Keller, "An Hypothesis for Approaching Swarms of Myxobacteria", J. Theor. Biol. 110, 257-274 (1984).

17. Lauffenburger, D.A., "Chemotaxis and Cell Aggregation", Lect. Notes Biomath. 55, 198-213 (1984).

18. Lauffenburger, D.A., "Stability of Colicin Plasmids in Continuous Culture: Mathematical Model and Analysis", Biotech. Prog. 1, 53-59 (1985).

19. Hertz, C.M., D.J. Graves, D.A. Lauffenburger and F.T. Serota, "Use of Cell Affinity Chromatography for Separation of Lymphocyte Subpopulations", Biotech. Bioeng. 27, 603-612 (1985).

20. Stickle, D.F., D.A. Lauffenburger and R.P. Daniele, "Measurement of Chemokinesis of Alveolar Macrophages Using the Linear Under-Agarose Assay", J. Leuk. Biol. 38, 383-401 (1985).

21. Tranquillo, R.T. and D.A. Lauffenburger, "Consequences of Chemosensory Receptor Phenomena for Leukocyte Orientation Behavior", Cell Biophys. 8, 1-46 (1986).

22. Lauffenburger, D.A., "Model for the Dynamics of Colicin Plasmids in Continuous Culture", Ann. NY Acad. Sci. 469, 97-103 (1986).

23. Rivero, M.A. and D.A. Lauffenburger, "Quantification of Bacterial Chemotaxis by Measurement of Model Parameters using the Capillary Assay", Biotech. Bioeng. 28, 1178-1190 (1986).

24. Linderman, J.J. and D.A. Lauffenburger, "Analysis of Intracellular Ligand/Receptor Sorting", Biophys. J. 50, 295- 305 (1986).

25. Leonard, E.F., K. Ikebe, D.A. Lauffenburger, and L. Muul, "Extracorporeal Cellular Immunotherapy", Trans. Am. Soc. Artif. Int. Orgs. 32, 633-638 (1986).

26. Fisher, E.S. and D.A. Lauffenburger, "Mathematical Analysis of Cell-Target Encounter Rates in Two Dimensions: the Effect of Chemotaxis", Biophys. J. 51, 705-716 (1987).

27. Alt, W. and D.A. Lauffenburger, "Transient Behavior of a Chemotaxis System Modeling Certain Types of Tissue Inflammation", J. Math. Biol. 24, 691-722 (1987).

28. Tranquillo, R.T. and D.A. Lauffenburger, "Stochastic Model of Chemosensory Cell Movement", J. Math. Biol. 25, 229-262 (1987).

29. Tranquillo, R.T. and D.A. Lauffenburger, "Analysis of Leukocyte Chemosensory Movement", Adv. Biosciences 66, 29-38 (1987).

30. Hammer, D.A. and D.A. Lauffenburger, "A Dynamical Model for Receptor-mediated Cell Adhesion to Surfaces", Biophys. J. 52, 475-487 (1987).

31. Hammer, D.A., J. . Linderman, D.J. Graves and D.A. Lauffenburger, "Affinity Chromatography for Cell Separation: Mathematical Model and Experimental Analysis", Biotech. Prog. 3, 189-204 (1987).

32. Lauffenburger, D.A., J. . Linderman and L. Berkowitz, "Analysis of Mammalian Cell Growth Factor Receptor Dynamics", Ann. NY Acad. Sci. 506, 147-162 (1987).

33. Lauffenburger, D.A., M.A. Rivero, F.X. Kelly, R.M. Ford and J. DiRienzo, "Bacterial Chemotaxis: Cell Flux Model, Parameter Measurement, Population Dynamics and Genetic Manipulation", Ann. NY Acad. Sci. 506, 281-295 (1987).

34. Lauffenburger, D.A., B.E. Farrell, R.T. Tranquillo, A. Kistler and S.H. Zigmond, "Commentary: Gradient Perception by Neutrophil Leukocytes, Continued", J. Cell Sci. 88, 415-416 (1987).

35. Tranquillo, R.T., D.A. Lauffenburger and S.H. Zigmond, "A Stochastic Model for Leukocyte Random Motility and Chemotaxis Based on Receptor Binding Fluctuations", J. Cell. Biol. 106, 303-309 (1988).

36. Staffeld, P.O., J.A. Quinn and D.A. Lauffenburger, "Analysis of Cell Transport Phenomena: Bacterial Chemotaxis in the Capillary Assay", Chem. Eng. Commun. 58, 339-351 (1988).

37. Fisher, E.S., D.A. Lauffenburger and R.P. Daniele, "Effect of Alveolar Macrophage Chemotaxis on Bacterial Clearance from the Lung Surface", Am. Rev. Resp. Dis. 137, 1129-1134 (1988).

38. Linderman, J.J. and D.A. Lauffenburger, "Analysis of Intracellular Receptor/Ligand Sorting in Endosomes", J. Theor. Biol. 132, 203-233 (1988).

39. Kelly, F.X., K.J. Dapsis and D.A. Lauffenburger, "Effects of Bacterial Chemotaxis on Dynamics of Microbial Competition", Microb. Ecol. 16, 115-131 (1988).

40. Lauffenburger, D.A., R.T. Tranquillo and S.H. Zigmond, "Concentration Gradients of Chemotactic Factor in Chemotaxis Assays", Meth. Enzymol. 162, 85-101 (1988).

41. Tranquillo, R.T., S.H. Zigmond and D.A. Lauffenburger, "Measurement of the Chemotaxis Coefficient for Polymorphonuclear Leukocytes in the Under-Agarose Assay", Cell Motility Cytoskel. 11, 1-15 (1988).

42. Rupnick, M.A., C.L., Stokes, S.K. Williams and D.A. Lauffenburger, "Quantitation of Random Motility of Human Microvessel Endothelial Cells Using a Linear Under-Agarose Assay", Lab Invest. 59, 363-372 (1988).

43. Tranquillo, R.T., B.E. Farrell, E.S. Fisher and D.A. Lauffenburger, "A Stochastic Model for Chemosensory Cell Movement: Application to Neutrophil and Macrophage Persistence and Orientation", Math. Biosci. 90, 287- 303 (1988).

44. Lauffenburger, D.A., "Bacterial Motility and Chemotaxis Effects on Microbial Population Growth", in Laboratory Models for Microbial Ecosystems, ed. J.W.T. Wimpenny, CRC Press, vol. II, pp 143-172 (1988).

45. Glasgow, J.E., B.E. Farrell, E.S. Fisher, D.A. Lauffenburger and R. P. Daniele, "The Motile Response of Alveolar Macrophages: An Experimental Study using Single-Cell and Cell Population Approaches", Am. Rev. Resp. Dis. 139, 320-329 (1989).

46. Buettner, H.M., D.A. Lauffenburger and S.H. Zigmond, "Cell Transport in the Millipore Filter Assay", AIChE J. 35, 459-465 (1989).

47. Lauffenburger, D.A. and C. Cozens, "Regulation of Mammalian Cell Growth by Autocrine Growth Factors: Analysis of Consequences for Inoculum Cell Density Effects", Biotech. Bioeng. 33, 1365-1378 (1989).

48. Hammer, D.A. and D.A. Lauffenburger, "A Dynamical Model for Receptor-Mediated Cell Adhesion to Surfaces in Viscous Shear Flow", Cell Biophys. 14, 139-173 (1989).

49. Lauffenburger, D.A., "A Simple Model for the Effects of Receptor-Mediated Cell/Substratum Adhesion on Cell Migration", Chem. Eng. Sci. 44, 1903-1914 (1989).

50. Mayo, K.H., M. Nunez, C. Burke, C. Starbuck, D.A. Lauffenburger and C.R. Savage, "Epidermal Growth Factor Receptor Binding is not a Simple One-Step Process", J. Biol. Chem. 264, 17838-17844 (1989).

51. Buettner, H.M., D.A. Lauffenburger and S.H. Zigmond, "Measurement of Leukocyte Motility and Chemotaxis Parameters with the Millipore Filter Assay", J. Immunol. Meth. 123, 25-37 (1989).

52. Rivero, M.A., R.T. Tranquillo, H.M. Buettner and D.A. Lauffenburger, "Transport Models for Chemotactic Cell Populations Based on Individual Cell Behavior", Chem. Eng. Sci. 44, 2881-2897 (1989).

53. Wattenbarger, M.R., D.J. Graves and D.A. Lauffenburger, "Specific Adhesion of Glycophorin Liposomes to a Lectin Surface under Shear Flow", Biophys. J. 57, 765-777 (1990).

54. Fisher, E.S. and D.A. Lauffenburger, "Analysis of the Effects of Immune Cell Motility and Chemotaxis on Target Elimination Dynamics", Math. Biosci. 98, 73-102 (1990).

55. Charnick, S. and D.A. Lauffenburger, "Mathematical Analysis of Cell-Target Encounter Rates in Three Dimensions: The Effect of Chemotaxis", Biophys. J. 57, 1009-1023 (1990).

56. Starbuck, C., H.S. Wiley and D.A. Lauffenburger, "Epidermal Growth Factor Binding and Trafficking Dynamics in Fibroblasts: Relationship to Cell Proliferation", Chem. Eng. Sci. 45, 2367-2373 (1990).

57. Cozens-Roberts, C., J.A. Quinn and D.A. Lauffenburger, "Receptor-Mediated Adhesion Phenomena: Model Studies with the Radial-Flow Detachment Assay", Biophys. J. 58, 107-125 (1990).

58. Farrell, B.E., R.P. Daniele and D.A. Lauffenburger, "Quantitative Relationships Between Single-Cell and Cell- Population Model Parameters for Chemosensory Migration Responses of Alveolar Macrophages to C5a", Cell Motility Cytoskel. 16: 279-293 (1990).

59. Stokes, C.L., P.B. Weisz, S.K. Williams and D.A. Lauffenburger, "Inhibition of Microvascular Endothelial Cell Migration by ß-Cyclodextrin Tetradecasulfate and Hydrocortisone", Microvasc. Res. 40: 279-284 (1990).

60. Cozens-Roberts, C., D.A. Lauffenburger and J.A. Quinn, "Receptor-Mediated Cell Attachment and Detachment Kinetics - Part I: Probabilistic Model and Analysis", Biophys. J. 58: 841-856 (1990).

61. Cozens-Roberts, C., J.A. Quinn and D.A. Lauffenburger, "Receptor-Mediated Cell Attachment and Detachment Kinetics - Part II: Experimental Model Studies with the Radial Flow Detachment Assay", Biophys. J. 58: 857-872 (1990).

62. Stokes, C.L., M.A. Rupnick, S.K. Williams and D.A. Lauffenburger, "Chemotaxis of Human Microvessel Endothelial Cells in Response to Acidic Fibroblast Growth Factor", Lab. Invest. 63: 657-668 (1990).

63. Stokes, C.L., D.A. Lauffenburger, and S.K. Williams, "Endothelial Cell Chemotaxis in Angiogenesis", Lect. Notes Biomath. 89: 442-452 (1990).

64. Ford, R.M., B.R. Phillips, J.A. Quinn, and D.A. Lauffenburger, "Measurement of Bacterial Random Motility and Chemotaxis Coefficients: I. Stopped-Flow Diffusion Chamber Assay", Biotech. Bioeng. 37: 647-660 (1991).

65. Ford, R.M. and D.A. Lauffenburger, "Measurement of Bacterial Random Motility and Chemotaxis Coefficients: II. Application of Single Cell-Based Mathematical Model", Biotechn. Bioeng. 37: 661-672 (1991).

66. DiMilla, P.A., K. Barbee, and D.A. Lauffenburger, "A Mathematical Model for the Effects of Adhesion and Mechanics on Cell Migration Speed", Biophys. J. 60: 15-37 (1991).

67. Wiley, H.S., J.J. Herbst, B.J. Walsh, D.A. Lauffenburger, M.G. Rosenfeld, and G.N. Gill, "The Role of Tyrosine Kinase Activity in Endocytosis, Compartmentation, and Downregulation of the EGF Receptor", J. Biol. Chem. 266: 11083-11094 (1991).

68. Stokes, C.L., S.K. Williams, and D.A. Lauffenburger, "Migration of Individual Microvessel Endothelial Cells: Stochastic Model and Parameter Measurement", J. Cell Sci. 99: 419-430 (1991).

69. Charnick, S., E.S. Fisher, and D.A. Lauffenburger, "Computer Simulations of the Effect of Chemotaxis on Cell/Target Encounter in Two Dimensions", Bull. Math. Biol. 53: 591-621 (1991).

70. Ford, R.M. and D.A. Lauffenburger, "Analysis of Chemotactic Bacterial Distributions in Population Migration Assays Using a Mathematical Model Applicable to Steep or Shallow Gradients", Bull. Math. Biol. 53: 721-749 (1991).

71. Cano, M.L., D.A. Lauffenburger, and S.H. Zigmond, "Kinetic Analysis of F-Acton Depolymerization in Polymorphonuclear Leukocyte Lysates Indicates that Chemoattractant Stimulation Increases Acton Filament Number Without Altering the Filament Length Distribution", J. Cell Biol. 115: 677-687 (1991).

72. Stokes, C.L., and D.A. Lauffenburger, "Analysis of the Roles of Microvessel Endothelial Cell Random Motility and Chemotaxis in Angiogenesis", J. Theor. Biol. 152: 377-403 (1991).

73. Forsten, K.E. and D.A. Lauffenburger, "Autocrine Ligand Binding to Cell Receptors: Mathematical Analysis of Competition by Solution 'Decoys'", Biophys. J.: 518-529 (1992).

74. Starbuck, C. and D.A. Lauffenburger, "Mathematical Model for the Effects of Epidermal Growth Factor Receptor Trafficking Dynamics on Fibroblast Proliferation Responses", Biotech. Progress 8: 132-143 (1992).

75. Ford, R.M. and D.A. Lauffenburger, "A Simple Expression for Quantifying Bacterial Chemotaxis Using Capillary Assay Data: Application to the Analysis of Enhanced Chemotactic Responses from Growth-Limited Cultures", Math. Biosci. 109: 127-149 (1992).

76. DiMilla, P.A., J.A. Quinn, S.M. Albelda, and D.A. Lauffenburger, "Measurement of Individual Cell Migration Parameters for Human Tissue Cells", AIChE J. 38: 1092-1104 (1992).

77. Forsten, K.E., and D.A. Lauffenburger, "Interrupting Autocrine Ligand-Receptor Binding: Comparison Between Receptor Blockers and Ligand Decoys", Biophys. J. 63: 857-861 (1992).

78. Nunez, M., K.H. Mayo, C. Starbuck, and D.A. Lauffenburger, "pH Sensitivity of Epidermal Growth Factor Complexes", J. Cell Biochem. 51: 312-321 (1993).

79. Saterbak, A., S.C. Kuo, and D.A. Lauffenburger, "Heterogeneity and Probabilistic Binding Contributions to Receptor-Mediated Cell Detachment Kinetics", Biophys. J. 65: 243-252 (1993).

80. DiMilla, P.A., J. Stone, S.M. Albelda, J.A. Quinn, and D.A. Lauffenburger, "Maximal Migration of Human Smooth Muscle Cells on Fibronectin and Collagen Type IV Occurs at an Intermediate Adhesiveness", J. Cell Biol. 122: 729-737 (1993).

81. Kuo, S.C. and D.A. Lauffenburger, "Relationship Between Receptor/Ligand Binding Affinity and Bond Strength", Biophys. J. 65: 2191-2200 (1993).

82. Schmidt, C.E., A.F. Horwitz, D.A. Lauffenburger, and M. P. Sheetz, "Integrin/Cytoskeleton Interactions in Migrating Fibroblasts are Dynamic, Asymmetric, and Regulated", J. Cell Biol. 123: 977-991 (1993).

83. Forsten, K.E. and D.A. Lauffenburger, "Probability of Autocrine Ligand Capture by Cell Surface Receptors: Implications for Ligand Secretion Measurements", J. Comp. Biol. 1: 15-23 (1994).

84. Herbst, J.J., L.K. Opresko, B.J. Walsh, D.A. Lauffenburger, and H.S. Wiley, "Regulation of Postendocytic Trafficking of the Epidermal Growth Factor Receptor through Endosomal Retention", J. Biol. Chem., 269: 12865-12873 (1994).

85. French, A.R., G.P. Sudlow, H.S. Wiley, and D.A. Lauffenburger, "Postendocytic Trafficking of Epidermal Growth Factor-Receptor Complexes is Mediated Through Saturable and Specific Endosomal Interactions," J. Biol. Chem., 269: 15749-15755 (1994).

86. Schmidt, C.E., T. Chen, and D.A. Lauffenburger, "Simulation and Analysis of Directed Integrin Transport on Migrating Fibroblasts," Biophys. J., 67: 461-474 (1994).

87. Wu, P., J. Hoying, S.K. Williams, B. Kozikowski, and D.A. Lauffenburger, "Soluble Integrin-Binding Competitor Either Inhibits or Enhances Endothelial Cell Migration, Predictably from Adhesion Effect", Ann. Biomed. Eng., 22: 144-152 (1994).

88. Forsten, K.E., and D.A. Lauffenburger, "The Role of Low-Affinity Interleukin-2 Receptors in Autocrine Ligand Binding", Molec. Immunol., 31: 739-751 (1994).

89. Reddy, C.C., A. Wells, and D.A. Lauffenburger, "Proliferative Response of Fibroblasts Expressing Internalization- Deficient EGF Receptors is Altered via Differential EGF Depletion Effects," Biotech. Progr., 10: 377-384 (1994).

90. Forsten, K.E., R.E. Kozack, D.A. Lauffenburger, and S. Subramaniam, "Numerical Solution of the Nonlinear Poisson-Boltzmann Equation for a Membrane-Electrolyte System," J. Phys. Chem. 98: 5580- 5586(1994).

91. Will, B.H., D.A. Lauffenburger, and H.S. Wiley, "Studies on Engineered Autocrine Systems: Requirements for Ligand Release from Cells Producing an Artificial Growth Factor", Tissue Eng. 1: 81-95 (1995).

92. French, A.R., D. Talaki, S.K. Niyogi, and D.A. Lauffenburger, "Intracellular Trafficking of Epidermal Growth Family Ligands is Directly Influenced by the pH Sensitivity of the Receptor/Ligand Interaction", J. Biol. Chem. 270: 4334-4340 (1995).

93. Lauffenburger, D.A., K.E. Forsten, B. Will, and H.S. Wiley, "Molecular/Cell Engineering Approach to Autocrine Ligand Control of Cell Function", Ann. Biomed. Eng. 23: 208-215 (1995).

94. Schmidt, C.E., J. Dai, D.A. Lauffenburger, M.P. Sheetz, and A.F. Horwitz, "Integrin-Cytoskeletal Interactions in Neuronal Growth Cones", J. Neurosci. 15: 3400-3407 (1995).

95. Schmidt, C.E., T. Chen, and D.A. Lauffenburger, "Modulation of Cell Migration Speed via Genetic Manipulation of Integrin/Cytoskeleton Linkage", J. Cell. Eng. 1: 3-12 (1995).

96. Robinson, A.S. and D.A. Lauffenburger, "Model for ER Chaperone Dynamics and Secretory Protein Interactions", AIChE Journal 42: 1443-1453 (1996).

97. Chu, L., H.S. Wiley, and D.A. Lauffenburger, "Endocytic Relay as a Potential Means for Enhancing Ligand Transport through Cellular Tissue Matrices: Analysis and Possible Implications for Drug Delivery", Tissue Eng. 2: 17-38 (1996).

98. Reddy, C.C., A. Wells, and D.A. Lauffenburger, "Receptor-Mediated Effects on Ligand Availability Influence Relative Mitogenic Potencies of EGF and TGFα", J. Cell. Physiol. 166: 512-522 (1996).

99. Lauffenburger, D.A., L. Chu, A. French, G. Oehrtman, C. Reddy, A. Wells, S.K. Niyogi, and H.S. Wiley, "Engineering Dynamics of Growth Factors and Other Therapeutic Ligands", Biotech. Bioeng. 52: 61-80 October 30, 2005 (1996).

100. Palecek, S., C.E. Schmidt, D.A. Lauffenburger, and A.F. Horwitz, "Integrin Dynamics on the Uropodal Region of Migrating Fibroblasts", J. Cell Sci. 109: 941-952 (1996).

101. French, A.R. and D.A. Lauffenburger, "Intracellular Receptor/Ligand Sorting: Endosomal Retention Component Model", Biotech. Bioeng. 51: 281-297 (1996).

102. Saterbak, E.A. and D.A. Lauffenburger, "Adhesion Mediated by Bonds in Series", Biotech. Progr. 12: 682-699 (1996).

103. Reddy, C.C., S.K. Niyogi, A. Wells, H.S. Wiley, and D.A. Lauffenburger, “Engineering Epidermal Growth Factor for Enhanced Mitogenic Potency”, Nature Biotech. 14: 1696-1699 (1996).

104. Palecek, S., J.C. Loftus, M.H. Ginsberg, D.A. Lauffenburger, and A.F. Horwitz, “Integrin/Ligand Binding Properties Govern Cell Migration Speed through Cell/Substratum Adhesiveness”, Nature 385: 537-540 (1997).

105. Schaffer, D.V., R.L. Neve, and D.A. Lauffenburger, “Use of the Green Fluorescent Protein as a Quantitative Reporter of Epidermal Growth Factor Receptor-Mediated Gene Delivery”, Tissue Eng. 3: 53-63 (1997).

106. Haugh, J.M. and D.A. Lauffenburger, “Physical Modulation of Intracellular Signaling Processes by Locational Regulation”, Biophys. J. 72: 2014-2031 (1997).

107. Kuo, S.C., D.A. Hammer, and D.A. Lauffenburger, “Simulation of Detachment of Specifically-Bound Particles from Surfaces by Shear Flow”, Biophys. J. 73: 517-531 (1997).

108. French, A.R. and D.A. Lauffenburger, “Design Principles for Controlling Receptor/Ligand Trafficking: Effects of Cellular and Molecular Properties on Endosomal Sorting Outcomes”, Ann. Biomed. Eng. 25: 690-707 (1997).

109. Ware, M.F., D.A. Tice, S.J. Parsons, and D.A. Lauffenburger, “Overexpression of c-Src in Fibroblasts Enhances Endocytic Internalization of EGF Receptor”, J. Biol. Chem. 272: 30185-30190 (1997).

110. Huttenlocher, A., S.P. Palecek, Q. Lu, W. Zhang, R.L. Mellgren, D.A. Lauffenburger, M.H. Ginsberg, and A.F. Horwitz, “Regulation of Cell Migration by the Calcium-Dependent Protease Calpain”, J. Biol. Chem. 272: 32719-32722 (1997).

111. Oehrtman, G.T., H.S. Wiley, and D.A. Lauffenburger, “Escape of Autocrine Ligands to Extracellular Medium: Experimental Test of Theoretical Model Predictions”, Biotech. Bioeng. 57: 571-582 (1998).

112. Leon, E.J., N. Verma, S. Zhang, D.A. Lauffenburger, and R.D. Kamm, “Mechanical Properties of a Class of Self- Assembling Oliogopeptide Biomaterials”, J. Biomed. Mat. Sci. Polymer Ed. 9: 293-308 (1998).

113. Palecek, S.P., A. Huttenlocher, A.F. Horwitz, and D.A. Lauffenburger, “Physical and Biochemical Regulation of Integrin Release During Rear Detachment of Migrating Cells”, J. Cell Sci. 111: 929-940 (1998).

114. Ware, M.F., A. Wells, and D.A. Lauffenburger, “EGF Alters Fibroblast Migration Speed and Directional Persistence Reciprocally and in Matrix-Dependent Manner”, J. Cell Sci. 111: 2423-2432 (1998).

115. Reddy, C.C., A. Wells, and D.A. Lauffenburger, “Comparative Mitogenic Potencies of EGF and TGFα Depend on Receptor-Limitation versus Ligand-Limitation”, Med. Biol. Eng. Comp. 36: 499-507 (1998).

116. Schaffer, D. and D.A. Lauffenburger, “Optimization of Cell Surface Binding Enhances Efficiency and Specificity of Molecular Conjugate Gene Delivery”, J. Biol. Chem. 273: 28004-28009 (1998).

117. Wiley, H.S., M. Woolf, L.K. Opresko, P. Burke, B. Will, J. Morgan, and D.A. Lauffenburger, “Removal of the Membrane-anchoring Domain of EGF Leads to Intracrine Signaling and Disruption of Mammary Epithelial Cell Organization”, J. Cell Biol. 143: 1317-1328 (1998).

118. Lauffenburger, D.A., G.T. Oehrtman, L. Walker, and H.S. Wiley, “Real-Time Quantitative Measurement of Autocrine Ligand Binding Indicates that Autocrine Loops Operate over a Short Range”, Proc. Natl. Acad. Sci. USA: 95: 15368-15373 (1998).

119. Xie, H., M.A. Pallero, K. Gupta, M.F. Ware, P. Chang, D.J. Kwiatkowski, D.A. Lauffenburger, J.E. Murphy- Ullrich, and A. Wells, “EGF Receptor Regulation of Cell-Substratum Interactions: EGF-Induced Disassembly of Focal Adhesions does not Require the Motility-Associated PLCγ Signaling Pathway”, J. Cell Sci. 111: 615- 624 (1998).

120. Haugh, J.M. and D.A. Lauffenburger, “Analysis of Receptor Internalization as a Mechanism for Modulating Signal Transduction Mediated by EGF Receptor”, J. Theor. Biol. 195: 187-218 (1998).

121. Haugh, J.M., K. Schooler, A. Wells, H.S. Wiley, and D.A. Lauffenburger, “Effect of Epidermal Growth Factor Receptor Internalization on Regulation of the Phospholipase C-γ Signaling Pathway”, J. Biol. Chem. 274: 8958-8965 (1999).

122. Wells, A., M.F. Ware, F.D. Allen, and D.A. Lauffenburger, “Shaping Up for Shipping Out: PLCγ Signaling of Morphology Changes in EGF-Stimulated Fibroblast Migration”, Cell Mot. Cytoskel. 44: 227-233 (1999).

123. Palecek, S.P., A.F. Horwitz, and D.A. Lauffenburger, “A Kinetic Model for Integrin-Mediated Adhesion Release during Cell Migration”, Annals Biomed. Eng. 27: 219-235 (1999).

124. Asthagiri, A., A.F. Horwitz, and D.A. Lauffenburger, “A Rapid and Sensitive Quantitative Kinase Activity Assay Using a Convenient 96-well Format”, Analyt. Biochem. 269: 342-347 (1999).

125. Maheshwari, G., A. Wells, L.G. Griffith, and D.A. Lauffenburger, “Biophysical Integration of Effects of Epidermal Growth Factor and Fibronectin on Fibroblast Migration”, Biophys. J. 76: 2814-2823 (1999).

126. Dong, J., L.K. Opresko, P.J. Dempsey, D.A. Lauffenburger, R.J. Coffey, H.S. Wiley, “Metalloprotease-Mediated Ligand Release Regulates Autocrine Signaling through the EGF receptor”, Proc. Natl. Acad. Sci. USA 96: 6235-6240 (1999).

127. Zhang, S., L. Yan, M. Altma, M. Lassle, H. Nugent, F. Frankel, D.A. Lauffenburger, G.M. Whitesides, and A. Rich, “Biological Surface Engineering: A Simple System for Cell Pattern Formation”, Biomaterials 20: 1213- 1220 (1999).

128. Orsello, C.E., Lauffenburger, D.A., and C.K. Colton, “Characterization of Cell Detachment from Hollow Fiber Affinity Membranes”, Biomed. Sci. Instr. 35: 315-320 (1999).

129. Asthagiri, A., C. Nelson, A.F. Horwitz, and D.A. Lauffenburger, “Quantitative Relation Between Integrin-Ligand Binding, Adhesion, and Signaling via Focal Adhesion Kinase and Extracellular-Signal Regulated Kinase 2”, J. Biol. Chem. 274: 27119-27127 (1999).

130. Haugh, J.M., A.C. Huang, H.S. Wiley, A. Wells, and D.A. Lauffenburger, “Internalized Epidermal Growth Factor Receptors Participate in the Activation of p21ras in Fibroblasts”, J. Biol. Chem. 274: 34350-34360 (1999).

131. Glading, A., P. Chang, D.A. Lauffenburger, and A. Wells, “EGF Receptor Activation of Calpain is Required for Fibroblast Motility and Occurs via an ERK/MAPK Signaling Pathway”, J. Biol. Chem. 275: 2390- 2398 (2000).

132. Schaffer, D.V., N. Fidelman, N. Dan, and D.A. Lauffenburger, “Vector Unpackaging is a Limiting Barrier to Molecular Conjugate Gene Delivery and Expression”, Biotech. Bioeng. 67: 598-606 (2000).

133. Fallon, E.M., S.F. Liparoto, K.J. Lee, T.L. Ciardelli, and D.A. Lauffenburger, “Increased Endosomal Sorting of Ligand to Recycling Enhances Potency of an Interleukin-2 Analog”, J. Biol. Chem. 275: 6790-6797 (2000).

134. Maheshwari, G., G. Brown, D.A. Lauffenburger, A. Wells, and L.G. Griffith, “Cell Adhesion and Motility Depend on Nanoscale RGD Clustering”, J. Cell. Sci. 113: 1677-1686 (2000).

135. Zandstra, P.W., H.-V. Lee, G. Daley, L.G. Griffith, and D.A. Lauffenburger, “Leukemia Inhibitor Factor (LIF) Modulates Embryonic Stem Cell Self-Renewal and Differentiation Independently of Proliferation”, Biotech. Bioeng. 69: 607-617 (2000).

136. Haugh, J.M., A. Wells, and D.A. Lauffenburger, “Mathematical Modeling of Epidermal Growth Factor Signaling through the Phospholipase C Pathway: Mechanistic Insights and Predictions for Molecular Interventions”, Biotech. Bioeng. 70: 225-238 (2000).

137. Fallon, E.M. and D.A. Lauffenburger, “Computational Model for the Effects of Ligand/Receptor Binding Properties on Interleukin-2 Trafficking Dynamics and T-Cell Proliferation Response”, Biotech. Progr. 16: 905-916 (2000).

138. Asthagiri, A.R., C.A. Reinhart, A.F. Horwitz, and D.A. Lauffenburger, “The Role of Transient ERK2 Signals in Fibronectin- and Insulin-Mediated DNA Synthesis”, J. Cell Sci. 113: 4499-4510 (2000).

139. Caplan, M.R., P.N. Moore, S. Zhang, R.D. Kamm, D.A. Lauffenburger, "Self-Assembly of a β-sheet Protein is Governed by Relief of Electrostatic Repulsion Relative to van der Waals Attraction", Biomacromolecules 1: 627-631 (2000).

140. Asthagiri, A.R. and D.A. Lauffenburger, “A Computational Study of Feedback Effects on Signal Propagation in a Mitogen-Activated Protein Kinase (MAPK) Pathway Model”, Biotech. Progr. 17: 227-239 (2001).

141. Glading, A., F. Ueberall, S.M. Keyse, D.A. Lauffenburger, and A. Wells, “Membrane-Proximal ERK Signaling is Required for M-calpain Activation Downstream of EGF Receptor Signaling”, J. Biol. Chem. 276: 23341-23348 (2001).

142. Dewitt, A., J.Y. Dong, H.S. Wiley, and D.A. Lauffenburger, “Quantitative Analysis of the EGF Receptor Autocrine System Reveals Cryptic Regulation of Cell Response by Ligand Capture”, J. Cell Sci. 114: 2301-2313 (2001).

143. Narang, A., K.K. Subramanian, and D.A. Lauffenburger, “Mathematical Model for Chemoattractant Gradient Sensing Based on Receptor-Regulated Membrane Phospolipid Signaling Dynamics”, Ann. Biomed. Eng. 29: 677-691 (2001).

144. Shvartsman, S.Y., H.S. Wiley, W.M. Deen, and D.A. Lauffenburger, “Spatial Range of Autocrine Signaling Loops: Modeling and Computational Analysis”, Biophys. J. 81: 1854-1867 (2001).

145. Hong, K., J. Sherley, and D.A. Lauffenburger, “Methylation of Episomal Plasmids as a Barrier to Transient Gene Expression via a Synthetic Delivery Vector”, Biomolec. Eng. 18: 185-192 (2001).

146. Varga, C.M., K. Hong, and D.A. Lauffenburger, “Quantitative Analysis of Synthetic Gene Delivery Vector Design Properties”, Molec. Ther. 4: 438-446 (2001).

147. Maheshwari, G., H.S. Wiley, and D.A. Lauffenburger, “Autocrine Epidermal Growth Factor Stimulates Directionally-Persistent Mammary Epithelial Cell Migration’, J. Cell Biol. 155: 1123-1128 (2001).

148. Caplan, M.R., E.M. Schwartzfarb, S. Zhang, R.D. Kamm, and D.A. Lauffenburger, “Control of Self- Assembling Oligopeptide Matrix Formation through Systematic Variation of Amino Acid Sequence”, Biomaterials 23: 219-227 (2002).

149. Shvartsman, S.V., P. Dent, H.S. Wiley, and D.A. Lauffenburger, “Context-Dependent Signaling in Autocrine Loops with Positive Feedback: Modeling and Experiments in the EGFR System”, Am. J. Physiol. – Cell Physiol. 282: C545-C559 (2002).

150. Viswanathan, S., T. Benatar, S. Rose-John, D.A. Lauffenburger, and P.W. Zandstra, “Ligand/Receptor Signaling Threshold Model Accounts for gp130-Mediated Embryonic Stem Cell Self-Renewal Responses to LIF and HIL6”, Stem Cells 20: 119-138 (2002).

151. Koo, L.Y., D.J. Irvine, A.M. Mayes, D.A. Lauffenburger, and L.G. Griffith, “Co-Regulation of Cell Adhesion by Nanoscale RGD Organization and Mechanical Stimulus”, J. Cell Sci. 115: 1423-1433 (2002).

152. Marini, D.M., W. Hwang, D.A. Lauffenburger, S. Zhang, and R.D. Kamm, “Left-handed Helical Ribbon Intermediates in the Self-Assembly of a β-sheet Peptide”, Nanoletters 2: 295-299 (2002).

153. Allen, F.D., C.F. Asnes, P. Chang, E.L. Elson, D.A. Lauffenburger, and A. Wells, “EGF Induces Acute Matrix Contraction and Subsequent Calpain-Modulated Relaxation”, Wound Rep. Regen. 10: 67-76 (2002).

154. Shvartsman, S.Y., C.B. Muratov, and D.A. Lauffenburger, “Modeling and Computational Analysis of EGF Receptor-Mediated Cell Communication in Drosophila Oogenesis”, Development 129: 2577-2589 (2002).

155. Caplan, M.R., E.M. Schwartzfarb, S. Zhang, R.D. Kamm, and D.A. Lauffenburger, “Effects of Systematic Variation of Amino Acid Sequence on the Mechanical Properties of a Self-Assembling Oligopeptide Biomaterial”, J. Biomat. Sci. Polymer Ed. 13: 225-236 (2002).

156. Sarkar, C.A., K. Lowenhaupt, T. Horan, T.C. Boone, B. Tidor, and D.A. Lauffenburger, “Rational Cytokine Design for Increased Lifetime and Enhanced Potency Using pH-Activated ‘Histidine Switching’”, Nature Biotech. 20: 908-913 (2002).

157. Dewitt, A., T. Iida, H.-Y. Lam, V. Hill, H.S. Wiley, and D.A. Lauffenburger, “Affinity Regulates Spatial Range of EGF Receptor Autocrine Ligands”, Develop. Biol. 250: 305-316 (2002).

158. Sarkar, C.A. and D.A. Lauffenburger, “Cell-Level Pharmacokinetic Model of GCSF: Implications for Ligand Lifetime and Potency in Vivo”, Molec. Pharmacol. 63: 147-158 (2003).

159. Hendriks, B., L.K. Opresko, H.S. Wiley, and D.A. Lauffenburger, “Co-Regulation of EGFR/HER2 Levels and Locations: Quantitative Analysis of HER2 Overexpression Effects”, Cancer Res. 63: 1130-1137 (2003).

160. Ricci, M.S., C.A. Sarkar, E.M. Fallon, D.A. Lauffenburger, and D.N. Brems, “pH Dependence of Structural Stability of IL-2 and GCSF”, Protein Sci. 12: 1030-1038 (2003).

161. Sarkar, C.A., Lowenhaupt, K., Wang, P.J., Horan, T., and D.A. Lauffenburger, “Parsing the Effects of Binding, Signaling, and Trafficking on the Mitogenic Potency of GCSF Analogs”, Biotech. Progr. 19: 955-964 (2003).

162. Hendriks, B., L.K. Opresko, H.S. Wiley, and D.A. Lauffenburger, “Quantitative Analysis of HER2-Mediated Effects on HER2 and EGFR Endocytosis: Distribution of Homo- and Hetero-dimers Depends on Relative HER2 Levels”, J. Biol. Chem. 278: 23343-23351 (2003).

163. Cheng, C., D.A. Lauffenburger, and T. Morales, “Motile Chondrocytes: Migration Properties and Synthesis of Collagen II”, Osteoarthr. Cart. 11: 603-612 (2003).

164. Mamoune, A., J.-H. Luo, D.A. Lauffenburger, and A. Wells, “Calpain-2 as a Target for Limiting Prostate Cancer Invasion”, Cancer Res. 63: 4632-4640 (2003).

165. Janes, K.A., J.G. Albeck, L.X. Peng, P.K. Sorger, D.A. Lauffenburger, and M.B. Yaffe, “High-Throughput Multiplex Kinase Assay for Monitoring Information Flow in Signaling Networks: Application to Sepsis- Apoptosis”, Molec. Cell. Proteomics 2: 463-473 (2003).

166. Hendriks, B., H.S. Wiley, and D.A. Lauffenburger, “HER2-Mediated Effects on EGFR Endosomal Sorting: Analysis of Biophyical Mechanisms”, Biophys. J. 85: 2732-2745 (2003).

167. Viswanathan, S., T. Benatar, M. Mileikovsky, D.A. Lauffenburger, A. Nagy, and P.W. Zandstra, “Supplementation-Dependent Differences in the Rates of Embryonic Stem Cell Self-Renewal, Differentiation, and Apoptosis”, Biotech. Bioeng. 84: 505-517 (2003).

168. Rao, B.J., A.T. Girvin, T. Ciardelli, D.A. Lauffenburger, and K.D. Wittrup, “Interleukin-2 Mutants with Enhanced α-Receptor Subunit Binding Affinity”, Protein Eng. 16: 1081-10877 (2003).

169. Maly, I., H.S. Wiley, and D.A. Lauffenburger, “Self-Organization of Polarized Cell Signaling via Autocrine EGFR Circuits: Computational Model Analysis”, Biophys. J. 86: 10-22 (2004).

170. Prudhomme, W., K. Duggar, G.Q. Daly, P.W. Zandstra, and D.A. Lauffenburger, “Multi-Variate Proteomic Analysis of Murine Embryonic Stem Cell Self-Renewal vs Differentiation Behavior”, Proc. Natl. Acad. Sci. USA 101: 2900-2905 (2004).

171. Iwabu, A., K. Smith, F.D. Allen, D.A. Lauffenburger, and A. Wells, “EGF Induces Fibroblast Contractility and Motility via a PKCδ-Dependent Pathway”, J. Biol. Chem. 279: 14551-14560 (2004).

172. Tschumperlin, D.J., G. Dai, I.V. Maly, L.H. Laiho, A.K. McVittie, P.T. So, D.A. Lauffenburger, R.D. Kamm, and J.M. Drazen, “Mechanotransduction via Growth Factor Shedding into a Compliant Extracellular Space”, Nature 429: 83-86 (2004).

173. Janes, K.A., J. R. Kelly, S. Gaudet, J.G.Albeck, P.K. Sorger, and D.A. Lauffenburger, “Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multi-Variate Signaling Network Measurements”, J. Comp. Biol. 11: 544-561 (2004).

174. Lu, H., L.Y. Koo, D.A. Lauffenburger, L.G. Griffith, and K.F. Jensen, “Microfluidic Shear Devices for Quantitative Analysis of Cell Adhesion”, Analyt. Chem. 76: 5257-5264 (2004).

175. Rao, B.M., I. Driver, D.A. Lauffenburger, and K.D. Wittrup, “IL-2 Variants Engineered for Increased IL-2Ra Affinity Exhibit Increased Potency Arising from a Cell Surface Ligand Reservoir Effect”, Molec. Pharmacol. 66: 864-869 (2004).

176. Maly, I., R.T. Lee, and D.A. Lauffenburger, “A Model for Mechanotransduction in Cardiac Muscle: Effects of Extracellular Matrix Deformation on Autocrine Signaling”, Ann. Biomed. Eng. 32: 1319-1335 (2004).

177. Prudhomme, W., K.H. Duggar, and D.A. Lauffenburger, “Kinetic Model for Deconvolution of Murine Embryonic Stem Cell Self-Renewal and Differentiation Responses to Cytokines and Extracellular Matrix”, Biotech. Bioeng. 88: 264-272 (2004).

178. Lazar, C.S., C.M. Cresson, D.A. Lauffenburger, and G.N. Gill, “The Na+/H+ Exchanger Regulatory Factor Stabilizes EGFR at the Cell Surface”, Molec. Biol. Cell 15: 5470-5480 (2004).

179. Said, M.R., T.J. Begley, A.V. Oppenheim, D.A. Lauffenburger, and L.D. Samson, “Global Network Analysis of Phenotypic Effects: Protein Networks and Toxicity Modulation in S. cerevisiae”, Proc. Natl. Acad. Sci. USA 101: 18006-18011 (2004).

180. Hendriks, B.S., G. Orr, A. Wells, H.S. Wiley, and D.A. Lauffenburger, “Parsing ERK Activation Reveals Quantitatively Equivalent Contributions from EGFR and HER2 in Human Mammary Epithelial Cells”, J. Biol. Chem. 280: 6157-6169 (2005).

181. Harms, B.D, G.M. Bassi, A.R. Horwitz, and D.A. Lauffenburger, “Directional Persistence of EGF-induced Cell Migration is Associated with Stabilization of Lamellipodal Protrusions”, Biophys. J. 88: 1479-1488 (2005).

182. Woolf, P.J., W. Prudhomme, L. Daheron, G.Q. Daley, and D.A. Lauffenburger, “Bayesian Analysis of Signaling Networks Governing Embryonic Stem Cell Fate Decisions”, Bioinformatics 21: 741-753 (2005).

183. Shults, M.D., K.A. Janes, D.A. Lauffenburger, and B. Imperiali, “A Multiplexed Fluorescence-Based Assay for Protein Kinase Activity in Cell Lysates”, Nature Methods 2: 277-284 (2005).

184. Monine, M.I., A.M. Berezhkovskii, E.J. Joslin, H.S. Wiley, D.A. Lauffenburger, and S.Y. Shvartsman, “Ligand Accumulation in Autocrine Cell Cultures”, Biophys. J. 88: 2384-2390 (2005).

185. Sachs, K., O. Perez, D. Pe’er, D.A. Lauffenburger, and G.P. Nolan, “Causal Protein Signaling Networks Derived From Multiparameter Single-Cell Data”, Science 308: 523-529 (2005).

186. Hautaniemi, S., S. Kharait, A. Iwabu, A. Wells, and D.A. Lauffenburger, “Modeling of Signal-Response Cascades using Decision Tree Analysis”, Bioinformatics 21: 2027-2035 (2005).

187. Dong, J., L.K. Opresko, W. Chrisler, G. Orr, R.D. Quesenberry, D.A. Lauffenburger, and H.S. Wiley, “The Membrane-Anchoring Domain of EGF Receptor Ligands Dictates Their Ability to Operate in Juxtacrine Mode”, Molec. Biol. Cell 16: 2984-2998 (2005).

188. Varga, C.M. N.C. Tedford, M. Thomas, A.M. Klibanov, L.G. Griffith, and D.A. Lauffenburger, “Quantitative Comparison of Polyethylenimine Formulations and Adenoviral Vectors in terms of Intracellular Gene Delivery Processes”, Gene Therapy 12: 1023-1032 (2005).

189. Hua, F., M.G. Cornejo, M.H. Cardone, C.L. Stokes, and D.A. Lauffenburger, “Effects of Bcl-2 Levels on Fas Signaling-Induced Caspase-3 Activation: Molecular Genetic Tests of Computational Model Predictions”, J. Immunol. 175: 985-995 (2005).

190. Yoshioka, J., R.N. Prince, H. Huang, S.B. Perkins, F.U. Cruz, C. MacGillivray, D.A. Lauffenburger, and R.T. Lee, “Cardiomyocyte Hypertrophy and Degradation of Connexin-43 through Spatially Restricted Autocrine/Paracrine HB-EGF”, Proc. Natl. Acad. Sci. USA 102: 10622-10627 (2005).

191. Zaman, M.H., R.D. Kamm, P.T. Matsudaira, and D.A. Lauffenburger, “Computational Model for Cell Migration in Three-Dimensional Matrices”, Biophys. J. 89: 1389-1397 (2005).

192. Rao, B.M., Driver I., D.A. Lauffenburger, and K.D. Wittrup, “High-Affinity CD25-Binding IL-2 Mutants Potently Stimulate Persistent T-Cell Growth”, Biochem. 44: 10696-10701 (2005).

193. Zhang, Y., A. Wolf-Yadlin, D.J. Pappin, J. Rush, D.A. Lauffenburger, and F.M. White, “Time-Resolved Mass Spectrometry of Tyrosine Phosphorylation Sites in the EGF Receptor Signaling Network Reveals Dynamic Modules”, Molec. Cell. Proteomics 4: 1240-1250 (2005).

194. Gaudet, S., K.A. Janes, J.G. Albeck, E.A. Pace, D.A. Lauffenburger, and P.K. Sorger, “A Compendium of Signals and Responses Triggered by Prodeath and Prosurvival Cytokines”, Molec. Cell. Proteomics 4: 1569-1590 (2005).

195. Viswanathan, S., D. Cheng, R.C. Raghu, D.A. Lauffenburger, and P.W. Zandstra, “Clonal Evolution of Stem and Differentiated Cells can be Predicted by Integrating Cell-Instrinsic and Extrinsic Parameters”, Biotech. Appl. Biochem. 42: 119-131 (2005).

196. Kamei, D.T., B.J. Lao, M.S. Ricci, R. Deshpande, H. Xu, B. Tidor, and D.A. Lauffenburger, “Quantitative Methods for Developing Fc Mutants with Extended Half-Lives”, Biotech. Bioeng. (2005, in press).

197. Janes, K.A., J.G. Albeck, S. Gaudet, P.K. Sorger, D.A. Lauffenburger, and M.B. Yaffe, “A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis”, Science 310: 1646-1653 (2005).

198. Semino, C.E., R.D. Kamm, and D.A. Lauffenburger, “Autocrine EGF Receptor Activation Mediates Endothelial Cell Migration and Vascular Morphogenesis Induced by VEGF Under Interstitial Flow”, Exptl. Cell Res. (2005, in press).

199. Hendriks, B.S., J. Cook, J.M. Burke, J.M. Beusmans, D.A. Lauffenburger, and D. deGraaf, “Computational Modeling of ErbB Family Phosphorylation Dynamics in Response to TGFα and Heregulin Indicates Spatial Compartmentation of Phosphatase Activity”, IEE Systems Biol. (2005, accepted).

Other articles

1. Lauffenburger, D.A., "Effects of Cell Motility Properties on Cell Populations in Ecosystems", ACS Symp. Series 207, 265-292 (1983).

2. Lauffenburger, D.A. and W. Alt, "Singular Perturbation Analysis of a Spatially-Distributed Model for the Inflammatory Response", AIChE Symp. Series 227, Vol. 79, 50-55 (1983).

3. Lauffenburger, D.A., J.J. Linderman and D.A. Hammer, "Mathematical Modeling of Receptor-Mediated Mammalian Cell Behavior", Biotech. Bioeng. Symp. Proc. 15, 675-688 (1986).

4. Hammer, D.A. and D.A. Lauffenburger, "Effects of Nonspecific Cell/Surface Interactions on Cell Affinity Chromatographic Separations", Mat. Res. Soc. Symp. Proc. 110: 739-745, eds. J. S. Hanker and B. L. Giammara (1989).

5. DiMilla, P.A., J.A. Stone, S.M. Albelda, D.A. Lauffenburger, and J.A. Quinn, "Measurement of Cell Adhesion and Migration on Protein-Coated Surfaces", Mat. Res. Soc. Symp. Proc. 252: 205-212 (1992).

6. Lauffenburger, D.A., Y-H. Khang, G. Sudlow, K.E. Forsten, and H.S. Wiley, "Quantitative Studies of EGF/EGF-Receptor Phenomena in Cell Proliferation", in Harnessing Biotechnology for the 21st Century, M. Ladisch and A. Bose, eds., ACS, pp. 341-344 (1992).

7. Lauffenburger, D.A., C. Starbuck, and H.S. Wiley, "Engineering Growth Factor/Receptor Processes: Effects of EGF Receptor Trafficking Dynamics on Cell Proliferation Responses to EGF", Proc. US/Japan Conference on Biotechnology, R. D. Tanner ed., Springer-Verlag, pp. 255-270 (1993).

8. Lauffenburger, D.A., “Engineering Cell Functions”, The NAE Bridge 27: 9-13 (1997).

Book reviews

1. Bacterial Chemotaxis as a Model Behavioral System (D.E. Koshland, Jr.) Math Biosci. 68, 151-153 (1984).

2. Cell Surface Dynamics (A. Perelson, C. DeLisi, and F. Wiegel, eds.), Math. Biosci. 76, 245-247 (1985).

3. Principles of Applied Mathematics (J.P. Keener), Bull. Math. Biol. 52, 319-321 (1990).

4. Physical Forces and the Mammalian Cell (J. Frangos, ed.) AIChE J. 40, 738-739 (1994).

5. Computational Cell Biology (C.P. Fall, E.S. Marland, J.M. Wagner, and J.J. Tyson, eds.) Cell 113: 7-8 (2003).

Patents

1. Granulocyte-Colony Stimulatory Factor Analog Composition and Methods (w/ C.A. Sarkar, B. Tidor, T. Horan & T. Boone); USA Patents #6946548 and #6790628 (2005).

2. Mutant Interleukin-2 Polypeptides; w/ K.D. Wittrup & B. Rao (application filed July 2003)

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