1. Arnold, K.B., A. Burgener, K. Birse, L. Romas, L.J. Dunphy, K. Shahabi, M. Abou, G.R. Westmacott, S. McCorrister, J. Kwatampora, B. Nyanga, J. Kimani, L. Masson, L.J. Liebenberg, S.S. Abdool Karim, J.S. Passmore, D.A. Lauffenburger, R. Kaul, L.R. McKinnon, “Increased Levels of Inflammatory Cytokines in the Female Reproductive Tract are Associated with Altered Expression of Proteases, Mucosal Barrier Proteins, and an Influx of HIV-Susceptible Target Cells”, Mucosal Immunol. 9: 194-205 (2016).
  2. Ip, B., N. Cilfone, A.C. Belkina, J. DeFuria, M. Jagannathan-Bogdan, M. Zhu, R. Kuchibhatla, M.E. McDonnell, Q. Xiao, T.B. Kepler, C.M. Apovian, D.A. Lauffenburger, and B.S. Nikolajczyk, “Th17 Cytokines and Downstream TNFa Production Impact Inflammation in Human Type 2 Diabetes&rduo;, Obesity 24: 102-112 (2016).
  3. Gordonov, S., M.K. Hwang, A. Wells, F.B. Gertler, D.A. Lauffenburger, and M. Bathe, “Time-Series Modeling of Live-Cell Shape Dynamics for Image-Based Phenotypic Profiling”, Integr. Biol. 8: 73-90 (2016).
  4. Oudin, M.J., S.K. Hughes, N. Rohani, M.N. Moufarrej, J.G. Jones, J.S. Condeelis, D.A. Lauffenburger, F.B. Gertler, “Characterization of the Expression of the Pro-Metastatic MenaINV Isoform during Breast Tumor Progression”, Clin. Exp. Metastasis 33: 249-261 (2016).
  5. Oudin, M.J., O. Jonas, T. Kosciuk, A. Riching, L.C. Broye, J. Wyckoff, S.K. Hughes, J.M. Lamar, S.B. Asokan, R. Langer, D.A. Lauffenburger, P. Keely, J.E. Bear, and F.B. Gertler, “MenaINV-Mediated Bi-Directional Signaling through a5b1 Integrin Supports Tumor Cell Haptotaxis and ECM Remodeling During Metastsis”, Canc. Disc. 6: 516-531 (2016).
  6. Archary, D., K.E. Seaton, J.S. Passmore, L. Werner, A. Deal, L.J. Dunphy, K.B. Arnold, N.L. Yates, D.A. Lauffenburger, P. Bergin, L.J. Liebenberg, N. Samsunder, M.W. Mureithi, M. Altfeld, N. Garrett, Q. Abdool Karim, S. Abdool Karim, L. Morris, and G.D. Tomaras, “Distinct Genital Tract HIV-Specific Antibody Profiles Associated with Tenofovir Gel”, Mucosal Immunol. 9: 834 (2016).
  7. Zhao, B., J.C. Sedlak, R. Srinivas, P. Creixell, J.R. Pritchard, B. Tidor, D.A. Lauffenburger, and M.T. Hemann, “Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution”, Cell 165: 234-246 (2016).
  8. Miller, M.A., M.J. Oudin, R.J. Sullivan, S.J. Wang, A.S. Meyer, H. Im, D.T. Frederick, J. Tadros, L.G. Griffith, H. Lee, R. Weissleder, K.T. Flaherty, F.B. Gertler, and D.A. Lauffenburger, “Reduced Proteolytic Shedding of Receptor Tyrosine Kinases is a Post-Translational Mechanism of Kinase Inhibitor Resistance”, Canc. Disc. 6: 382-399 (2016).
  9. Tape, C.J., S. Ling, M. Dimitriadi, K.M. McMahon, J.D. Worboys, H.S. Leong, I.C. Norrie, C.J. Miller, G. Poulogiannis, D.A. Lauffenburger, and C. Jorgensen, “Oncogenic K-Ras Regulates Tumor Cell Signaling via Stromal Reciprocation”, Cell 165: 1818 (2016).
  10. Chitforoushzadeh, Z., Z. Ye, Z. Sheng, S. LaRue, R.C. Fry, D.A. Lauffenburger, and K.A. Janes, “TNF-Insulin Crosstalk at the Transcription Factor GATA6 is Revealed by a Model that Links Signaling and Transcriptomic Data Tensors”, Sci. Signaling 9: ra59 (2016).
  11. Wilson, J.L., S. Dalin, S. Gosline, M. Hemann, E. Fraenkel, and D.A. Lauffenburger, “Pathway-Based Network Modeling finds Hidden Genes in shRNA Screen for Regulators of Acute Lymphoblastic Leukemia”, Integr. Biol. 8: 761-774 (2016).
  12. Zevin, A.S., I.Y. Xie, K. Birse, K. Arnold, L. Romas, G. Westmacott, R.M. Novak, S. McCorrister, L.R. McKinnon, C.R. Cohen, R. Mackelprang, J. Lingappa, D.A. Lauffenburger, N.R. Klatt, and A.D Burgener, “Microbiome Composition and Function Drives Wound-Healing Impairment in the Female Genital Tract”, PLoS Pathogens 12: e1005889 (2016).
  13. Oudin, M.J., M.A. Miller, J.A. Klazen, T. Kosciuk, A. Lussiez, S.K. Hughes, J. Tadros, J.E. Bear, D.A. Lauffenburger, and F.B. Gertler, “MenaINV Mediates Synergistic Crosstalk between Signaling Pathways driving Chemotaxis and Haptotaxis”, Molec. Biol. Cell 27: 2085-3094 (2016).
  14. Schrier, S.B., A.S. Hill, D. Plana, and D.A. Lauffenburger, “Synergistic Communication Between CD4+ T Cells and Monocytes Impacts the Cytokine Environment”, Sci. Reports 6: 34942 (2016).
  15. Morris, M.K., D.C. Clarke, L.C. Osimiri, and D.A. Lauffenburger, “Systematic Analysis of Quantitative Logic Model Ensembles Predicts Drug Combination Effects on Cell Signaling Networks”, CPT: Pharmacometrics & Systems Pharmacology 5: 544-553 (2016).
  16. Balsamo, M., C. Mondal, G. Carmona, L.M. McClain, D.N. Riquelme, J. Tadros, D. Ma, E. Vasile, J.S. Condeelis, D.A. Lauffenburger, and F.B. Gertler, “The Alternatively-Included 11a Sequence Modifies the Effects of Mena on Actin Cytoskeletal Organization and Cell Behavior”, Sci. Reports 6: 35298 (2016).
  17. Lu, L.L., A.W. Chung, T.R. Rosebrock, M. Ghebremichael, W.H. Yu, P.S. Grace, M.K. Schoen, F. Tafesse, C. Martin, V. Leung, A.E. Mahan, M. Sips, M.P. Kumar, J. Tedesco, H. Robinson, E. Tkachenko, M. Draghi, K.J. Freedberg, H. Streeck, T.J. Suscovich, D.A. Lauffenburger, B.I. Restrepo, C. Day, S.M. Fortune, and G. Alter, “A Functional Role for Antibodies in Tuberculosis”, Cell 167: 433-443 (2016).
  18. Nagel, Z.D., G.J. Kitange, S.K. Gupta, B.A. Joughin, I.A. Chaim, P. Mazzacuto, D.A. Lauffenburger, J.N. Sarkaria, and L.D. Samson, “DNA Repair Capacity in Multiple Pathways Predicts Chemoresistance in Glioblastoma Multiforme”, Cancer Res. 77: 198-206 (2016).
  19. Moynihan, K.D., C.F. Opel, G.L. Szeto, A. Tzeng, E.F. Zhu, J.M. Engreitz, R.T. Williams, K. Rakhra, M.H. Zhang, A.M. Rothschilds, S. Kumari, R.L. Kelly, B.H. Kwan, W. Abraham, K. Hu, N.K. Mehta, M.J. Krauke, H. Suh, J.R. Cochran, D.A. Lauffenburger, K.D. Wittrup, and D.J. Irvine, “Eradication of Large Established Tumors in Mice by Combination Immunotherapy that Engages Innate and Adaptive Immune Responses”, Nature Medicine 22: 1402-1410 (2016).
  20. Clark, A.M., S.E. Wheeler, C.L. Young, L. Stockdale, J. Shepard Neiman, W. Zhao, D.B. Stolz, R. Venkataramanan, D.A. Lauffenburger, L. Griffith, and A. Wells, “A Liver Microphysiological System of Tumor Cell Dormancy and Inflammatory Responsiveness is Affected by Scaffold Properties”, Lab on a Chip 17:156-168 (2016).
  21. Sun, D., S. Dalin, M.T. Hemann, D.A. Lauffenburger, and B. Zhao, “Differential Selective Pressure Alters Rate of Drug Resistance Acquisition in Heterogeneous Tumor Populations”, Sci. Reports 6: 36198 (2016).
  22. Oudin, M.J., L. Barbier, C. Schafer, T. Kosciuk, M.A. Miller, S. Han, O. Jonas, D.A. Lauffenburger, and F.B. Gertler, “Mena Confers Resistance to Paclitaxel in Triple-Negative Breast Cancer”, Molec. Canc. Ther. 16: 143-155 (2017).
  23. Jones, D.S., A.P. Jenney, J.L. Swantek, J.M. Burke, D.A. Lauffenburger, and P.K. Sorger, “Profiling Drugs for Rheumatoid Arthritis that Inhibit Synovial Fibroblast Activation”, Nature Chem. Biol. 13: 38-45 (2017).
  24. Li, R., J.D. Hebert, T.A. Lee, H. Xing, A. Boussommier-Calleja, R.O. Hynes, D.A. Lauffenburger, and R.D. Kamm, “Macrophage-Secreted TNFa and TGFb1 Influence Migration Speed and Persistence of Cancer Cells in 3D Tissue Culture via Independent Pathways”, Cancer Res. 77: 279-290 (2017).
  25. Tan, L. D. Gurbani, E.L. Weisberg, D.S. Jones, S. Rao, W.D. Singer, F.M. Bernard, S. Mowafy, A. Jenney, G. Du, A. Nonami, J.D. Griffith, D.A. Lauffenburger, K.D. Westover, P.K. Sorger, and N.S Gray, “Studies of TAK1-Centered Polypharmacology with Novel Covalent TAK1 Inhibitors”, Bioorg. Med. Chem. 25: 1320-1328 (2017).
  26. Dugast, A.S., K.B. Arnold, G. Lofano, S. Moore, M. Hoffner, M. Simek, P. Poignard, M. Seaman, T.J. Suscovich, F. Pereyra, B.D. Walker, D. Lauffenburger, D.S. Kwon, B.F. Keele, and G. Alter, “Virus-Driven Inflammation is Associated with the Development of bNAbs in Spontaneous Controllers of HIV”, Clin. Infect. Dis. 64: 1098-11-4 (2017).
  27. Nicolas, D., E.A. Proctor, F.M. Raval, B.C. Ip, C. Habib, E. Ritou, T.N. Grammatopoulos, D. Steenkamp, H. Dooms, C.M. Apovian, D.A. Lauffenburger, and B.S. Nikolajczyk, “Advances in the Quantification of Mitochondrial Function in Primary Human Immune Cells through Extracellular Flux”, PLoS One 12: e0170975 (2017).
  28. Conrad, C., M.A. Miller, J.W. Bartsch, U. Schlomann, and D.A. Lauffenburger, “Simultaneous Detection of Metalloprotease Activities in Complex Biological Samples Using the PrAMA (Proteolytic Activity Matrix Assay) Method”, Methods Molec. Biol. 1574: 243-253 (2017).
  29. Cook, C.D., A.S. Hill, M. Guo, L. Stockdale, J.P. Papps, K.B. Isaacson, D.A. Lauffenburger, and L.G. Griffith, “Local Remodeling of Synthetic Extracellular Matrix Microenvironments by Co-Cultured Endometrial Epithelial and Stromal Cells Enables Long-Term Dynamic Physiological Function”, Integr. Biol. 9: 271-289 (2017).
  30. Valdez, J. C.D. Cook, C.C. Ahrens, A.J. Wang, A. Brown, M. Kumar, L. Stockdale, D. Rothenberg, K. Renggli, E. Gordon, D. Lauffenburger, F. White, and L. Griffith, “On-Demand Dissolution of Modular Synthetic Extracellular Matrix Reveals Local Epithelial-Stromal Communication Networks”, Biomaterials 130: 90-103 (2017).
  31. Jorgensen, H. A.S. Hill, M.T. Beste, M.P. Kumar, E. Chiswick, P. Federcsak, K.B. Isaacson, D.A. Lauffenburger, L.G. Griffith, and E. Qvigstad, “Peritoneal Fluid Cytokines Related to Endometriosis in Patients Evaluated for Infertility”, Fertil. Steril. 107: 1191-1199 (2017).
  32. Sarkar, U., K.C. Ravindra, E. Large, C.L. Young, D. Rivera-Burgos, J. Yu, M. Cirit, D.J. Hughes, J.S. Wishnok, D.A. Lauffenburger, L.G. Griffith, and S.R. Tannenbaum, “Integrated Assessment of Diclofenac Biotransformation, Pharmacokinetics, and Omics-Based Toxicity in a Three-Dimensional Human Liver-Immunocompetent Co-Culture System”, Drug Metab. Dispos. 45: 855-866 (2017).
  33. Conrad, C., K. Dorzweiler, M.A. Miller, D.A. Lauffenburger, H. Strik, and J.W. Bartsch, “Profiling of Metalloprotease Activities in Cerebrospinal Fluids of Patients with Neoplastic Meningitis”, Fluids Barriers CNS 14: 22 (2017).
  34. Liebenberg, L.J., L. Masson, K.B. Arnold, L.R. McKinnon, L. Werner, E. Proctor, D. Archary, L.E. Mansoor, D.A. Lauffenburger, Q. Abdool Karim, S.S. Abdool Karim, and J.S. Passmore, “Genital-Systemic Chemokine Gradients and the Risk of HIV Acquisition in Women”, J. AIDS 74: 318-325 (2017).
  35. Chen, W.L.K., C. Edington, E. Suter, J. Yu, J.J. Velazquez, J.G. Velazquez, M. Schockley, E.M. Large, R. Venkataramanan, D.J. Hughes, C.L. Stokes, D.L. Trumper, R.L. Carrier, M. Cirit, L.G. Griffith, and D.A. Lauffenburger, “Integrated Gut/Liver Microphysiological Systems Elucidates Inflammatory Inter-Tissue Crosstalk”, Biotech. Bioeng. 114: 2648-2659 (2017).
  36. Zweemer, A.J., C.B. French, J. Mesfin, S. Gordonov, A.S. Meyer, and D.A. Lauffenburger, “Apoptotic Bodies Elicit Gas6-Mediated Migration of AXL-Expressing Tumor Cells”, Molec. Canc. Res. 15: 1656-1666 (2017).
  37. Yoneyama, T., M. Gorry, M.A. Miller, A. Gaither-Davis, Y. Lin, M.L. Moss, L.G. Griffith, D.A. Lauffenburger, L.P. Stabile, J.G. Herman, and N.L. Vujanovic, “Modification of Proteolytic Activity Matrix to Measure ADAM10 and ADAM17 Sheddase Activities in Cell and Tissue Lysates”, J. Cancer 8: 3916-3932 (2017).
  38. Soltis, A.R., N.J. Kennedy, X. Xin, F. Zhou, S.B. Ficarro, Y.S. Yap, B.J. Matthews, D.A. Lauffenburger, F.M. White, J.A. Marto, R.J. Davis, and E. Fraenkel, “Hepatic Dysfunction Caused by Consumption of a High-Fat Diet”, Cell Reports 21: 3317-3328 (2017).
  39. Shao, H., D. Lauffenburger, and A. Wells, “Tyro3 Carboxyl Terminal Region Confers Stability and Contains the Autophosphorylation Sites”, Biochem. Biophys. Res. Comm. 490: 1074-1079 (2017).
  40. Wilson, J.L., E. Kefaloyianni, L. Stopfer, C. Harrison, V. Sabbisetti, E. Fraenkel, D.A. Lauffenburger, and A. Herrlich, “Functional Genomic Identification of Novel Signaling Regulators of TGFα Ectodomain Shedding”, Molec. Canc. Res. 16: 147-161 (2017).
  41. Sadanand, S., J. Das, A.W. Chung, M.K. Schoen, S. Lane, T.J. Suscovich, H. Streeck, D.M. Smith, S.J. Little, D.A. Lauffenburger, D.D. Richman, and G. Alter, “Temporal Variation in HIV-Specific Subclass Antibodies during Acute Infection Differentiates Spontaneous Controllers from Chronic Progressors”, AIDS 32: 443-450 (2018).
  42. Soltis, A.R., N.J. Kennedy, X. Xin, F. Zhou, S.B. Ficcarro, Y.S. Yap, B.J. Matthews, D.A. Lauffenburger, F.M. White, J.A. Marto, R.J. Davis, and E. Fraenkel, “Hepatic Dysfunction Caused by Consumption of a High-Fat Diet”, Cell Reports 21: 3317-3328 (2018).
  43. Fleury, M., A.C. Belkina, E.A. Proctor, C. Zammitti, R.W. Simms, D.A. Lauffenburger, J.E. Snyder-Cappone, R. Lafyatis, and H. Dooms, “Increased Expression and Modulated Regulatory Activity of Co-Inhibitory Receptors PD-1, TIGIT, and TIM-3 in Lymphocytes from Patients with Systemic Sclerosis”, Arth. Rheumatol. 70: 566-577 (2018).
  44. Clark, A.M., M.P. Kumar, S.E. Wheeler, C.L. Young, R. Venkataramanan, D.B. Stolz, L.G. Griffith, D.A. Lauffenburger, and A. Wells, “A Model of Dormant-Emergent Metastatic Breast Cancer Progression Enabling Exploration of Biomarker Signatures”, Molec. Cell Proteomics 17: 619-630 (2018).
  45. Lyons, J., D.K. Brubaker, P.C. Ghazi, K.R. Baldwin, A. Edwards, M. Boukhali, S.D. Strasser, L. Suarez-Lopez, Y.J. Lin, V. Yajnik, J.L. Kissil, W. Haas, D.A. Lauffenburger, and K.M. Haigis, “Integrated In Vivo Multi-Omics Analysis Identifies p21-Activated Kinase Signaling as a Driver of Colitis”, Sci. Signaling 11: eaan3580 (2018).
  46. Jones, D.S., A.P. Jenney, B.A. Joughin, P.K. Sorger, and D.A. Lauffenburger, “Inflammatory but not Mitogenic Contexts Prime Synovial Fibroblasts for Compensatory Signaling to p38 Inhibition”, Sci. Signaling 11: eaal1601 (2018).
  47. Edington, C.D., W.L.K. Chen, E. Geishecker, T. Kassis, L.R. Soenksen, B.M. Bhushan, D. Freake, J. Kirschner, C. Maass, N. Tsamandouras, J. Valdez, C.D. Cook, T. Parent, S. Snyder, J. Yu, E. Suter, M. Shockley, J. Velazquez, J.J. Velazquez, L. Stockdale, J.P. Papps, I. Lee, N. Vann, M. Gamboa, M.E. LaBarge, Z. Zhong, X. Wang, L.A. Boyer, D.A. Lauffenburger, R.L. Carrier, C. Communal, S.R. Tannenbaum, C.L. Stokes, D.J. Hughes, G. Rohatgi, D.L. Trumper, M. Cirit, and L.G. Griffith, “Inter-Connected Micro-Physiological Systems for Quantitative Biology and Pharmacology Studies”, Sci. Reports 8: 4530 (2018).
  48. Lyons, J., P.C. Ghazi, A. Starchenko, A. Tovaglieri, K.R. Baldwin, E.J. Poulin, J.J. Gierut, C. Genetti, V. Yajnik, D.T. Breault, D.A. Lauffenburger, and K.M. Haigis, “The Colonic Epithelium Plays an Active Role in Promoting Colitis by Shaping the Tissue Cytokine Profile”, PLoS Biol. 16: e2002417 (2018).
  49. Yu, W.H., P. Zhao, M. Draghi, C. Arevalo, C.B. Karsten, T.J. Suscovich, B. Gunn, H. Streeck, A.L. Brass, M. Tiemeyer, M. Seaman, J.R. Mascola, L. Wells, D.A. Lauffenburger, and G. Alter, “Exploiting Glycan Topography for Computational Design of Env Glycoprotein Antigenicity”, PLoS Comp. Biol. 14: e1006093 (2018).
  50. Yoneyama, T., M. Gorry, A. Sobo-Vujanovic, Y. Lin, L. Vujanovic, A. Gaither-Davis, M.L. Moss, M.A. Miller, L.G. Griffith, D.A. Lauffenburger, L.P. Stabile, J. Herman, and N.L. Vujanovic, “ADAM10 Sheddase Activity is a Potential Lung Cancer Biomarker”, J. Cancer 9: 2559-2570 (2018).
  51. Gunn, B.M., W.H. Yu, M.M. Karim, J.M. Brannan, A.S. Herbert, A.Z. Wec, P.J. Halfmann, M.L. Fusco, S.L. Schendel, K. Gangarvarapu, T. Krause, X. Qiu, S. He, J. Das, T.J. Suscovich, J. Lai, K. Chandran, L. Zeitlin, J.E. Crowe Jr, D.A. Lauffenburger, Y. Kawaoka, G.P. Kobinger, K.G. Anderson, J.M. Dye, E.O. Saphire, and G. Alter, “A Role for Fc Function in Therapeutic Monoclonal Antibody-Mediated Protection Against Ebola Virus”, Cell Host Microbe 24: 221-233 (2018).
  52. Lofano, G., M.J. Gorman, A.S. Yousif, W.H. Yu, J.M. Fox, A.S. Dugast, M.E. Ackerman, T.J. Suscovich, J. Weiner, D. Barouch, H. Streeck, S. Little, D. Smith, D. Richman, D.A. Lauffenburger, B.D. Walker, M.S. Diamond, and G. Alter, “Antigen-Specific Antibody Fc Glycosylation Enhances Humoral Immunity via the Recruitment of Complement”, Science Immunol. 3: eaat7796 (2018).
  53. Ackerman, M.E., J. Das, S. Pittala, T. Broge, C. Linde, T.J. Suscovich, E.P. Brown, T. Bradley, H. Hatarajan, S. Lin, J.K. Sassic, S. O’Keefe, N. Mehta, D. Goodman, M. Sips, J.A. Weiner, G.D. Tomaras, B.F. Haynes, D.A. Lauffenburger, C. Bailey-Kellogg, M. Roederer, and G. Alter, “Route of Immunization Defines Multiple Mechanisms of Vaccine-Mediated Protection Against SIV”, Nature Med. s41591-018-01610 (2018).
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