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Publications

Key Publications

  1. Lee, M.J., Ye, A.S., Gardino, A.K., Heijink, A.M., Sorger, P.K., Macbeath, G., Yaffe, M.B. (2012). Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 149, 780-794. PubMed PMID: 22579283.
  2. Godin, M., Delgado, F.F., Son, S.M., Grover, W.H., Bryan, A.K., Tzur, A., Jorgensen, P., Payer, K., Grossman, A.D., Kirschner, M.W., et al. (2010). Using buoyant mass to measure the growth of single cells. Nature Methods 7, 387-U370. PMID: 20383132. PMCID: PMC2862099.
  3. Chen, W. W., Schoeberl, B., Jasper, P. J., Niepel, M., Nielsen, U. B., Lauffenburger, D. A., and Sorger, P. K. (2009). Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol 5, 239. PMID: 19156131. PMCID: PMC2644173.
  4. Spencer, S. L., Gaudet, S., Albeck, J. G., Burke, J. M., and Sorger, P. K. (2009). Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. PMID: 19363473. PMCID: PMC2858974.
  5. Albeck, J. G., Burke, J. M., Spencer, S. L., Lauffenburger, D. A., and Sorger, P. K. (2008). Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol 6, 2831-2852. PMID: 19053173. PMCID: PMC2592357.
  6. Burg, T., Godin, M., Knudsen, S., Shen, W., Carlson, G., Foster, J., Babcock, K., and Manalis, S. (2007). Weighing of biomolecules, single cells and single nanoparticles in fluid. Nature 446, 1066-1069. PMID: 17460669.
  7. Miller-Jensen, K., Janes, K. A., Brugge, J. S., and Lauffenburger, D. A. (2007). Common effector processing mediates cell-specific responses to stimuli. Nature 448, 604-608. PMID: 17637676.
  8. Janes, K. A., Gaudet, S., Albeck, J. G., Nielsen, U. B., Lauffenburger, D. A., and Sorger, P. K. (2006). The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 124, 1225-1239. PMID: 16564013.
  9. Wolf-Yadlin, A., Kumar, N., Zhang, Y., Hautaniemi, S., Zaman, M., Kim, H.-D., Grantcharova, V., Lauffenburger, D., and White, F. (2006). Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol 2:54. PMID: 17016520. PMCID: PMC1682017.
  10. Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K., Lauffenburger, D. A., and Yaffe, M. B. (2005). A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653. PMID: 16339439.

Full List

2014

  1. Bryan AK, Hecht VC, Shen W, Payer K, Grover WH, and Manalis SR (2014). Measuring Single Cell Mass, Volume, and Density with Dual Suspended Microchannel Resonators. Lab Chip 14(3), 569-576. PMC3895367 PMID: 24296901.
  2. Sarkar A, Kolitz S, Lauffenburger DA, and Han J (2014). Microfluidic Probe for Single-Cell Analysis in Adherent Tissue Culture. Nat Commun 5(3421. PMC4179103 PMID: 24594667.
  3. Kallenberger SM, Beaudouin J, Claus J, Fischer C, Sorger PK, Legewie S, and Eils R (2014). Intra- and Interdimeric Caspase-8 Self-Cleavage Controls Strength and Timing of Cd95-Induced Apoptosis. Sci Signal 7(316), ra23. PMCNIHMS627852 PMID: 24619646.
  4. Ebrahimkhani MR, Neiman JA, Raredon MS, Hughes DJ, and Griffith LG (2014). Bioreactor Technologies to Support Liver Function in Vitro. Adv Drug Deliv Rev 69-70(132-157. PMC4144187 PMID: 24607703.
  5. Field SL, Dasgupta T, Cummings M, and Orsi NM (2014). Cytokines in Ovarian Folliculogenesis, Oocyte Maturation and Luteinisation. Mol Reprod Dev 81(4), 284-314. PMID: 24273059.
  6. Buck LD, Inman SW, Rusyn I, and Griffith LG (2014). Co-Regulation of Primary Mouse Hepatocyte Viability and Function by Oxygen and Matrix. Biotechnol Bioeng 111(5), 1018-1027. PMC4110975 PMID: 24222008.
  7. Dasgupta T, Croll DH, Owen JA, Vander Heiden MG, Locasale JW, Alon U, Cantley LC, and Gunawardena J (2014). A Fundamental Trade-Off in Covalent Switching and Its Circumvention by Enzyme Bifunctionality in Glucose Homeostasis. J Biol Chem 289(19), 13010-13025. PMC4036316 PMID: 24634222.
  8. Cheow LF, Sarkar A, Kolitz S, Lauffenburger D, and Han J (2014). Detecting Kinase Activities from Single Cell Lysate Using Concentration-Enhanced Mobility Shift Assay. Anal Chem 86(15), 7455-7462. PMC4144746 PMID: 25025773.
  9. Griffith LG, Wells A, and Stolz DB (2014). Engineering Liver. Hepatology 60(4), 1426-1434. PMC4176555 PMID: 24668880.

2013

  1. Chen CH, Miller MA, Sarkar A, Beste MT, Isaacson KB, Lauffenburger DA, Griffith LG, and Han J (2013). Multiplexed Protease Activity Assay for Low-Volume Clinical Samples Using Droplet-Based Microfluidics and Its Application to Endometriosis. J Am Chem Soc 135(5), 1645-1648. PMC3566300 PMID: 23157326.
  2. Morris MK, Melas I, and Saez-Rodriguez J (2013). Construction of Cell Type-Specific Logic Models of Signaling Networks Using Cellnopt. Methods Mol Biol 930(179-214. PMID: 23086842.
  3. Clarke DC, Morris MK, and Lauffenburger DA (2013). Normalization and Statistical Analysis of Multiplexed Bead-Based Immunoassay Data Using Mixed-Effects Modeling. Mol Cell Proteomics 12(1), 245-262. PMC3536905 PMID: 23071098.
  4. Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, and Sorger PK (2013). Properties of Cell Death Models Calibrated and Compared Using Bayesian Approaches. Mol Syst Biol 9(644. PMC3588908 PMID: 23385484.
  5. Lopez CF, Muhlich JL, Bachman JA, and Sorger PK (2013). Programming Biological Models in Python Using Pysb. Mol Syst Biol 9(646. PMC3588907 PMID: 23423320.
  6. Dutta S, Chen TS, and Keating AE (2013). Peptide Ligands for Pro-Survival Protein Bfl-1 from Computationally Guided Library Screening. ACS Chem Biol 8(4), 778-788. PMC3631442 PMID: 23363053.
  7. Gujral TS, Karp ES, Chan M, Chang BH, and MacBeath G (2013). Family-Wide Investigation of Pdz Domain-Mediated Protein-Protein Interactions Implicates Beta-Catenin in Maintaining the Integrity of Tight Junctions. Chem Biol 20(6), 816-827. PMC3728706 PMID: 23790492.
  8. Feijo Delgado F, Cermak N, Hecht VC, Son S, Li Y, Knudsen SM, Olcum S, Higgins JM, Chen J, Grover WH, and Manalis SR (2013). Intracellular Water Exchange for Measuring the Dry Mass, Water Mass and Changes in Chemical Composition of Living Cells. PLoS One 8(7), e67590. PMC3699654 PMID: 23844039.
  9. Wagner JP, Wolf-Yadlin A, Sevecka M, Grenier JK, Root DE, Lauffenburger DA, and MacBeath G (2013). Receptor Tyrosine Kinases Fall into Distinct Classes Based on Their Inferred Signaling Networks. Sci Signal 6(284), ra58. PMC3987808 PMID: 23861540.
  10. Tsukamoto K, Buck L, Inman W, Griffith L, Kocher O, and Krieger M (2013). Challenges in Using Cultured Primary Rodent Hepatocytes or Cell Lines to Study Hepatic Hdl Receptor Sr-Bi Regulation by Its Cytoplasmic Adaptor Pdzk1. PLoS One 8(7), e69725. PMC3720616 PMID: 23936087.
  11. Reinhardt HC, and Yaffe MB (2013). Phospho-Ser/Thr-Binding Domains: Navigating the Cell Cycle and DNA Damage Response. Nat Rev Mol Cell Biol 14(9), 563-580. PMID: 23969844.
  12. Heavner ME, Gueguen G, Rajwani R, Pagan PE, Small C, and Govind S (2013). Partial Venom Gland Transcriptome of a Drosophila Parasitoid Wasp, Leptopilina Heterotoma, Reveals Novel and Shared Bioactive Profiles with Stinging Hymenoptera. Gene 526(2), 195-204. PMC3905606 PMID: 23688557.
  13. Lim D, Gold DA, Julien L, Rosowski EE, Niedelman W, Yaffe MB, and Saeij JP (2013). Structure of the Toxoplasma Gondii Rop18 Kinase Domain Reveals a Second Ligand Binding Pocket Required for Acute Virulence. J Biol Chem 288(48), 34968-34980. PMC3843107 PMID: 24129568.
  14. Hang TC, Tedford NC, Reddy RJ, Rimchala T, Wells A, White FM, Kamm RD, and Lauffenburger DA (2013). Vascular Endothelial Growth Factor (Vegf) and Platelet (Pf-4) Factor 4 Inputs Modulate Human Microvascular Endothelial Signaling in a Three-Dimensional Matrix Migration Context. Mol Cell Proteomics 12(12), 3704-3718. PMC3861718 PMID: 24023389.

2012

  1. Luckert K, Gujral TS, Chan M, Sevecka M, Joos TO, Sorger PK, Macbeath G, and Potz O (2012). A Dual Array-Based Approach to Assess the Abundance and Posttranslational Modification State of Signaling Proteins. Sci Signal 5(206), pl1. PMC3465074 PMID: 22234610.
  2. Clarke DC, and Lauffenburger DA (2012). Multi-Pathway Network Analysis of Mammalian Epithelial Cell Responses in Inflammatory Environments. Biochem Soc Trans 40(1), 133-138. PMID: 22260679.
    Mohammad DH, and Yaffe MB (2012). Fixin’ to Divide. Mol Cell 45(3), 273-275. PMC3501254 PMID: 22325348.
  3. Maiwald T, Blumberg J, Raue A, Hengl S, Schilling M, Sy SK, Becker V, Klingmuller U, and Timmer J (2012). In Silico Labeling Reveals the Time-Dependent Label Half-Life and Transit-Time in Dynamical Systems. BMC Syst Biol 6(13. PMC3395849 PMID: 22369292.
  4. Morris MK, Shriver Z, Sasisekharan R, and Lauffenburger DA (2012). Querying Quantitative Logic Models (Q2lm) to Study Intracellular Signaling Networks and Cell-Cytokine Interactions. Biotechnol J 7(3), 374-386. PMC3292705 PMID: 22125256.
  5. Kholodenko B, Yaffe MB, and Kolch W (2012). Computational Approaches for Analyzing Information Flow in Biological Networks. Sci Signal 5(220), re1. PMID: 22510471.
  6. Gaudet S, Spencer SL, Chen WW, and Sorger PK (2012). Exploring the Contextual Sensitivity of Factors That Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis. PLoS Comput Biol 8(4), e1002482. PMC3343095 PMID: 22570596.
  7. Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, MacBeath G, and Yaffe MB (2012). Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks. Cell 149(4), 780-794. PMC3501264 PMID: 22579283.
  8. Beyer EM, and MacBeath G (2012). Cross-Talk between Receptor Tyrosine Kinase and Tumor Necrosis Factor-Alpha Signaling Networks Regulates Apoptosis but Not Proliferation. Mol Cell Proteomics 11(6), M111 013292. PMC3433887 PMID: 22323825.
  9. Powers TR, Virk SM, Trujillo-Provencio C, and Serrano EE (2012). Probing the Xenopus Laevis Inner Ear Transcriptome for Biological Function. BMC Genomics 13(225. PMC3532188 PMID: 22676585.
  10. Chen TS, and Keating AE (2012). Designing Specific Protein-Protein Interactions Using Computation, Experimental Library Screening, or Integrated Methods. Protein Sci 21(7), 949-963. PMC3403433 PMID: 22593041.
  11. Loerke D, le Duc Q, Blonk I, Kerstens A, Spanjaard E, Machacek M, Danuser G, and de Rooij J (2012). Quantitative Imaging of Epithelial Cell Scattering Identifies Specific Inhibitors of Cell Motility and Cell-Cell Dissociation. Sci Signal 5(231), rs5. PMID: 22763340.
  12. Niedelman W, Gold DA, Rosowski EE, Sprokholt JK, Lim D, Farid Arenas A, Melo MB, Spooner E, Yaffe MB, and Saeij JP (2012). The Rhoptry Proteins Rop18 and Rop5 Mediate Toxoplasma Gondii Evasion of the Murine, but Not the Human, Interferon-Gamma Response. PLoS Pathog 8(6), e1002784. PMC3386190 PMID: 22761577.
  13. Son S, Tzur A, Weng Y, Jorgensen P, Kim J, Kirschner MW, and Manalis SR (2012). Direct Observation of Mammalian Cell Growth and Size Regulation. Nat Methods 9(9), 910-912. PMC3433595 PMID: 22863882.
  14. Joughin BA, Liu C, Lauffenburger DA, Hogue CW, and Yaffe MB (2012). Protein Kinases Display Minimal Interpositional Dependence on Substrate Sequence: Potential Implications for the Evolution of Signalling Networks. Philos Trans R Soc Lond B Biol Sci 367(1602), 2574-2583. PMC3415838 PMID: 22889908.
  15. Kolitz SE, and Lauffenburger DA (2012). Measurement and Modeling of Signaling at the Single-Cell Level. Biochemistry 51(38), 7433-7443. PMID: 22954137.
  16. Jaqaman K, and Grinstein S (2012). Regulation from Within: The Cytoskeleton in Transmembrane Signaling. Trends Cell Biol 22(10), 515-526. PMC3754899 PMID: 22917551.
  17. Naegle KM, White FM, Lauffenburger DA, and Yaffe MB (2012). Robust Co-Regulation of Tyrosine Phosphorylation Sites on Proteins Reveals Novel Protein Interactions. Mol Biosyst 8(10), 2771-2782. PMC3501258 PMID: 22851037.
  18. Hopker K, Hagmann H, Khurshid S, Chen S, Hasskamp P, Seeger-Nukpezah T, Schilberg K, Heukamp L, Lamkemeyer T, Sos ML, Thomas RK, Lowery D, Roels F, Fischer M, Liebau MC, Resch U, Kisner T, Rother F, Bartram MP, Muller RU, Fabretti F, Kurschat P, Schumacher B, Gaestel M, Medema RH, Yaffe MB, Schermer B, Reinhardt HC, and Benzing T (2012). Aatf/Che-1 Acts as a Phosphorylation-Dependent Molecular Modulator to Repress P53-Driven Apoptosis. EMBO J 31(20), 3961-3975. PMC3474921 PMID: 22909821.
  19. Sorger PK, and Schoeberl B (2012). An Expanding Role for Cell Biologists in Drug Discovery and Pharmacology. Mol Biol Cell 23(21), 4162-4164. PMC3484093 PMID: 23112228.
  20. Lee J, Sharei A, Sim WY, Adamo A, Langer R, Jensen KF, and Bawendi MG (2012). Nonendocytic Delivery of Functional Engineered Nanoparticles into the Cytoplasm of Live Cells Using a Novel, High-Throughput Microfluidic Device. Nano Lett 12(12), 6322-6327. PMC3521073 PMID: 23145796.
  21. Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, and Alexopoulos LG (2012). Non Linear Programming (Nlp) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways. PLoS One 7(11), e50085. PMC3511450 PMID: 23226239.

2011

  1. Aldridge, B.B., Gaudet, S., Lauffenburger, D.A., Sorger, P.K. (2012). Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis. Mol Syst Biol. 7, 553. doi: 10.1038/msb.2011.85. PMID: 22108795.
  2. Alexander, J., Lim, D., Joughin, B.A., Hegemann, B., Hutchins, J.R., Ehrenberger, T., Ivins, F., Sessa, F., Hudecz, O., Nigg, E.A., Fry, A.M., Musacchio, A., Stukenberg, P.T., Mechtler, K., Peters, J.M., Smerdon, S.J., Yaffe, M.B. (2011). Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Science Signal. 4, ra42. PMID: 21712545.
  3. Banko, M.R., Allen, J.J., Schaffer, B.E., Wilker, E.W., Tsou, P., White, J.L., Villén, J., Wang, B., Kim, S.R., Sakamoto, K., Gygi, S.P., Cantley, L.C., Yaffe, M.B., Shokat, K.M., Brunet, A. (2011). Chemical Genetic Screen for AMPKα2 Substrates Uncovers a Network of Proteins Involved in Mitosis. Molecular Cell. 44, 878-892. PMID: 22137581.
  4. Cannell, I.G., Yaffe, M.B. (2011). Salvaging the septic heart through targeting the interleukin-6/p38 mitogen-activated protein kinase signaling network. Crit Care Med. 39, 1836-7. PMID: 21685754.
  5. Chen, C.H., Sarkar, A., Song, Y.A., Miller, M.A., Kim, S.J., Griffith, L.G., Lauffenburger, D.A., Han, J. (2011). Enhancing protease activity assay in droplet-based microfluidics using a biomolecule concentrator. J Am Chem Soc. 133, 10368-10371. PMID: 21671557.
  6. Dextras, P., Payer, K.R., Burg, T.P., Shen, W.J., Wang, Y.C., Han, J.Y., and Manalis, S.R. (2011). Fabrication and Characterization of an Integrated Microsystem for Protein Preconcentration and Sensing. Journal of Microelectromechanical Systems 20, 221-230. doi: 10.1109/JMEMS.2010.2093563.
  7. Gardino, A.K., Yaffe, M.B. (2011). 14-3-3 proteins as signaling integration points for cell cycle control and apoptosis. Semin Cell Dev Biol. 22, 688-689. PMID: 21765407.
  8. Grover, W.H., Bryan, A.K., Diez-Silva, M., Suresh, S., Higgins, J.M., Manalis, S.R. (2011). Measuring single-cell density. Proc  Natl Acad of Sci USA 108, 10992-10996. PMID: 21690360.
  9. Hegemann, B., Hutchinsm, J.R., Hudecz, O., Novatchkova, M., Rameseder, J., Sykora, M.M., Liu, S., Mazanek, M., Lénárt, P., Hériché, J.K., Poser, I., Kraut, N., Hyman, A.A., Yaffe, M.B., Mechtler, K., Peters, J.M. (2011). Systematic phosphorylation analysis of human mitotic protein complexes. Science Signal. 4, rs12. PMID: 22067460.
  10. Hsu, P.P., Kang, S.A., Rameseder, J., Zhang, Y., Ottina, K.A., Lim, D., Peterson, T.R., Choi, Y., Gray, N.S., Yaffe, M.B., Marto, J.A., Sabatini, D.M. (2011). The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 332, 1317-1322. PMID: 21659604.
  11. Jaqaman, K., Kuwata, H., Touret, N., Collins, R., Trimble, W.S., Danuser, G., Grinstein S. Cytoskeletal Control of CD36 Diffusion Propotes its Receptor and Signaling Function. Cell 146, 593-606. 2011. PMID: 21854984.
  12. Kleiman, L.B., Maiwald, T., Conzelmann, H., Lauffenburger, D.A., Sorger, P.K. (2011). Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell. 43, 723-737. PMID: 21884975.
  13. Krall, J.A., Beyer, E.M., and MacBeath, G. (2011). High- and Low-Affinity Epidermal Growth Factor Receptor-Ligand Interactions Activate Distinct Signaling Pathways. Plos One 6, e15945.1-10. PMID: 21264347. External link to article
  14. Lee, J., Chunara, R., Shen, W., Payer, K., Babcock, K., Burg, T.P., and Manalis, S.R. (2011). Suspended microchannel resonators with piezoresistive sensors. Lab on a Chip 11, 645-651. PMID: 21180703. External link to article
  15. Liu, F., Park, J.E., Qian, W.J., Lim, D., Gräber, M., Berg, T., Yaffe, M.B., Lee, K.S., Burke, T.R. Jr. (2011). Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel. Nat Chem Biol. 7, 595-560. PMID: 21765407.
  16. Luckert, K., Gotschel, F., Sorger, P.K., Hecht, A., Joos, T.O., and Potz, O. (2011). Snapshots of Protein Dynamics and Post-translational Modifications In One Experiment-beta-Catenin and Its Functions. Molecular & Cellular Proteomics 10: M110.007377. PMID: 21378377. External link to article
  17. Millard, B.L., Niepel, M., Menden, M.P., Muhlich, J.L., and Sorger, P.K. (2011). Adaptive informatics for multifactorial and high-content biological data. Nat Methods 8, 487-492. PMID: 21516115. External link to article
  18. Morris, M.K., Saez-Rodriguez, J., Clarke, D.C., Sorger, P.K., and Lauffenburger, D.A. (2011). Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. PLoS Computational Biology 7, e1001099. PMID: 21408212. External link to article
  19. Palmer, M.J., Mahajan, V.S., Chen, J., Irvine, D.J., and Lauffenburger, D.A. (2011). Signaling thresholds govern heterogeneity in IL-7-receptor-mediated responses of naïve CD8(+) T cells. Immunol Cell Biol. 2011 Feb 22. [Epub ahead of print] PMID: 21339767. External link to article
  20. Prill, R.J., Saez-Rodriguez, J., Alexopoulos, L.G., Sorger, P.K., Stolovitzky, G. (2011). Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal. 4, mr7. PubMed PMID: 21900204.
  21. Ramírez-Gordillo, D., Trujillo-Provencio, C.. Knight, V.B., Serrano, E.E. (2011). Comparison of three gene delivery methods in chinese hamster ovary (CHO) and Xenopus laevis kidney (A6) Cells In vitro. Cell Dev Biology. Animal 47, 640-652. PMID: 21959846.
  22. Reinhardt, H.C., Cannell, I.G., Morandell, S., and Yaffe, M.B. (2011). Is post-transcriptional stabilization, splicing and translation of selective mRNAs a key to the DNA damage response? Cell Cycle 10, 23-27. PMID: 21173571. External link to article
  23. Sader, J.E., Burg, T.P., Lee, J., Manalis, S.R. (2011). Energy dissipation in microfluidic beam resonators: Effect of Poisson’s ratio. Physical Review E, 84. PMID: 21929087.
  24. Saez-Rodriguez, J., Alexopoulos, L.G., Zhang, M., Morris, M.K., Lauffenburger, D.A., Sorger, P.K. (2011). Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res. 71, 5400-5411. PMID: 21742771.
  25. Sarkar, A., Han, J. (2011). Non-Linear and Linear Enhancement of Enzymatic Reaction Kinetics using a Biomolecule Concentrator. Lab on a Chip 11, 2569-2576. PMID: 21677981.
  26. Sevecka, M., Wolf-Yadlin, A., and MacBeath, G. (2011). Lysate Microarrays Enable High-throughput, Quantitative Investigations of Cellular Signaling. Molecular & Cellular Proteomics 10, M110.005363. PMID: 21296872. External link to article
  27. Spencer, S.L., and Sorger, P.K. (2011). Measuring and Modeling Apoptosis in Single Cells. Cell 144, 926-939. PMID: 21414484. External link to article

2010

  1. Alexopoulos, L.G., Saez-Rodriguez, J., Cosgrove, B.D., Lauffenburger, D.A., and Sorger, P.K. (2010). Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes. Molecular & Cellular Proteomics 9, 1849-1865. PubMed PMID: 20460255. External link to article
  2. Bryan, A.K., Goranov, A., Amon, A., and Manalis, S.R. (2010). Measurement of mass, density, and volume during the cell cycle of yeast. Proceedings of the National Academy of Sciences of the United States of America 107, 999-1004. PMID: 20080562. External link to article
  3. Chen, W.W., Niepel, M., and Sorger, P.K. (2010). Classic and contemporary approaches to modeling biochemical reactions. Genes & Development 24, 1861-1875.PMID: 20810646. External link to article
  4. Ciaccio, M.F., Wagner, J.P., Chuu, C.P., Lauffenburger, D.A., and Jones, R.B. (2010). Systems analysis of EGF receptor signaling dynamics with microwestern arrays. Nature Methods 7, 148-155. PMID: 20101245. External link to article
  5. Cosgrove, B.D., Alexopoulos, L.G., Hang, T.C., Hendriks, B.S., Sorger, P.K., Griffith, L.G., and Lauffenburger, D.A. (2010). Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol Biosyst. 6, 1195-1206. PMID: 20361094. External link to article
  6. Dutta, S., Gullá, S., Chen, T.S., Fire, E., Grant, R.A., Keating, and A.E. (2010). Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol. 398, 747-762. PMID: 20363230. External link to article
  7. Flannagan, R. S., Harrison, R. E., Yip, C. M, Jaqaman, K. Grinstein, S. (2010). Dynamic macrophage “probing” is required for the efficient capture of phagocytic targets. Journal of Cell Biology 191, 1205-1218. PMID: 21135140. External link to article
  8. Fire, E., Gulla, S.V., Grant, R.A., and Keating, A.E. (2010). Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes. Protein Science 19, 507-519. PMID: 20066663. External link to article
  9. Godin, M., Delgado, F.F., Son, S.M., Grover, W.H., Bryan, A.K., Tzur, A., Jorgensen, P., Payer, K., Grossman, A.D., Kirschner, M.W., et al. (2010). Using buoyant mass to measure the growth of single cells. Nature Methods 7, 387-U370. PMID: 20383132. External link to article
  10. Gujral, T.S., and MacBeath, G. (2010). A System-Wide Investigation of the Dynamics of Wnt Signaling Reveals Novel Phases of Transcriptional Regulation. PLoS One 5, e10024.1-10. PMID: 20383323. External link to article
  11. Kim, S.J., Song, Y.A., and Han, J. Nanofluidic concentration devices for biomolecules utilizing ion concentration polarization: theory, fabrication, and applications.  (2010). Chem Soc Rev. 39, 912-922. PMID: 20179814. External link to article
  12. Kreeger, P.K., Wang, Y., Haigis, K.M., and Lauffenburger, D.A. Integration of multiple signaling pathway activities resolves K-RAS/N-RAS mutation paradox in colon epithelial cell response to inflammatory cytokine stimulation. (2010). Integr Biol (Camb). 2, 202-208. PMID: 20473400. External link to article
  13. Morris, M.K., Saez-Rodriguez, J., Sorger, P.K., and Lauffenburger, D.A. (2010). Logic-based models for the analysis of cell signaling networks. Biochemistry. 49, 3216-3224. PMID: 20225868. External link to article
  14. Paddibhatla, I., Lee, M.J., Kalamarz, M.E., Ferrarese, R., and Govind, S. (2010) Role for sumoylation in systemic inflammation and immune homeostasis in Drosophila larvae. PLoS Pathog. 6, e1001234. PMID: 21203476. External link to article
  15. Pennell, S., Westcott, S., Ortiz-Lombardia, M., Patel, D., Li, J.J., Nott, T.J., Mohammed, D., Buxton, R.S., Yaffe, M.B., Verma, C., et al. (2010). Structural and Functional Analysis of Phosphothreonine-Dependent FHA Domain Interactions. Structure 18, 1587-1595. PMID: 21134638. External link to article
  16. Powers, T., Virk, S., and Serrano, E. E. Strategies for enhanced annotation of a microarray probe set. Int J Bioinform Res Appl. 2010;6(2):163-78. External link to article
  17. Prill, R.J., Marbach, D., Saez-Rodriguez, J., Sorger, P.K., Alexopoulos, L.G., Xue, X., Clarke, N.D., Altan-Bonnet, G., and Stolovitzky, G. (2010). Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One. 5, e9202. PMID: 20186320. External link to article
  18. Reinhardt, H.C., Hasskamp, P., Schmedding, I., Morandell, S., van Vugt, M., Wang, X.Z., Linding, R., Ong, S.E., Weaver, D., Carr, S.A., et al. (2010). DNA Damage Activates a Spatially Distinct Late Cytoplasmic Cell-Cycle Checkpoint Network Controlled by MK2-Mediated RNA Stabilization. Molecular Cell 40, 34-49. PMID: 20932473. External link to article
  19. Sader, J.E., Lee, J., and Manalis, S.R. (2010). Energy dissipation in microfluidic beam resonators: Dependence on mode number. Journal of Applied Physics 108, 114507. doi:10.1063/1.3514100.
  20. van Vugt, M., Gardino, A.K., Linding, R., Ostheimer, G.J., Reinhardt, H.C., Ong, S.E., Tan, C.S., Miao, H., Keezer, S.M., Li, J.J., et al. (2010). A Mitotic Phosphorylation Feedback Network Connects Cdk1, Plk1, 53BP1, and Chk2 to Inactivate the G2/M DNA Damage Checkpoint. Plos Biology 8, e1000287. PMID: 20126263. External link to article
  21. Wen, J., Wilker, E.W., Yaffe, M.B., and Jensen, K.F. (2010). Microfluidic Preparative Free-Flow Isoelectric Focusing: System Optimization for Protein Complex Separation. Analytical Chemistry 82, 1253-1260. PMID: 20092256. External link to article
  22. Yang, R., Niepel, M., Mitchison, T.K., and Sorger, P.K. (2010). Dissecting variability in responses to cancer chemotherapy through systems pharmacology. Clin Pharmacol Ther. 88, 34-38. PMID: 20520606. External link to article

2009

  1. Aldridge, B. B., Saez-Rodriguez, J., Muhlich, J. L., Sorger, P. K., and Lauffenburger, D. A. (2009). Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. PLoS Comput Biol 5, e1000340. PMID:19343194
  2. Chen, W. W., Schoeberl, B., Jasper, P. J., Niepel, M., Nielsen, U. B., Lauffenburger, D. A., and Sorger, P. K. (2009). Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol 5, 239. PMID:19156131
  3. Cosgrove, B. D., King, B. M., Hasan, M. A., Alexopoulos, L. G., Farazi, P. A., Hendriks, B. S., Griffith, L. G., Sorger, P. K., Tidor, B., Xu, J. J., and Lauffenburger, D. A. (2009). Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity. Toxicol Appl Pharmacol. PMID:19362101
  4. Kreeger, P.K., Mandhana, R., Alford, S.K., Haigis, K.M., snf Lauffenburger, D.A. (2009). RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects. Cancer Res. 69, 8191-8199. PMID: 19789336. External link to article
  5. Mitsos, A., Melas, I.N., Siminelakis, P., Chairakaki, A.D., Saez-Rodriguez, J., and Alexopoulos, L.G. (2009). Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. PLoS Comput Biol. 5, e1000591. PMID: 19997482. External link to article
  6. Sachs, K., Itani, S., Carlisle, J., Nolan, G. P., Pe’er, D., and Lauffenburger, D. A. (2009). Learning signaling network structures with sparsely distributed data. J Comput Biol 16, 201-212. PMID:19193145
  7. Saez-Rodriguez, J., Alexopoulos, L. G., Epperlein, J., Samaga, R. , Lauffenburger, D. A., Klamt, S. and Sorger, P. K. (2009). Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology, 5:331. PMID: 19953085
  8. Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S. The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol. 2009 Aug;5(8):e1000438. Epub 2009 Aug 7. PubMed PMID: 19662154; PubMed Central PMCID: PMC2710522. External link to article
  9. Spencer, S. L., Gaudet, S., Albeck, J. G., Burke, J. M., and Sorger, P. K. (2009). Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. PMID:19363473
  10. Trujillo-Provencio, C., Powers, T. R., Sultemeier, D. R., and Serrano, E. E. (2009). RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 493, 3-20. PMID:18839338

2008

  1. Adamo, A., and Jensen, K. F. (2008). Microfluidic based single cell microinjection. Lab on a Chip 8, 1258-1261. PMID:18651065
  2. Albeck, J. G., Burke, J. M., Spencer, S. L., Lauffenburger, D. A., and Sorger, P. K. (2008). Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol 6, 2831-2852. PMID:19053173
  3. Albeck, J. G., Burke, J. M., Aldridge, B. B., Zhang, M., Lauffenburger, D. A., and Sorger, P. K. (2008). Quantitative analysis of pathways controlling extrinsic apoptosis in single cells. Mol Cell 30, 11-25. PMID:18406323
  4. Apgar, J. F., Toettcher, J. E., Endy, D., White, F. M., and Tidor, B. (2008). Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol 4, e30. PMID:18282085
  5. Cosgrove, B. D., Cheng, C., Pritchard, J. R., Stolz, D. B., Lauffenburger, D. A., and Griffith, L. G. (2008). An inducible autocrine cascade regulates rat hepatocyte proliferation and apoptosis responses to tumor necrosis factor-alpha. Hepatology 48, 276-288. PMID:18536058
  6. Cosgrove, B. D., Griffith, L. G., and Lauffenburger, D. A. (2008). Fusing Tissue Engineering and Systems Biology Toward Fulfilling Their Promise. Cellular and Molecular Bioengineering 1, 33-41. DOI:10.1007/s12195-008-0007-9
  7. Grover, W. H., von Muhlen, M. G., and Manalis, S. R. (2008). Teflon films for chemically-inert microfluidic valves and pumps. Lab on a Chip 8, 913-918. PMID:18497911
  8. Janes, K. A., Reinhardt, H. C., and Yaffe, M. B. (2008). Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 135, 343-354. PMID:18957207
  9. Palmer, M. J., Mahajan, V. S., Trajman, L. C., Irvine, D. J., Lauffenburger, D. A., and Chen, J. (2008). Interleukin-7 receptor signaling network: an integrated systems perspective. Cell Mol Immunol 5, 79-89. PMID:18445337
  10. Sabouri-Ghomi, M., Wu, Y., Hahn, K., and Danuser, G. (2008). Visualizing and quantifying adhesive signals. Current Opinion in Cell Biology 20, 541-550. PMID:18586481
  11. Son, S., Grover, W. H., Burg, T. P., and Manalis, S. R. (2008). Suspended microchannel resonators for ultralow volume universal detection. Analytical chemistry 80, 4757-4760. PMID:18489125
  12. Squires, T. M., Messinger, R. J., and Manalis, S. R. (2008). Making it stick: convection, reaction and diffusion in surface-based biosensors. NATURE BIOTECHNOLOGY 26, 417-426. PMID:18392027
  13. Saez-Rodriguez, J., Goldsipe, A., Muhlich, J., Alexopoulos, L. G., Millard, B., Lauffenburger, D. A., and Sorger, P. K. (2008). Flexible Informatics for Linking Experimental Data to Mathematical Models via DataRail. Bioinformatics. PMID:18218655
  14. Wang, Y.-C., and Han, J. (2008). Pre-binding dynamic range and sensitivity enhancement for immuno-sensors using nanofluidic preconcentrator. Lab on a Chip. DOI:10.1039/b717220f
  15. Zizlsperger, N., Malashkevich, V. N., Pillay, S., and Keating, A. E. (2008). Analysis of coiled-coil interactions between core proteins of the spindle pole body. Biochemistry 47, 11858-11868. PMID:18850724

2007

  1. Albrecht, J. W., El-Ali, J., and Jensen, K. F. (2007). Cascaded free-flow isoelectric focusing for improved focusing speed and resolution. Anal Chem 79, 9364-9371. PMID:17994708
  2. Albrecht, J. W., and Jensen, K. F. (2007). Patent Application: Isoelectric focusing systems and methods. MIT Case No.: 12421.
  3. Burg, T., Godin, M., Knudsen, S., Shen, W., Carlson, G., Foster, J., Babcock, K., and Manalis, S. (2007). Weighing of biomolecules, single cells and single nanoparticles in fluid. Nature 446, 1066-1069. PMID:17460669
  4. Chellappan, S., Kiran Kumar Reddy, G. S., Ali, A., Nalam, M. N., Anjum, S. G., Cao, H., Kairys, V., Fernandes, M. X., Altman, M. D., Tidor, B., Rana, T. M., Schiffer, C. A., and Gilson, M. K. (2007). Design of Mutation-resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis. Chem Biol Drug Des 69, 298-313. PMID:17539822
  5. Chunara, R., Burg, T. P., Payer, K., Dextras, P., and Manalis, S. (2007). Suspended microchannel resonators with integrated electronic readout for biomolecular and single cell analysis, In The 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2007) (Paris, France).
  6. Chunara, R., Godin, M., Knudsen, S. M., and Manalis, S. R. (2007). Mass-based readout for agglutination assays. Applied Physics Letters. DOI:10.1063/1.2806197
  7. Fu, X., Apgar, J. R., and Keating, A. E. (2007). Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. J Mol Biol 371, 1099-1117. PMID:17597151
  8. Godin, M., Bryan, A. K., Burg, T. P., Babcock, K., and Manalis, S. R. (2007). Measuring the mass, density, and size of particles and cells using a suspended microchannel resonator. Applied Physics Letters 91, 123121. DOI:10.1063/1.2789694
  9. Grover, W. H., Weng, Y. C., and Manalis, S. R. (2007). A microfluidic autosampler with true Teflon valves: Design and application to the suspended microchannel resonator mass sensor, In The 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2007) (Paris, France).
  10. Huang, P. H., Cavenee, W. K., Furnari, F. B., and White, F. M. (2007). Uncovering therapeutic targets for glioblastoma: a systems biology approach. Cell Cycle 6, 2750-2754. PMID:17986864
  11. Huang, P. H., Mukasa, A., Bonavia, R., Flynn, R., Brewer, Z., Cavenee, W., Furnari, F., and White, F. (2007). Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci U S A 104, 12867-12872. PMID:17646646
  12. Kemp, M. L., Wille, L., Lewis, C. L., Nicholson, L. B., and Lauffenburger, D. A. (2007). Quantitative Network Signal Combinations Downstream of TCR Activation Can Predict IL-2 Production Response. J Immunol 178, 4984-4992. PMID:17404280
  13. Kim, S. J., Wang, Y.-C., Lee, J. H., Jang, H., and Han, J. (2007). Concentration Polarization and Nonlinear Electrokinetic Flow near a Nanofluidic Channel. Physical Review Letters 99. PMID:17678369
  14. Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A., Jørgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J. G., Samson, L. D., Woodgett, J. R., Russell, R. B., Bork, P., Yaffe, M. B., and Pawson, T. (2007). Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415-1426. PMID:17570479
  15. Miller-Jensen, K., Janes, K. A., Brugge, J. S., and Lauffenburger, D. A. (2007). Common effector processing mediates cell-specific responses to stimuli. Nature 448, 604-608. PMID:17637676
  16. Quick, Q. A., and Serrano, E. E. (2007). Cell proliferation during the early compartmentalization of the Xenopus laevis inner ear. Int J Dev Biol 51, 201-209. PMID:17486540
  17. Sakarya, O., Armstrong, K. A., Adamska, M., Adamski, M., Wang, I. F., Tidor, B., Degnan, B. M., Oakley, T. H., and Kosik, K. S. (2007). A post-synaptic scaffold at the origin of the animal kingdom. PLoS ONE 2. PMID:17551586
  18. Tian, Y., Kolb, R., Hong, J. H., Carroll, J., Li, D., You, J., Bronson, R., Yaffe, M. B., Zhou, J., and Benjamin, T. (2007). TAZ promotes PC2 degradation through a SCFbeta-Trcp E3 ligase complex. Mol Cell Biol 27, 6383-6395. PMID:17636028
  19. Wang, Y.-C., Liu, V., and Han, J. (2007). Nanofluidic preconcentration device for sensitive and wide dynamic range immunosensing, In The 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2007) (Paris, France).
  20. Wilker, E. W., van Vugt, M. A., Artim, S. A., Huang, P. H., Petersen, C. P., Reinhardt, H. C., Feng, Y., Sharp, P. A., Sonenberg, N., White, F. M., and Yaffe, M. B. (2007). 14-3-3sigma controls mitotic translation to facilitate cytokinesis. Nature 446, 329-332. PMID:17361185
  21. Wilkins, A. K., Barton, P. I., and Tidor, B. (2007). The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism. PLoS Comput Biol 3, e242. PMID:18085817
  22. Wille, L., Kemp, M., Sandy, P., Lewis, C., and Lauffenburger, D. (2007). Epi-allelic Erk1 and Erk2 knockdown series for quantitative analysis of T cell Erk regulation and IL-2 production. Molecular Immunology 44, 3085-3091. PMID:17418417
  23. Wolf-Yadlin, A., Hautaniemi, S., Lauffenburger, D. A., and White, F. M. (2007). Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A. PMID:17389395
  24. Yaffe, M. B., and White, F. M. (2007). Signaling netwErks get the global treatment. Genome Biol 8, 202. PMID:17274840
  25. Ye, L., Zhang, M., Alexopoulos, L. G., Sorger, P. K., and Jensen, K. F. (2007). Microfluidic devices for studying the response of adherent cells under short time stimuli treatment, Paper presented at: The 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2007) (Paris, France).

2006

  1. Adamo, A., and Jensen, K. F. (2006). Microfluidics for controlled single cell microinjection, Paper presented at: The 10th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2006) (Tokyo, Japan).
  2. Adiwijaya, B. S., Barton, P. I., and Tidor, B. (2006). Biological network design strategies: discovery through dynamic optimization. Mol Biosyst 2, 650-659. PMID:17216046
  3. Albeck, J., Macbeath, G., White, F., Sorger, P., Lauffenburger, D., and Gaudet, S. (2006). Collecting and organizing systematic sets of protein data. Nature Reviews Molecular Cell Biology 7, 803-812. PMID:17057751
  4. Albrecht, J., and Jensen, K. F. (2006). Multi-stage free-flow isoelectric focusing for enhanced separation speed and resolution, Paper presented at: The 10th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2006) (Tokyo, Japan).
  5. Albrecht, J. W., and Jensen, K. F. (2006). Micro free flow isoelectric focusing enhanced by active cooling and functionalized gels. Electrophoresis 27, 4960-4969. PMID:17117380
  6. Aldridge, B., Burke, J., Lauffenburger, D., and Sorger, P. (2006). Physicochemical modelling of cell signalling pathways. Nature Cell Biology 8, 1195-1203. PMID:17060902
  7. Aldridge, B. B., Haller, G., Sorger, P. K., and Lauffenburger, D. A. (2006). Direct Lyapunov exponent analysis enables parametric study of transient signalling governing cell behaviour. Syst Biol (Stevenage) 153, 425-432. PMID:17186704
  8. Burg, T. P., Mirza, A. R., Milovic, N., Tsau, C. H., Popescu, G. A., Foster, J. S., and Manalis, S. R. (2006). Vacuum-packaged suspended microchannel resonant mass sensor for biomolecular detection. Microelectromechanical Systems, Journal of 15, 1466-1476. DOI:10.1109/JMEMS.2006.883568
  9. El-Ali, J., and Jensen, K. F. (2006). Microcarrier enabled microfluidic assays of anchorage dependant cells, Paper presented at: The 10th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2006) (Tokyo, Japan).
  10. El-Ali, J., Sorger, P. K., and Jensen, K. F. (2006). Cells on chips. Nature 442, 403-411. PMID:16871208
  11. Fitzgerald, J. B., Schoeberl, B., Nielsen, U. B., and Sorger, P. K. (2006). Systems biology and combination therapy in the quest for clinical efficacy. Nat Chem Biol 2, 458-466. PMID:16921358
  12. Gervais, T., El-Ali, J., Günther, A., and Jensen, K. F. (2006). Flow-induced deformation of shallow microfluidic channels. Lab Chip 6, 500-507. PMID:16572212
  13. Gervais, T., and Jensen, K. (2006). Mass transport and surface reactions in microfluidic systems. Chemical Engineering Science 61, 1102-1121. DOI:10.1016/j.ces.2005.06.024 10.1016/j.ces.2005.06.024
  14. Heinrichs, A., Kritikou, E., Pulverer, B., and Raftopoulou, M., eds. (2006). Systems biology: a user’s guide (New York, NY: Nature Publishing Group).
  15. Hong, J. H., and Yaffe, M. B. (2006). TAZ: a beta-catenin-like molecule that regulates mesenchymal stem cell differentiation. Cell Cycle 5, 176-179. PMID:16397409
  16. Hua, F., Hautaniemi, S., Yokoo, R., and Lauffenburger, D. A. (2006). Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways. J R Soc Interface 3, 515-526. PMID:16849248
  17. Ideker, T., Winslow, L., and Lauffenburger, D. A. (2006). Bioengineering and Systems Biology. Annals of Biomedical Engineering 34, 257-264. PMID:16929563
  18. Janes, K., and Yaffe, M. (2006). Data-driven modelling of signal-transduction networks. Nature Reviews Molecular Cell Biology 7, 820-828. PMID:17057752
  19. Janes, K. A., Gaudet, S., Albeck, J. G., Nielsen, U. B., Lauffenburger, D. A., and Sorger, P. K. (2006). The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 124, 1225-1239. PMID:16564013
  20. Janes, K. A., and Lauffenburger, D. A. (2006). A biological approach to computational models of proteomic networks. Curr Opin Chem Biol 10, 73-80. PMID:16406679
  21. Kim, J. E., and White, F. M. (2006). Quantitative analysis of phosphotyrosine signaling networks triggered by CD3 and CD28 costimulation in jurkat cells. J Immunol 176, 2833-2843. PMID:16493040
  22. Knight, V. B., and Serrano, E. E. (2006). Tissue and Species Differences in the Application of Quantum Dots as Probes for Biomolecular Targets in the Inner Ear and Kidney. Nanobioscience, IEEE Transactions on 5, 251-262. PMID:17181024
  23. Miller-Jensen, K., Janes, K. A., Wong, Y. L., Griffith, L. G., and Lauffenburger, D. A. (2006). Adenoviral vector saturates Akt pro-survival signaling and blocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis. J Cell Sci 119, 3788-3798. PMID:16940353
  24. Schmelzle, K., and White, F. M. (2006). Phosphoproteomic approaches to elucidate cellular signaling networks. Curr Opin Biotechnol 17, 406-414. PMID:16806894
  25. Wolf-Yadlin, A., Kumar, N., Zhang, Y., Hautaniemi, S., Zaman, M., Kim, H.-D., Grantcharova, V., Lauffenburger, D., and White, F. (2006). Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol 2:54. PMID:17016520
  26. Yeang, C. H., and Jaakkola, T. (2006). Modeling the combinatorial functions of multiple transcription factors. J Comput Biol 13, 463-480. PMID:16597252

2005

  1. Albrecht, J., Gaudet, S., and Jensen, K. F. (2005). Rapid free flow isoelectric focusing via novel electrode structures, Paper presented at: The 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2005) (Boston, USA).
  2. Altman, M. D., Bardhan, J. P., White, J. K., and Tidor, B. (2005). An Accurate Surface Formulation for Biomolecule Electrostatics in Non-Ionic Solutions, Paper presented at: Engineering in Medicine and Biology Society, 2005. IEEE-EMBS 2005. 27th Annual International Conference of the. PMID:17282038
  3. El-Ali, J., Gaudet, S., Günther, A., Sorger, P. K., and Jensen, K. F. (2005). Cell stimulus and lysis in a microfluidic device with segmented gas-liquid flow. Anal Chem 77, 3629-3636. PMID:15924398
  4. El-Ali, J., Gaudet, S., Murhpy, Nielsen, U. B., and Jensen, K. F. (2005). Microfluidic device with integrated antibody arrays for cell signaling analysis, Paper presented at: The 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2005) (Boston, USA).
  5. Gaudet, S., Janes, K. A., Albeck, J. G., Pace, E. A., Lauffenburger, D. A., and Sorger, P. K. (2005). A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics 4, 1569-1590. PMID:16030008
  6. Gervais, T., Tsau, C., Ali, E., Manalis, S. R., and Jensen, K. F. (2005). Convection-limited Surface Transport In Nanofluidic Channels, Paper presented at: The 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2005).
  7. Goldberg, I. G., Allan, C., Burel, J. M., Creager, D., Falconi, A., Hochheiser, H., Johnston, J., Mellen, J., Sorger, P. K., and Swedlow, J. R. (2005). The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6. PMID:15892875
  8. Hong, J. H., Hwang, E. S., McManus, M. T., Amsterdam, A., Tian, Y., Kalmukova, R., Mueller, E., Benjamin, T., Spiegelman, B. M., Sharp, P. A., Hopkins, N., and Yaffe, M. B. (2005). TAZ, a transcriptional modulator of mesenchymal stem cell differentiation. Science 309, 1074-1078. PMID:16099986
  9. Hua, F., Cornejo, M. G., Cardone, M. H., Stokes, C. L., and Lauffenburger, D. A. (2005). Effects of Bcl-2 levels on Fas signaling-induced caspase-3 activation: molecular genetic tests of computational model predictions. J Immunol 175, 985-995. PMID:16002698
  10. Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K., Lauffenburger, D. A., and Yaffe, M. B. (2005). A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653. PMID:16339439
  11. Kim, J. E., Tannenbaum, S. R., and White, F. M. (2005). Global phosphoproteome of HT-29 human colon adenocarcinoma cells. J Proteome Res 4, 1339-1346. PMID:16083285
  12. Lu, H., and Jensen, K. (2005). Cellular and Subcellular Analysis on Chip, In Lab-on-Chips for Cellomics, pp. 273-298. DOI:10.1007/978-1-4020-2975-2_11
  13. Lu, H., Schmidt, M. A., and Jensen, K. F. (2005). A microfluidic electroporation device for cell lysis. Lab Chip 5, 23-29. PMID:15616736
  14. Sachs, K., Perez, O., Pe’er, D., Lauffenburger, D., and Nolan, G. (2005). Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data. Science 308, 523-529. PMID:15845847
  15. Shults, M. D., Janes, K. A., Lauffenburger, D. A., and Imperiali, B. (2005). A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates. Nat Methods 2, 277-283. PMID:15782220
  16. Sorger, P. K. (2005). A reductionist’s systems biology: opinion. Curr Opin Cell Biol 17, 9-11. PMID:15661513
  17. Wang, Y.-C., Tsau, C. H., Burg, T. P., Manalis, S., and Han, J. (2005). Efficient Biomolecule Pre-concentration by Nanofilter-triggered Electrokinetic Trapping, In The 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS2005) (Boston, MA).
  18. Wilker, E. W., Grant, R. A., Artim, S. C., and Yaffe, M. B. (2005). A structural basis for 14-3-3sigma functional specificity. J Biol Chem 280, 18891-18898. PMID:15731107
  19. Yeang, C. H., Mak, H. C., McCuine, S., Workman, C., Jaakkola, T., and Ideker, T. (2005). Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol 6. PMID:15998451
  20. Zhang, Y., Wolf-Yadlin, A., Ross, P. L., Pappin, D. J., Rush, J., Lauffenburger, D. A., and White, F. M. (2005). Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics 4, 1240-1250. PMID:15951569

2004

  1. Brown, G. E., Stewart, M. Q., Bissonnette, S. A., Elia, A. E., Wilker, E., and Yaffe, M. B. (2004). Distinct ligand-dependent roles for p38 MAPK in priming and activation of the neutrophil NADPH oxidase. J Biol Chem 279, 27059-27068. PMID:15102856
  2. Janes, K. A., Kelly, J. R., Gaudet, S., Albeck, J. G., Sorger, P. K., and Lauffenburger, D. A. (2004). Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J Comput Biol 11, 544-561. PMID:15579231
  3. Kim, J. E., and Tannenbaum, S. R. (2004). Insulin regulates cleavage of procaspase-9 via binding of X chromosome-linked inhibitor of apoptosis protein in HT-29 cells. Cancer Res 64, 9070-9075. PMID:15604274
  4. Kim, J.-E., and Tannenbaum, S. (2004). S-Nitrosation Regulates the Activation of Endogenous Procaspase-9 in HT-29 Human Colon Carcinoma Cells. J Biol Chem 279, 9758-9764. PMID:14701803
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