National Centers for Systems Biology National Institutes of Health Sandia National Laboratories Los Alamos National Laboratory UNM Cancer Center The University of New Mexico New Mexico Consortium
© Copyright 2012 The New Mexico Center for the Spatiotemporal Modeling of Cell Signaling

Publications

Download summary of publications, 2009/2010

Download summary of publications, 2008/2009

Download summary of publications, 2002-Present


Selected Publications 2012

Cell Signaling and Microscopy:

  1. Spendier K, DS Lidke, KA Lidke and JL Thomas. 2012. Single-particle tracking of immunoglobulin E receptors (FcεRI) in micron-sized clusters and receptor patches. FEBS Lett. 586:416-421. PMID: 22265688.
    FEBS Letters pdf pdf icon

Reviews:

  1. Chigaev A and Sklar LA. Overview: assays for studying integrin-dependent cell adhesion. Methods Mol Biol 757: 3-14, 2012.

  2. Spendier, K. and J.L. Thomas. "Spatial Patterns in Mast Cell Activation", in Mast Cells: Phenotype, Function and Role in Immunity, David B. Murray, Ed. Nova Publishers, 2012. in press.

  3. Carroll-Portillo A, Surviladze Z, Cambi A, Lidke DS and Wilson BS (2012) Mast cell synapses and exosomes: membrane contacts for information exchange.Front. Immun. 3:46. doi: 10.3389/fimmu.2012.00046
    Front. Immun. pdf pdf icon

Selected Publications 2010/2011

Cell Signaling and Microscopy:

  1. Chigaev A, Smagley Y and Sklar LA. Nitric oxide/cGMP pathway signaling actively down-regulates alpha4beta1-integrin affinity: an unexpected mechanism for inducing cell de-adhesion. BMC Immunol 12: 28, 2011.

  2. Chigaev A, Wu Y, Williams DB, Smagley Y and Sklar LA. Discovery of very late antigen-4 (VLA-4, {alpha}4{beta}1 integrin) allosteric antagonists. J Biol Chem 286: 5455-5463, 2011.

  3. Shalini T Low-Nam, Keith A Lidke, Patrick J Cutler, Rob C Roovers, Paul M P van Bergen en Henegouwen, Bridget S Wilson & Diane S Lidke. ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding. Nature Structural & Molecular Biology (2011). Published online 23 October 2011
    Nature Structural & Molecular Biology pdf pdf icon

  4. Carroll-Portillo, A, K Spendier, J Pfeiffer, G Griffiths, H Li, J M Oliver, D Lidke, K Lidke, J Thomas, BS Wilson and J Timlin. 2010. FcεRI membrane dynamics upon binding mobile or immobile ligands on surfaces: formation of a mast cell synapse. J. Immunology 184:1328-1338. PMID: 20042583. PMCID: PMC3087819
    Journal of Immunology article
    Journal of Immunology pdfpdf icon

  5. Spendier, K, A Carroll-Portillo, K Lidke, BS Wilson, JA Timlin and JL Thomas. 2010. Distribution and dynamics of RBL IgE receptors (FcεRI) on planar ligand-presenting surfaces. Biophysical J. 99:388-397.

  6. Lidke, DS, F. Huang, J.N. Post, B. Rieger, J. Wilsbacher, J.L. Thomas, J. Pouysségur, T.M. Jovin and P. Lenormand. 2010. “ERK nuclear translocation is dimerization-independent but controlled by the rate of phosphorylation.” Journal of Biological Chemistry. 285:3092-3102. PMCID: PMC2823437.
    Journal of Biological Chemistry pdfpdf icon

  7. Cannon, J.L., Mody, P.D., Blaine, K.M., Nelson, A.D., Sayles, L., Moore, T.V., Clay, B.S., Bandukwala, H.S., Dulin, N.O., Shilling, R.A., Sperling, A.I. 2011. CD43 interaction with ERM proteins regulates T cell trafficking and CD43 phosphorylation. Molecular Biology of the Cell, 22: 954-63. PMID: 21289089
    Molecular Biology of the Cell pdfpdf icon

  8. Lidke, DS, S.T. Low-Nam, P.J. Cutler, K.A. Lidke. “Determining FcεRI diffusional dynamics via single quantum dot tracking.” Methods in Molecular Biology: Immune Receptors. (In press)

  9. Low-Nam, ST, KA Lidke, PJ Cutler, RC Roovers, P van Bergen en Henegouwen, BS Wilson and DS Lidke. Visualization of ErbB1 dimers: ligand-induced stability and repeated encounters in domains. Nature Structural and Molecular Biology, In Press.

  10. M Steinkamp, S Yang, ST Low-Nam, X Meng, M Smith, DS Lidke and BS Wilson. 2011. ErbB3 is an active kinase driven by sequential heterodimer and homodimer interactions. Submitted.

  11. François Girodon, Mara P. Steinkamp, Cédric Cleyrat, Sylvie Hermouet and Bridget S. Wilson. 2011. "Confocal imaging studies cast doubt on nuclear localization of JAK2 V617F." doi: 10.1182/blood-2011-02-336479 Blood September 1, 2011 vol. 118 no. 9 2633-2634.
    Blood pdfpdf icon
Image Analysis and Modeling:
  1. Hsieh, M, S Yang, M Raymond-Stinz, JS Edwards and BS Wilson. 2010. Spatio-temporal modeling of signaling protein recruitment to EGFR. BMC Systems Biology 4:57.

  2. Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS. 2010. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys. J. 98:48-56. PMCID: PMC2800967

  3. Banerjee S. and M. E. Moses. 2010. Scale Invariance of Immune System Response Rates and Times: Perspectives on Immune System Architecture and Implications for Artificial Immune Systems. Swarm Intelligence 4(4): 301-308.

  4. Yang J, Meng X, Hlavacek WS. 2011. Rule-based modeling and simulation of biochemical systems with molecular finite automata. IET Syst. Biol. 4:453-466. PMCID: PMC3070173

  5. Yang, J. and W. S. Hlavacek. 2011. Efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems. Phys. Biol. NIHMSID: NIHMS288900
    Phys. Biol. pdfpdf icon

  6. Costa MN, Radhakrishnan K, Edwards JS. 2011. Monte Carlo simulations of the plasma membrane corral-induced EGFR clustering. Journal of Biotechnology 151 (2011) 261–270
    Journal of Biotechnology pdfpdf icon

  7. Lemons NW, Hu B, Hlavacek WS. 2011. Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics 12:45. PMC Journal – In Process (The paper is freely available online http://www.biomedcentral.com/1471-2105/12/45)

  8. Espinoza, FA, J. M. Oliver, B. S. Wilson, S. L. Steinberg. 2011. Using Hierarchical Clustering and Dendrograms to Quantify the Clustering of Membrane Proteins. Bulletin of Mathematical Biology. E-pub ahead of print.
    Bulletin of Mathematical Biology pdfpdf icon

  9. Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. 2011. Guidelines for visualizing and annotating rule-based models. Mol. BioSyst. (submitted)

  10. Banerjee S., D. Levin, M. E. Moses, F. Koster, S. Forrest, “The Value of Inflammatory Signals in Adaptive Immune Responses” 2011. Proceedings of the 10th International Conference on Artificial Immune Systems (ICARIS) (accepted).

  11. Tektonidis, M., H. Hatzikirou*, A. Chauviere, M. Simon, C. Schaller and A. Deutsch. 2011. Identifications of the intrinsic mechanisms for glioma tumor invasion. J. Theor. Biol. (submitted)

  12. Spendier K and JL Thomas. 2011. Image Correlation Spectroscopy of Randomly Distributed Disks. J. Biol. Phys. 37:477-492
    J. Biol. Phys. pdf pdf icon

  13. F. A. Espinoza, M. J. Wester, J. M. Oliver, B. S. Wilson, N. Andrews, D. S. Lidke and S. L. Steinberg. Insights Into Cell Membrane Microdomain Organization from Live Cell Single Particle Tracking of the High Affinity IgE Receptor, FceRI, of Mast Cells. Submitted for publication August 2011.

  14. Frieboes, H., M. A. Chaplain, A. Thompson, E. L. Bearer, J. Lowengrub, and V. Cristini (2011). "Physical oncology: a bench-to-bedside quantitative and predictive approach." Cancer Res 71(2): 298-302.

  15. Deisboeck, T., Z. Wang, P. Macklin, and V. Cristini. (2011). "Multiscale Cancer Modeling." Annual Review of Biomedical Engineering 13(1).

  16. Pham, K., H. Frieboes, V. Cristini, and J. Lowengrub (2011). "Predictions of tumour morphological stability and evaluation against experimental observations." J R Soc Interface 8(54): 16-29.

  17. Wise, S., J. Lowengrub, and V. Cristini (2011). "An Adaptive Multigrid Algorithm for Simulating Solid Tumor Growth Using Mixture Models." Math Comput Model 53(1-2): 1-20.

  18. Pham, K., A. Chauviere, H. Hatzikirou, X. Li, H. Byrne, V. Cristini, and J. Lowengrub (2011). “Density-dependent quiescence in glioma invasion: instability in a simple reaction-diffusion model for the migration/proliferation dichotomy.” J Biol Dynam. (in press).

  19. De Magalhaes, N., L. Liaw, M. Berns, V. Cristini, Z. Chen, D. Stupack, and J. Lowengrub (2010). "Applications of a new In vivo tumor spheroid based shell-less chorioallantoic membrane 3-D model in bioengineering research." J Biomed Sci Eng 3(1): 20-26.

  20. Chauviere, A., H. Hatzikirou, J. Lowengrub, H. Frieboes, A. Thompson, and V. Cristini (2010). "Mathematical Oncology: How Are the Mathematical and Physical Sciences Contributing to the War on Breast Cancer?" Curr Breast Cancer Rep 2(3): 121-129.

  21. Frieboes, H., F. Jin, Y. Chuang, S. Wise, J. Lowengrub, and V. Cristini (2010). "Three-dimensional multispecies nonlinear tumor growth-II: Tumor invasion and angiogenesis." J Theor Biol 264(4): 1254-1278.

  22. Lowengrub, J., H. Frieboes, F. Jin, Y. Chuang, X. Li, P. Macklin, S. Wise, and V. Cristini (2010). "Nonlinear modelling of cancer: bridging the gap between cells and tumours." Nonlinearity 23(1): R1-R9.
Enabling Technologies:
  1. Wu M, Singh AK. Single-cell protein analysis, Curr Opin Biotechnol (2011), doi:10.1016/j.copbio.2011.11.023
    Curr Opin Biotechnol pdfpdf icon

  2. Yilmaz S, Singh AK. Single cell genome sequencing, Curr Opin Biotechnol (2011), doi:10.1016/j.copbio.2011.11.018
    Curr Opin Biotechnol pdfpdf icon

  3. Nowak-Lovato, KL, BS Wilson and KD Rector. 2010. SERS nanosensors that report pH of endocytic compartments during FcεRI transit. Analytical and Bioanalytical Chemistry 398:2019-2029.

  4. Wells, NP, GA Lessard, PM Goodwin, ME Phipps, PJ Cutler, DS Lidke, BS Wilson, JH Werner. 2010. Time-resolved three-dimensional molecular tracking in live cells. NanoLetters 10:4732-4737.
    NanoLetters pdfpdf icon

  5. Bradbury AR, Sidhu S, Dubel S, McCafferty J. 2011. Beyond natural antibodies: the power of in vitro display technologies. Nature Biotechnology 29: 245-254.
    Nature Biotechnology pdfpdf icon

  6. Huang, F, SL Schwartz, JM Byars, KA Lidke. 2011. Simultaneous Multiple-emitter Fitting for Single Molecule Super-Resolution Imaging. Biomed. Opt. Express 2: 1377-1393. PMID: 21559149. PMCID: PMC3087594
    http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-2-5-1377

  7. Ferrara, F., Listwan, P., Waldo, G.S., and Bradbury, A.R.M. 2011. Using split GFP to fluorescently label antibody fragments. PLoS One (submitted).
Reviews:
  1. Radhakrishnan K, Halász A, Vlachos D, Edwards JS. 2010. Quantitative understanding of cell signaling: the importance of membrane organization. Curr Op Biotechnol. 21: 677-682.
    ScienceDirect pdfpdf icon

  2. Wilson, BS, J.M. Oliver, D.S. Lidke. 2011. Spatiotemporal signaling in mast cells. In: Mast Cell Biology, Contemporary and Emerging Topics, Editors, Dean Metcalfe and Alasdair Gilfillan. Landes BioScience and Springer Science. 716: 91-106 (ISBN-13: 9781441995322)
    Spatiotemporal signaling in mast cells pdfpdf icon

  3. Hlavacek WS. 2011. Two challenges of systems biology. In Handbook of Statistical Systems Biology (Stumpf MPH, Balding DJ, Girolami MA, Editors) Wiley-Blackwell, Ch. 1. ISBN 9780470710869(in press, scheduled to appear Oct 2011).

  4. Chauviere, A, H. Hatzikirou, Y. Kevrekidis, J. Lowengrub, V. Cristini. 2011. Multiscale modeling of solid tumor growth. IEEE Transactions in Biomedical Engineering (submitted)

  5. Hatzikirou, H, A. Chauviere, A. Bauer, P. Macklin, A. Leier, T. Marquez, M. Lewis, E. Bearer, V. Cristini. 2011. Integrative mathematical oncology. WIREs Systems Biology and Medicine (submitted)

  6. Singh, AK et al. 2011. “Biochemical analysis of single cells” in Current Opinion in Biotechnology. In preparation.

  7. Singh, AK et al. 2011. “Autonomous lab on a chip technologies” in Springer’s series Chemical Sensors and Biosensors edited by Prof. Gerald Urban. In preparation.

  8. Hlavacek WS. 2011. "Guidelines for visualizing and annotating rule-based models" in Molecular bioSystems. NIHMSID: NIHMS301574.
    Molecular bioSystems pdfpdf icon

Selected Publications, 2009/2010

Cell Signaling, Microscopy and Image Analysis:

  1. Andrews, NL, JR Pfeiffer, AM Martinez, DM Haaland, RW Davis, T Kawakami, JM Oliver, BS Wilson and DS Lidke. 2009. Small, Mobile FcεRI Receptor Aggregates Are Signaling Competent. Immunity 31:469–479. PMCID: PMC2828771
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2828771/?tool=pubmed
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2828771/pdf/nihms146102.pdfpdf icon

  2. Carroll-Portillo, A, K Spendier, J Pfeiffer, G Griffiths, H Li, JM Oliver, D Lidke, J Thomas, BS Wilson and J Timlin. 2010. FcεRI Membrane Dynamics upon Binding Mobile or Immobile Ligands on Surfaces: Formation of a Mast Cell Synapse. J Immunol. 184:1328-38. PMCID: pending
    http://www.jimmunol.org/cgi/content/full/184/3/1328
    http://www.jimmunol.org/cgi/reprint/184/3/1328.pdfpdf icon

  3. Kathrin Spendier, Amanda Carroll-Portillo, Keith A. Lidke, Bridget S. Wilson, Jerilyn A. Timlin, and James L. Thomas, "Distribution and Dynamics of Rat Basophilic Leukemia Immunoglobulin E Receptors (FcɛRI) on Planar Ligand-Presenting Surfaces" Biophysical Journal, Volume 99, Issue 2, 2010. 99:388-397. PMID: 20643056
    http://www.cell.com/biophysj/abstract/S0006-3495%2810%2900527-8
    Biophysical Journal pdfpdf icon

  4. Smith, CS, N Joseph, B Rieger and KA Lidke. 2010. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat Methods. 2010 May;7(5):373-5. Epub 2010 Apr 4. PMCID: PMC2862147
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862147/?tool=pubmed
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862147/pdf/nihms-187624.pdfpdf icon

Modeling:
  1. Radhakrishnan, K, J Edwards, D Lidke, T Jovin, B Wilson, and J Oliver. 2009. Sensitivity Analysis Predicts that the ERK-pMEK Interaction Regulates ERK Nuclear Translocation. IET Systems Biology 3: 329-341.
    http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5243211pdf icon

  2. Hsieh, G, W Shu, BS Wilson and JS Edwards. 2010. ErbB family receptor dynamic modeling quantitatively predicts signaling dynamics. BMC Systems Biology. 4:57. PMCID: PMC2877007
    http://www.biomedcentral.com/1752-0509/4/57
    http://www.biomedcentral.com/content/pdf/1752-0509-4-57.pdfpdf icon

  3. Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS. 2010. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys. J. 98:48-56. PMCID: PMC2800967
    ScienceDirect article
    ScienceDirect pdfpdf icon

  4. Radhakrishnan K, Halasz A, Vlachos D, and Edwards JS "Quantitative understanding of cell signaling: the importance of membrane organization". Curr Opin Biotechnol 2010;21:677-682. PMID: 20829029. PMCID: PMC2967365
    View article pdfpdf icon

  5. Costa MN, Radhakrishnan K, and Edwards JS "Monte Carlo simulations of plasma membrane corral-induced EGFR clustering". J Biotechnol, accepted for publication.
    ScienceDirect article

  6. Collins, S, M Stamatakis and DG Vlachos, Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes BMC Bioinformatics 2010, 11:218
    View article pdfpdf icon
Review:
  1. Lidke, DS and BS Wilson. 2009. Caught in the act: quantifying protein behaviour in living cells. Trends Cell Biol. 19:566-74. PMCID: PMC2783887
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783887/?tool=pubmed
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783887/pdf/nihms142662.pdfpdf icon

Selected Publications, 2008/2009

Cell Signaling, Microscopy and Image Analysis:

  1. Andrews, NL, KA Lidke, JR. Pfeiffer, AR Burns, BS Wilson, JM Oliver, and DS Lidke. 2008. Actin restricts FcεRI diffusion and facilitates antigen-induced receptor immobilization. Nature Cell Biol. 10: 955-963.
    http://www.nature.com/ncb/journal/v10/n8/full/ncb1755.html
    http://www.nature.com/ncb/journal/v10/n8/pdf/ncb1755.pdfpdf icon

  2. JI Kashiwakura, S Xiao, J Kitaura, Y Kawakami, M Maeda-Yamamoto, JR Pfeiffer, BS Wilson, U Blank and T Kawakami. 2008. Pivotal Advance: IgE accelerates in vitro development of mast cells and modifies their phenotype. J. Leukocyte Biol. 84: 357-367. (Cover)
    http://www.jleukbio.org/content/84/2/357.long
    http://www.jleukbio.org/content/84/2/357.full.pdf+htmlpdf icon

  3. L Andrews, JR Pfeiffer, AM Martinez, DM Haaland, RW Davis, T Kawakami, JM Oliver, BS Wilson, D S Lidke. Small, mobile FcεRI aggregates are signaling competent. 2009. Immunity, 31:469-479.
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2828771/?tool=pubmed
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2828771/pdf/nihms146102.pdfpdf icon

  4. N Wells, GA Lessard, ME Phipps, PM Goodwin, DS Lidke, BS Wilson, JH Werner. (2009) Going beyond 2D: Following membrane diffusion and topography in the IgE–FcεRI system using 3-dimensional tracking microscopy. Proceedings SPIE In press.
    www.osti.gov/energycitations/product.biblio.jsp?osti_id=962289
    www.osti.gov/energycitations/servlets/purl/962289-mv0fq3/962289.pdfpdf icon

  5. Oliver, JM CA Tarleton, L Gilmartin, T Archibeque, CR Qualls, L Diehl, BS Wilson, M Schuyler. 2010. Reduced FcεRI-mediated release of asthma-promoting cytokines and chemokines from human basophils during Omalizumab therapy. Internat. Archives Allergy Immunology, 151:275-284
    http://www.ncbi.nlm.nih.gov/pubmed/19844128

Mathematical Modeling:
  1. Niehaus, AM, DG Vlachos, & JS Edwards. 2008. Microscopic simulation of epidermal growth factor receptor diffusion on corralled membrane surfaces. Biophysical J. 94: 1551-1564.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242759/
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242759/pdf/1551.pdfpdf icon

  2. Zhang, J., SL Steinberg, BS Wilson, JM Oliver & LR Williams. 2008. Markov random field modeling of the spatial distribution of proteins on cell membranes. Bulletin of Mathematical Biology. 70: 297-321.
    http://www.ncbi.nlm.nih.gov/pubmed/17906899
    http://www.springerlink.com/content/l044446137507975/fulltext.pdfpdf icon

  3. Hsieh, W Shu, S Yang, M Raymond-Stintz, D Vlahos, S Steinberg, BS Wilson and J Edwards. 2008 Stochastic simulations of ErbB homo and hetero-dimerization: potential impacts of receptor conformational state and spatial segregation. IET Systems Biology 2(5): 256-272.
    IEEE Xplore article

  4. Goldstein, B, D. Coombs, J. R. Faeder and W. S. Hlavacek. "Kinetic Proofreading Model." Adv Exp Med Biol. 640:82-94
    http://www.springerlink.com/content/pt633121047w2383/
    http://www.springerlink.com/content/pt633121047w2383/fulltext.pdfpdf icon

  5. Lipniacki, T, B Hat, JR Faeder and W.S. Hlavacek. 2008. Stochastic effects and bistability in T cell receptor signaling. J. Theor. Biol. 254, 110-122.
    ScienceDirect article
    ScienceDirect pdfpdf icon

  6. Yang, J, MI Monine, J. Faeder and WS Hlavacek. 2008. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys. Rev. E 78, 031910.
    http://pre.aps.org/abstract/PRE/v78/i3/e031910
    http://pre.aps.org/pdf/PRE/v78/i3/e031910

  7. Faeder, JR, ML Blinov and WS Hlavacek. Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol. In Systems Biology (I. V. Maly, Editor) Humana Press, Totowa, NJ.
    http://www.springerlink.com/content/nn1v343vw2kmj00w/#section=54512&page=1
    http://www.springerlink.com/content/nn1v343vw2kmj00w/fulltext.pdfpdf icon

  8. Ying, W, G Huerta, SL Steinberg and M Zuniga. 2009. Time Series Analysis of Particle Tracking Data for Molecular Motion on the Cell Membrane. Bull. Math. Biol. 71:1967-2024.
    http://www.ncbi.nlm.nih.gov/pubmed/19657701
    http://www.springerlink.com/content/f8870v11m621u570/fulltext.pdfpdf icon

  9. Nag, A, MI Monine, JR Faeder and B Goldstein. 2009. Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys. J. 96:2604-23.
    ScienceDirect article
    ScienceDirect pdfpdf icon

  10. T Mazel, R Raymond, M Raymond-Stinz, S Jett and BS Wilson. 2009. Stochastic modeling of calcium in 3D geometry. Biophysical Journal. 96:1691-1706.
    ScienceDirect article
    ScienceDirect pdf

  11. MN Costa, K Radhakrishnan, BS Wilson, DG Vlachos and JS Edwards. 2009. Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction. PLoS One, 4: e63216.
    PLoS ONE article
    PLoS ONE pdfpdf icon

  12. Hlavacek WS, JR Faeder. 2009. The complexity of cell signaling and the new for a new mechanics. Sci Signal 2(81):pe46.
    www.ncbi.nlm.nih.gov/pubmed/19638613
    www.ccbb.pitt.edu/Faculty/Faeder/Publications/Reprints/Faeder_SciSignal_2009.pdfpdf icon

  13. Hu B, M. Fricke, JR Faeder, RG Posner, WS Hlavacek. 2009. GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics 25(11)1457-60.
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2682519/
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2682519/pdf/btp173.pdfpdf icon

  14. Colvin J, MI Monine, JR Faeder, WS Hlavacke, DD Von Hoff, RG Posner. 2009. Simulation of large-scale rule-based models. Bioinformatics 25(7)910-7
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660871/
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660871/pdf/btp066.pdfpdf icon

  15. Ming-yu Hsieh, Shujie Yang, Mary Ann Raymond-Stinz, Jeremy S Edwards and Bridget S Wilson. 2010. Spatio-temporal modeling of signaling protein recruitment to EGFR. BMC Syst Biol. 2010; 4: 57. PMCID: PMC2877007
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2877007/?tool=pubmed
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2877007/pdf/1752-0509-4-57.pdfpdf icon

Technology Development:
  1. Meagher, RJ, YK Light and AK Singh. 2008. Rapid, continuous purification of proteins in a microfluidic device using genetically-engineered partition tags. Lab Chip 8: 527-32.
    http://pubs.rsc.org/en/Content/ArticleLanding/2008/LC/b716462a
    http://pubs.rsc.org/en/Content/ArticlePDF/2008/LC/B716462A/2008-02-25pdf icon

  2. G. Sommer. G, AK Singh and AV Hatch. 2008. On-chip Isoelectric Focusing Using Photopolymerized Immobilized pH Gradients. Anal. Chem. 80: 3327-3333.
    http://pubs.acs.org/doi/abs/10.1021/ac702523g
    http://pubs.acs.org/doi/pdf/10.1021/ac702523gpdf icon

  3. Lassen, K., Bradbury, A.R.M., Rehfeld, J.F. and Heegaard, N.H.H. 2008. Microscale characterization of the binding specificity and affinity of a monoclonal anti-sulfo-tyrosyl IgG antibody, Electrophoresis 29: 2557-64.
    http://onlinelibrary.wiley.com/doi/10.1002/elps.200700908/abstract
    http://onlinelibrary.wiley.com/doi/10.1002/elps.200700908/pdfpdf icon

  4. Dai, M., Temirov, J., Pesavento, E., Kiss, C., Velappan, N., Pavlik, P., Werner, J. and Bradbury, A.R.M. 2008. Using T7 phage display to select GFP based binders, Protein Eng Des Sel. 21: 413-424.
    http://peds.oxfordjournals.org/content/21/7/413.abstract
    http://peds.oxfordjournals.org/content/21/7/413.full.pdf+htmpdf icon

  5. Secco, P., D'Agostino, E., Marzari, R., Licciulli, M., Di Niro, R., D'Angelo, S., Bradbury, A.R.M., Dianzani, U., Santoro, C. and Sblattero, D. 2009. Antibody library selection by the ß-lactamase Protein Fragment Complementation Assay. Prot. Eng. Design Selection in press
    http://www.ncbi.nlm.nih.gov/pubmed/18829449
    http://peds.oxfordjournals.org/content/22/3/149.full.pdf+htmlpdf icon

  6. Srivastava N, JS Brennen, RF Renzi, M Wu, SS Branda, AK Singh, AE Herr. 2009. Fully integrated microfluidic platform enabling authomated phosphoprofiling of macrophase response. Anal. Chem 81:3261-9.
    http://pubs.acs.org/doi/abs/10.1021/ac8024224
    http://pubs.acs.org/doi/pdf/10.1021/ac8024224pdf icon

  7. Sommer GJ, AK Singh, AV Hatch. 2009. Enrichment and fractionation of proteins via microscale pore limit electrophoresis. Lab Chip 21:2729-37.
    http://www.ncbi.nlm.nih.gov/pubmed/19704990

  8. Perroud TD, RJ Meagher, MP Kanouff, RF Renzi, M Wu, AK Singh, KD Patel. 2009. Isotropically etched radial micropore for cell concentration, immobilization and picodroplet generation. Lab Chip 9:507-15.
    http://www.ncbi.nlm.nih.gov/pubmed/19190785

Home > Publications
New Mexico Center for the SpatioTemporal Modeling of Cell Signaling