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The University of New Mexico Health Sciences Center

Publications

Selected Publications 2020

  1. Emanuel Salazar-Cavazos, Carolina Franco Nitta , Bridget S. Wilson, Keith A Lidke, William Hlavacek and Diane S. Lidke. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Molecular Biology of the Cell, in press. 2020

Selected Publications 2019

  1. Cesar A. López, Mark F. Swift, Xiao-Ping Xu, Dorit Hanein, Niels Volkmann, S. Gnanakaran (2019) Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM. Structure, 2019, ISSN 0969-2126, I Kinjyo, D Bragin, R Grattan, SS Winter and BS Wilson. (2019) Leukemia-derived exosomes and cytokines pave the way for entry into the brain. Journal of Leukocyte Biology, doi: 10.1002/JLB.3A0218-054R Epub ahead of print.
  2. Bayesian Multiple Emitter Fitting using Reversible Jump Markov Chain Monte Carlo. Fazel M, Wester MJ, Mazloom-Farsibaf H, Meddens MBM, Eklund AS, Schlichthaerle T, Schueder F, Jungmann R, Lidke KA. Sci Rep. 2019 Sep 24;9(1):13791. doi: 10.1038/s41598-019-50232-x.
  3. Combinatorial diversity of Syk recruitment driven by its multivalent engagement with FcεRIγ. Travers T, Kanagy WK, Mansbach RA, Jhamba E, Cleyrat C, Goldstein B, Lidke DS, Wilson BS, Gnanakaran S. Mol Biol Cell. 2019 Aug 1;30(17):2331-2347. doi: 10.1091/mbc.E18-11-0722. Epub 2019 Jun 19.
  4. PD-L1 Expression in Mastocytosis. Williams M, Lidke DS, Hartmann K, George TI. Int J Mol Sci. 2019 May 13;20(9). pii: E2362. doi: 10.3390/ijms20092362.
  5. Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation. Kumar S, Gu Y, Abudu YP, Bruun JA, Jain A, Farzam F, Mudd M, Anonsen JH, Rusten TE, Kasof G, Ktistakis N, Lidke KA, Johansen T, Deretic V. Dev Cell. 2019 Apr 8;49(1):130-144.e6. doi: 10.1016/j.devcel.2019.01.027. Epub 2019 Feb 28.
  6. Changes in Fluorescence Recovery After Photobleaching (FRAP) as an indicator of SOX9 transcription factor activity. Govindaraj K, Hendriks J, Lidke DS, Karperien M, Post JN. Biochim Biophys Acta Gene Regul Mech. 2019 Jan;1862(1):107-117. doi: 10.1016/j.bbagrm.2018.11.001. Epub 2018 Nov 20.
  7. Dual Actions of Ketorolac in Metastatic Ovarian Cancer. Hudson LG, Cook LS, Grimes MM, Muller CY, Adams SF, Wandinger-Ness A. Cancers (Basel). 2019 Jul 24;11(8). pii: E1049. doi: 10.3390/cancers11081049.
  8. Distributed Adaptive Search in T Cells: Lessons From Ants. Moses ME, Cannon JL, Gordon DM, Forrest S. Front Immunol. 2019 Jun 13;10:1357. doi: 10.3389/fimmu.2019.01357
  9. Cesar A. López, Mark F. Swift, Xiao-Ping Xu, Dorit Hanein, Niels Volkmann, S. Gnanakaran (2019) Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM. Structure, 2019, ISSN 0969-2126, https://doi.org/10.1016/j.str.2019.03.013.
  10. I Kinjyo, D Bragin, R Grattan, SS Winter and BS Wilson. (2019) Leukemia-derived exosomes and cytokines pave the way for entry into the brain. Journal of Leukocyte Biology, doi: 10.1002/JLB.3A0218-054R Epub ahead of print.

Selected Publications 2018

  1. Hudson LG, Gillette JM, Kang H, Rivera MR, Wandinger-Ness A. (2018) Ovarian Tumor Microenvironment Signaling: Convergence on the Rac1 GTPase. Cancers (Basel). 2018 Sep 27;10(10). pii: E358. doi: 10.3390/cancers10100358. Review. PMID: 30261690
  2. Palsuledesai CC, Surviladze Z, Waller A, Miscioscia TF, Guo Y, Wu Y, Strouse J, Romero E, Salas VM, Curpan R, Young S, Carter M, Foutz T, Galochkina Z, Ames H, Haynes MK, Edwards BS, Nicolotti O, Luo L, Ursu O, Bologa CG, Oprea TI, Wandinger-Ness A, Sklar LA. (2018) Activation of Rho Family GTPases by Small Molecules. ACS Chem Biol. 2018 Jun 15;13(6):1514-1524. doi: 10.1021/acschembio.8b00038. Epub 2018 May 24. PMID: 29746086
  3. Peretti AS, Dominguez D, Grimes MM, Hathaway HJ, Prossnitz ER, Rivera MR, Wandinger-Ness A, Kusewitt DF, Hudson LG. (2018) The R-Enantiomer of Ketorolac Delays Mammary Tumor Development in Mouse Mammary Tumor Virus-Polyoma Middle T Antigen (MMTV-PyMT) Mice. Am J Pathol. 2018 Feb;188(2):515-524. doi: 10.1016/j.ajpath.2017.10.018. Epub 2017 Nov 21. PMID: 29169987
  4. Saito-Reis, C, Marjon, KD, Pascetti, EM, Floren, M, Gillette JM. “The Tetraspanin CD82 regulates Bone Marrow Homing and Engraftment of Hematopoietic Stem and Progenitor Cells.” Mol Biol Cell. 2018. Nov 26;29(24):2946-2958. Special Issue on Stem Cell Biology.
  5. Chelsea A. Saito-Reis, Kristopher D. Marjon, Erica M. Pascetti, Muskan Floren, Jennifer M. Gillette, and David Traver (2018) The tetraspanin CD82 regulates bone marrow homing and engraftment of hematopoietic stem and progenitor cells. Molecular Biology of the Cell 2018 29:24, 2946-2958
  6. Civciristov S, Ellisdon AM, Suderman R, Pon CK, Evans BA, Kleifeld O, Charlton SJ, Hlavacek WS, Canals M, Halls ML (2018) Pre-assembled GPCR signaling complexes mediate unique cellular responses to ultralow ligand concentrations. Sci Signal 11: eaan1188.
  7. Chylek LA, Holowka DA, Baird BA, and Hlavacek WS (2018) Quantitative modeling of mast cell signaling. In Systems Immunology: An Introduction to Modeling Methods for Scientists (Das J, Jayaprakash C, Editors), CRC Press, Boca Raton, FL, Ch 13, pp 213-226. ISBN-13: 978-1-4987-1740-3
  8. Munsky B, Hlavacek WS, Tsimring LS, Editors (2018) Quantitative Biology: Theory, Computational Methods, and Models. The MIT Press, Cambridge, MA. ISBN: 978-0-262-03808-9
  9. Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS (2018) Generalizing Gillespie's direct method to enable network-free simulations. Bull Math Biol doi: 10.1007/s11538-018-0418-2
  10. Prashant Dogra, Natalie L. Adolphi, Zhihui Wang, Yu-Shen Lin, Kimberly S. Butler, Paul N. Durfee, Jonas G. Croissant, Achraf Noureddine, Eric N. Coker, Elaine L. Bearer, Vittorio Cristini & C. Jeffrey Brinker. (2018) Establishing the effects of mesoporous silica nanoparticle properties on in vivo disposition using imaging-based pharmacokinetics. Nature Communications. DOI: 10.1038/s41467-018-06730-z
  11. Tasnim, H., Fricke, G.M., Byrum, J.R., Sotiris, J.O., Cannon, J.L.*, Moses, M.E. 2018. Quantitative measurement of naïve T cell association with dendritic cells, FRCs, and blood vessels in lymph nodes. Frontiers in Immunology. Jul 26;9:1571. *corresponding author. PMID: 30093900 PMCID: PMC6070610 DOI: 10.3389/fimmu.2018.01571
  12. Heydarian, H., F. Schueder, M.T. Strauss, B. van Werkhoven, M. Fazel, K.A. Lidke, R. Jungmann, S. Stallinga, and B. Rieger. (2018) Template-free 2D particle fusion in localization microscopy. Nature Methods.
  13. Pallikkuth, S., C. Martin, F. Farzam, J.S. Edwards, M.R. Lakin, D.S. Lidke, and K.A. Lidke. (2018) Sequential super-resolution imaging using DNA strand displacement. PLOS ONE.
  14. Graus, M.S., M.J. Wester, D.W. Lowman, D.L. Williams, M.D. Kruppa, C.M. Martinez, J.M. Young, H.C. Pappas, K.A. Lidke, and A.K. Neumann. (2018) Mannan Molecular Substructures Control Nanoscale Glucan Exposure in Candida. Cell Reports.
  15. Brandsma, A.M., S.L. Schwartz, M.J. Wester, C.C. Valley, G.L.A. Blezer, G. Vidarsson, K.A. Lidke, T. ten Broeke, D.S. Lidke, and J.H.W. Leusen. (2018) Mechanisms of inside-out signaling of the high-affinity IgG receptor FcγRI. Science Signaling.
  16. Kumar, S., A. Jain, F. Farzam, J.Y. Jia, Y.X. Gu, S.W. Choi, M.H. Mudd, A. Claude-Taupin, M.J. Wester, K.A. Lidke, T.E. Rusten, and V. Deretic. (2018) Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins. Journal of Cell Biology.
  17. López CA, Unkefer CJ, Swanson BI, Swanson JMJ, Gnanakaran S. (2018) Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans. (2018) PLoS Comput Biol 14(2): e1005972.

Selected Publications 2017

  1. Termini, CM and Gillette, JM. (2017) Tetraspanins as Regulators of Cellular Signaling. Front Cell Dev Biol. April 6;5:34. PMID:28428953 PMCID:5382171
  2. C Cleyrat, R Girard, EH Choi, E Jeziorski, T Lavabre-Bertrand, S Hermouet, S Carillo, BS Wilson. (2017) Functional rescue of a novel Mpl K39N/W272 double mutant associated with congenital amegakaryocytic thrombocytopenia (CAMT) using genome editing. Blood Advances, 1(21): 1815-1826. PMID: 29296828  PMCID: PMC5728092
  3. Mrass, P., Oruganti, S.R., Fricke, G.M., Tafoya, J., Byrum, J. Yang, L., Hamilton, S.L., Miller, M.J., Moses, M.E., Cannon, J.L. 2017. ROCK regulates the intermittent mode of interstitial T cell migration in inflamed lungs. Nature Communications. 8(1): 1010. doi:10.1038/s41467-017-01032-2. PMID:29044117 PMCID: PMC5647329
  4. Cannon, J.L., Oruganti, S.R., Vidrine, D.W. 2017. Molecular regulation of T-ALL cell infiltration into the CNS. Oncotarget, 8(49):84626-84627. PMID:29156664 PMCID: PMC5689554
  5. Oruganti, S.R., Torres, D. J., Krebsbach, S., Winters, J., Asperti-Boursin, F., Matlawska-Wasowska, K., Winter, S.S., Halsey, C., Cannon, J.L. 2017. CARMA1 is a novel regulator of T-ALL cell migration to the CNS. Leukemia. doi: 10.1038/leu.2016.272.  PMID:27698445 Free PMC article. Recommended by F1000Prime.
  6. Harmon B, Chylek LA, Liu Y, Mitra ED, Mahajan A, Saada EA, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WS & Singh AK (2017) Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Scientific Reports 7, article 15586. PMID:29138425 PMCID: PMC5686181
  7. Peretti, A.S., M. Rivera, H.L. Hathaway, E.R. Prossnitz, A. Wandinger-Ness, D.F. Kusewitt, and L.G. Hudson. (2017) The R-enantiomer of ketorolac delays mammary tumor development in Mouse Mammary Tumor Virus-polyoma middle T antigen (MMTV-PyMT) mice. Am. J. Pathol. S0002-9440(7)30445-5. PMID:29169987 PMC PENDING
  8. Munsky B, Hlavacek WS, Tsimring LS, Editors (in press) Quantitative Biology: Theory, Computational Methods and Examples of Models. The MIT Press, Cambridge, MA. PMCID: Exempt
  9. Schwartz SL, Cleyrat C, Olah MJ, Relich PK, Phillips GK, Hlavacek WS, Lidke KA, Wilson BS, Lidke DS (2017) Differential mast cell outcomes are sensitive to FcεRI-Syk binding kinetics. Mol Biol Cell 10.1091/mbc.E17-06-0350 https://doi.org/10.1101/147595 [Featured in Highlights from MBoC, ASCB Newsletter] PMCID:  *PUBLIC ACCESS
  10. Marek Kochańczyk, William S. Hlavacek, Tomasz Lipniacki; (2017) SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. Bioinformatics 2017 btx456. doi: 10.1093/bioinformatics/btx456. PMID:29036531/NO PMC YET
  11. Medina, C. S., Manifold-Wheeler, B., Gonzales, A., & Bearer, E. L. (2017). Automated computational processing of 3-D MR images of mouse brain for phenotyping of living animals. Current Protocols in Molecular Biology, 119, 29A.5.1–29A.5.38. doi: 10.1002/cpmb.40 PMID:28678440/NO PMC YET
  12. Kinjyo I, Matlawska-Wasowska K, Chen X,et al. (2017) Characterization of the anti-CD22 targeted therapy, moxetumomab pasudotox, for B-cell precursor acute lymphoblastic leukemia. Pediatr Blood Cancer. 2017;00:e26604.
  13. Graus MS, Neumann AK, Timlin JA. (2017) Hyperspectral fluorescence microscopy detects autofluorescent factors that can be exploited as a diagnostic method for Candida species differentiation. J. Biomed. Opt. 0001;22(1):016002. PMCID:28056142 PMC5216876
  14. Chylek LA, Holowka DA, Baird BA, Hlavacek WS (in press) Quantitative modeling of mast cell signaling. In Systems Immunology: An Introduction to Modeling Methods for Scientists (Das J, Jayaprakas C, Editors), Taylor & Francis. PMID:25480645/NO PMC YET
  15. Medina CS, Biris O, Falzone TL, Zhang X, Zimmerman AJ, Bearer EL. Hippocampal to basal forebrain transport of Mn2+ is impaired by deletion of KLC1, a subunit of the conventional kinesin microtubule-based motor. Neuroimage. 2017 Jan 15;145(Pt A):44-57. doi: 10.1016/j.neuroimage.2016.09.035.  PMID:27751944 PMCID:5457905
  16. Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błonska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T (2017) Relaxation oscillations and hierarchy of feedbacks in MAPK signaling. Sci Rep 7: 38244. PMID:28045041 PMC5206726
  17. Mahajan A, Youssef LA, Cleyrat C, Grattan R, Lucero SR, Mattison CP, Erasmus MF, Jacobson B, Tapia L, Hlavacek WS, Schuyler M, Wilson BS (2017) Allergen valency, dose and FcεRI occupany set thresholds for secretory responses to Pen a 1 and motivate design of hypoallergens. J Immunol 198: 1034–1046. PMCID:2803904 PMC5263102
  18. Maston, L.D., Jones, D.T., Giermakowska, W., Howard, T. Cannon, J.L., Wang, W., Wei, Y., Xuan, W., Resta, T.C., Gonzalez-Bosc, L.V. Central Role of T Helper 17 Cells in Chronic Hypoxia-Induced Pulmonary Hypertension. 2017. American Journal of Physiology-Lung Cellular and Molecular Physiology. Feb 17:ajplung.00531.2016. PMID:28213473 PMC5451600
  19. Rojas-Hernandez CM, Nemunaitis J, Marjon KD, Bustamante D, Zhang QY, Gillette JM.Chronic lymphocytic leukemia with clinical debut as neurological involvement: a rare phenomenon and the need for better predictive markers. BMC Hematol. 2017 Feb 2;17:3. doi: 10.1186/s12878-017-0073-0.  PMCID:28174663 PMC5290634

Selected Publications 2016

  1. M F Erasmus, K Matlawska, A Mahajan, SS Winter, L Xu, M Horowitz, DS Lidke and BS Wilson. (2016) Dynamic pre-BCR homodimers fine tune autonomous signals for B lineage ALL survival. Science Signaling, Nov 29;9(456):ra116. PMCID: pending
  2. Termini CM, Lidke KA, Gillette JM. Tetraspanin CD82 Regulates the Spatiotemporal Dynamics of PKCα in Acute Myeloid Leukemia. Sci Rep. 2016 Jul 15;6:29859. PMCID: PMC4945921
  3. Kerketta, R., Halász, Á. M., Steinkamp, M. P., Wilson, B. S., & Edwards, J. S. (2016). Effect of Spatial Inhomogeneities on the Membrane Surface on Receptor Dimerization and Signal Initiation. Frontiers in Cell and Developmental Biology, 4, 81. http://do.org/10.3389/fcell.2016.00081
  4. Meddens, M.B.M., S. Liu, P.S. Finnegan, T.L. Edwards, C.D. James, and K.A. Lidke. (2016) Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution. Biomedical Optics Express, 2016. 7(6): p. 2219-2236.
  5. J Ruan, V Jin, Y Huang, H Xu, JS Edwards, Y Chen, Z Zhao (2016) "Education, collaboration, and innovation: intelligent biology and medicine in the era of big data" BMC Genomics 16 (Suppl 7), S1. PMCID: PMC4474420
  6. Drew Levin, Stephanie Forrest, Soumya Banerjee, Candice Clay, Judy Cannon, Melanie Moses, Frederick Koster. 2016. A spatial model of the efficiency of T cell search in the influenza-infected lung. Journal of Theoretical Biology. Feb 23;398:52-63. do: 10.1016/j.jtbi.2016.02.022. PMID: 26920246 [PubMed - in process]
  7. Fricke, G.M., Letendre, K.L, Moses, M.E., Cannon, J.L. 2016. Persistence and adaptation in immunity: T cells balance the extent and thoroughness of search. PLoS Computational Biology. Mar 18;12(3):e1004818. PMID: 26990103. PMCID: PMC4798282
  8. Hansen SG, Wu HL, Burwitz BJ, César A. López, Gnanakaran S, Sacha JB, Picker LJ. (2016) "Broadly targeted CD8+ T cell responses restricted by major histocompatibility complex E." Science. 2016 Jan 21. pii: aac9475. [Epub ahead of print]
  9. Kanigel Winner K, Steinkamp MP, Lee RJ, Swat M, Muller CY, Moses ME, Jiang Y, Wilson BS. (2016) "Spatial modeling of drug delivery routes for treatment of disseminated ovarian cancer," Cancer Research 76(6):1320-34. PMCID: PMC4794352
  10. Marjon KD, Termini CM, Karlen KL, Saito-Reis C, Soria CE, Lidke KA, Gillette JM, Tetraspanin CD82 regulates bone marrow homing of acute myeloid leukemia by modulating the molecular organization of N-cadherin. Oncogene. 2016 Aug 4;35(31):4132-40. PMCID: PMC4877306
  11. Fricke, G.M., Hecker, J.P. Cannon, J.L., Moses, M.E., 2016. Immunological Search Strategies Applied to a Robot Swarm. Robotica. Aug. volume 34, issue 08, pp. 1791-1810s.

Selected Publications 2015

  1. Carroll-Portillo A, Cannon JL, te Riet J, Holmes A, Kawakami Y, Kawakami T, Cambi A, Lidke DS. (2015) Mast cells and dendritic cells form synapses that facilitate antigen transfer for T cell activation. J Cell Biol. 2015 Aug 31;210(5):851-64. do: 10.1083/jcb.201412074. Epub 2015 Aug 24. PMID: 26304724. PMCID: PMC4555818
  2. Letendre K, Donnadieu E, Moses ME, Cannon JL. (2015) Bringing statistics up to speed with data in analysis of lymphocyte motility. PLoS One. 2015 May 14;10(5):e0126333. do: 10.1371/journal.pone.0126333. eCollection 2015. PMID: 25973755
  3. G Wan, C Pehlke, R Pepermans, JL Cannon, D Lidke and A Rajput. (2015) The H1047R point mutation in p110 alpha changes the morphology of human colon HCT116 cancer cells. Cell Death Discovery (2015) 1, 15044; do:10.1038/cddiscovery.2015.44; published online 19 October 2015
  4. Nieuwenhuizen RPJ, Bates M, Szymborska A, Lidke KA, Rieger B, Stallinga S (2015) Correction: Quantitative Localization Microscopy: Effects of Photophysics and Labeling Stoichiometry. PLoS ONE 10(9): e0139071. do:10.1371/journal.pone.0139071
  5. M. Pryor, M.P. Steinkamp, A.M. Halasz , Y. Chen , S. Yang, M.S. Smith, G. Zahoransky-Kohalmi, M. Swift, X. Xu, D. Hanien, N. Volkmann, D.S. Lidke, J.S. Edwards and B.S. Wilson. (2016) "Orchestration of ErbB3 signaling through hetero and homo-interactions." Molecular Biology of the Cell. 26: 4109-23. PMCID: PMC4710241
  6. Marisa Ponpuak, Michael A Mandell, Tomonori Kimura, Santosh Chauhan, Cédric Cleyrat, Vojo Deretic. (2015) Secretory autophagy. Current Opinion in Cell Biology. 2015. PMCID: PMC4529791
  7. Valley CC, Liu S, Lidke DS, Lidke KA. (2015) Sequential Superresolution Imaging of Multiple Targets Using a Single Fluorophore. Plos One. 2015
  8. Broeken J, Johnson H, Lidke DS, Liu S, Nieuwenhuizen RPJ, Stallinga S, Lidke KA, Rieger B. (2015) Resolution improvement by 3D particle averaging in localization microscopy. Methods and Applications in Fluorescence. 2015
  9. Schwartz SL, Yan Q, Telmer CA, Lidke KA, Bruchez MP, Lidke DS. (2015) Fluorogen-Activating Proteins Provide Tunable Labeling Densities for Tracking FcεRI Independent of IgE. ACS Chemical Biology. 2015
  10. Szymańska P, Martin KR, MacKeigan JP, Hlavacek WS#, Lipniacki T# (2015) Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLOS ONE 10: e0116550. #Co-corresponding authors. PMCID: PMC4356596
  11. Stites EC, Aziz M, Creamer MS, Von Hoff DD, Posner RG, Hlavacek WS (2015) Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys J 108: 1819–1829. PMCID: PMC4390817
  12. Chylek LA, Harris LA, Faeder JR, Hlavacek WS (2015) Modeling for (physical) biologists: an introduction to the rule-based approach. Phys Biol 12: 045007. PMCID: In Process
  13. Oana Coban, Laura C. Zanetti-Dominguez, Daniel R. Matthews, Daniel J. Rolfe, Gregory Weitsman, Paul R. Barber, Jody Barbeau, Viviane Devauges, Florian Kampmeier, Martyn Winn, Borivoj Vojnovic, Peter J. Parker, Keith A. Lidke, Diane S. Lidke, Simon M. Ameer-Beg, Marisa L. Martin-Fernandez, and Tony Ng. (2015) Effect of Phosphorylation on EGFR Dimer Stability Probed by Single-Molecule Dynamics and FRET/FLIM. Biophysical Journal Volume 108, Issue 5, 10 March 2015, Pages 1013–1026. http://www.sciencedirect.com/science/article/pii/S0006349515000661
  14. Vu TQ, Lam WY, Hatch EW, Lidke DS. (2015) Quantum dots for quantitative imaging: from single molecules to tissue. Cell Tissue Res. 2015 Jan 27. [Epub ahead of print]

Selected Publications 2014

  1. Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y. (2014) The Seventh q-bio Conference: meeting report and preface. Phys Biol. 2014 Aug;11(4):040301
  2. Lund TC, Patrinostro X, Kramer AC, Stadem P, Higgins LA, Markowski TW, Wroblewski MS, Lidke DS, Tolar J, Blazar BR. (2014) sdf1 Expression reveals a source of perivascular-derived mesenchymal stem cells in zebrafish. Stem Cells. 2014 Oct;32(10):2767-79
  3. Itano MS, Graus MS, Pehlke C, Wester MJ, Liu P, Lidke KA, et al. (2014) Super-resolution imaging of C-type lectin spatial rearrangement within the dendritic cell plasma membrane at fungal microbe contact sites. Frontiers in Physics. 2014;2. do: 10.3389/fphy.2014.00046. PMID: 24874253. PMCID: PMC4038466.
  4. C Cleyrat, A Dareshouri, M Vilaine, MP Steinkamp, D Boasa, M Ellisman, S Hermouet and BS Wilson. (2014) Mpl traffic to the cell surface through unconventional and conventional routes. Traffic. 2014 15(9):961-82. PMID: 24931576.
  5. Graus MS, Pehlke C, Wester MJ, Davidson LB, Steinberg SL, Neumann AK. (2014) A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction. PLoS Comput Biol 10(5): e1003639. do:10.1371/journal.pcbi.1003639. PMID: 24874253. PMCID: PMC4038466.
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  6. A Keller, Y Ghosh, MS DeVore, ME Phipps, MH Stewart, DS Lidke, BS Wilson, JA Hollingsworth and JH Werner. (2014) 3-dimensional tracking of non-blinking 'giant' quantum dots in live cells. Advanced Functional Materials. PMCID: PMC4412170.
  7. Liu P, Wang X, Itano MS, Neumann AK, de Silva AM, Jacobson K, Thompson NL. (2014) Low Copy Numbers of DC-SIGN in Cell Membrane Microdomains: Implications for Structure and Function. Traffic. 2014 Feb; 15(2): 179-96. PMID: 2431390.
  8. Marjon K.D. and Gillette. J.M. (2014) Measurement of intercellular transfer to signaling endosomes, Methods Enzymol. 534: 207-21. 2014. PMID: 24359956.
  9. Termini C.M., Cotter M.L., Marjon K.D., Buranda T., Lidke K.A., Gillette J.M. (2014) "The membrane scaffold CD82 regulates cell adhesion by altering α4 integrin stability and molecular density." Mol Biol Cell. 2014 May 15;25(10):1560-73. PMID: 24623721. PMCID: PMC4019488.
  10. Valley CC, Lidke KA, Lidke DS. "The Spatiotemporal Organization of ErbB Receptors: Insights from Microscopy." In Signaling by Receptor Tyrosine Kinases. Cold Spring Harbor Perspectives in Biology. J Schlessinger and MA Lemmon, eds. 2014. PMID: 24370847.
  11. Yan Q, Schwartz SL, Maji S, Huang F, Szent-Gyorgyi C, Lidke DS, Lidke KA and Bruchez MP. (2014) Localization Microscopy using Noncovalent Fluorogen Activation by Genetically Encoded Fluorogen-Activating Proteins. Chemphyschem. PMID: 24194371. PMCID: PMC3967550.
  12. A Mahajan, D Burua, P Cutler, DS Lidke, ARM Bradbury, C-S Tung, FA Espinoza, C Pehlke, R Grattan, Y Kawakami, WS Hlavacek and BS Wilson (2014) Optimal aggregation of FceRI with a structurally-defined trivalent ligand overrides negative regulation driven by phosphatases. ACS Chemical Biology, May 2 Epub ahead of print. PMID: 24784318.
  13. Chylek LA, Holowka DA, Baird BA, Hlavacek WS. (2014) An interaction network for the FceRI signaling network. Frontiers Immunol. 5:172
  14. Westrate LM, Drocco JA, Martin KR, Hlavacek WS, Mackeigen JP. (2014) Mitochondrial morphological features are associated with fission and fusion events. PLoS One 9(4):e95265. PMID: 24733410. PMCID: 3986258.
  15. Kozer N, Barua D, Henderson C, Nice EC, Burgess AW, Hlavacek WS, Clayton AH. (2014) Recruitment of the adaptor protein Grb2 to EGFR tetramers. Biochemistry. 53(16):2594-604. . PMID: 24697349. PMCID: PMC4010257.
  16. Wu M, Frieboes HB, Chaplain MA, McDougall SR, Cristini V, Lowengrub J. (2014) The effect of interstitial pressure on therapeutic agent transport: coupling with the tumor blood and lymphatic vascular systems. J Theor Biol. Apr 18. PMID: 24751927.
  17. Tang L, van de Ven AL, Guo D, Andasari V, Cristini V, Li KC, Zhou X. (2014) Computational modeling of 3D tumor growth and angiogenesis for chemotherapy evaluation. PLoS One. 9(1):e83962. PMID: 24404145. PMCID: PMC3880288.
  18. Wandinger-Ness A and Marino Zerial. (2014) Rab proteins and the compartmentalization of the endosomal system. Cold Spring Harbor Monograph Volume: Endocytosis Ed. A. Sorkin, M. Zerial and S. Schmid. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. ISBN 978-087969-941-3. In Press.
  19. L. A. Chylek, L. A. Harris, C.-S. Tung, J. R. Faeder, C. F. Lopez and W. S. Hlavacek. (2014) Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.Wiley Interdiscip. Rev. Syst. Biol. Med. 6, 13-36. PMID: 24123887. PMCID: PMC3947470.
  20. O. Resnekov, B. Munsky and W. S. Hlavacek (2014) Perspective on the q-bio Summer School and Conference: 2007–2014 and beyond. Quant. Biol. 2, 54-58
  21. L. A. Chylek,* V. Akimov,* J. Dengjel,* K. T. G. Rigbolt, B. Hu, W. S. Hlavacek and B. Blagoev (2014) Phosphorylation site dynamics of early T-cell receptor signaling. PLOS ONE 9: e104240. *These authors contributed equally.
  22. L. A. Chylek, B. S. Wilson and W. S. Hlavacek (2014) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Adv. Exp. Med. Biol. 844, 245-262.

Selected Publications 2013

  1. Pascal J, Ashley CE, Wang Z, Brocato TA, Butner JD, Carnes EC, Koay EJ, Brinker, CJ, Cristini V. (2013) Mechanistic modeling identifies drug-uptake history as predictor of tumor drug resistance and nano-carrier-mediated response. ACS Nano. 7(12):11174-82. PMID: 24187963. PMCID: PMC3891887.
  2. Yan Q, Schwartz SL, Maji S, Huang F, Szent-Gyorgyi C, Lidke DS, Lidke KA, Bruchez MP. (2013) Localization Microscopy using Noncovalent Fluorogen Activation by Genetically Encoded Fluorogen-Activating Proteins Chemphyschem. 2013 Nov 5. do: 10.1002/cphc.201300757. [Epub ahead of print]. PMID: 24194371. PMCID: PMC3967550.
  3. MP. Steinkamp, ST. Low-Nam, S Yang, KA Lidke, DS Lidke, BS Wilson (2014) ErbB3 is an active tyrosine kinase capable of homo- and hetero-interactions. Mol. Cell. Biol. 34(6):965-977. PMID: 24379439. PMCID: PMC3958038.
  4. Liu, S., E.B. Kromann, W.D. Krueger, J. Bewersdorf, and K.A. Lidke, Three dimensional single molecule localization using a phase retrieved pupil function. Optics Express, 2013. 21(24): p. 29462-29487. PMID: 24514501. PMCID: PMC3867195.
  5. Liu, S. and K.A. Lidke, A Multiemitter Localization Comparison of 3D Superresolution Imaging Modalities. ChemPhysChem, 2013: p. n/a-n/a. PMID: 24281982.
  6. James E. Casanova, Victor W. Hsu, Catherine L. Jackson, Richard A. Kahn, Craig R. Roy, Jennifer L. Stow, Angela Wandinger-Ness, Elizabeth Sztul. (2013) Meeting report – Arf and Rab family G proteins. Journal of Cell Science 126, 5313–5316. PMID: 24293329.
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  7. Lund TC, Kobs AJ, Kramer A, Nyquist M, Kuroki MT, Osborn J, Lidke DS, Low-Nam ST, Blazar BR, Tolar J. (2013) Bone Marrow Stromal and Vascular Smooth Muscle Cells Have Chemosensory Capacity via Bitter Taste Receptor Expression. PLoS ONE 8(3): e58945. PMID: 23520545. PMCID: PMC3592821.
  8. Jesse Williams, Douglas Yau, Nan Sethakorn, Jacob Kach, Eleanor Reed, Tamson Moore, Judy Cannon, Xiaohua Jin, Heming Xing, Anthony Muslin, Anne Sperling, and Nickolai Dulin. (2013) RGS3 controls T lymphocyte migration in a model of Th2-mediated airway inflammation. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2013 Nov;305(10):L693-701. do: 10.1152/ajplung.00214.2013. Epub 2013 Sep 27. PMID: 24077945. PMCID: PMC3840273.
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  9. Cannon J.L., Asperti-Boursin, F., Letendre, K., Brown, I.K., Korzekwa, K.E., Blaine, K. M. Oruganti, S.R., Sperling, A.I., Moses, M.E. (2013) PKCθ regulates T cell motility via Ezrin-Radixin-Moesin localization to the uropod. PLOS One. 2013 Nov 8;8(11):e78940. do: 10.1371/journal.pone.0078940. PMID: 24250818. PMCID: PMC3826749.
  10. Cleyrat C, Darehshouri A, Anderson KL, Page C, Lidke DS, Volkmann N, Hanein D, Wilson BS. (2013) The architectural relationship of components controlling mast cell endocytosis. J Cell Sci. 2013 Nov 1;126(Pt 21):4913-25. PMC3820241
  11. 27. McCabe MM, ST Low-Nam, A Halasz, DS Lidke, BS Wilson and JS Edwards. (2013) Dynamic transition states of ErbB1 phosphorylation predicted by spatial-stochastic modeling. Biophys J. 2013 Sep 17; 105(6):1533-43. PMID: 24048005. PMCID: PMC3785885.
  12. Barua D, Hlavacek WS. (2013) Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PLoS Comput Biol. 2013 Sep;9(9):e1003217. do: 10.1371/journal.pcbi.1003217. PMID: 24086117. PMCID: PMC3784502..
  13. Chylek LA, Wilson BS, Hlavacek WS. (accepted, 2013) Modeling biomolecular site dynamics in immunoreceptor signaling systems. In A Systems Biology Approach to Blood (Corey SJ, Kimmel M, Editors), Springer. A preprint is freely available online: http://openwetware.org/images/f/fe/LA-UR-12-23058.pdf pdf icon
  14. L. A. Chylek, E. C. Stites, R. G. Posner and W. S. Hlavacek (2013) Innovations of the rule-based modeling approach. In Systems Biology: Integrative Biology and Simulation Tools, Vol. 1, Ch. 9, pp. 273-300 (A. Prokop and B. Csukás, Editors), Springer, Dordrecht. ISBN: 978-94-007-6803-1 (Online) http://openwetware.org/images/3/37/LA-UR-12-10375.pdf pdf icon
  15. R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grunwald, S. Stallinga, and B. Rieger. (2013) Measuring image resolution in optical nanoscopy. Nature Methods. 2013 Jun;10(6):557-62. do: 10.1038/nmeth.2448. Epub 2013 Apr 28. PMID: 23624665. NIHMSID: 615954 (PMC pending).
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  16. K. van den Dries, S. L. Schwartz, J. Byars, M. B. M. Meddens, M. Bolomini-Vittori, D. S. Lidke, C. G. Figdor, K. A. Lidke, A. Cambi. (2013) Dual color super-resolution microscopy reveals nanoscale organization of mechanosensory podosomes. Molecular Biology of the Cell. 2013 Jul;24(13):2112-23. do: 10.1091/mbc.E12-12-0856. Epub 2013 May 1. PMID: 23637461. PMCID: PMC3694795.
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  17. Kozer N*, Barua D*, Orchard S, Nice EC, Burgess AW, Hlavacek WS, Clayton AHA. (Apr 2013, online publication date) Exploring higher-order EGFR oligomerisation and phosphorylation – a combined experimental and theoretical approach. Mol Biosyst. 2013 Jul;9(7):1849-63. do: 10.1039/c3mb70073a. Epub 2013 Apr 30. *These authors contributed equally. PMID: 23629589. PMC3698845.
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  18. Patrick J. Cutler, Michael D. Malik, Sheng Liu, Jason M. Byars, Diane S. Lidke, Keith A. Lidke. (2013) Multi-color Quantum Dot Tracking using a High-Speed Hyperspectral Line-Scanning Microscope. PLoS One. 2013 May 22;8(5):e64320. do: 10.1371/journal.pone.0064320. Print 2013. PMID: 23717596 [PubMed - in process]. PMCID: PMC3661486.
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  19. Liu Y, D Barua, G Zwartz, P Liu, BS Wilson, JM Oliver, WS Hlavacek and A Singh. (2013) Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLoS One. 2013;8(3):e60159. do: 10.1371/journal.pone.0060159. PMID: 23544131. PMCID: PMC3609784.
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  20. Liu, Y. and A. K. Singh. (2013) Microfluidic platforms for single-cell protein analysis. Journal of Lab Automation. 2013 Dec;18(6):446-54. do: 10.1177/2211068213494389. Epub 2013 Jul 2. PMID: 23821679 [PubMed - in process]
  21. Martin KR, Barua D, Kauffman AL, Westrate LM, Posner RG, Hlavacek WS, Mackeigan JP. (2013) Computational model for autophagic vesicle dynamics in single cells. Autophagy. 2013 Jan 1;9(1):74-92. PMID: 23196898. PMCID: PMC3542220.
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  22. Matlawska-Wasowska K, K E Ward, S Stevens, Y Wang, R Herbst, SS Winter and BS Wilson. (2013) Macrophage and NK-mediated killing of precursor-B acute lymphoblastic leukemia cells targeted with a-fucosylated anti-CD19 humanized antibodies. Leukemia. 2013 Jun;27(6):1263-74. do: 10.1038/leu.2013.5. Epub 2013 Jan 11. PMID: 23307031. NIHMSID: 619930 (PMC pending).
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  23. Steinkamp MP, Winner KK, Davies S, Muller C, Zhang Y, Hoffman RM, Shirinifard A, Moses, M, Jiang Y and Wilson BS. (2013) Ovarian tumor attachment, invasion, and vascularization reflect unique microenvironments in the peritoneum: insights from xenograft and mathematical models. Front. Oncol. 3:97. do:10.3389/fonc.2013.00097. PMID: 23730620. PMC3656359
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  24. Stéphane Ory, Mara Ceridono, Fanny Momboisse, Sébastien Houy, Sylvette Chasserot-Golaz, Dimitri Heintz, Valérie Calco, Anne-Marie Haeberlé, Flor A. Espinoza, Peter J. Sims, Yannick Bailly, Marie-France Bader, and Stéphane Gasman. Phospholipid Scramblase-1-Induced Lipid Reorganization Regulates Compensatory Endocytosis in Neuroendocrine Cells. The Journal of Neuroscience, February 20, 2013 • 33(8):3545–3556 • 3545. PMID: 23426682. PMC3677529
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Selected Publications 2012

  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. PMCID: PMC3413461.
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  2. Maienschein-Cline M, Dinner AR, Hlavacek WS, Mu F. (2012) Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Res. 40:e175. PMID: 22923524. PMCID: PMC3526315.
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  3. Larochelle, A, Gillette, J.M.*, Desmond, R., Ichwan, B., Cantilena, A., Cerf, A., Barrett, A.J., Wayne, A.S. Lippincott-Schwartz, J., and C.E. Dunbar. (2012) Bone marrow homing and engraftment of hematopoietic stem and progenitor cells is mediated by CD82 polarity. Blood 119:1848-55. PMID: 22228628. PMCID: PMC3293639.
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  4. Pullen NA, BO Barstein, YT Flanga, Z Want, R Suzuki, TDL Tamang, MC Khurant, EA Harry, P Draber, KD Bunging, K Mizuno, BS Wilson and JJ Ryan. (2012) A novel mechanism for FcεRI-mediated Stat5 tyrosine phosphorylation and the selective influence of Stat5B over mast cell cytokine production. J. of Biological Chemistry, 287:2045-54 PMID: 22130676. PMCID: PMC3265884.
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  5. Stephen, T-L, BS Wilson and TM Laufer. (2012) Subcellular distribution of Lck during CD4 T cell maturation in the thymic medulla regulates the T cell activation threshold. Proc. Natl. Acad. Sci. USA, 109:7415-20. PMID: 22529380. PMCID: PMC3358885.
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  6. K. A. Lidke. (2012) "A new intercellular transfer phenomenon is uncovered by three-dimensional particle tracking.," Biophysical journal 103, 1820. PMID: 23199909. PMCID: PMC3491699.
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  7. Barua D, Goldstein B. (2012) A Mechanistic Model of Early FceRI Signaling: Lipid Rafts and the Question of Protection from Dephosphorylation. PLoS ONE 7(12): e51669. do:10.1371/journal.pone.0051669. PMID: 23284735. PMCID: PMC3524258.
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  8. Jones HDT, Haaland DM, Sinclair MB, Melgaard DK, Collins AM, and Timlin JA. (2012) Preprocessing Strategies to Improve MCR Analyses of Hyperspectral Images. Chemom. Intell. Lab. Syst. 117, 149-158 (2012).
  9. Yang J, Pearson, JE. Origins of concentration dependence of waiting times for single-molecule fluorescence binding. J. Chem. Phys. 136, 244506 (2012); do: 10.1063/1.4729947. PMID: 22755586. PMCID: PMC3396705.
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  10. Creamer, MS, EC Stites, JA Cahill, CW Tan, ME Berens, H Han, KJ Bussey, DD Von Hoff, WS Hlavacek and RG Posner. (2012) Specification, annotation, visualization and simulation of a large rule-based model for ErbB receptor signaling. BMC Systems Biology. BMC Syst Biol. 2012 Aug 22;6:107. PMID: 22913808. PMCID: PMC3485121.
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  11. Seamster, PE, M Loewenberg, J Pascal, A Chauviere, A Gonzales, V Cristini, and EL Bearer. (2012) Quantitative measurements and modeling of cargo-motor interactions during fast transport in the living axon. Physical Biology 9: 055005. PMID: 23011729. PMC3625656.
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  12. Espinoza, FA, MJ Wester, JM Oliver, BS Wilson, NL Andrews, DS Lidke and SL Steinberg. (2012) Insights Into Cell Membrane Microdomain Organization from Live Cell Single Particle Tracking of the IgE High Affinity Receptor FcεRI of Mast Cells. Bull. Math. Biol. 74; 1857-1911. Published online: 26 June 2012. PMID: 22733211. PMCID: PMC3677563.
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  13. Barua D, WS Hlavacek and T Lipniacki. (2012) A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J. Immunol. 189, 646-658. Published online: 18 June 2012. PMID: 22711887. PMCID: PMC3392547.
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  14. Archuleta (Costa), MN, JE McDermott, JS Edwards, and H Resat. (2012) An adaptive coarse graining method for signal transduction in three dimensions. Fundam. Inform. 118(4): 371-384 (2012). PMID: 24357890. PMC3865981
  15. Espinoza, FA, JM Oliver, BS Wilson, SL Steinberg. (2012) Using Hierarchical Clustering and Dendrograms to Quantify the Clustering of Membrane Proteins. Bulletin of Mathematical Biology. 74: 190-211, 2012. PMID: 21751075. PMCID: PMC3429354.
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  16. Lidke, KA (2012). Super resolution for common probes and common microscopes. Nature Methods, 9(2), 139-141. PMID: 22290184. PMCID: Pending.
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  17. Chigaev, A. and LA Sklar. (2012) Overview: assays for studying integrin-dependent cell adhesion. Methods Mol.Biol. 757:3-14. PMID: 21909902. PMC3805125.
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  18. Radhakrishnan, K, A Halász, MM McCabe, JS Edwards and BS Wilson (2012) Mathematical simulation of membrane protein clustering for efficient signal transduction. PMID: 22669501. PMC3822010. Annals of Biomedical Engineering special issue.
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  19. Lidke, DS and KA Lidke. (2012) "Advances in High-Resolution Imaging: Techniques for 3D Imaging of Cellular Structures." J. Cell Sci. 125, 2571-2580. PMID: 22685332. PMC3706075.
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  20. 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. EXEMPT (Book Chapter).
  21. Carroll-Portillo A, Z Surviladze, A Cambi, DS Lidke and BS Wilson. (2012) Mast cell synapses and exosomes: membrane contacts for information exchange. Frontiers in Immunology 3:46; 1-9, 2012. PMID: 22566928. PMCID: PMC3342342.
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  22. Cambi, A and DS Lidke. (2012) Nanoscale Membrane Organization: Where Biochemistry Meets Advanced Microscopy. ACS CHEMICAL BIOLOGY 7: 139-149. PMID: 22004174. PMCID: PMC3262946.
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  23. Wu, M. and AK Singh. (2012) Single cell protein analysis, Current Opinion in Biotechnology, 2012, 23(1):83-8. PMID: 22189001. PMCID: PMC3283030.
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  24. Hatzikirou H, A Chauviere, AL Bauer , A Leier, MT Lewis, P Macklin, TT Marquez-Lago, EL Bearer and V Cristini. (2012). Integrative physical oncology. Wiley Interdiscip Rev Syst Biol Med. 4(1):1-14. PMID: 21853537. PMCID: PMC3622087.
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Selected Publications 2011

  1. Sethi A, Goldstein B, Gnanakaran S (2011) Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2- Sos1 Complex. PLoS Comput Biol 7(10): e1002192. do:10.1371/journal.pcbi.1002192. PMID: 2202247. PMCID: PMC3192808.
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  2. de Keijzer, S. M. Meddens, D. Kilic, B. Joosten, I. Reinieren-Beeren, D.S. Lidke, S. Grinstein and A. Cambi. (2011) "Interleukin 4 alters early phagosome phenotype by modulating class I PI3K dependent lipid remodeling and protein recruitment." PLoS ONE. 6(7): e22328. PMID: 21799824. PMCID: PMC3143135.
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  3. Chigaev A, Smagley Y and Sklar LA. (2011) Nitric oxide/cGMP pathway signaling actively down-regulates alpha4beta1-integrin affinity: an unexpected mechanism for inducing cell de-adhesion. BMC Immunol 12: 28. PMID: 21586157. PMCID: PMC3125286.
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  4. Chigaev A, Y Wu, DB Williams, Y Smagley and LA Sklar. (2011) Discovery of very late antigen-4 (VLA-4, α4β1 integrin) allosteric antagonists. J Biol Chem 286: 5455-5463. PMID: 21131351. PMCID: PMC3037658.
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  5. Low-Nam, ST, KA Lidke, PJ Cutler, RC Roovers, P van Bergen en Henegouwen, BS Wilson and DS Lidke. (2011) ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand. Nature Structural and Molecular Biology, 18:1244-9 PMID: 22020299. PMCID: PMC3210321.
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  6. 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. PMCID: PMC3069020.
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  7. Lidke, DS., ST Low-Nam, PJ Cutler and KA Lidke. (2011) Determining FcεRI diffusional dynamics via single quantum dot tracking. Methods In Molecular Biology, Clifton NJ, 748, 121-132. PMID: 21701970. EXEMPT (Book Chapter).
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  8. 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." do: 10.1182/blood-2011-02-336479 Blood September 1, 2011 vol. 118 no. 9 2633-2634. PMID: 21885612. NIHMSID: 619874 (PMC pending).
    Blood pdf pdf icon
  9. 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 PMID: 21073243. PMCID: PMC3070173.
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  10. Yang, J. and W. S. Hlavacek. (2011) Yang J and WS Hlavacek (2011) The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems. Phys. Biol. 8:055009. PMCID: PMC3168694. PMID: 21832806.
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  11. 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. PMID: 21167222. PMCID: PMC3822008.
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  12. Lemons NW, Hu B, Hlavacek WS. (2011) Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics 12:45. PMCID: PMC152790. PMID: 21288338.
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  13. 13. Espinoza, FA, J. M. Oliver, B. S. Wilson, S. L. Steinberg. Using Hierarchical Clustering and Dendrograms to Quantify the Clustering of Membrane Proteins. Bulletin of Mathematical Biology. Bull Math Biol. 2012 Jan;74(1):190-211. PMID: 21751075. PMCID: PMC3429354.
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  14. Chylek LA, EC Stites, RG Posner and WS Hlavacek (invited and in review) Innovations of the rule-based modeling approach. In Systems Biology: Integrative Biology and Simulation Tools, Volume 1 (Prokop A, Csukas B, Editors) Springer.
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  15. Banerjee S., D. Levin, M. E. Moses, F. Koster, S. Forrest. (2011) "The Value of Inflammatory Signals in Adaptive Immune Responses". Proceedings of the 10th International Conference on Artificial Immune Systems (ICARIS) (accepted).
  16. M. Tektonidis, H. Hatzikirou, A. Chauviere, M. Simon, K. Schaller and A. Deutsch. (2011) Identification of intrinsic in vitro cellular mechanisms for glioma invasion. Journal of Theoretical Biology 287, 131-147 . PMID: 21816160.
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  17. Spendier K and JL Thomas. (2011) Image Correlation Spectroscopy of Randomly Distributed Disks. J. Biol. Phys. 37:477-492. PMID: 2294248. PMCID: PMC3169693.
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  18. Frieboes, H., M Chaplain, A Thompson, EL Bearer, J Lowengrub and V Cristini. (2011) Physical Oncology: Bench to bedside quantitative and predictive approach. Cancer Res. 71(2):298-302. PMID: 21224346. PMCID: PMC3073485.
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  19. Deisboeck, T., Z. Wang, P. Macklin, and V. Cristini. (2011) "Multiscale Cancer Modeling." Annual Review of Biomedical Engineering 13(1).
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  20. 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. PMID: 20519213. PMCID: PMC3024820.
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  21. 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. PMID: 20519213. PMCID: PMC3024820.
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  22. K. Pham, A. Chauviere, H. Hatzikirou, X. Li, H.M. Byrne, V. Cristini and J. Lowengrub. (2011) Density-dependent quiescence in glioma invasion: instability in a simple reaction-diusion model for the migration/proliferation dichotomy.of Biological Journal dynamics (Published online June 2011; DOI:10.1080/17513758.2011.590610). PMID: 22873675. PMC3024820.
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  23. Huang, F, SL Schwartz, JM Byars and KA Lidke. (2011) Simultaneous multiple-emitter fitting for single molecule super-resolution imaging. Biomedical optics express, 2(5), 1377-93. do:10.1364/BOE.2.001377 PMID: 21559149. PMCID: PMC3087594.
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  24. Chylek LA, B Hu, ML Blinov, T Emonet, JR Faeder, B Goldstein, RN Gutenkunst, JM Haugh, T Lipniacki, RG Posner, Y Yang and WS Hlavacek. (2011) Guidelines for visualizing and annotating rule-based models. Mol. BioSyst. 7:2779-2795. PMC3168731 PMID: 21647530. PMCID: PMC3168731.
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  25. Xu MY, AD Aragon, MR Mascarena, N Torrez-Martinez and JS Edwards. (2011) Protocol: Dual Primer Emulsion PCR for Next-Generation DNA Sequencing. Biotechniques Protocol Edition. PMID: 20569215. PMCID: PMC4049327.
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  26. Zhou, YE, JP O'Rourke, JS Edwards and SA Ness. (2011) Single Molecule Analysis of c-myb Alternative Splicing Reveals Novel Classifiers for Precursor B-ALL. PLoS ONE. PMID: 21853052. PMCID: PMC3154906.
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  27. Wu M, Singh AK. (2011) Single-cell protein analysis, Curr Opin Biotechnol (2011), do:10.1016/j.copbio.2011.11.023. PMID: 22189001. PMCID: PMC3283030.
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  28. Yilmaz, S and AK Singh. (2011) Single cell genome sequencing, Current Opinion in Biotechnology, 23:1–7. PMID: 22154471. PMCID: PMC3318999.
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  29. Bradbury AR, Sidhu S, Dubel S, McCafferty J. (2011) Beyond natural antibodies: the power of in vitro display technologies. Nature Biotechnology 29: 245-254. PMID: 21390033. PMCID: PMC3057417.
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  30. Ferrara F, P Listwan, GS Waldo and ARM Bradbury (2011) Fluorescent Labeling of Antibody Fragments Using Split GFP. PLoS One 6: e25727. PMID: 21998685. PMCID: PMC3187779
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  31. 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). PMID: 21713653. PMCID: PMC3285534.

Selected Publications 2010

  1. 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 pdf pdf icon
  2. 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. PMID: 20643056. PMCID: PMC2905106.
  3. 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 pdf pdf icon
  4. 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. PMID: 20459599. PMCID: PMC2877007.
  5. 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. PMID: 20085718. PMCID: PMC2800967.
    ScienceDirect article
    ScienceDirect pdfpdf icon
  6. 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.
  7. 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. PMID: 21243108. PMCID: PMC3019609.
  8. 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. PMID: 20303982 PMCID: PMC2912164.
  9. 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. PMID: 20808719. PMCID: PMC2929802.
  10. 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. PMID: 20842349. PMCID: PMC3285537.
  11. 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. PMID: 20957984. PMCID: PMC3061257.
    NanoLetters pdf pdf icon
  12. 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. PMID: 20829029. PMCID: PMC2967365.
    ScienceDirect pdf pdf icon
  13. 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. PMID: 21151486. PMCID: PMC2987530.
  14. Kathrin Spendier, Amanda Carroll-Portillo, Keith A. Lidke, Bridget S. Wilson, Jerilyn A. Timlin, and James L. Thomas. (2010) "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. PMCID: PMC2905106.
    http://www.cell.com/biophysj/abstract/S0006-3495%2810%2900527-8
    Biophysical Journal pdf pdf icon
  15. Hsieh, G, W Shu, BS Wilson and JS Edwards. (2010) ErbB family receptor dynamic modeling quantitatively predicts signaling dynamics. BMC Systems Biology. 4:57. PMID: 20459599. PMCID: PMC2877007.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862147/?tool=pubmed
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862147/pdf/nihms-187624.pdf pdf icon
  16. Collins, S, M Stamatakis and DG Vlachos. (2010) Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes BMC Bioinformatics 2010, 11:218. PMID: 20429923. PMCID: PMC2868014.
    View article pdf pdf icon

Selected Publications 2009

  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. PMID: 19747859. PMCID: PMC2828771.
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2828771/?tool=pubmed
    www.ncbi.nlm.nih.gov/pmc/articles/PMC2828771/pdf/nihms146102.pdf pdf icon
  2. 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. PMID: 21028924. PMCID: PMC3097028.
    http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5243211 pdf icon
  3. Lidke, DS and BS Wilson. (2009) Caught in the act: quantifying protein behaviour in living cells. Trends Cell Biol. 19:566-74. PMID: 19801189. PMCID: PMC2783887.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783887/?tool=pubmed
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783887/pdf/nihms142662.pdf pdf icon
  4. 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. PMC2996128.
  5. 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 IgEFceRI system using 3-dimensional tracking microscopy. Proceedings SPIE 7185: 71850Z. NIHMSID: 619937 (PMC pending).
  6. 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. PMC2710010