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Preassembled GPCR signaling complexes mediate distinct cellular responses to ultralow ligand concentrations.

Civciristov S, Ellisdon AM, Suderman R, Pon CK, Evans BA, Kleifeld O, Charlton SJ, Hlavacek WS, Canals M, Halls ML.

Sci Signal. 2018 Oct 9;11(551). pii: eaan1188. doi: 10.1126/scisignal.aan1188.


Using both qualitative and quantitative data in parameter identification for systems biology models.

Mitra ED, Dias R, Posner RG, Hlavacek WS.

Nat Commun. 2018 Sep 25;9(1):3901. doi: 10.1038/s41467-018-06439-z.


Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling.

Rukhlenko OS, Khorsand F, Krstic A, Rozanc J, Alexopoulos LG, Rauch N, Erickson KE, Hlavacek WS, Posner RG, Gómez-Coca S, Rosta E, Fitzgibbon C, Matallanas D, Rauch J, Kolch W, Kholodenko BN.

Cell Syst. 2018 Aug 22;7(2):161-179.e14. doi: 10.1016/j.cels.2018.06.002. Epub 2018 Jul 11.


Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics.

Lin YT, Chylek LA, Lemons NW, Hlavacek WS.

J Phys Chem B. 2018 Jun 21;122(24):6351-6356. doi: 10.1021/acs.jpcb.8b02960. Epub 2018 Jun 8.


Generalizing Gillespie's Direct Method to Enable Network-Free Simulations.

Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS.

Bull Math Biol. 2018 Mar 28. doi: 10.1007/s11538-018-0418-2. [Epub ahead of print]


New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling.

Erickson KE, Rukhlenko OS, Posner RG, Hlavacek WS, Kholodenko BN.

Semin Cancer Biol. 2018 Mar 5. pii: S1044-579X(17)30285-7. doi: 10.1016/j.semcancer.2018.02.008. [Epub ahead of print] Review.


A phase 2 trial of personalized cytotoxic therapy based on tumor immunohistochemistry in previously treated metastatic pancreatic cancer patients.

Ramanathan RK, Weiss GJ, Posner RG, Rajeshkumar NV, Jameson G, Aziz M, Hoering A, Bolejack V, Maitra A, Fulk M, Stites EC, Hlavacek WS, Gatalica Z, Xiu J, Hidalgo M, Von Hoff DD, Barrett MT.

J Gastrointest Oncol. 2017 Dec;8(6):925-935. doi: 10.21037/jgo.2017.09.05.


Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation.

Harmon B, Chylek LA, Liu Y, Mitra ED, Mahajan A, Saada EA, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WS, Singh AK.

Sci Rep. 2017 Nov 14;7(1):15586. doi: 10.1038/s41598-017-15568-2.


SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

Kochanczyk M, Hlavacek WS, Lipniacki T.

Bioinformatics. 2017 Nov 15;33(22):3667-3669. doi: 10.1093/bioinformatics/btx456.


Differential mast cell outcomes are sensitive to FcεRI-Syk binding kinetics.

Schwartz SL, Cleyrat C, Olah MJ, Relich PK, Phillips GK, Hlavacek WS, Lidke KA, Wilson BS, Lidke DS.

Mol Biol Cell. 2017 Nov 7;28(23):3397-3414. doi: 10.1091/mbc.E17-06-0350. Epub 2017 Aug 30.


Relaxation oscillations and hierarchy of feedbacks in MAPK signaling.

Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T.

Sci Rep. 2017 Jan 3;7:38244. doi: 10.1038/srep38244.


Allergen Valency, Dose, and FcεRI Occupancy Set Thresholds for Secretory Responses to Pen a 1 and Motivate Design of Hypoallergens.

Mahajan A, Youssef LA, Cleyrat C, Grattan R, Lucero SR, Mattison CP, Erasmus MF, Jacobson B, Tapia L, Hlavacek WS, Schuyler M, Wilson BS.

J Immunol. 2017 Feb 1;198(3):1034-1046. doi: 10.4049/jimmunol.1601334. Epub 2016 Dec 30.


The eighth q-bio conference: meeting report and special issue preface.

Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O.

Phys Biol. 2015 Dec 30;12(6):060401. doi: 10.1088/1478-3975/12/6/060401. No abstract available.


BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

Thomas BR, Chylek LA, Colvin J, Sirimulla S, Clayton AH, Hlavacek WS, Posner RG.

Bioinformatics. 2016 Mar 1;32(5):798-800. doi: 10.1093/bioinformatics/btv655. Epub 2015 Nov 9.


Enhanced dimerization drives ligand-independent activity of mutant epidermal growth factor receptor in lung cancer.

Valley CC, Arndt-Jovin DJ, Karedla N, Steinkamp MP, Chizhik AI, Hlavacek WS, Wilson BS, Lidke KA, Lidke DS.

Mol Biol Cell. 2015 Nov 5;26(22):4087-99. doi: 10.1091/mbc.E15-05-0269. Epub 2015 Sep 2.


Modeling for (physical) biologists: an introduction to the rule-based approach.

Chylek LA, Harris LA, Faeder JR, Hlavacek WS.

Phys Biol. 2015 Jul 16;12(4):045007. doi: 10.1088/1478-3975/12/4/045007. Review.


Use of mechanistic models to integrate and analyze multiple proteomic datasets.

Stites EC, Aziz M, Creamer MS, Von Hoff DD, Posner RG, Hlavacek WS.

Biophys J. 2015 Apr 7;108(7):1819-1829. doi: 10.1016/j.bpj.2015.02.030.


Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1.

Szymańska P, Martin KR, MacKeigan JP, Hlavacek WS, Lipniacki T.

PLoS One. 2015 Mar 11;10(3):e0116550. doi: 10.1371/journal.pone.0116550. eCollection 2015.


Modeling biomolecular site dynamics in immunoreceptor signaling systems.

Chylek LA, Wilson BS, Hlavacek WS.

Adv Exp Med Biol. 2014;844:245-62. doi: 10.1007/978-1-4939-2095-2_12. Review.


Phosphorylation site dynamics of early T-cell receptor signaling.

Chylek LA, Akimov V, Dengjel J, Rigbolt KT, Hu B, Hlavacek WS, Blagoev B.

PLoS One. 2014 Aug 22;9(8):e104240. doi: 10.1371/journal.pone.0104240. eCollection 2014.


The Seventh q-bio Conference: meeting report and preface.

Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y.

Phys Biol. 2014 Aug;11(4):040301. doi: 10.1088/1478-3975/11/4/040301. Epub 2014 Jul 30. No abstract available.


Optimal aggregation of FcεRI with a structurally defined trivalent ligand overrides negative regulation driven by phosphatases.

Mahajan A, Barua D, Cutler P, Lidke DS, Espinoza FA, Pehlke C, Grattan R, Kawakami Y, Tung CS, Bradbury AR, Hlavacek WS, Wilson BS.

ACS Chem Biol. 2014 Jul 18;9(7):1508-19. doi: 10.1021/cb500134t. Epub 2014 May 15.


An Interaction Library for the FcεRI Signaling Network.

Chylek LA, Holowka DA, Baird BA, Hlavacek WS.

Front Immunol. 2014 Apr 15;5:172. doi: 10.3389/fimmu.2014.00172. eCollection 2014. Review.


Mitochondrial morphological features are associated with fission and fusion events.

Westrate LM, Drocco JA, Martin KR, Hlavacek WS, MacKeigan JP.

PLoS One. 2014 Apr 14;9(4):e95265. doi: 10.1371/journal.pone.0095265. eCollection 2014.


Recruitment of the adaptor protein Grb2 to EGFR tetramers.

Kozer N, Barua D, Henderson C, Nice EC, Burgess AW, Hlavacek WS, Clayton AH.

Biochemistry. 2014 Apr 29;53(16):2594-604. doi: 10.1021/bi500182x. Epub 2014 Apr 21.


Perspective on the q-bio Summer School and Conference: 2007 - 2014 and beyond.

Resnekov O, Munsky B, Hlavacek WS.

Quant Biol. 2014 Mar 1;2(1):54-58. No abstract available.


Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):13-36. doi: 10.1002/wsbm.1245. Epub 2013 Sep 30. Review.


Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells.

Barua D, Hlavacek WS.

PLoS Comput Biol. 2013;9(9):e1003217. doi: 10.1371/journal.pcbi.1003217. Epub 2013 Sep 26.


Special section dedicated to The Sixth q-bio Conference: meeting report and preface.

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR.

Phys Biol. 2013 Jun;10(3):030301. doi: 10.1088/1478-3975/10/3/030301. Epub 2013 Jun 4. No abstract available.


Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach.

Kozer N, Barua D, Orchard S, Nice EC, Burgess AW, Hlavacek WS, Clayton AH.

Mol Biosyst. 2013 Jul;9(7):1849-63. doi: 10.1039/c3mb70073a. Epub 2013 Apr 30.


Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform.

Liu Y, Barua D, Liu P, Wilson BS, Oliver JM, Hlavacek WS, Singh AK.

PLoS One. 2013;8(3):e60159. doi: 10.1371/journal.pone.0060159. Epub 2013 Mar 27.


Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.

Nowak-Lovato K, Alexandrov LB, Banisadr A, Bauer AL, Bishop AR, Usheva A, Mu F, Hong-Geller E, Rasmussen KØ, Hlavacek WS, Alexandrov BS.

PLoS Comput Biol. 2013;9(1):e1002881. doi: 10.1371/journal.pcbi.1002881. Epub 2013 Jan 17.


Computational model for autophagic vesicle dynamics in single cells.

Martin KR, Barua D, Kauffman AL, Westrate LM, Posner RG, Hlavacek WS, Mackeigan JP.

Autophagy. 2013 Jan;9(1):74-92. doi: 10.4161/auto.22532. Epub 2012 Nov 29.


Improved predictions of transcription factor binding sites using physicochemical features of DNA.

Maienschein-Cline M, Dinner AR, Hlavacek WS, Mu F.

Nucleic Acids Res. 2012 Dec;40(22):e175. doi: 10.1093/nar/gks771. Epub 2012 Aug 25.


Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling.

Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Han H, Bussey KJ, Von Hoff DD, Hlavacek WS, Posner RG.

BMC Syst Biol. 2012 Aug 22;6:107. doi: 10.1186/1752-0509-6-107.


A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn.

Barua D, Hlavacek WS, Lipniacki T.

J Immunol. 2012 Jul 15;189(2):646-58. doi: 10.4049/jimmunol.1102003. Epub 2012 Jun 18.


The Brucella TIR-like protein TcpB interacts with the death domain of MyD88.

Chaudhary A, Ganguly K, Cabantous S, Waldo GS, Micheva-Viteva SN, Nag K, Hlavacek WS, Tung CS.

Biochem Biophys Res Commun. 2012 Jan 6;417(1):299-304. doi: 10.1016/j.bbrc.2011.11.104. Epub 2011 Nov 29.


The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems.

Yang J, Hlavacek WS.

Phys Biol. 2011 Oct;8(5):055009. doi: 10.1088/1478-3975/8/5/055009. Epub 2011 Aug 10.


Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing.

Nemenman I, Faeder JR, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

Phys Biol. 2011 Oct;8(5):050301. doi: 10.1088/1478-3975/8/5/050301. Epub 2011 Aug 10.


Scaffold-mediated nucleation of protein signaling complexes: elementary principles.

Yang J, Hlavacek WS.

Math Biosci. 2011 Aug;232(2):164-73. doi: 10.1016/j.mbs.2011.06.003. Epub 2011 Jun 12.


Guidelines for visualizing and annotating rule-based models.

Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS.

Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7.


Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds.

Mu F, Unkefer CJ, Unkefer PJ, Hlavacek WS.

Bioinformatics. 2011 Jun 1;27(11):1537-45. doi: 10.1093/bioinformatics/btr177. Epub 2011 Apr 8.


Hierarchical graphs for rule-based modeling of biochemical systems.

Lemons NW, Hu B, Hlavacek WS.

BMC Bioinformatics. 2011 Feb 2;12:45. doi: 10.1186/1471-2105-12-45.


Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

Bauer AL, Hlavacek WS, Unkefer PJ, Mu F.

PLoS Comput Biol. 2010 Nov 18;6(11):e1001007. doi: 10.1371/journal.pcbi.1001007.


Rule-based modelling and simulation of biochemical systems with molecular finite automata.

Yang J, Meng X, Hlavacek WS.

IET Syst Biol. 2010 Nov;4(6):453-66. doi: 10.1049/iet-syb.2010.0015.


The Third q-bio Conference on Cellular Information Processing.

Nemenman I, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

IET Syst Biol. 2010 Nov;4(6):331-3. doi: 10.1049/iet-syb.2010.9133. No abstract available.


RuleMonkey: software for stochastic simulation of rule-based models.

Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG.

BMC Bioinformatics. 2010 Jul 30;11:404. doi: 10.1186/1471-2105-11-404.


Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates.

Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS.

Biophys J. 2010 Jan 6;98(1):48-56. doi: 10.1016/j.bpj.2009.09.043.


The complexity of cell signaling and the need for a new mechanics.

Hlavacek WS, Faeder JR.

Sci Signal. 2009 Jul 28;2(81):pe46. doi: 10.1126/scisignal.281pe46.


Rule-based modeling of biochemical systems with BioNetGen.

Faeder JR, Blinov ML, Hlavacek WS.

Methods Mol Biol. 2009;500:113-67. doi: 10.1007/978-1-59745-525-1_5.


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