| Year |
Citation |
Score |
| 2020 |
Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. Journal of Integrative Bioinformatics. PMID 32628633 DOI: 10.1515/Jib-2020-0015 |
0.335 |
|
| 2020 |
Salazar-Cavazos E, Nitta CF, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Molecular Biology of the Cell. mbcE19090548. PMID 31913761 DOI: 10.1091/Mbc.E19-09-0548 |
0.371 |
|
| 2019 |
Mitra ED, Hlavacek WS. Parameter Estimation and Uncertainty Quantification for Systems Biology Models. Current Opinion in Systems Biology. 18: 9-18. PMID 32719822 DOI: 10.1016/J.Coisb.2019.10.006 |
0.323 |
|
| 2019 |
Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS. PyBioNetFit and the Biological Property Specification Language. Iscience. 19: 1012-1036. PMID 31522114 DOI: 10.1016/J.Isci.2019.08.045 |
0.337 |
|
| 2019 |
Lin YT, Feng S, Hlavacek WS. Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks. The Journal of Chemical Physics. 150: 244101. PMID 31255063 DOI: 10.1063/1.5096774 |
0.616 |
|
| 2019 |
Hlavacek WS, Csicsery-Ronay JA, Baker LR, Ramos Álamo MDC, Ionkov A, Mitra ED, Suderman R, Erickson KE, Dias R, Colvin J, Thomas BR, Posner RG. A Step-by-Step Guide to Using BioNetFit. Methods in Molecular Biology (Clifton, N.J.). 1945: 391-419. PMID 30945257 DOI: 10.1007/978-1-4939-9102-0_18 |
0.316 |
|
| 2019 |
Suderman R, Fricke GM, Hlavacek WS. Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules. Methods in Molecular Biology (Clifton, N.J.). 1945: 33-42. PMID 30945241 DOI: 10.1007/978-1-4939-9102-0_2 |
0.306 |
|
| 2019 |
Shirin A, Klickstein IS, Feng S, Lin YT, Hlavacek WS, Sorrentino F. Prediction of Optimal Drug Schedules for Controlling Autophagy. Scientific Reports. 9: 1428. PMID 30723233 DOI: 10.1038/S41598-019-38763-9 |
0.594 |
|
| 2019 |
Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. Plos Computational Biology. 15: e1006706. PMID 30653502 DOI: 10.1371/Journal.Pcbi.1006706 |
0.403 |
|
| 2018 |
Civciristov S, Ellisdon AM, Suderman R, Pon CK, Evans BA, Kleifeld O, Charlton SJ, Hlavacek WS, Canals M, Halls ML. Preassembled GPCR signaling complexes mediate distinct cellular responses to ultralow ligand concentrations. Science Signaling. 11. PMID 30301787 DOI: 10.1126/Scisignal.Aan1188 |
0.347 |
|
| 2018 |
Mitra ED, Dias R, Posner RG, Hlavacek WS. Using both qualitative and quantitative data in parameter identification for systems biology models. Nature Communications. 9: 3901. PMID 30254246 DOI: 10.1038/S41467-018-06439-Z |
0.314 |
|
| 2018 |
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, et al. Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Systems. PMID 30007540 DOI: 10.1016/J.Cels.2018.06.002 |
0.315 |
|
| 2018 |
Lin YT, Chylek LA, Lemons NW, Hlavacek WS. Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics. The Journal of Physical Chemistry. B. PMID 29851484 DOI: 10.1021/Acs.Jpcb.8B02960 |
0.308 |
|
| 2018 |
Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS. Generalizing Gillespie's Direct Method to Enable Network-Free Simulations. Bulletin of Mathematical Biology. PMID 29594824 DOI: 10.1007/S11538-018-0418-2 |
0.622 |
|
| 2018 |
Salazar-Cavazos E, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Integrating Multiplex Single-Molecule Pull-Down (SiMPull) Data and Computational Modeling to Understand EGFR Signaling Biophysical Journal. 114: 463a. DOI: 10.1016/J.Bpj.2017.11.2554 |
0.311 |
|
| 2017 |
Harmon B, Chylek LA, Liu Y, Mitra ED, Mahajan A, Saada EA, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WS, Singh AK. Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Scientific Reports. 7: 15586. PMID 29138425 DOI: 10.1038/S41598-017-15568-2 |
0.356 |
|
| 2017 |
Kochanczyk M, Hlavacek WS, Lipniacki T. SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. Bioinformatics (Oxford, England). PMID 29036531 DOI: 10.1093/Bioinformatics/Btx456 |
0.345 |
|
| 2017 |
Schwartz SL, Cleyrat C, Olah MJ, Relich PK, Phillips GK, Hlavacek WS, Lidke KA, Wilson BS, Lidke DS. Differential Mast Cell Outcomes Are Sensitive to FcεRI-Syk Binding Kinetics. Molecular Biology of the Cell. PMID 28855374 DOI: 10.1091/Mbc.E17-06-0350 |
0.328 |
|
| 2016 |
Mahajan A, Youssef LA, Cleyrat C, Grattan R, Lucero SR, Mattison CP, Erasmus MF, Jacobson B, Tapia L, Hlavacek WS, Schuyler M, Wilson BS. Allergen Valency, Dose, and FcεRI Occupancy Set Thresholds for Secretory Responses to Pen a 1 and Motivate Design of Hypoallergens. Journal of Immunology (Baltimore, Md. : 1950). PMID 28039304 DOI: 10.4049/Jimmunol.1601334 |
0.302 |
|
| 2016 |
Salazar-Cavazos E, Contreras-Vidal LG, Wilson BS, Hlavacek WS, Lidke DS. Systems Biology Approach Reveals the Importance of SHC1-GRB2 Interactions in EGFR Phosphorylation Kinetics Biophysical Journal. 110: 144a. DOI: 10.1016/J.Bpj.2015.11.815 |
0.363 |
|
| 2015 |
Chylek LA, Harris LA, Faeder JR, Hlavacek WS. Modeling for (physical) biologists: an introduction to the rule-based approach. Physical Biology. 12: 045007. PMID 26178138 DOI: 10.1088/1478-3975/12/4/045007 |
0.35 |
|
| 2015 |
Stites EC, Aziz M, Creamer MS, Von Hoff DD, Posner RG, Hlavacek WS. Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophysical Journal. 108: 1819-29. PMID 25863072 DOI: 10.1016/J.Bpj.2015.02.030 |
0.37 |
|
| 2015 |
Szyma?ska P, Martin KR, MacKeigan JP, Hlavacek WS, Lipniacki T. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. Plos One. 10: e0116550. PMID 25761126 DOI: 10.1371/Journal.Pone.0116550 |
0.358 |
|
| 2015 |
Valley CC, Arndt-Jovin DJ, Jovin TM, Steinkamp MP, Chizhik AI, Karedla N, Hlavacek WS, Wilson BS, Lidke KA, Lidke DS. Inside-Out Signaling of Oncogenic EGFR Mutants Promotes Ligand-Independent Dimerization Biophysical Journal. 108: 351a. DOI: 10.1016/J.Bpj.2014.11.1921 |
0.303 |
|
| 2014 |
Chylek LA, Wilson BS, Hlavacek WS. Modeling biomolecular site dynamics in immunoreceptor signaling systems. Advances in Experimental Medicine and Biology. 844: 245-62. PMID 25480645 DOI: 10.1007/978-1-4939-2095-2_12 |
0.365 |
|
| 2014 |
Chylek LA, Akimov V, Dengjel J, Rigbolt KT, Hu B, Hlavacek WS, Blagoev B. Phosphorylation site dynamics of early T-cell receptor signaling. Plos One. 9: e104240. PMID 25147952 DOI: 10.1371/Journal.Pone.0104240 |
0.383 |
|
| 2014 |
Mahajan A, Barua D, Cutler P, Lidke DS, Espinoza FA, Pehlke C, Grattan R, Kawakami Y, Tung CS, Bradbury AR, Hlavacek WS, Wilson BS. Optimal aggregation of FcεRI with a structurally defined trivalent ligand overrides negative regulation driven by phosphatases. Acs Chemical Biology. 9: 1508-19. PMID 24784318 DOI: 10.1021/Cb500134T |
0.334 |
|
| 2014 |
Chylek LA, Holowka DA, Baird BA, Hlavacek WS. An Interaction Library for the FcεRI Signaling Network. Frontiers in Immunology. 5: 172. PMID 24782869 DOI: 10.3389/Fimmu.2014.00172 |
0.404 |
|
| 2014 |
Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 6: 13-36. PMID 24123887 DOI: 10.1002/Wsbm.1245 |
0.397 |
|
| 2013 |
Barua D, Hlavacek WS. Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. Plos Computational Biology. 9: e1003217. PMID 24086117 DOI: 10.1371/Journal.Pcbi.1003217 |
0.321 |
|
| 2013 |
Kozer N, Barua D, Orchard S, Nice EC, Burgess AW, Hlavacek WS, Clayton AH. Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach. Molecular Biosystems. 9: 1849-63. PMID 23629589 DOI: 10.1039/C3Mb70073A |
0.329 |
|
| 2013 |
Liu Y, Barua D, Liu P, Wilson BS, Oliver JM, Hlavacek WS, Singh AK. Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. Plos One. 8: e60159. PMID 23544131 DOI: 10.1371/Journal.Pone.0060159 |
0.33 |
|
| 2013 |
Martin KR, Barua D, Kauffman AL, Westrate LM, Posner RG, Hlavacek WS, Mackeigan JP. Computational model for autophagic vesicle dynamics in single cells. Autophagy. 9: 74-92. PMID 23196898 DOI: 10.4161/Auto.22532 |
0.375 |
|
| 2012 |
Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Han H, Bussey KJ, Von Hoff DD, Hlavacek WS, Posner RG. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. Bmc Systems Biology. 6: 107. PMID 22913808 DOI: 10.1186/1752-0509-6-107 |
0.432 |
|
| 2012 |
Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. Journal of Immunology (Baltimore, Md. : 1950). 189: 646-58. PMID 22711887 DOI: 10.4049/Jimmunol.1102003 |
0.349 |
|
| 2012 |
Stites EC, Creamer MS, Aziz M, Hlavacek WS, Posner RG. Large Scale, High Resolution Models of Receptor Tyrosine Kinase Signaling Networks Biophysical Journal. 102: 513a-514a. DOI: 10.1016/J.Bpj.2011.11.2812 |
0.404 |
|
| 2011 |
Yang J, Hlavacek WS. The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems. Physical Biology. 8: 055009. PMID 21832806 DOI: 10.1088/1478-3975/8/5/055009 |
0.365 |
|
| 2011 |
Yang J, Hlavacek WS. Scaffold-mediated nucleation of protein signaling complexes: elementary principles. Mathematical Biosciences. 232: 164-73. PMID 21683720 DOI: 10.1016/J.Mbs.2011.06.003 |
0.342 |
|
| 2011 |
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models. Molecular Biosystems. 7: 2779-95. PMID 21647530 DOI: 10.1039/C1Mb05077J |
0.349 |
|
| 2010 |
Yang J, Meng X, Hlavacek WS. Rule-based modelling and simulation of biochemical systems with molecular finite automata. Iet Systems Biology. 4: 453-66. PMID 21073243 DOI: 10.1049/Iet-Syb.2010.0015 |
0.36 |
|
| 2010 |
Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG. RuleMonkey: software for stochastic simulation of rule-based models. Bmc Bioinformatics. 11: 404. PMID 20673321 DOI: 10.1186/1471-2105-11-404 |
0.36 |
|
| 2010 |
Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophysical Journal. 98: 48-56. PMID 20085718 DOI: 10.1016/J.Bpj.2009.09.043 |
0.336 |
|
| 2009 |
Hlavacek WS, Faeder JR. The complexity of cell signaling and the need for a new mechanics. Science Signaling. 2: pe46. PMID 19638613 DOI: 10.1126/Scisignal.281Pe46 |
0.364 |
|
| 2009 |
Faeder JR, Blinov ML, Hlavacek WS. Rule-based modeling of biochemical systems with BioNetGen. Methods in Molecular Biology (Clifton, N.J.). 500: 113-67. PMID 19399430 DOI: 10.1007/978-1-59745-525-1_5 |
0.392 |
|
| 2009 |
Hu B, Matthew Fricke G, Faeder JR, Posner RG, Hlavacek WS. GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics (Oxford, England). 25: 1457-60. PMID 19321734 DOI: 10.1093/Bioinformatics/Btp173 |
0.34 |
|
| 2009 |
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG. Simulation of large-scale rule-based models. Bioinformatics (Oxford, England). 25: 910-7. PMID 19213740 DOI: 10.1093/Bioinformatics/Btp066 |
0.386 |
|
| 2009 |
Hlavacek WS. How to deal with large models? Molecular Systems Biology. 5: 240. PMID 19156132 DOI: 10.1038/Msb.2008.80 |
0.361 |
|
| 2008 |
Goldstein B, Coombs D, Faeder JR, Hlavacek WS. Kinetic proofreading model. Advances in Experimental Medicine and Biology. 640: 82-94. PMID 19065786 DOI: 10.1007/978-0-387-09789-3_8 |
0.345 |
|
| 2008 |
Dreisigmeyer DW, Stajic J, Nemenman I, Hlavacek WS, Wall ME. Determinants of bistability in induction of the Escherichia coli lac operon. Iet Systems Biology. 2: 293-303. PMID 19045824 DOI: 10.1049/Iet-Syb:20080095 |
0.307 |
|
| 2008 |
Yang J, Monine MI, Faeder JR, Hlavacek WS. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 78: 031910. PMID 18851068 DOI: 10.1103/Physreve.78.031910 |
0.361 |
|
| 2008 |
Lipniacki T, Hat B, Faeder JR, Hlavacek WS. Stochastic effects and bistability in T cell receptor signaling. Journal of Theoretical Biology. 254: 110-22. PMID 18556025 DOI: 10.1016/J.Jtbi.2008.05.001 |
0.376 |
|
| 2007 |
Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I, Wall ME. Q-bio 2007: a watershed moment in modern biology. Molecular Systems Biology. 3: 148. PMID 18059443 DOI: 10.1038/Msb4100193 |
0.303 |
|
| 2007 |
Faeder J, Monine M, Nag A, Goldstein B, Hlavacek W. Rule-based modeling of signal transduction Journal of Critical Care. 22: 349-350. DOI: 10.1016/J.Jcrc.2007.10.033 |
0.338 |
|
| 2006 |
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. Rules for modeling signal-transduction systems. Science's Stke : Signal Transduction Knowledge Environment. 2006: re6. PMID 16849649 DOI: 10.1126/Stke.3442006Re6 |
0.376 |
|
| 2006 |
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Bio Systems. 83: 136-51. PMID 16233948 DOI: 10.1016/J.Biosystems.2005.06.014 |
0.404 |
|
| 2005 |
Wall ME, Dunlop MJ, Hlavacek WS. Multiple functions of a feed-forward-loop gene circuit. Journal of Molecular Biology. 349: 501-14. PMID 15890368 DOI: 10.1016/J.Jmb.2005.04.022 |
0.351 |
|
| 2005 |
Faeder JR, Blinov ML, Goldstein B, Hlavacek WS. Rule-based modeling of biochemical networks: Research Articles Complexity. 10: 22-41. DOI: 10.1002/Cplx.V10:4 |
0.31 |
|
| 2005 |
Faeder JR, Blinov ML, Goldstein B, Hlavacek WS. Rule-based modeling of biochemical networks Complexity. 10: 22-41. DOI: 10.1002/Cplx.20074 |
0.306 |
|
| 2004 |
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics (Oxford, England). 20: 3289-91. PMID 15217809 DOI: 10.1093/Bioinformatics/Bth378 |
0.381 |
|
| 2004 |
Goldstein B, Faeder JR, Hlavacek WS. Mathematical and computational models of immune-receptor signalling. Nature Reviews. Immunology. 4: 445-56. PMID 15173833 DOI: 10.1038/Nri1374 |
0.389 |
|
| 2004 |
Wall ME, Hlavacek WS, Savageau MA. Design of gene circuits: lessons from bacteria. Nature Reviews. Genetics. 5: 34-42. PMID 14708014 DOI: 10.1038/Nrg1244 |
0.544 |
|
| 2003 |
Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B. The complexity of complexes in signal transduction. Biotechnology and Bioengineering. 84: 783-94. PMID 14708119 DOI: 10.1002/Bit.10842 |
0.539 |
|
| 2003 |
Wall ME, Hlavacek WS, Savageau MA. Design principles for regulator gene expression in a repressible gene circuit. Journal of Molecular Biology. 332: 861-76. PMID 12972257 DOI: 10.1016/S0022-2836(03)00948-3 |
0.578 |
|
| 2003 |
Faeder JR, Hlavacek WS, Reischl I, Blinov ML, Metzger H, Redondo A, Wofsy C, Goldstein B. Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model. Journal of Immunology (Baltimore, Md. : 1950). 170: 3769-81. PMID 12646643 DOI: 10.4049/Jimmunol.170.7.3769 |
0.364 |
|
| 2002 |
Hlavacek WS, Redondo A, Wofsy C, Goldstein B. Kinetic proofreading in receptor-mediated transduction of cellular signals: receptor aggregation, partially activated receptors, and cytosolic messengers. Bulletin of Mathematical Biology. 64: 887-911. PMID 12391861 DOI: 10.1006/Bulm.2002.0306 |
0.329 |
|
| 2002 |
Posner RG, Savage PB, Peters AS, Macias A, DelGado J, Zwartz G, Sklar LA, Hlavacek WS. A quantitative approach for studying IgE-FcepsilonRI aggregation. Molecular Immunology. 38: 1221-8. PMID 12217387 DOI: 10.1016/S0161-5890(02)00067-6 |
0.32 |
|
| 2002 |
Goldstein B, Faeder JR, Hlavacek WS, Blinov ML, Redondo A, Wofsy C. Modeling the early signaling events mediated by FcepsilonRI. Molecular Immunology. 38: 1213-9. PMID 12217386 DOI: 10.1016/S0161-5890(02)00066-4 |
0.368 |
|
| 2002 |
Hlavacek WS, Percus JK, Percus OE, Perelson AS, Wofsy C. Retention of antigen on follicular dendritic cells and B lymphocytes through complement-mediated multivalent ligand-receptor interactions: theory and application to HIV treatment. Mathematical Biosciences. 176: 185-202. PMID 11916508 DOI: 10.1016/S0025-5564(02)00091-3 |
0.461 |
|
| 2001 |
Hlavacek WS, Redondo A, Metzger H, Wofsy C, Goldstein B. Kinetic proofreading models for cell signaling predict ways to escape kinetic proofreading. Proceedings of the National Academy of Sciences of the United States of America. 98: 7295-300. PMID 11390967 DOI: 10.1073/Pnas.121172298 |
0.388 |
|
| 1999 |
Hlavacek WS, Perelson AS, Sulzer B, Bold J, Paar J, Gorman W, Posner RG. Quantifying aggregation of IgE-FcepsilonRI by multivalent antigen. Biophysical Journal. 76: 2421-31. PMID 10233059 DOI: 10.1016/S0006-3495(99)77397-2 |
0.3 |
|
| 1997 |
Hlavacek WS, Savageau MA. Completely uncoupled and perfectly coupled gene expression in repressible systems. Journal of Molecular Biology. 266: 538-58. PMID 9067609 DOI: 10.1006/Jmbi.1996.0811 |
0.581 |
|
| 1996 |
Hlavacek WS, Savageau MA. Rules for coupled expression of regulator and effector genes in inducible circuits. Journal of Molecular Biology. 255: 121-39. PMID 8568860 DOI: 10.1006/Jmbi.1996.0011 |
0.581 |
|
| 1995 |
Hlavacek WS, Savageau MA. Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. Journal of Molecular Biology. 248: 739-55. PMID 7752237 DOI: 10.1006/Jmbi.1995.0257 |
0.583 |
|
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