| Year |
Citation |
Score |
| 2025 |
Sauro HM, Agmon E, Blinov ML, Gennari JH, Hellerstein J, Heydarabadipour A, Hunter P, Jardine BE, May E, Nickerson DP, Smith LP, Bader GD, Bergmann F, Boyle PM, Drager A, ... ... Laubenbacher R, et al. From FAIR to CURE: Guidelines for Computational Models of Biological Systems. Arxiv. PMID 40034129 |
0.304 |
|
| 2025 |
Fonseca LL, Böttcher L, Mehrad B, Laubenbacher RC. Optimal control of agent-based models via surrogate modeling. Plos Computational Biology. 21: e1012138. PMID 39808665 DOI: 10.1371/journal.pcbi.1012138 |
0.646 |
|
| 2024 |
Niarakis A, Laubenbacher R, An G, Ilan Y, Fisher J, Flobak Å, Reiche K, Rodríguez Martínez M, Geris L, Ladeira L, Veschini L, Blinov ML, Messina F, Fonseca LL, Ferreira S, et al. Immune digital twins for complex human pathologies: applications, limitations, and challenges. Npj Systems Biology and Applications. 10: 141. PMID 39616158 DOI: 10.1038/s41540-024-00450-5 |
0.618 |
|
| 2024 |
Knapp AC, Cruz DA, Mehrad B, Laubenbacher RC. Personalizing computational models to construct medical digital twins. Biorxiv : the Preprint Server For Biology. PMID 39574674 DOI: 10.1101/2024.05.31.596692 |
0.315 |
|
| 2024 |
Fonseca LL, Böttcher L, Mehrad B, Laubenbacher RC. Surrogate modeling and control of medical digital twins. Arxiv. PMID 38827450 |
0.664 |
|
| 2024 |
Böttcher L, Fonseca LL, Laubenbacher RC. Control of Medical Digital Twins with Artificial Neural Networks. Biorxiv : the Preprint Server For Biology. PMID 38562787 DOI: 10.1101/2024.03.18.585589 |
0.705 |
|
| 2024 |
Böttcher L, Fonseca LL, Laubenbacher RC. Control of Medical Digital Twins with Artificial Neural Networks. Arxiv. PMID 38562447 |
0.705 |
|
| 2024 |
Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, et al. Toward mechanistic medical digital twins: some use cases in immunology. Frontiers in Digital Health. 6: 1349595. PMID 38515550 DOI: 10.3389/fdgth.2024.1349595 |
0.626 |
|
| 2024 |
Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, et al. Forum on immune digital twins: a meeting report. Npj Systems Biology and Applications. 10: 19. PMID 38365857 DOI: 10.1038/s41540-024-00345-5 |
0.641 |
|
| 2024 |
Murrugarra D, Veliz-Cuba A, Dimitrova E, Kadelka C, Wheeler M, Laubenbacher R. Modular Control of Biological Networks. Arxiv. PMID 38344220 |
0.357 |
|
| 2023 |
Kadelka C, Wheeler M, Veliz-Cuba A, Murrugarra D, Laubenbacher R. Modularity of biological systems: a link between structure and function. Journal of the Royal Society, Interface. 20: 20230505. PMID 37876275 DOI: 10.1098/rsif.2023.0505 |
0.366 |
|
| 2023 |
Kadelka C, Wheeler M, Veliz-Cuba A, Murrugarra D, Laubenbacher R. Modularity of biological systems: a link between structure and function. Biorxiv : the Preprint Server For Biology. PMID 37745485 DOI: 10.1101/2023.09.11.557227 |
0.366 |
|
| 2022 |
Adhikari B, Scindia Y, Sordo Vieira L, de Assis Lopes Ribeiro H, Masison J, Yang N, Fonseca LL, Wheeler M, Knapp AC, Mei Y, Helba B, Atkinson C, Schroeder W, Mehrad B, Laubenbacher R. Computational Modeling of Macrophage Iron Sequestration during Host Defense against Aspergillus. Msphere. e0007422. PMID 35862797 DOI: 10.1128/msphere.00074-22 |
0.623 |
|
| 2022 |
Knapp AC, Sordo Vieira L, Laubenbacher R, Chifman J. SteadyCellPhenotype: A web-based tool for the modeling of biological networks with ternary logic. Bioinformatics (Oxford, England). PMID 35179549 DOI: 10.1093/bioinformatics/btac097 |
0.307 |
|
| 2020 |
Paul E, Pogudin G, Qin W, Laubenbacher R. The Dynamics of Canalizing Boolean Networks. Complexity. 2020. PMID 37538387 DOI: 10.1155/2020/3687961 |
0.381 |
|
| 2020 |
Paul E, Pogudin G, Qin W, Laubenbacher R. The Dynamics of Canalizing Boolean Networks Complexity. 2020: 1-14. DOI: 10.1155/2020/3687961 |
0.378 |
|
| 2019 |
Sordo Vieira L, Laubenbacher RC, Murrugarra D. Control of Intracellular Molecular Networks Using Algebraic Methods. Bulletin of Mathematical Biology. 82: 2. PMID 31919596 DOI: 10.1007/s11538-019-00679-w |
0.394 |
|
| 2019 |
Ha S, Dimitrova E, Hoops S, Altarawy D, Ansariola M, Deb D, Glazebrook J, Hillmer R, Shahin H, Katagiri F, McDowell J, Megraw M, Setubal J, Tyler BM, Laubenbacher R. PlantSimLab - a modeling and simulation web tool for plant biologists. Bmc Bioinformatics. 20: 508. PMID 31638901 DOI: 10.1186/S12859-019-3094-9 |
0.429 |
|
| 2019 |
Posner R, Laubenbacher R. Connecting the molecular function of microRNAs to cell differentiation dynamics. Journal of the Royal Society, Interface. 16: 20190437. PMID 31551049 DOI: 10.1098/Rsif.2019.0437 |
0.343 |
|
| 2018 |
Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P. An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology. PMID 30047562 DOI: 10.1111/Mmi.14086 |
0.323 |
|
| 2017 |
Kadelka C, Kuipers J, Laubenbacher R. The influence of canalization on the robustness of Boolean networks Physica D: Nonlinear Phenomena. 353: 39-47. DOI: 10.1016/J.Physd.2017.05.002 |
0.453 |
|
| 2016 |
An G, Fitzpatrick BG, Christley S, Federico P, Kanarek A, Neilan RM, Oremland M, Salinas R, Laubenbacher R, Lenhart S. Optimization and Control of Agent-Based Models in Biology: A Perspective. Bulletin of Mathematical Biology. PMID 27826879 DOI: 10.1007/S11538-016-0225-6 |
0.39 |
|
| 2015 |
Arat S, Bullerjahn GS, Laubenbacher R. A network biology approach to denitrification in Pseudomonas aeruginosa. Plos One. 10: e0118235. PMID 25706405 DOI: 10.1371/Journal.Pone.0118235 |
0.356 |
|
| 2015 |
Oremland M, Laubenbacher R. Optimal harvesting for a predator-prey agent-based model using difference equations. Bulletin of Mathematical Biology. 77: 434-59. PMID 25559457 DOI: 10.1007/S11538-014-0060-6 |
0.333 |
|
| 2015 |
Veliz-Cuba A, Aguilar B, Laubenbacher R. Dimension Reduction of Large Sparse AND-NOT Network Models Electronic Notes in Theoretical Computer Science. 316: 83-95. DOI: 10.1016/J.Entcs.2015.06.012 |
0.411 |
|
| 2014 |
Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R. A mathematical model of skeletal muscle disease and immune response in the mdx mouse. Biomed Research International. 2014: 871810. PMID 25013809 DOI: 10.1155/2014/871810 |
0.699 |
|
| 2014 |
Veliz-Cuba A, Aguilar B, Hinkelmann F, Laubenbacher R. Steady state analysis of Boolean molecular network models via model reduction and computational algebra. Bmc Bioinformatics. 15: 221. PMID 24965213 DOI: 10.1186/1471-2105-15-221 |
0.34 |
|
| 2014 |
Vera-Licona P, Jarrah A, Garcia-Puente LD, McGee J, Laubenbacher R. An algebra-based method for inferring gene regulatory networks. Bmc Systems Biology. 8: 37. PMID 24669835 DOI: 10.1186/1752-0509-8-37 |
0.753 |
|
| 2014 |
Oremland M, Laubenbacher R. Using difference equations to find optimal tax structures on the SugarScape Journal of Economic Interaction and Coordination. 9: 233-253. DOI: 10.1007/S11403-014-0133-5 |
0.319 |
|
| 2014 |
Brunson JC, Fassino S, McInnes A, Narayan M, Richardson B, Franck C, Ion P, Laubenbacher R. Evolutionary events in a mathematical sciences research collaboration network Scientometrics. 99: 973-998. DOI: 10.1007/S11192-013-1209-Z |
0.437 |
|
| 2014 |
Veliz-Cuba A, Murrugarra D, Laubenbacher R. Structure and dynamics of acyclic networks Discrete Event Dynamic Systems: Theory and Applications. 24: 647-658. DOI: 10.1007/S10626-013-0174-2 |
0.396 |
|
| 2013 |
Kadelka C, Murrugarra D, Laubenbacher R. Stabilizing gene regulatory networks through feedforward loops Chaos. 23. PMID 23822505 DOI: 10.1063/1.4808248 |
0.444 |
|
| 2013 |
Martins A, Vera-Licona P, Laubenbacher R. Computational systems biology: Discrete models of gene regulation networks Undergraduate Mathematics For the Life Sciences: Models, Processes, and Directions. 189-200. DOI: 10.5948/UPO9781614443162.032 |
0.313 |
|
| 2013 |
Veliz-Cuba A, Buschur K, Hamershock R, Kniss A, Wolff E, Laubenbacher R. AND-NOT logic framework for steady state analysis of boolean network models Applied Mathematics and Information Sciences. 7: 1263-1274. DOI: 10.12785/Amis/070401 |
0.485 |
|
| 2013 |
Laubenbacher R, Mendes P. Top-Down Dynamical Modeling of Molecular Regulatory Networks Computational Systems Biology: From Molecular Mechanisms to Disease: Second Edition. 223-239. DOI: 10.1016/B978-0-12-405926-9.00011-3 |
0.412 |
|
| 2012 |
Murrugarra D, Veliz-Cuba A, Aguilar B, Arat S, Laubenbacher R. Modeling stochasticity and variability in gene regulatory networks. Eurasip Journal On Bioinformatics & Systems Biology. 2012: 5. PMID 22673395 DOI: 10.1186/1687-4153-2012-5 |
0.387 |
|
| 2012 |
Chifman J, Kniss A, Neupane P, Williams I, Leung B, Deng Z, Mendes P, Hower V, Torti FM, Akman SA, Torti SV, Laubenbacher R. The core control system of intracellular iron homeostasis: a mathematical model. Journal of Theoretical Biology. 300: 91-9. PMID 22286016 DOI: 10.1016/J.Jtbi.2012.01.024 |
0.334 |
|
| 2012 |
Murrugarra D, Laubenbacher R. The number of multistate nested canalyzing functions Physica D: Nonlinear Phenomena. 241: 929-938. DOI: 10.1016/J.Physd.2012.02.011 |
0.44 |
|
| 2012 |
Veliz-Cuba A, Laubenbacher R. On the computation of fixed points in Boolean networks Journal of Applied Mathematics and Computing. 39: 145-153. DOI: 10.1007/S12190-011-0517-9 |
0.422 |
|
| 2011 |
Murrugarra D, Laubenbacher R. Regulatory patterns in molecular interaction networks. Journal of Theoretical Biology. 288: 66-72. PMID 21872607 DOI: 10.1016/J.Jtbi.2011.08.015 |
0.462 |
|
| 2011 |
Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R. ADAM: analysis of discrete models of biological systems using computer algebra. Bmc Bioinformatics. 12: 295. PMID 21774817 DOI: 10.1186/1471-2105-12-295 |
0.389 |
|
| 2011 |
Laubenbacher R. Algebraic methods in mathematical biology. Bulletin of Mathematical Biology. 73: 701-5. PMID 21400021 DOI: 10.1007/S11538-011-9643-7 |
0.422 |
|
| 2011 |
Hinkelmann F, Murrugarra D, Jarrah AS, Laubenbacher R. A mathematical framework for agent based models of complex biological networks. Bulletin of Mathematical Biology. 73: 1583-602. PMID 20878493 DOI: 10.1007/S11538-010-9582-8 |
0.756 |
|
| 2011 |
Hinkelmann F, Laubenbacher R. Boolean models of bistable biological systems Discrete and Continuous Dynamical Systems - Series S. 4: 1443-1456. DOI: 10.3934/Dcdss.2011.4.1443 |
0.447 |
|
| 2011 |
Dimitrova E, Garca-Puente LD, Hinkelmann F, Jarrah AS, Laubenbacher R, Stigler B, Stillman M, Vera-Licona P. Parameter estimation for Boolean models of biological networks Theoretical Computer Science. 412: 2816-2826. DOI: 10.1016/J.Tcs.2010.04.034 |
0.762 |
|
| 2010 |
Dimitrova ES, Licona MP, McGee J, Laubenbacher R. Discretization of time series data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 853-68. PMID 20583929 DOI: 10.1089/Cmb.2008.0023 |
0.423 |
|
| 2010 |
Veliz-Cuba A, Jarrah AS, Laubenbacher R. Polynomial algebra of discrete models in systems biology. Bioinformatics (Oxford, England). 26: 1637-43. PMID 20448137 DOI: 10.1093/Bioinformatics/Btq240 |
0.789 |
|
| 2010 |
Jarrah AS, Laubenbacher R, Veliz-Cuba A. The dynamics of conjunctive and disjunctive Boolean network models. Bulletin of Mathematical Biology. 72: 1425-47. PMID 20087672 DOI: 10.1007/S11538-010-9501-Z |
0.761 |
|
| 2009 |
Laubenbacher R, Jarrah AS. Algebraic models of biochemical networks. Methods in Enzymology. 467: 163-96. PMID 19897093 DOI: 10.1016/S0076-6879(09)67007-5 |
0.769 |
|
| 2009 |
Laubenbacher R, Hower V, Jarrah A, Torti SV, Shulaev V, Mendes P, Torti FM, Akman S. A systems biology view of cancer. Biochimica Et Biophysica Acta. 1796: 129-39. PMID 19505535 DOI: 10.1016/J.Bbcan.2009.06.001 |
0.737 |
|
| 2009 |
Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV. A general map of iron metabolism and tissue-specific subnetworks. Molecular Biosystems. 5: 422-43. PMID 19381358 DOI: 10.1039/B816714C |
0.334 |
|
| 2009 |
Laubenbacher R, Jarrah A, Dimitrova E, Stigler B, Vera-Licona P. System identification for discrete polynomial models of gene regulatory networks Ifac Proceedings Volumes (Ifac-Papersonline). 15: 39-41. DOI: 10.3182/20090706-3-Fr-2004.00005 |
0.774 |
|
| 2008 |
Sontag E, Veliz-Cuba A, Laubenbacher R, Jarrah AS. The effect of negative feedback loops on the dynamics of boolean networks. Biophysical Journal. 95: 518-26. PMID 18375509 DOI: 10.1529/Biophysj.107.125021 |
0.745 |
|
| 2008 |
Shapiro M, Duca KA, Lee K, Delgado-Eckert E, Hawkins J, Jarrah AS, Laubenbacher R, Polys NF, Hadinoto V, Thorley-Lawson DA. A virtual look at Epstein-Barr virus infection: simulation mechanism. Journal of Theoretical Biology. 252: 633-48. PMID 18371986 DOI: 10.1016/J.Jtbi.2008.01.032 |
0.703 |
|
| 2008 |
Vera-Licona P, Laubenbacher R. Inference of ecological interaction networks Annales Zoologici Fennici. 45: 459-464. DOI: 10.5735/086.045.0509 |
0.408 |
|
| 2008 |
Dimitrova ES, Stigler B, Jarrah AS, Laubenbacher R. Applications of the gröbner fan to gene network reconstruction (abstract only) Acm Communications in Computer Algebra. 42: 69. DOI: 10.1145/1394042.1394079 |
0.756 |
|
| 2008 |
Martins AM, Vera-Licona P, Laubenbacher R. 'Model your genes the mathematical way' - A mathematical biology workshop for secondary school teachers Teaching Mathematics and Its Applications. 27: 91-101. DOI: 10.1093/Teamat/Hrn003 |
0.389 |
|
| 2008 |
Oosawa C, Savageau MA, Jarrah AS, Laubenbacher RC, Sontag ED. Stabilizing and destabilizing effects of embedding 3-node subgraphs on the state space of boolean networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5191: 100-107. DOI: 10.1007/978-3-540-79992-4_13 |
0.347 |
|
| 2007 |
Jarrah AS, Raposa B, Laubenbacher R. Nested Canalyzing, Unate Cascade, and Polynomial Functions. Physica D. Nonlinear Phenomena. 233: 167-174. PMID 18437250 DOI: 10.1016/J.Physd.2007.06.022 |
0.728 |
|
| 2007 |
Duca KA, Shapiro M, Delgado-Eckert E, Hadinoto V, Jarrah AS, Laubenbacher R, Lee K, Luzuriaga K, Polys NF, Thorley-Lawson DA. A virtual look at Epstein-Barr virus infection: biological interpretations. Plos Pathogens. 3: 1388-400. PMID 17953479 DOI: 10.1371/Journal.Ppat.0030137 |
0.717 |
|
| 2007 |
Camacho D, Vera Licona P, Mendes P, Laubenbacher R. Comparison of reverse-engineering methods using an in silico network. Annals of the New York Academy of Sciences. 1115: 73-89. PMID 17925358 DOI: 10.1196/Annals.1407.006 |
0.433 |
|
| 2007 |
Stigler B, Jarrah A, Stillman M, Laubenbacher R. Reverse engineering of dynamic networks Annals of the New York Academy of Sciences. 1115: 168-177. PMID 17925347 DOI: 10.1196/Annals.1407.012 |
0.773 |
|
| 2007 |
Castiglione F, Duca K, Jarrah A, Laubenbacher R, Hochberg D, Thorley-Lawson D. Simulating Epstein-Barr virus infection with C-ImmSim. Bioinformatics (Oxford, England). 23: 1371-7. PMID 17341499 DOI: 10.1093/Bioinformatics/Btm044 |
0.7 |
|
| 2007 |
Dimitrova ES, Jarrah AS, Laubenbacher R, Stigler B. A Gröbner fan method for biochemical network modeling Proceedings of the International Symposium On Symbolic and Algebraic Computation, Issac. 122-126. DOI: 10.1145/1277548.1277566 |
0.375 |
|
| 2007 |
Jarrah AS, Laubenbacher R, Stigler B, Stillman M. Reverse-engineering of polynomial dynamical systems Advances in Applied Mathematics. 39: 477-489. DOI: 10.1016/J.Aam.2006.08.004 |
0.75 |
|
| 2007 |
Jarrah AS, Laubenbacher R. Discrete models of biochemical networks: The toric variety of nested canalyzing functions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4545: 15-22. |
0.371 |
|
| 2006 |
Laubenbacher R, Pareigis B. Update schedules of sequential dynamical systems Discrete Applied Mathematics. 154: 980-994. DOI: 10.1016/J.Dam.2005.10.010 |
0.338 |
|
| 2006 |
Garcia LD, Jarrah AS, Laubenbacher R. Sequential dynamical systems over words Applied Mathematics and Computation. 174: 500-510. DOI: 10.1016/J.Amc.2005.04.101 |
0.725 |
|
| 2006 |
Laubenbacher R, Mendes P. A discrete approach to top-down modeling of biochemical networks Computational Systems Biology. 229-247. DOI: 10.1016/B978-012088786-6/50031-9 |
0.403 |
|
| 2005 |
Colón-Reyes O, Laubenbacher R, Pareigis B. Boolean monomial dynamical systems Annals of Combinatorics. 8: 425-439. DOI: 10.1007/S00026-004-0230-6 |
0.348 |
|
| 2004 |
Laubenbacher R, Stigler B. A computational algebra approach to the reverse engineering of gene regulatory networks. Journal of Theoretical Biology. 229: 523-37. PMID 15246788 DOI: 10.1016/J.Jtbi.2004.04.037 |
0.472 |
|
| 2004 |
Jarrah AS, Laubenbacher R. Generic Cohen-Macaulay Monomial Ideals Annals of Combinatorics. 8: 45-61. DOI: 10.1007/S00026-004-0204-8 |
0.687 |
|
| 2003 |
Jarrah AS, Laubenbacher R, Romanovski V. The Sibirsky component of the center variety of polynomial differential systems Journal of Symbolic Computation. 35: 577-589. DOI: 10.1016/S0747-7171(03)00016-6 |
0.707 |
|
| 2003 |
Laubenbacher R, Pareigis B. Decomposition and simulation of sequential dynamical systems Advances in Applied Mathematics. 30: 655-678. DOI: 10.1016/S0196-8858(02)00554-7 |
0.358 |
|
| 2003 |
Laubenbacher R. A Computer Algebra Approach to Biological Systems Proceedings of the International Symposium On Symbolic and Algebraic Computation, Issac. 5-6. |
0.393 |
|
| 2001 |
Laubenbacher R, Pareigis B. Equivalence Relations on Finite Dynamical Systems Advances in Applied Mathematics. 26: 237-251. DOI: 10.1006/Aama.2000.0717 |
0.347 |
|
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