| H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations R Anandakrishnan, B Aguilar, AV Onufriev Nucleic acids research 40 (W1), W537-W541, 2012 | 1533 | 2012 |
| Modeling stochasticity and variability in gene regulatory networks D Murrugarra, A Veliz-Cuba, B Aguilar, S Arat, R Laubenbacher EURASIP Journal on Bioinformatics and Systems Biology 2012, 1-11, 2012 | 85 | 2012 |
| Steady state analysis of Boolean molecular network models via model reduction and computational algebra A Veliz-Cuba, B Aguilar, F Hinkelmann, R Laubenbacher BMC bioinformatics 15, 1-8, 2014 | 80 | 2014 |
| Identification of control targets in Boolean molecular network models via computational algebra D Murrugarra, A Veliz-Cuba, B Aguilar, R Laubenbacher BMC systems biology 10, 1-11, 2016 | 73 | 2016 |
| Boolean nested canalizing functions: A comprehensive analysis Y Li, JO Adeyeye, D Murrugarra, B Aguilar, R Laubenbacher Theoretical Computer Science 481, 24-36, 2013 | 68 | 2013 |
| Reducing the secondary structure bias in the generalized Born model via R6 effective radii B Aguilar, R Shadrach, AV Onufriev Journal of Chemical Theory and Computation 6 (12), 3613-3630, 2010 | 60 | 2010 |
| Statistics and physical origins of pK and ionization state changes upon protein-ligand binding B Aguilar, R Anandakrishnan, JZ Ruscio, AV Onufriev Biophysical journal 98 (5), 872-880, 2010 | 57 | 2010 |
| Protein–ligand electrostatic binding free energies from explicit and implicit solvation S Izadi, B Aguilar, AV Onufriev Journal of chemical theory and computation 11 (9), 4450-4459, 2015 | 49 | 2015 |
| Efficient computation of the total solvation energy of small molecules via the R6 generalized Born model B Aguilar, AV Onufriev Journal of chemical theory and computation 8 (7), 2404-2411, 2012 | 41 | 2012 |
| Introducing charge hydration asymmetry into the generalized Born model A Mukhopadhyay, BH Aguilar, IS Tolokh, AV Onufriev Journal of Chemical Theory and Computation 10 (4), 1788-1794, 2014 | 38 | 2014 |
| Intricate genetic programs controlling dormancy in Mycobacterium tuberculosis EJR Peterson, AA Abidi, ML Arrieta-Ortiz, B Aguilar, JT Yurkovich, A Kaur, ... Cell reports 31 (4), 2020 | 34 | 2020 |
| Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions AV Onufriev, B Aguilar Journal of Theoretical and Computational Chemistry 13 (03), 1440006, 2014 | 27 | 2014 |
| Exploring Approaches for Predictive Cancer Patient Digital Twins: Opportunities for Collaboration and Innovation EA Stahlberg, MH Abdel-Rahman, B Aguilar, A Asadpoure, RA Beckman, ... Frontiers in Digital Health, 191, 2022 | 23 | 2022 |
| A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma B Aguilar, DL Gibbs, DJ Reiss, M McConnell, SA Danziger, A Dervan, ... Gigascience 9 (7), giaa075, 2020 | 22 | 2020 |
| Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding EV Katkova, AV Onufriev, B Aguilar, VB Sulimov Journal of Molecular Graphics and Modelling 72, 70-80, 2017 | 18 | 2017 |
| Dimension reduction of large sparse AND-NOT network models A Veliz-Cuba, B Aguilar, R Laubenbacher Electronic Notes in Theoretical Computer Science 316, 83-95, 2015 | 17 | 2015 |
| Cell death as a trigger for morphogenesis B Aguilar, A Ghaffarizadeh, CD Johnson, GJ Podgorski, I Shmulevich, ... PLoS One 13 (3), e0191089, 2018 | 14 | 2018 |
| A near-optimal control method for stochastic boolean networks B Aguilar, P Fang, R Laubenbacher, D Murrugarra Letters in biomathematics 7 (1), 67, 2020 | 11 | 2020 |
| Flexibility of boolean network reservoir computers in approximating arbitrary recursive and non-recursive binary filters M Echlin, B Aguilar, M Notarangelo, DL Gibbs, I Shmulevich Entropy 20 (12), 954, 2018 | 11 | 2018 |
| Atom diffusion of small Cu clusters across facet–facet barriers over Cu {1 1 1} surfaces BH Aguilar, JC Flores, AM Coronado, H Huang Modelling and Simulation in Materials Science and Engineering 15 (5), 419, 2007 | 11 | 2007 |
Alexey OnufrievVirginia TechVerified email at vt.edu
