Modeling stochasticity and variability in gene regulatory networks. - David Murrugarra; Alan Veliz-Cuba; Boris Aguilar; Seda Arat; Reinhard C. Laubenbacher (EURASIP J. Bioinform. Syst. Biol., 2012)

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. - Ramu Anandakrishnan; Boris Aguilar; Alexey Onufriev (Nucleic Acids Res., 2012)

Dimension Reduction of Large AND-NOT Network Models. - Alan Veliz-Cuba; Reinhard C. Laubenbacher; Boris Aguilar (CoRR, 2013)

Boolean nested canalizing functions: A comprehensive analysis. - Yuan Li; John O. Adeyeye; David Murrugarra; Boris Aguilar; Reinhard C. Laubenbacher (Theor. Comput. Sci., 2013)

Steady state analysis of Boolean molecular network models via model reduction and computational algebra. - Alan Veliz-Cuba; Boris Aguilar; Franziska Hinkelmann; Reinhard C. Laubenbacher (BMC Bioinform., 2014)

Dimension Reduction of Large Sparse AND-NOT Network Models. - Alan Veliz-Cuba; Boris Aguilar; Reinhard C. Laubenbacher (SASB, 2014)

Identification of control targets in Boolean molecular network models via computational algebra. - David Murrugarra; Alan Veliz-Cuba; Boris Aguilar; Reinhard C. Laubenbacher (BMC Syst. Biol., 2016)

Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters. - Moriah Echlin; Boris Aguilar; Max Notarangelo; David L. Gibbs; Ilya Shmulevich (Entropy, 2018)

Multi-omics data integration in the Cloud: Analysis of Statistically Significant Associations Between Clinical and Molecular Features in Breast Cancer. - Kawther Abdilleh; Boris Aguilar; J. Ross Thomson (BCB, 2020)

Multi-omics characterization of Microtubule-actin cross linking factor 1 (MACF1) using the ISB-Cancer Genomics Cloud. - Dondra Bailey; Kawther Abdilleh; Boris Aguilar; Alexis McClary (BCB, 2020)

Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. - Eric A. Stahlberg; Mohamed Abdel-Rahman; Boris Aguilar; Alireza Asadpoure; Robert A. Beckman; Lynn L. Borkon; Jeffrey N. Bryan; Colleen M. Cebulla; Young Hwan Chang; Ansu Chatterjee; Jun Deng; Sepideh Dolatshahi; et al. (Frontiers Digit. Health, 2022)

Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model. - Moriah Echlin; Boris Aguilar; Ilya Shmulevich (Entropy, 2023)

A framework towards digital twins for type 2 diabetes. - Yue Zhang 024; Guangrong Qin; Boris Aguilar; Noa Rappaport; James T. Yurkovich; Lance Pflieger; Sui Huang; Leroy Hood; Ilya Shmulevich (Frontiers Digit. Health, 2024)

LM-Merger: a workflow for merging logical models with an application to gene regulatory network models. - Luna Xingyu Li; Boris Aguilar; John H. Gennari; Guangrong Qin (BMC Bioinform., 2025)