Increased Flexibility in Genetic Algorithms: the Use of variable Boltzmann Selective pressure to control Propagation. - Michael de la Maza; Bruce Tidor (Computer Science and Operations Research, 1992)

An Analysis of Selection Procedures with Particular Attention Paid to Proportional and Boltzmann Selection. - Michael de la Maza; Bruce Tidor (ICGA, 1993)

Fast methods for simulation of biomolecule electrostatics. - Shihhsien S. Kuo; Michael D. Altman; Jaydeep P. Bardhan; Bruce Tidor; Jacob K. White 001 (ICCAD, 2002)

FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation. - Michael D. Altman; Jaydeep P. Bardhan; Bruce Tidor; Jacob K. White 001 (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2006)

Efficient optimization of electrostatic interactions between biomolecules. - Jaydeep P. Bardhan; Michael D. Altman; Jacob K. White 001; Bruce Tidor (CDC, 2007)

The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism. - A. Katharina Wilkins; Paul I. Barton; Bruce Tidor (PLoS Comput. Biol., 2007)

Optimal Drug Cocktail Design: Methods for Targeting Molecular Ensembles and Insights from Theoretical Model Systems. - Mala L. Radhakrishnan; Bruce Tidor (J. Chem. Inf. Model., 2008)

A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics. - Shih-Hsien Kuo; Bruce Tidor; Jacob White 001 (ACM J. Emerg. Technol. Comput. Syst., 2008)

Stimulus Design for Model Selection and Validation in Cell Signaling. - Joshua F. Apgar; Jared E. Toettcher; Drew Endy; Forest M. White; Bruce Tidor (PLoS Comput. Biol., 2008)

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. - Daniel Machado; Rafael S. Costa; Miguel Rocha 001; Isabel Rocha; Bruce Tidor; Eugénio C. Ferreira (IWANN (2), 2009)

MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. - Bracken M. King; Bruce Tidor (Bioinform., 2009)

Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. - Michael D. Altman; Jaydeep P. Bardhan; Jacob K. White 001; Bruce Tidor (J. Comput. Chem., 2009)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Rotamer optimization for protein design through MAP estimation and problem-size reduction. - Eun-Jong Hong; Shaun M. Lippow; Bruce Tidor; Tomás Lozano-Pérez (J. Comput. Chem., 2009)

Sensitivity Analysis for Oscillating Dynamical Systems. - A. Katharina Wilkins; Bruce Tidor; Jacob K. White 001; Paul I. Barton (SIAM J. Sci. Comput., 2009)

Model Transformation of Metabolic Networks using a Petri Net Based Framework. - Daniel Machado; Rafael S. Costa; Miguel Rocha 001; Isabel Rocha; Bruce Tidor; Eugénio C. Ferreira (ACSD/Petri Nets Workshops, 2010)

Biochemical oscillator sensitivity analysis in the presence of conservation constraints. - Jared E. Toettcher; Anya Castillo; Bruce Tidor; Jacob White 001 (DAC, 2011)

An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability. - XiaoNa Wei; Bu-Cong Han; Jing-Xian Zhang; X. H. Liu; C. Y. Tan; Yu Yang Jiang; Boon Chuan Low; Bruce Tidor; Yuzong Chen 002 (BMC Syst. Biol., 2011)

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology. - Tina Toni; Bruce Tidor (PLoS Comput. Biol., 2013)