Using a standard clock technique for efficient simulation. - Pirooz Vakili (Oper. Res. Lett., 1991)

Correlation of Markov Chains Simulated in Parallel. - Paul Glasserman; Pirooz Vakili (WSC, 1992)

Ordinal optimization of DEDS. - Yu-Chi Ho; R. S. Sreenivas; Pirooz Vakili (Discret. Event Dyn. Syst., 1992)

Massively Parallel and Distributed Simulation of a Class of Discrete Event Systems: A Different Perspective. - Pirooz Vakili (ACM Trans. Model. Comput. Simul., 1992)

Parallel replicated simulation of Markov chains: implementation and variance reduction. - Simon Streltsov; Pirooz Vakili (WSC, 1993)

Uniformization based sensitivity estimation for a class of discrete-event systems. - Pirooz Vakili; Guo-Xiang Yu (Discret. Event Dyn. Syst., 1994)

Optimality of hedging point policies in the production control of failure prone manufacturing systems. - Jian-Qiang Hu; Pirooz Vakili; Guo-Xiang Yu (IEEE Trans. Autom. Control., 1994)

Variance Reduction for Discrete Event Systems Driven by Poisson Processes. - Pirooz Vakili (WSC, 1995)

Variance reduction algorithms for parallel replicated simulation of uniformized Markov chains. - Simon Streltsov; Pirooz Vakili (Discret. Event Dyn. Syst., 1996)

Periodic and chaotic dynamics of a switched-server system under corridor policies. - Guo-Xiang Yu; Pirooz Vakili (IEEE Trans. Autom. Control., 1996)

A Non-myopic Utility Function for Statistical Global Optimization Algorithms. - Simon Streltsov; Pirooz Vakili (J. Glob. Optim., 1999)

Optimality of index policies for a sequential sampling problem. - David A. Castañón; Simon Streltsov; Pirooz Vakili (IEEE Trans. Autom. Control., 1999)

Optimal allocation of heterogeneous resources: a control-theoretic approach. - Yanfeng Wang; James R. Perkins; Pirooz Vakili; Anil Khurana (CDC, 2001)

Development of a discrete event dynamic systems curriculum using a Web-based "real-time" simulated factory. - Christos G. Cassandras; Meimei Deng; Jian-Qiang Hu; Christos G. Panayiotou; Pirooz Vakili; Chenming Zhao (ACC, 2004)

Value of flexibility in a finite horizon decision process. - Leonardo P. Santiago; Pirooz Vakili (CDC, 2004)

Capacity and Production Managment in a Single Product Manufacturing System. - Jian-Qiang Hu; Pirooz Vakili; Lei Huang (Ann. Oper. Res., 2004)

A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. - Ioannis Ch. Paschalidis; Yang Shen 001; Sandor Vajda; Pirooz Vakili (CDC/ECC, 2005)

On the Value of Flexibility in R&D Projects. - Leonardo P. Santiago; Pirooz Vakili (Manag. Sci., 2005)

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. - Ioannis Ch. Paschalidis; Yang Shen 001; Pirooz Vakili; Sandor Vajda (EMBC, 2006)

A new efficient simulation strategy for pricing path-dependent options. - Gang Zhao; Yakun Zhou; Pirooz Vakili (WSC, 2006)

Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. - Yang Shen 001; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2007)

Efficient estimation of option price and price sensitivities via structured database Monte Carlo (SDMC). - Gang Zhao; Tarik Borogovac; Pirooz Vakili (WSC, 2007)

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. - Ioannis Ch. Paschalidis; Yang Shen 001; Pirooz Vakili; Sandor Vajda (IEEE Trans. Autom. Control., 2007)

Control variate technique: A constructive approach. - Tarik Borogovac; Pirooz Vakili (WSC, 2008)

Monotonicity and stratification. - Gang Zhao; Pirooz Vakili (WSC, 2008)

A Control Variate Approach for Improving Efficiency of Ensemble Monte Carlo - Tarik Borogovac; Francis J. Alexander; Pirooz Vakili (CoRR, 2008)

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. - Yang Shen 001; Ioannis Ch. Paschalidis; Pirooz Vakili; Sandor Vajda (PLoS Comput. Biol., 2008)

Control variates for sensitivity estimation. - Tarik Borogovac; Na Sun; Pirooz Vakili (WSC, 2010)

Importance sampling for parametric estimation. - Xiaojin Tang; Pirooz Vakili (WSC, 2010)

A new approach to rigid body minimization with application to molecular docking. - Hanieh Mirzaei; Dima Kozakov; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Pirooz Vakili (CDC, 2012)

A message passing approach to Side Chain Positioning with applications in protein docking refinement. - Mohammad Moghadasi; Dima Kozakov; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2012)

Flexible refinement of protein-ligand docking on manifolds. - Hanieh Mirzaei; Elizabeth A. Villar; Scott E. Mottarella; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov; Pirooz Vakili (CDC, 2013)

A new distributed algorithm for side-chain positioning in the process of protein docking. - Mohammad Moghadasi; Dima Kozakov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2013)

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. - Feng Nan; Mohammad Moghadasi; Pirooz Vakili; Sandor Vajda; Dima Kozakov; Ioannis Ch. Paschalidis (CDC, 2014)

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. - Pirooz Vakili; Hanieh Mirzaei; Shahrooz Zarbafian; Ioannis Ch. Paschalidis; Dima Kozakov; Sandor Vajda (CDC, 2014)

The Impact of Side-Chain Packing on Protein Docking Refinement. - Mohammad Moghadasi; Hanieh Mirzaei; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis; Dima Kozakov (J. Chem. Inf. Model., 2015)

Focused grid-based resampling for protein docking and mapping. - Artem B. Mamonov; Mohammad Moghadasi; Hanieh Mirzaei; Shahrooz Zarbafian; Laurie E. Grove; Tanggis Bohnuud; Pirooz Vakili; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov (J. Comput. Chem., 2016)

Improved prediction of MHC-peptide binding using protein language models. - Nasser Hashemi; Boran Hao; Mikhail Ignatov; Ioannis Ch. Paschalidis; Pirooz Vakili; Sandor Vajda; Dima Kozakov (Frontiers Bioinform., 2023)