Learning Instance-Independent Value Functions to Enhance Local Search. - Robert Moll; Andrew G. Barto; Theodore J. Perkins; Richard S. Sutton (NIPS, 1998)

Machine Learning for Subproblem Selection. - Robert Moll; Theodore J. Perkins; Andrew G. Barto (ICML, 2000)

Lyapunov-Constrained Action Sets for Reinforcement Learning. - Theodore J. Perkins; Andrew G. Barto (ICML, 2001)

Heuristic Search in Infinite State Spaces Guided by Lyapunov Analysis. - Theodore J. Perkins; Andrew G. Barto (IJCAI, 2001)

Scheduling Contract Algorithms on Multiple Processors. - Daniel S. Bernstein; Theodore J. Perkins; Shlomo Zilberstein; Lev Finkelstein (AAAI/IAAI, 2002)

Reinforcement Learning for POMDPs Based on Action Values and Stochastic Optimization. - Theodore J. Perkins (AAAI/IAAI, 2002)

On the Existence of Fixed Points for Q-Learning and Sarsa in Partially Observable Domains. - Theodore J. Perkins; Mark D. Pendrith (ICML, 2002)

A Convergent Form of Approximate Policy Iteration. - Theodore J. Perkins; Doina Precup (NIPS, 2002)

Lyapunov Design for Safe Reinforcement Learning. - Theodore J. Perkins; Andrew G. Barto (J. Mach. Learn. Res., 2002)

Reverse Engineering the Gap Gene Network of Drosophila melanogaster. - Theodore J. Perkins; Johannes Jaeger; John Reinitz; Leon Glass (PLoS Comput. Biol., 2006)

Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation. - Sean M. Cory; Theodore J. Perkins (PLoS Comput. Biol., 2008)

Maximum likelihood trajectories for continuous-time Markov chains. - Theodore J. Perkins (NIPS, 2009)

Statistical lower bounds on protein copy number from fluorescence expression images. - Lee Zamparo; Theodore J. Perkins (Bioinform., 2009)

Estimating the Stochastic Bifurcation Structure of Cellular Networks. - Carl Song; Hilary Phenix; Vida Abedi; Matthew Scott 001; Brian P. Ingalls; Mads Kærn; Theodore J. Perkins (PLoS Comput. Biol., 2010)

A Trade-Off between Sample Complexity and Computational Complexity in Learning Boolean Networks from Time-Series Data. - Theodore J. Perkins; Michael T. Hallett (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data. - Hilary Phenix; Katy Morin; Cory Batenchuk; Jacob Parker; Vida Abedi; Liu Yang; Lioudmila Tepliakova; Theodore J. Perkins; Mads Kærn (PLoS Comput. Biol., 2011)

Automatic Detection of Filopodia from Fluorescence Microscopy Images. - Sharmin Nilufar; Theodore J. Perkins; Anne Morrow; Jonathan Lee (IWBBIO, 2013)

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. - Parameswaran Ramachandran; Gareth A. Palidwor; Christopher J. Porter; Theodore J. Perkins (Bioinform., 2013)

FiloDetect: automatic detection of filopodia from fluorescence microscopy images. - Sharmin Nilufar; Anne Morrow; Jonathan Lee; Theodore J. Perkins (BMC Syst. Biol., 2013)

Learning a Cost Function for Interactive Microscope Image Segmentation. - Sharmin Nilufar; Theodore J. Perkins (AAAI Workshop: Modern Artificial Intelligence for Health Analytics, 2014)

Learning a cost function for microscope image segmentation. - Sharmin Nilufar; Theodore J. Perkins (EMBC, 2014)

Learning to Detect Contours with Dynamic Programming Snakes. - Sharmin Nilufar; Theodore J. Perkins (ICPR, 2014)

The potential power of dynamics in epistasis analysis. - Aseel Awdeh; Hilary Phenix; Mads Kærn; Theodore J. Perkins (BCB, 2015)

State Sequence Analysis in Hidden Markov Models. - Yuri Grinberg; Theodore J. Perkins (UAI, 2015)

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach. - Mohamed A. Ghadie; Nathalie Japkowicz; Theodore J. Perkins (Bioinform., 2015)

On cross-conditional and fluctuation correlations in competitive RNA networks. - Daniel Sánchez-Taltavull; Matthew MacLeod; Theodore J. Perkins (Bioinform., 2016)

Super-enhancer Dynamics Throughout Myogenesis. - Basma Abdelkarim; Theodore J. Perkins (BCB, 2017)

Analysis of Controls in ChIP-seq. - Aseel Awdeh; Theodore J. Perkins (BCB, 2017)

Learning-based interactive segmentation using the maximum mean cycle weight formalism. - Sharmin Nilufar; Dao Sen Wang; John Girgis; Carmen G. Palii; D. Yang; A. Blais; M. Brand; Doina Precup; Theodore J. Perkins (Image Processing, 2017)

Fully polynomial-time computation of maximum likelihood trajectories in Markov chains. - Yuri Grinberg; Theodore J. Perkins (Inf. Process. Lett., 2017)

Dynamics in Epistasis Analysis. - Aseel Awdeh; Hilary Phenix; Mads Kærn; Theodore J. Perkins (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Optimal Risk in Multiagent Blind Tournaments. - Theodore J. Perkins (AAMAS, 2019)

RECAP reveals the true statistical significance of ChIP-seq peak calls. - Justin G. Chitpin; Aseel Awdeh; Theodore J. Perkins (Bioinform., 2019)

WACS: improving ChIP-seq peak calling by optimally weighting controls. - Aseel Awdeh; Marcel Turcotte; Theodore J. Perkins (BMC Bioinform., 2021)

BATL: Bayesian annotations for targeted lipidomics. - Justin G. Chitpin; Anuradha Surendra; Thao T. Nguyen; Graeme Taylor; Hongbin Xu; Irina Alecu; Roberto Ortega; Julianna J. Tomlinson; Angela M. Crawley; Michaeline McGuinty; Michael G. Schlossmacher; Rachel Saunders-Pullman; et al. (Bioinform., 2022)

A Model of Cell Population Dynamics in Skeletal Muscle Regeneration. - Renad Al-Ghazawi; Theodore J. Perkins; Xiaojian Shao (BCB, 2023)