2011
C.-C. Chan, S. Scoggin, D. Wang, S. Cherry, T. Dembo, B. Greenberg, E. J. Jin, C. Kuey, A. Lopez, S. Q. Mehta, T. J. Perkins, M. Brankatschk, A. Rothenfluh, M. Buszczak, P. R. Hiesinger (2011) "Systematic Discovery of Rab GTPases with Synaptic Functions in Drosophila" Current Biology, Vol. 21, Iss. 20, pp. 1704-1715. [Access On-Line]
T. J. Perkins, A. Y. Weiße, P. S. Swain (2011) "Chance and Memory" In Quantitative Biology: From Molecular to Cellular Systems, M. E. Wall (ed.), CRC Press. [Book at Amazon]
H. Phenix, K. Morin, C. Batenchuk, J. Parker, V. Abedi, L. Yang, L. Tepliakova, T.J. Perkins, M. Kærn (2011) "Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data" PLoS Computational Biology Vol. 7, No. 5, Art. e1002048. [Access On-Line]
D. Charlebois, T. J. Perkins and M. Kaern (2011) "Stochastic gene expression and the processing of propagation of noisy signals in genetic networks" In Information Processing and Biological Systems, S. Niiranen and A. Ribeiro (Eds.), Springer. [Book website]
2010
G. Summer and T. J. Perkins (2010) "Functional data analysis for identifying nonlinear models of gene regulatory networks" BMC Genomics, Vol. 11 (Suppl 4), Art. S18. [Access On-Line]
A. N. Husainy, A. A. Morrow, T. J. Perkins and J. M. Lee (2010) "Robust patterns in the stochastic organization of filopodia" BMC Cell Biology, Vol. 11, Art. 86. [Access On-Line]
T. J. Perkins, R. Wilds and L. Glass (2010) "Robust dynamics in minimal hybrid models of genetic networks" Philosophical Transactions of the Royal Society A, Vol. 368, pp. 4961-4975. [Access On-Line]
G. A. Palidwor, T. J. Perkins and X. Xia (2010) "A General Model of Codon Bias Due to GC Mutational Bias" PLoS ONE 5(10): e13431. [Access On-Line]
M. Salehi and T. J. Perkins (2010) "Maximum Probability Reaction Sequences in Stochastic Chemical Kinetic Systems" Frontiers in Systems Biology 1:137 [Access On-Line] [Supporting material]
C. Song, H. Phenix, V. Abedi, M. Scott, B. P. Ingalls, M. Kaern and T. J. Perkins (2010) "Estimating the Stochastic Bifurcation Structure of Cellular Networks" PLoS Computational Biology, Vol. 6, No. 3, Art. e1000699. [Access On-Line] [Supporting material]
T. J. Perkins and M. T. Hallett (2010) "A trade-off between sample complexity and computational complexity in learning Boolean networks from time-series data" IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 1, pp. 118-125. [Access On-Line]
2009
T. J. Perkins and P. S. Swain (2009) "Strategies for cellular decision-making" Molecular Systems Biology, Vol. 5, Article 326. [Access On-Line]
L. Zamparo and T. J. Perkins (2009) "Statistical lower bounds on protein copy number from fluorescence expression images" Bioinformatics, Vol. 25, pp. 2670-2676. [Access On-Line] [Supporting material]
T. J. Perkins (2009) "Maximum likelihood trajectories for continuous-time Markov chains" In Advances in Neural Information Processing Systems 22 (NIPS-2009). [Access On-Line] (Search the page for "Perkins")
2008
S. Mitra, S. Datta, T. J. Perkins and G. Michailidis (2008) Introduction to Machine Learning and Bioinformatics. Taylor and Francis Group, Chapman & Hall/CRC Press. [At Amazon]
S. Cory and T. J. Perkins (2008) "Implementing Arithmetic and Other Analytic Operations by Transcriptional Regulation" PLoS Computational Biology, Vol. 4(4), e1000064. [Access On-Line]
2007
T. J. Perkins (2007) "The Gap Gene System of Drosophila melanogaster: Model-fitting and Validation" Annals of the New York Academy of Sciences, Vol. 1115, pp. 116-131. [Access On-Line]
E. Libby, T. J. Perkins, P. S. Swain (2007) "Noisy information processing through transcriptional regulation" Proceedings of the National Academy of Sciences, Vol. 104, No. 17, pp. 7151-7156. [Access On-Line]
2006
T. J. Perkins, J. Jaeger, J. Reinitz, L. Glass (2006) "Reverse Engineering the Gap Gene System of Drosophila Melanogaster" PLoS Computational Biology, Vol. 2, No. 5, e51. [Access On-Line]
N. Rosenfeld, T. J. Perkins, U. Alon, M. B. Elowitz, P. S. Swain (2006) "A fluctuation method to quantify in vivo fluorescence data" Biophysical Journal, Vol. 91, No. 2, pp. 759-66. [Access On-Line]
T. J. Perkins, M. Hallett, L. Glass (2006) "Dynamical properties of model gene networks and implications for the inverse problem" BioSystems, Vol. 84, Iss. 2, pp. 115-123. [Access On-Line]
2005
L. Glass, T. J. Perkins, J. Mason, H. T. Siegelmann, R. Edwards (2005) "Chaotic Dynamics in an Electronic Model of a Genetic Network" Journal of Statistical Physics, Vol. 121, No. 5-6, pp. 969-994. [Access On-Line]
M. Scott, T. J. Perkins, S. Bunnell, F. Pepin, D. Y. Thomas, M. Hallett (2005) "Identifying Regulatory Subnetworks for a Distinguished Set of Genes" Molecular and Cellular Proteomics, Vol. 4, pp. 683-692. [Access On-Line]
2004
T. J. Perkins, M. Hallett and L. Glass (2004) "Inferring Models of Gene Expression Dynamics." Journal of Theoretical Biology, Vol. 230, pp. 289-299. [Access On-Line]
2003
T. J. Perkins and D. Precup (2003) "A Convergent Form of Approximate Policy Iteration" In Advances in Neural Information Processing Systems 15 (NIPS-2002), pp. 1595-1602.
2002
T. J. Perkins (2002) "Lyapunov Methods for Safe Intelligent Agent Design" Ph.D. Thesis, University of Massachusetts Amherst.
T. J. Perkins and A. G. Barto (2002) "Lyapunov Design for Safe Reinforcement Learning" Journal of Machine Learning Research, Volume 3(Dec), pp. 803-823.
T. J. Perkins and M. D. Pendrith (2002) "On the Existence of Fixed Points for Q-Learning and Sarsa in Partially Observable Domains" In Proceedings of the Nineteenth International Conference on Machine Learning (ICML-2002), pp. 490-497.
T. J. Perkins (2002) "Reinforcement Learning for POMDPs based on Action Values and Stochastic Optimization" In Proceedings of the Eighteenth National Conference on Artificial Intelligence (AAAI-2002), pp. 199-204.
D. S. Bernstein, T. J. Perkins, S. Zilberstein, and L. Finkelstein (2002) "Scheduling Contract Algorithms on Multiple Processors" In Proceedings of the Eighteenth National Conference on Artificial Intelligence (AAAI-2002), pp. 702--706.
2001
T. J. Perkins and A. G. Barto (2001) "Lyapunov-Constrained Action Sets for Reinforcement Learning" In Proceedings of the Eighteenth International Conference on Machine Learning (ICML-01), pp. 409-416.
T. J. Perkins and A. G. Barto (2001) "Heuristic Search in Infinite State Spaces Guided by Lyapunov Analysis" In Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence (IJCAI-01), pp. 242-247.
2000
R. Moll, T. J. Perkins, and A. G. Barto (2000) "Machine Learning for Subproblem Selection" In Proceedings of the Seventeenth International Conference on Machine Learning (ICML-2k), pp. 615-622.