Theodore J. Perkins, Ph.D. - Publications

Affiliations: 
University of Massachusetts, Amherst, Amherst, MA 
Area:
Reinforcement Learning

34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Benyoucef A, Palii CG, Wang C, Porter CJ, Chu A, Dai F, Tremblay V, Rakopoulos P, Singh K, Huang S, Pflumio F, Hébert J, Couture JF, Perkins TJ, Ge K, et al. UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia. Genes & Development. 30: 508-21. PMID 26944678 DOI: 10.1101/gad.276790.115  1
2015 Ramachandran P, Palidwor GA, Perkins TJ. BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. Epigenetics & Chromatin. 8: 33. PMID 26388941 DOI: 10.1186/s13072-015-0028-2  1
2015 Ghadie MA, Japkowicz N, Perkins TJ. Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach. Bioinformatics (Oxford, England). PMID 25847008 DOI: 10.1093/bioinformatics/btv192  1
2015 Grinberg Y, Perkins TJ. State sequence analysis in hidden Markov models Uncertainty in Artificial Intelligence - Proceedings of the 31st Conference, Uai 2015. 336-344.  1
2014 Perkins TJ, Foxall E, Glass L, Edwards R. A scaling law for random walks on networks. Nature Communications. 5: 5121. PMID 25311870 DOI: 10.1038/ncomms6121  1
2014 Palii CG, Vulesevic B, Fraineau S, Pranckeviciene E, Griffith AJ, Chu A, Faralli H, Li Y, McNeill B, Sun J, Perkins TJ, Dilworth FJ, Perez-Iratxeta C, Suuronen EJ, Allan DS, et al. Trichostatin A enhances vascular repair by injected human endothelial progenitors through increasing the expression of TAL1-dependent genes. Cell Stem Cell. 14: 644-57. PMID 24792117 DOI: 10.1016/j.stem.2014.03.003  1
2014 Li K, Precup D, Perkins TJ. Pooled screening for synergistic interactions subject to blocking and noise Plos One. 9. PMID 24454940 DOI: 10.1371/journal.pone.0085864  1
2014 Nilufar S, Perkins TJ. Learning to detect contours with dynamic programming snakes Proceedings - International Conference On Pattern Recognition. 984-989. DOI: 10.1109/ICPR.2014.179  1
2013 Nilufar S, Morrow AA, Lee JM, Perkins TJ. FiloDetect: Automatic detection of filopodia from fluorescence microscopy images Bmc Systems Biology. 7. PMID 23880086 DOI: 10.1186/1752-0509-7-66  1
2013 Soleimani VD, Palidwor GA, Ramachandran P, Perkins TJ, Rudnicki MA. Chromatin tandem affinity purification sequencing Nature Protocols. 8: 1525-1534. PMID 23845964 DOI: 10.1038/nprot.2013.088  1
2013 Ramachandran P, Palidwor GA, Porter CJ, Perkins TJ. MaSC: Mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data Bioinformatics. 29: 444-450. PMID 23300135 DOI: 10.1093/bioinformatics/btt001  1
2012 Levin P, Lefebvre J, Perkins TJ. What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems Journal of the Royal Society Interface. 9: 3411-3425. PMID 22977098 DOI: 10.1098/rsif.2012.0633  1
2012 Soleimani VD, Punch VG, Kawabe Y, Jones AE, Palidwor GA, Porter CJ, Cross JW, Carvajal JJ, Kockx CE, van IJcken WF, Perkins TJ, Rigby PW, Grosveld F, Rudnicki MA. Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Developmental Cell. 22: 1208-20. PMID 22609161 DOI: 10.1016/j.devcel.2012.03.014  1
2012 Lefebvre J, Perkins TJ. Neural population densities shape network correlations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 021914. PMID 22463251 DOI: 10.1103/PhysRevE.85.021914  1
2012 Iacucci E, Zingg HH, Perkins TJ. Methods for determining the statistical significance of enrichment or depletion of gene ontology classifications under weighted membership Frontiers in Genetics. 3. DOI: 10.3389/fgene.2012.00024  1
2011 Chan CC, Scoggin S, Wang D, Cherry S, Dembo T, Greenberg B, Jin EJ, Kuey C, Lopez A, Mehta SQ, Perkins TJ, Brankatschk M, Rothenfluh A, Buszczak M, Hiesinger PR. Systematic discovery of Rab GTPases with synaptic functions in Drosophila. Current Biology : Cb. 21: 1704-15. PMID 22000105 DOI: 10.1016/j.cub.2011.08.058  1
2011 Phenix H, Morin K, Batenchuk C, Parker J, Abedi V, Yang L, Tepliakova L, Perkins TJ, Kærn M. Quantitative epistasis analysis and pathway inference from genetic interaction data. Plos Computational Biology. 7: e1002048. PMID 21589890 DOI: 10.1371/journal.pcbi.1002048  1
2011 Charlebois DA, Perkins TJ, Kaern M. Stochastic gene expression and the processing and propagation of noisy signals in genetic networks Intelligent Systems Reference Library. 11: 89-112. DOI: 10.1007/978-3-642-19621-8_5  1
2010 Salehi M, Perkins TJ. Maximum probability reaction sequences in stochastic chemical kinetic systems. Frontiers in Physiology. 1: 170. PMID 21629860 DOI: 10.3389/fphys.2010.00170  1
2010 Summer G, Perkins TJ. Functional data analysis for identifying nonlinear models of gene regulatory networks. Bmc Genomics. 11: S18. PMID 21143801 DOI: 10.1186/1471-2164-11-S4-S18  1
2010 Husainy AN, Morrow AA, Perkins TJ, Lee JM. Robust patterns in the stochastic organization of filopodia. Bmc Cell Biology. 11: 86. PMID 21083909 DOI: 10.1186/1471-2121-11-86  1
2010 Palidwor GA, Perkins TJ, Xia X. A general model of codon bias due to GC mutational bias. Plos One. 5: e13431. PMID 21048949 DOI: 10.1371/journal.pone.0013431  1
2010 Perkins TJ, Wilds R, Glass L. Robust dynamics in minimal hybrid models of genetic networks. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 368: 4961-75. PMID 20921006 DOI: 10.1098/rsta.2010.0139  1
2010 Song C, Phenix H, Abedi V, Scott M, Ingalls BP, Kaern M, Perkins TJ. Estimating the stochastic bifurcation structure of cellular networks. Plos Computational Biology. 6: e1000699. PMID 20221261 DOI: 10.1371/journal.pcbi.1000699  1
2010 Perkins TJ, Hallett MT. 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 / Ieee, Acm. 7: 118-25. PMID 20150674 DOI: 10.1109/TCBB.2008.38  1
2009 Perkins TJ. Maximum likelihood trajectories for continuous-time Markov chains Advances in Neural Information Processing Systems 22 - Proceedings of the 2009 Conference. 1437-1445.  1
2006 Perkins TJ, Jaeger J, Reinitz J, Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. Plos Computational Biology. 2: e51. PMID 16710449 DOI: 10.1371/journal.pcbi.0020051  1
2006 Rosenfeld N, Perkins TJ, Alon U, Elowitz MB, Swain PS. A fluctuation method to quantify in vivo fluorescence data. Biophysical Journal. 91: 759-66. PMID 16648159 DOI: 10.1529/biophysj.105.073098  1
2005 Glass L, Perkins TJ, Mason J, Siegelmann HT, Edwards R. Chaotic dynamics in an electronic model of a genetic network Journal of Statistical Physics. 121: 989-994. DOI: 10.1007/s10955-005-7009-y  1
2003 Perkins TJ, Barto AG. Lyapunov design for safe reinforcement learning Journal of Machine Learning Research. 3: 803-832.  1
2003 Perkins TJ, Precup D. A convergent form of approximate policy iteration Advances in Neural Information Processing Systems 1
2002 Bernstein DS, Perkins TJ, Zilberstein S, Finkelstein L. Scheduling contract algorithms on multiple processors Proceedings of the National Conference On Artificial Intelligence. 702-706.  1
2001 Perkins TJ, Barto AG. Heuristic search in infinite state spaces guided by Lyapunov analysis Ijcai International Joint Conference On Artificial Intelligence. 242-247.  1
1999 Moll R, Barto AG, Perkins TJ, Sutton RS. Learning instance-independent value functions to enhance local search Advances in Neural Information Processing Systems. 1017-1023.  1
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