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Theodore J. Perkins, Ph.D. - Publications

Affiliations: 
University of Massachusetts, Amherst, Amherst, MA 
Area:
Reinforcement Learning
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33 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
2020 Gillespie MA, Palii CG, Sanchez-Taltavull D, Shannon P, Longabaugh WJR, Downes DJ, Sivaraman K, Espinoza HM, Hughes JR, Price ND, Perkins TJ, Ranish JA, Brand M. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Molecular Cell. PMID 32330456 DOI: 10.1016/J.Molcel.2020.03.031  0.35
2019 Bashkeel N, Perkins TJ, Kærn M, Lee JM. Human gene expression variability and its dependence on methylation and aging. Bmc Genomics. 20: 941. PMID 31810449 DOI: 10.1186/S12864-019-6308-7  0.306
2018 Soleimani VD, Nguyen D, Ramachandran P, Palidwor GA, Porter CJ, Yin H, Perkins TJ, Rudnicki MA. Cis-regulatory determinants of MyoD function. Nucleic Acids Research. PMID 30016497 DOI: 10.1093/Nar/Gky388  0.306
2018 Rothberg JLM, Maganti HB, Jrade H, Porter CJ, Palidwor GA, Cafariello C, Battaion HL, Khan ST, Perkins TJ, Paulson RF, Ito CY, Stanford WL. Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis. Cell Discovery. 4: 21. PMID 29736258 DOI: 10.1038/S41421-018-0022-5  0.318
2017 Ramachandran P, Sánchez-Taltavull D, Perkins TJ. Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks. Plos One. 12: e0183103. PMID 28817636 DOI: 10.1371/journal.pone.0183103  0.331
2017 Chen Z, Chang WY, Etheridge A, Strickfaden H, Jin Z, Palidwor G, Cho JH, Wang K, Kwon SY, Doré C, Raymond A, Hotta A, Ellis J, Kandel RA, Dilworth FJ, ... Perkins TJ, et al. Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape. Aging Cell. PMID 28597562 DOI: 10.1111/Acel.12621  0.308
2017 Awdeh A, Phenix H, Kaern M, Perkins T. Dynamics in Epistasis Analysis. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28092574 DOI: 10.1109/Tcbb.2017.2653110  0.326
2016 Sánchez-Taltavull D, Ramachandran P, Lau N, Perkins TJ. Bayesian Correlation Analysis for Sequence Count Data. Plos One. 11: e0163595. PMID 27701449 DOI: 10.1371/Journal.Pone.0163595  0.319
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  0.347
2015 Cassar PA, Carpenedo RL, Samavarchi-Tehrani P, Olsen JB, Park CJ, Chang WY, Chen Z, Choey C, Delaney S, Guo H, Guo H, Tanner RM, Perkins TJ, Tenenbaum SA, Emili A, et al. Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. Embo Reports. 16: 1334-57. PMID 26265008 DOI: 10.15252/Embr.201540974  0.346
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  0.334
2015 Jahani-Asl A, Yin H, Soleimani V, Chang N, Sincennes M, Luchman HA, Sidharth P, Scott A, Lorimer I, Perkins T, Ligon K, Weiss S, Rudnicki M, Bonni A. CSIG-06EGFRvIII REQUIRES OSMR AS A CO-RECEPTOR TO DRIVE GLIOBLASTOMA PATHOGENESIS Neuro-Oncology. 17: v67.2-v67. DOI: 10.1093/Neuonc/Nov210.06  0.314
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  0.306
2013 Phenix H, Perkins T, Kærn M. Identifiability and inference of pathway motifs by epistasis analysis Chaos. 23. PMID 23822501 DOI: 10.1063/1.4807483  0.344
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  0.312
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: 24. PMID 22375144 DOI: 10.3389/Fgene.2012.00024  0.35
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  0.359
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  0.354
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  0.352
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  0.348
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  0.335
2009 Zamparo L, Perkins TJ. Statistical lower bounds on protein copy number from fluorescence expression images. Bioinformatics (Oxford, England). 25: 2670-6. PMID 19574287 DOI: 10.1093/Bioinformatics/Btp415  0.321
2008 Cory SM, Perkins TJ. Implementing arithmetic and other analytic operations by transcriptional regulation. Plos Computational Biology. 4: e1000064. PMID 18437243 DOI: 10.1371/Journal.Pcbi.1000064  0.355
2007 Perkins TJ. The gap gene system of Drosophila melanogaster: model-fitting and validation. Annals of the New York Academy of Sciences. 1115: 116-31. PMID 17934052 DOI: 10.1196/Annals.1407.015  0.366
2007 Libby E, Perkins TJ, Swain PS. Noisy information processing through transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America. 104: 7151-6. PMID 17420464 DOI: 10.1073/Pnas.0608963104  0.336
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  0.375
2006 Perkins TJ, Hallett M, Glass L. Dynamical properties of model gene networks and implications for the inverse problem. Bio Systems. 84: 115-23. PMID 16386356 DOI: 10.1016/J.Biosystems.2005.09.010  0.335
2005 Scott MS, Perkins T, Bunnell S, Pepin F, Thomas DY, Hallett M. Identifying regulatory subnetworks for a set of genes. Molecular & Cellular Proteomics : McP. 4: 683-92. PMID 15722371 DOI: 10.1074/Mcp.M400110-Mcp200  0.342
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  0.324
2004 Perkins TJ, Hallett M, Glass L. Inferring models of gene expression dynamics. Journal of Theoretical Biology. 230: 289-99. PMID 15302539 DOI: 10.1016/J.Jtbi.2004.05.022  0.357
2003 Perkins TJ, Barto AG. Lyapunov design for safe reinforcement learning Journal of Machine Learning Research. 3: 803-832.  0.465
2001 Perkins TJ, Barto AG. Heuristic search in infinite state spaces guided by Lyapunov analysis Ijcai International Joint Conference On Artificial Intelligence. 242-247.  0.461
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.  0.563
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