Publications
2019
D. M. Blackburn, F. Lazure, A. H. Corchado, T. J. Perkins, H. S. Najafabadi, V. D. Soleimani (2019) “High-resolution genome-wide expression analysis of single myofibers using SMART-Seq” Journal of Biological Chemistry, Vol. 294, Iss. 52, pp. 20097-20108. [Access Online]
R. L. Carpenedo, S. Y. Kwon, R. M. Tanner, J. Yockell-Lelièvre, C. Choey, C. Doré, M. Ho, D. J. Stewart, T. J. Perkins, W. L. Stanford (2019) "Transcriptomically Guided Mesendoderm Induction of Human Pluripotent Stem Cells Using a Systematically Defined Culture Scheme" Stem Cell Reports, Vol. 13, Iss. 6, pp. 1111-1125. [Access Online]
N. Bashkeel, T. J. Perkins, M. Kærn, J. M. Lee (2019) "Human gene expression variability and its dependence on methylation and aging" BMC Genomics, Vol. 20, Iss. 1, Art. 941. [Access Online]
J. G. Chitpin, A. Awdeh, T. J. Perkins (2019) "RECAP reveals the true statistical significance of ChIP-seq peak calls" Bioinformatics, Vol. 35, Iss. 19, pp. 3592-3598. [Access Online][Software]
N. Bharathy, et al. (2019) "Preclinical rationale for entinostat in embryonal rhabdomyosarcoma" Skeletal Muscle, Vol. 9, Art. 12 (10 pages). [Access Online]
2018
A. Awdeh, H. Phenix. M. Kaern, T. J. Perkins (2018) "Dynamics in Epistasis Analysis" IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 3, pp. 878--891. [Access Online]
N. Bharathy, et al. (2018) "The HDAC3--SMARCA4--miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma" Science Signalling, Vol. 11, Iss. 557, Art. eaau7632 (13 pages). [Access Online]
H. B. Maganti, et al. (2018) "Targeting the MTF2--MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy" Cancer Discovery, Vol. 8, Iss. 11, pp. 1376--1389. [Access Online]
V. D. Soleimani, D. Nguyen, P. Ramachandran, G. A. Palidwor, C. J. Porter, H. Yin, T. J. Perkins, M. A. Rudnicki (2018) "Cis-regulatory determinants of MyoD function" Nucleic Acids Research, Vol. 46, No. 14, pp. 7221--7235. [Access Online]
J. L. M. Rothberg, H. B. Maganti, H. Jrade, C. J. Porter, G. A. Palidwor, C. Cafariello, H. L. Battaion, S. T. Khan, T. J. Perkins, R. F. Paulson, C. Y. Ito, W. L. Stanford (2018) "Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis" Cell Discovery, Vol. 4, Art. 21 (16 pages). [Access Online]
2017
P. Ramachandran, D. Sanchez-Taltavull, T. J. Perkins (2017) "Uncovering Robust Patterns of MicroRNA Co-Expression across Cancers using Bayesian Relevance Networks" PLoS ONE, Vol. 12, No. 8, Art. e0183103 (25 pages). [Access Online] Also appeared at GLBIO 2017, where it won "Outstanding Presentation".
S. Nilufar, D. S. Wang, J. Girgis, C. G. Palii, D. Yang, A. Blais, M. Brand, D. Precup, T. J. Perkins (2017) "Learning-Based Interactive Segmentation using the Maximum Mean Cycle Weight Formalism" Proceedings of SPIE Medical Imaging 2017: Image Processing, Art. 101332S (20 pages). [Access Online]
A. Awdeh, H. Phenix. M. Kaern, T. J. Perkins (2017) "Dynamics in Epistasis Analysis" Preprint in IEEE Transactions on Computational Biology and Bioinformatics. [Access Online]
Y. Grinberg, T. J. Perkins (2017) "Fully Polynomial-Time Computation of Maximum Likelihood Trajectories in Markov Chains" In Information Processing Letters, Vol. 118, pp. 53-57.
P. K. Shah, M. R. Tanner, I. Kovacevic, A. Rankin, T. E. Marshall, N. Noblett, N. N. Tran, T. Roenspies, J. Hung, Z. Chen, C. Slatculescu, T. J. Perkins, Z. Bao, A. Colavita (2017) "PCP and SAX-3/Robo Pathways Cooperate to Regulate Convergent Extension-Based Nerve Cord Assembly in C. elegans." Developmental Cell, Vol. 41, Iss. 2, pp. 195-203. [Access Online]
R. Kumar, A. Gont, T. J. Perkins, J. E. L. Hanson, I. A. J. Lorimer (2017) "Induction of senescence in primary glioblastoma cells by serum and TGFß." Scientific Reports, Vol. 7, Iss. 1, Art. 2156. [Access Online]
Z. Chen, W. Y. Chang, A. Etheridge, H. Strickfaden, Z. Jin, G. Palidwor, J.-H. Cho, K. Wang, S. Y. Kwon, C. Doré, A. Raymond, A. Hotta, J. Ellis, R. A. Kandel, F. J. Dilworth, T. J. Perkins, M. J. Hendzel, D. J. Galas, W. L. Stanford (2017) "Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape." Aging Cell, Vol. 16, Iss. 4, pp. 870--887. [Access Online]
S. Fraineau, C.G. Palii, B. McNeill, M. Ritso, W.C. Shelley, N. Prasain, A. Chu, E. Vion, K. Rieck, S. Nilufar, T.J. Perkins, M.A. Rudnicki, D.S. Allan, M.C. Yoder, E.J. Suuronen, M. Brand (2017) "Epigenetic activation of pro-angiogenic signaling pathways in human endothelial progenitors increases vasculogenesis." Stem Cell Reports, Vol. 9, No. 5, pp. 1573-1587. [Access Online]
2016
D. Sanchez-Taltavull, P. Ramachandran, N. Lau, T. J. Perkins (2016) "Bayesian Correlation Analysis for Sequence Count Data" In PLoS ONE, Vol. 11, No. 10, Art. e0163595. [Access Online]
J. Bar, M. S. Hasim, T. Baghai, N. Niknejad, T. J. Perkins, D. J. Stewart, H. S. Sekhon, P. J. Villeneuve, J. Dimitroulakos (2016) "Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells." In Neoplasia, Vol. 18, No. 9, pp. 525--535. [Access Online]
D. Sanchez-Taltavull, M. MacLeod, T. J. Perkins (2016) "On cross-conditional and fluctuation correlations in competitive RNA networks" In Bioinformatics, Vol. 32, No. 17, pp. i790-i797. [Access Online]
A. Jahani-Asl et al. (2016) "Control of glioblastoma tumorigenesis by feed-forward cytokine signaling" In Nature Neuroscience, Vol. 19, pp. 798-806. [Access Online]
A. Benyoucef et al. (2016) "UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia" In Genes and Development, Vol. 30, pp. 508-521. [Access Online]
2015
P. Ramachandran, G. Palidwor, T. J. Perkins (2015) "BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates" In Epigenetics and Chromatin, Vol 8, Art. 33 (16 pages). [Access Online]
A. Awdeh, H. Phenix, M. Kaern, T. J. Perkins (2015) "The Potential Power of Dynamics in Epistasis Analysis" In BCB'15: Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, ACM New York, NY, USA, pp. 106-115. [Access Online]
Y. Grinberg, T. J. Perkins "State Sequence Analysis in Hidden Markov Models" In Uncertainty in Artificial Intelligence: Proceedings of the Thirty-First Conference (2015), Eds. M. Meila, T. Heskes, AUAI Press Corvallis, Oregon, USA, pp. 336-344. [Access Online]
P. A. Cassar, R. L. Carpenedo, P. Samavarchi-Tehrani, et al. "Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network" In EMBO Reports, published online Aug 11, 2015. [Access Online]
M. A. Ghadie, N. Japkowicz, T. J. Perkins "Gene Selection for the Reconstruction of Stem Cell Differentiation Trees: A Linear Programming Approach" Bioinformatics, Vol. 31, No. 16, pp. 2676-2682. [Access Online]
J. Bar, I. Gorn-Hondermann, P. Moretto, T. J. Perkins, N. Niknejad, D. J. Stewart, G. D. Goss, J. Dimitroulakos "miR Profiling Identifies Cyclin-Dependent Kinase 6 Downregulation as a Potential Mechanism of Acquired Cisplatin Resistance in Non–Small-Cell Lung Carcinoma" Clinical Lung Cancer, published online Feb 2, 2015. [Access Online]
2014
T. J. Perkins, E. Foxall, L. Glass, R. Edwards (2014) "A scaling law for random walks on networks" Nature Communications, Vol. 5, Art. 5121 (7 pages). [Access Online]
C. G. Palii et al. (2014) "Trichostatin A Enhances Vascular Repair by Injected Human Endothelial Progenitors through Increasing the Expression of TAL1-Dependent Genes" Cell Stem Cell, Vol. 14, Iss. 5, pp. 644-657. [Access Online]
S. Nilufar, T. J. Perkins (2014) "Learning a Cost Function for Microscope Image Segmentation" 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 5506-5509. [Access Online]
S. Nilufar, T. J. Perkins (2014) "Learning to Detect Contours with Dynamic Programming Snakes" 22nd International Conference on Pattern Recognition. [Access Online]
K. Li, D. Precup, T. J. Perkins (2014) "Pooled Screening for Synergistic Interactions Subject to Blocking and Noise" PLoS ONE, Vol. 9, Iss. 1, Art. e85864 (12 pages). [Access Online]
2013
P. Ramachandran, T. J. Perkins (2013) "Adaptive Bandwidth Kernel Density Estimation for Next-Generation Sequencing Data" BMC Proceedings, Vol. 7 (Suppl. 7), Art. S7 (10 pages). [Access Online] [Software]
S. Nilufar, A. A. Morrow, J. M. Lee, T. J. Perkins (2013) "FiloDetect: Automatic Detection of Filopodia from Fluorescence Microscopy Images" BMC Systems Biology, Vol. 7, Art. 66. [Access Online] [Software]
V. D. Soleimani, G. A. Palidwor, P. Ramachandran, T. J. Perkins, M. A. Rudnicki (2013) "Chromatin tandem affinity purification sequencing" Nature Protocols, Vol. 8, No. 8, pp. 1525-1534. [Access Online]
H. Phenix, T. J. Perkins, M. Kaern (2013) "Identifiability and inference of pathway motifs by epistasis analysis" Chaos, Vol. 23, No. 2, Art. 025103 (9 pages). [Access Online]
P. Ramachandran, G. A. Palidwor, C. J. Porter, T. J. Perkins (2013) "MaSC: Mappability-Sensitive Cross-Correlation for Estimating Mean Fragment Length of Single-End Short Read Sequencing Data" Bioinformatics, Vol. 29, No. 4, pp. 444-450. [Access Online] [Software]
2012
P. Levin, J. Lefebvre, T. J. Perkins (2012) "What Do Molecules Do When We're Not Looking? State Sequence Analysis for Stochastic Chemical Systems" Journal of the Royal Society Interface, Vol. 9, No. 77, pp. 3411-3425. [Access On-Line] [Software]
V. D. Soleimani, V. G. Punch, Y-i Kawabe, A. E. Jones, G. A. Palidwor, C. J. Porter, J. W. Cross, J. J. Carvajal, C. E. M. Kockx, W. F. J. van IJcken, T. J. Perkins, P. W. J. Ribgy, F. Grosveld, M. A. Rudnicki (2012) "Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs" Developmental Cell, Vol. 22, Iss. 6, pp. 1208-1220. [Access On-Line]
J. Lefebvre, T. J. Perkins (2012) "Neural population densities shape network correlations" Physical Review E , Vol. 85, No. 2, Art. 021914. [Access On-Line]
R. Edwards, E. Foxall, T. J. Perkins (2012) "Scaling Properties of Paths on Graphs" Electronic Journal of Linear Algebra, Vol. 23, pp. 966-988. [Access Online]
E. Iacucci, H. H. Zingg, T. J. Perkins (2012) "Methods for determining the statistical significance of enrichment or depletion of gene ontology classifications under weighted membership" Frontiers in Genetics, Vol. 3, Art. 24. [Access On-Line]
T. J. Perkins, A. Y. Weiße, P. S. Swain (2012) "Chance and Memory" In Quantitative Biology: From Molecular to Cellular Systems, M. E. Wall (ed.), CRC Press. [Book at Amazon]
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]
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 and 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]
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]
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]
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.