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P. Ramachandran, D. Sanchez-Taltavull, T. J. Perkins (2017) "Uncovering Robust Patterns of MicroRNA Co-Expression across Cancers using Bayesian Relevance Networks" To appear at GLBIO 2017. [Access Online] 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. 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] 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] 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]