SELECTED PUBLICATIONS

  1. Surana A, Chen C, Rajapakse I. "Hypergraph Dissimilarity Measures." arXiv:2106.08206, 2021

  2. Wang, R., Chen, T., Yao, P., Liu, S., Rajapakse, I., & Hero, A. (2021). ASK: Adversarial Soft k-Nearest Neighbor Attack and Defense. arXiv preprint arXiv:2106.14300.

  3. Wang, R., Chen, T., Yao, P., Liu, S., Rajapakse, I., & Hero, A. (2021). Immuno-mimetic Deep Neural Networks (Immuno-Net). (Accepted at the ICML 2021)

  4. Dotson GA, Ryan CW, Chen C, Muir L, Rajapakse I. "Cellular reprogramming: Mathematics meets medicine." WIREs Mech Dis. 2020;e1515. https://doi.org/10.1002/wsbm.1515

  5. Lindsly S, Chen C, Liu S, Ronquist S, Dilworth S, Perlman M, Rajapakse I. "4DNvestigator: time series genomic data analysis toolbox." Nucleus, 12:1, 58-64, DOI: 10.1080/19491034.2021.1910437 (2021) .

  6. Chen C, Surana A, Bloch A, Rajapakse I. "Controllability of Hypergraphs." IEEE Transactions on Network Science and Engineering, Accepted (2021).

  7. Lindsly S, Jia W, Chen H, Liu S, Ronquist S, Chen C, Wen X, Stansbury C, Dotson G, Ryan C, Rehemtulla A, Omenn G, Wicha M, Li S, Muir L, Rajapakse I. "Functional Organization of the Maternal and Paternal Human 4D Nucleome." bioRxiv doi: 10.1101/2020.03.15.992164 (2021).

  8. Brown M, Dotson G, Ronquist S, Emons G, Rajapakse I, Ried T. "TCF7L2 Silencing Reprograms the 4D Nucleome of Colorectal Cancer Cells." Neoplasia, February 2021, Pages 257-269

  9. Sweeney P, Chen C, Rajapakse I, Cone R. "Network Dynamics of Hypothalamic Feeding Neurons." Proceedings of the National Academy of Sciences, 118.14 (2021).

  10. Chen C, Rajapakse I. "Tensor Entropy for Uniform Hypergraphs." IEEE Transactions on Network Science and Engineering 7.4 (2020): 2889-2900.

  11. Chen C, Surana A, Bloch A, Rajapakse I. "Multilinear Control Systems Theory." SIAM Journal on Control and Optimization, 59.1 (2021): 749-776.

  12. Sun Y, Dotson GA, Muir L, Ronquist S, Oravecz-Wilson K, Peltier D, Seike K, Li L, Meixner W, Rajapakse I, Reddy P. "Cohesin Releasing Factor WAPL Regulates Genome Structure and Function of Mature T Cells." bioRxiv doi: 10.1101/2021.01.23.427857 (2020).

  13. Wang R, Chen T, Lindsly S, Rehemtulla A, Hero A, Rajapakse I. "RAILS: A Robust Adversarial Immune-inspired Learning System" arXiv preprint arXiv:2012.10485. (2020)

  14. Lindsly S, Gupta M, Stansbury C, Rajapakse I. "Understanding Memory B Cell Selection." arXiv preprint arXiv:2012.05817. (2021)

  15. Chen C, Surana A, Bloch A, Rajapakse I. "Data-Driven Model Reduction for Multilinear Control Systems via Tensor Trains." arXiv preprint arXiv:1912.03569 (2020)

  16. Ali H, Liu S, Yilmaz Y, Couillet R, Rajapakse I, Hero A. "Latent Heterogeneous Multilayer Community Detection." IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 8142-8146) (2019).

  17. Braun R, Ronquist S, Wangsa D, Chen H, Anthuber L, Gemoll T, Wangsa D, Koparde V, Hunn C, Habermann J, Heselmeyer-Haddad K, Rajapakse I, Ried T. "Single Chromosome Aneuploidy Induces Genome-wide Perturbation of Nuclear Organization and Gene Expression." Neoplasia (2019).

  18. Chen C, Surana A, Bloch A, Rajapakse I. "Multilinear Time Invariant System Theory." 2019 Proceedings of SIAM Conference on Control and its Applications, (pp. 118-125.) (2019).

  19. Chen P, Wu L, Liu S, Rajapakse I. "Fast Incremental von Neumann Graph Entropy Computation: Theory, Algorithm, and Applications." 2019 International Conference on Machine Learning (2019).

  20. Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Muir LA, Rajapakse I. "Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming." iScience (2018).

  21. Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha M, Bloch A, Brockett R and Rajapakse I. "Algorithm for Cellular Reprogramming." Proceedings of the National Academy of Sciences 114.45 (2017): 11832-11837.

  22. Ried T and Rajapakse I. "The 4D Nucleome." Methods 123 (2017): 1-2.

  23. Seaman L, and Rajapakse I. "4D Nucleome Analysis Toolbox: Analysis of Hi-C Data with Abnormal Karyotype and Time Series Capabilities." Bioinformatics 34.1 (2017): 104-106.

  24. Ronquist S, Meixner W, Rajapakse I, Snyder J. "Insight into Dynamic Genome Imaging: Canonical framework identification and high-throughput analysis." Methods 123 (2017): 119-127.

  25. Seaman L, Chen H, Brown M, Wangsa D, Patterson G, Camps J, Omenn G, Ried T and Rajapakse I. "Nucleome Analysis Reveals Structure–Function Relationships for Colon Cancer." Molecular Cancer Research 15.7 (2017): 821-830.

  26. Rajapakse I, and Smale S. "Emergence of Function from Coordinated Cells in a Tissue." Proceedings of the National Academy of Sciences 114.7 (2017): 1462-1467.

  27. Rajapakse I, and Smale S. "The Pitchfork Bifurcation." International Journal of Bifurcation and Chaos 27.09 (2017): 1750132.

  28. Rajapakse I, and Smale S. "Mathematics of the Genome." Foundations of Computational Mathematics 17.5 (2017): 1195-1217.

  29. Surana A, Patterson G, Rajapakse I. "Dynamic Tensor Time Series Modeling and Analysis." Decision and Control (CDC), 2016 IEEE 55th Conference on. IEEE, 2016.

  30. Chen J, Hero A, and Rajapakse I. "Spectral Identification of Topological Domains." Bioinformatics 32.14 (2016): 2151-2158.

  31. Chen H, Chen J, Muir LA, Ronquist S, Meixner W, Ljungman M, Ried T, Smale S, Rajapakse I. "Functional Organization of the Human 4D Nucleome. " Proceedings of the National Academy of Sciences 112.26 (2015): 8002-8007.