Rajapakse, Indika. "Conversation with Dr. Steve Smale and Dr. Lee Hartwell." NOTICES OF THE AMERICAN MATHEMATICAL SOCIETY 68, no. 9. 

Joshua Pickard, Ram Prakash, Marc Andrew Choi, Natalie Oliven, Cooper Stansbury, Jillian Cwycyshyn, Alex Gorodetsky, Alvaro Velasquez, and Indika Rajapakse, "Language Model Powered Digital Biology with BRAD," arXiv preprint arXiv:2409.02864v3 (2024)

Rajapakse I, Moler C. Kuramoto Model of Self-synchronizing Oscillators, Working paper

C. Stansbury, J. Cwycyshyn, J. Pickard, W. Meixner, I. Rajapakse, and L. A. Muir, “Data-guided direct reprogramming of human fibroblasts into the hematopoietic lineage,” Aug. 26, 2024, bioRxiv

Rajapakse I, Lindsly, Brockett R, Hartwell L. A Mathematical Theory of Learning Guided by the Immune System. (unpublished)

Rajapakse I and Hartwell L. Biological Controllability and Templating. (unpublished)

Cwycyshyn, Jillian, Cooper Stansbury, Walter Meixner, James B. Hoying, Lindsey A. Muir, and Indika Rajapakse. "A Programmable Platform for Probing Cell Migration and Proliferation." APL Bioengineering, 2024. 

Joshua Pickard, Cooper Stansbury, Amit Surana, Anthony Bloch, and Indika Rajapakse. "Biomarker Selection for Adaptive Systems." arXiv preprint arXiv:2405.09809 (2024). 

Joshua Pickard, Cooper Stansbury, Amit Surana, Indika Rajapakse, and Anthony Bloch. "Geometric Aspects of Observability of Hypergraphs." SIAM Journal on Matrix Analysis and Applications, 45(3), 1621-1642  (2024). 

Pickard J, Stansbury C, Chen C, Surana A, Bloch A, Rajapakse I. Kronecker product of tensors and hypergraphs, SIAM Journal on Matrix Analysis and Applications, 45(3), 1621-1642  (2024) 

Znaidi, M. R., Sia, J., Ronquist, S., Rajapakse, I., Jonckheere, E., & Bogdan, P. (2023). A unified approach of detecting phase transition in time-varying complex networks. Scientific Reports, 13(1), 17948. 

Pickard J, Surana A, Bloch A, Rajapakse I. Observability of hypergraphs. In 2023 62nd IEEE Conference on Decision and Control (CDC) 2023 Dec 13 (pp. 2445-2451). IEEE. 

Pickard J,  Can C, Salman R, Stansbury C, Kim S, Surana A, Rajapakse I. “HAT: Hypergraph Analysis Toolbox,” PLOS Computional Biology, 2023 

Dotson, Gabrielle A., Can Chen, Stephen Lindsly, Anthony Cicalo, Sam Dilworth, Charles Ryan, Sivakumar Jeyarajan et al. "Deciphering Multi-way Interactions in the Human Genome." Nature Communications 13, no. 1 (2022): 5498. 

Surana A, Chen C, Rajapakse I. "Hypergraph Similarity Measures."  IEEE Transactions on Network Science and Engineering,  2022

Sun Y, Dotson GA, Muir LA, Ronquist S, Oravecz-Wilson K, Peltier D, Seike K, Li L, Meixner W, Rajapakse I, Reddy P. Rearrangement of T Cell genome architecture regulates GVHD. iScience. 2022 Sep 16;25(9):104846. 

Wang R, Chen T, Lindsly S, Rehemtulla A, Hero A, Rajapakse I. "RAILS: A Robust Adversarial Immune-inspired Learning System", IEEE Access 10 (2022): 22061-22078 

Muir L, ...., Rajapakse I, O’Rourke R, Lumeng L. "Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters." Journal of Clinical Investigation (2022)

Lindsly S, Gupta M, Stansbury C, Rajapakse I. "Understanding Memory B Cell Selection." Journal of Theoretical Biology (2021) 

Stansbury, Cooper M., Gabrielle A. Dotson, Harrison Pugh, Alnawaz Rehemtulla, Indika Rajapakse, and Lindsey A. Muir. "A lipid-associated macrophage lineage rewires the spatial landscape of adipose tissue in early obesity." JCI Insight. 2023 .  

Wang R, Chen T, Yao P, Liu S. Rajapakse I, Hero A. "ASK: Adversarial Soft k-Nearest Neighbor Attack and Defense." IEEE Access 2022 (2022)

Wang R, Chen T, Lindsly S, Stansbury C, Rajapakse, I, Hero, A. "Immuno-mimetic Deep Neural Networks (Immuno-Net).", ICML 2021

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  (2021)

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) .

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

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." iScience, Volume 24, Issue 12, 17 December 2021, 103452 

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

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

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

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

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)

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).

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).

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).

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).

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). 

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. 

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

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. 

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. 

Macedonia CR, Johnson CT, Rajapakse I. Advanced Research and Data Methods in Women's Health. Obstetrics & Gynecology. 2017 Feb 1;129(2):249-64. 

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.

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. 

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

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

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

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

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. 

Chen HM, DeLong CJ, Bame M, Rajapakse I, Herron TJ, McInnis MG, O’shea KS.  "Transcripts involved in calcium signaling and telencephalic neuronal fate are altered in induced pluripotent stem cells from bipolar disorder patients." Translational psychiatry 4.3 (2014): e375-e375. 

Rajapakse I, Groudine M, Mesbahi M. Dynamics and control of state-dependent networks for probing genomic organization. Proceedings of the National Academy of Sciences. 2011 Oct 18;108(42):17257-62. 

Rajapakse I, Groudine M. On emerging nuclear order. Journal of Cell Biology. 2011 Mar 7;192(5):711-21. 

Rajapakse I, Groudine M, Mesbahi M. What can systems theory of networks offer to biology?. PLoS computational biology. 2012 Jun 28;8(6):e1002543. 

Hannum G, Guinney J,  ....... Rajapakse I, Friend S, Ideker T, Zhang K. Genome-wide methylation profiles reveal quantitative views of human aging rates. Molecular cell. 2013 Jan 24;49(2):359-67.