PUBLICATIONS

  1. Ali H, Liu S, Yilmaz Y, Couillet R, Rajapakse I, Hero A. "Latent heterogeneous multilayer community detection." ICASSP 2019-2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 8142-8146). IEEE (2019).
  2. Chen C, Surana A, Bloch A, Rajapakse I, "Model Identification Framework for Multilinear Time Invariant Systems." Submitted (2019)
  3. Bushnell G, Hardas T, Hartfield R, Zhang Y, Oakes R, Ronquist S, Chen H, Rajapakse I, Wicha M, Jeruss J, Shea L. "Biomaterial scaffolds recruit an aggressive population of metastatic tumor cells in vivo." Cancer Research: canres-2502. (2019)
  4. Ronquist S, Liu S, Perlman M, Rajapakse I. "4DNvestigator: a toolbox for the analysis of time series Hi-C and RNA-seq data." Submitted (2019)
  5. 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)
  6. Chen C, Surana A, Bloch A, Rajapakse I. "Multilinear Time Invariant System Theory." Submitted (2019)
  7. 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).
  8. 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).
  9. Muir LA, Kiridena S, Griffin C, DelProposto JB, Geletka L, Martinez-Santibañez G, Zamarron BF, Lucas H, Singer K, O' Rourke RW, Lumeng CN. "Frontline Science: Rapid adipose tissue expansion triggers unique proliferation and lipid accumulation profiles in adipose tissue macrophages." Biol. 2018 Apr;103(4):615-628. doi: 10.1002/JLB.3HI1017-422R. Epub 2018 Mar 1.
  10. Liu S, Chen PY, Hero A, Rajapakse I. "Dynamic Network Analysis of the 4D Nucleome." bioRxiv (2018): 268318.
  11. Liu S, Chen PY, Rajapakse I, Hero A. "First-order bifurcation detection for dynamic complex networks." 2018 IEEE International Conference on Acoustics, Speech and Signal Processing (2018).
  12. 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.
  13. Ried T and Rajapakse I. "The 4D Nucleome." Methods 123 (2017): 1-2.
  14. Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Muir LA, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Rajapakse I. "Genome Architecture Leads a Bifurcation in Cell Identity." bioRxiv (2017): 151555.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. Chen H, Seaman L, Liu S, Ried T & Rajapakse I. "Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers." Nucleus 8.4 (2017): 383-391.
  20. Macedonia C, Johnson C, Rajapakse I. "Advanced research and data methods in Women's health: big data analytics, adaptive studies, and the road ahead." Obstetrics & Gynecology 129.2 (2017): 249-264.
  21. Chen H, Liu S, Seaman L, Najarian C, Wu W, Ljungman M, Higgins G, Hero A, Wicha M, Rajapakse I. "Parental allele-specific genome architecture and transcription during the cell cycle." bioRxiv(2017): 201715.
  22. Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Muir LA, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Rajapakse I. "Genome Architecture Leads a Bifurcation in Cell Identity." bioRxiv (2017): 151555.
  23. Rajapakse I, and Smale S. "The Pitchfork Bifurcation." International Journal of Bifurcation and Chaos27.09 (2017): 1750132.
  24. Rajapakse I, and Smale S. "Mathematics of the genome." Foundations of Computational Mathematics 17.5 (2017): 1195-1217.
  25. Muir LA, Neeley C, Meyer KA, Baker NA, Brosius AM, Washabaugh AR, Varban OA, Finks JF, Zamarron BF, Flesher CG, Chang JS, DelProposto JB, Geletka L, Martinez-Santibanez G, Kaciroti N, Lumeng CN, O'Rourke RW. "Adipose tissue fibrosis, hypertrophy, and hyperplasia: Correlations with diabetes in human obesity." Obesity (Silver Spring). 2016 Mar;24(3):597-605. doi: 10.1002/oby.21377.
  26. Muir LA, Murry CE, Chamberlain JS. "Prosurvival Factors Improve Functional Engraftment of Myogenically Converted Dermal Cells into Dystrophic Skeletal Muscle.". Stem Cells Dev. 2016 Sep 7
  27. Surana A, Patterson G, Rajapakse I. "Dynamic tensor time series modeling and analysis." Decision and Control (CDC), 2016 IEEE 55th Conference on. IEEE, 2016.
  28. Chen J, Hero A, and Rajapakse I. "Spectral identification of topological domains." Bioinformatics 32.14 (2016): 2151-2158.
  29. Seaman L, Meixner W, Snyder J, Rajapakse I. "Periodicity of nuclear morphology in human fibroblasts." Nucleus 6.5 (2015): 408-416.
  30. 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.
  31. Chen H, Comment N, Chen J, Ronquist S, Hero A, Ried T, Rajapakse I. "Chromosome conformation of human fibroblasts grown in 3-dimensional spheroids." Nucleus 6.1 (2015): 55-65.
  32. Muir LA, Nguyen QG, Hauschka SD, Chamberlain JS. "Engraftment potential of dermal fibroblasts following in vivo myogenic conversion in immunocompetent dystrophic skeletal muscle." Mol Ther Methods Clin Dev. 2014 Jun 25;1:14025.
  33. Chen H, DeLong C, Bame M, Rajapakse I, Herron T, McInnis MG, O'Shea S . "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.
  34. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K. "Genome-wide methylation profiles reveal quantitative views of human aging rates." Molecular cell49.2 (2013): 359-367.
  35. Rajapakse I, Perlman MD, Martin PJ, Hansen JA, Kooperberg C. "Multivariate Detection of Gene‐Gene Interactions." Genetic epidemiology 36.6 (2012): 622-630.
  36. Rajapakse I, Groudine M, Mehran M. "What can systems theory of networks offer to biology?." PLoS computational biology 8.6 (2012): e1002543.
  37. Rajapakse I, Scalzo D, Groudine M. "Losing control: Cancer's catastrophic transition." nucleus 2.4 (2011): 249-252.
  38. Rajapakse I, Groudine M, Mesbahi M. "Dynamics and control of state-dependent networks for probing genomic organization." Proceedings of the National Academy of Sciences 108.42 (2011): 17257-17262.
  39. Rajapakse I, Groudine M. "On emerging nuclear order." The Journal of cell biology 192.5 (2011): 711-721.
  40. Pitt J, Rajapakse I, Ferre-D’Amare A. "SEWAL: an open-source platform for next-generation sequence analysis and visualization." Nucleic acids research 38.22 (2010): 7908-7915.
  41. Rajapakse I, Scalzo D, Tapscott SJ, Kosak ST, Groudine M. "Networking the nucleus." Molecular systems biology 6.1 (2010): 395.
  42. Rajapakse I, Perlman MD, Scalzo D, Kooperberg C, Groudine M, Kosak ST.. "The emergence of lineage-specific chromosomal topologies from coordinate gene regulation." Proceedings of the National Academy of Sciences 106.16 (2009): 6679-6684.
  43. Kooperberg C, Leblanc M, Dai JY, Rajapakse I. "Structures and assumptions: Strategies to harness gene× gene and gene× environment interactions in GWAS." Statistical science: a review journal of the Institute of Mathematical Statistics 24.4 (2009): 472.
  44. Groudine M, Rajapakse I. et al "Dynamics of Genomic Organization.." Blood 114.22 (2009): SCI-17. Web. 07 Feb. 2019.
  45. Rajapakse I, Muir L, Martin P. "Hardy’s “Small” Discovery Remembered." Notices of the AMS 55.3 (2008).
  46. Tschirgi M, Rajapakse I, Chandra M. "Functional consequence of mutation in rat cardiac troponin T is affected differently by myosin heavy chain isoforms." The Journal of physiology 574.1 (2006): 263-273.
  47. Chandra M, Tschirgi ML, Rajapakse I, Ken Campbell. "Troponin T modulates sarcomere length-dependent recruitment of cross-bridges in cardiac muscle." Biophysical journal 90.8 (2006): 2867-2876.