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Indika Rajapakse, Ph.D. - Publications

Affiliations: 
2004 Washington State University, Pullman, WA, United States 
Area:
Mathematics, Neuroscience Biology
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Znaidi MR, Sia J, Ronquist S, Rajapakse I, Jonckheere E, Bogdan P. A unified approach of detecting phase transition in time-varying complex networks. Scientific Reports. 13: 17948. PMID 37864007 DOI: 10.1038/s41598-023-44791-3  0.754
2023 Stansbury CM, Dotson GA, Pugh H, Rehemtulla A, Rajapakse I, Muir LA. A lipid-associated macrophage lineage rewires the spatial landscape of adipose tissue in early obesity. Jci Insight. PMID 37651193 DOI: 10.1172/jci.insight.171701  0.766
2023 Pickard J, Chen C, Salman R, Stansbury C, Kim S, Surana A, Bloch A, Rajapakse I. HAT: Hypergraph analysis toolbox. Plos Computational Biology. 19: e1011190. PMID 37276238 DOI: 10.1371/journal.pcbi.1011190  0.429
2022 Dotson GA, Chen C, Lindsly S, Cicalo A, Dilworth S, Ryan C, Jeyarajan S, Meixner W, Stansbury C, Pickard J, Beckloff N, Surana A, Wicha M, Muir LA, Rajapakse I. Deciphering multi-way interactions in the human genome. Nature Communications. 13: 5498. PMID 36127324 DOI: 10.1038/s41467-022-32980-z  0.797
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. 25: 104846. PMID 36043052 DOI: 10.1016/j.isci.2022.104846  0.786
2022 Muir LA, Cho KW, Geletka LM, Baker NA, Flesher CG, Ehlers AP, Kaciroti N, Lindsly S, Ronquist S, Rajapakse I, O'Rourke RW, Lumeng CN. Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters. Jci Insight. PMID 34990410 DOI: 10.1172/jci.insight.146563  0.734
2021 Lindsly S, Jia W, Chen H, Liu S, Ronquist S, Chen C, Wen X, Stansbury C, Dotson GA, Ryan C, Rehemtulla A, Omenn GS, Wicha M, Li SC, Muir L, ... Rajapakse I, et al. Functional organization of the maternal and paternal human 4D Nucleome. Iscience. 24: 103452. PMID 34877507 DOI: 10.1016/j.isci.2021.103452  0.776
2021 Lindsly S, Gupta M, Stansbury C, Rajapakse I. Understanding memory B cell selection. Journal of Theoretical Biology. 531: 110905. PMID 34543633 DOI: 10.1016/j.jtbi.2021.110905  0.752
2021 Sweeney P, Chen C, Rajapakse I, Cone RD. Network dynamics of hypothalamic feeding neurons. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33795520 DOI: 10.1073/pnas.2011140118  0.39
2021 Lindsly S, Chen C, Liu S, Ronquist S, Dilworth S, Perlman M, Rajapakse I. 4DNvestigator: Time Series Genomic Data Analysis Toolbox. Nucleus (Austin, Tex.). PMID 33794739 DOI: 10.1080/19491034.2021.1910437  0.782
2021 Brown MA, Dotson GA, Ronquist S, Emons G, Rajapakse I, Ried T. TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization. Neoplasia (New York, N.Y.). 23: 257-269. PMID 33422939 DOI: 10.1016/j.neo.2020.12.010  0.793
2020 Dotson GA, Ryan CW, Chen C, Muir L, Rajapakse I. Cellular reprogramming: Mathematics meets medicine. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. e1515. PMID 33289324 DOI: 10.1002/wsbm.1515  0.788
2019 Braun R, Ronquist S, Wangsa D, Chen H, Anthuber L, Gemoll T, Wangsa D, Koparde V, Hunn C, Habermann JK, Heselmeyer-Haddad K, Rajapakse I, Ried T. Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression. Neoplasia (New York, N.Y.). 21: 401-412. PMID 30909073 DOI: 10.1016/J.Neo.2019.02.003  0.818
2019 Bushnell GG, Hardas TP, Hartfield RM, Zhang Y, Oakes RS, Ronquist S, Chen H, Rajapakse I, Wicha MS, Jeruss JS, Shea LD. Biomaterial scaffolds recruit an aggressive population of metastatic tumor cells in vivo. Cancer Research. PMID 30808673 DOI: 10.1158/0008-5472.Can-18-2502  0.779
2018 Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Muir LA, Rajapakse I. Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming. Iscience. 6: 232-246. PMID 30240614 DOI: 10.1016/J.Isci.2018.08.002  0.779
2017 Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha MS, Bloch A, Brockett R, Rajapakse I. Algorithm for cellular reprogramming. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078370 DOI: 10.1073/Pnas.1712350114  0.778
2017 Seaman L, Rajapakse I. 4D Nucleome Analysis Toolbox: Analysis of Hi-C data with abnormal karyotype and time series capabilities. Bioinformatics (Oxford, England). PMID 28961756 DOI: 10.1093/Bioinformatics/Btx484  0.797
2017 Ronquist S, Meixner W, Rajapakse I, Snyder J. Insight into Dynamic Genome Imaging: Canonical Framework Identification and High-Throughput Analysis. Methods (San Diego, Calif.). PMID 28461134 DOI: 10.1016/J.Ymeth.2017.04.022  0.793
2017 Seaman L, Chen H, Brown M, Wangsa D, Patterson G, Camps J, Omenn GS, Ried T, Rajapakse I. Nucleome Analysis Reveals Structure-function Relationships for Colon Cancer. Molecular Cancer Research : McR. PMID 28258094 DOI: 10.1158/1541-7786.Mcr-16-0374  0.813
2017 Rajapakse I, Smale S. Emergence of function from coordinated cells in a tissue. Proceedings of the National Academy of Sciences of the United States of America. PMID 28137861 DOI: 10.1073/Pnas.1621145114  0.38
2017 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 (Austin, Tex.). 0. PMID 28129029 DOI: 10.1080/19491034.2017.1280209  0.804
2016 Chen J, Hero AO, Rajapakse I. Spectral Identification of Topological Domains. Bioinformatics (Oxford, England). PMID 27153657 DOI: 10.1093/Bioinformatics/Btw221  0.335
2016 Rajapakse I, Smale S. Mathematics of the Genome Foundations of Computational Mathematics. 1-23. DOI: 10.1007/S10208-016-9316-X  0.421
2015 Seaman L, Meixner W, Snyder J, Rajapakse I. Periodicity of nuclear morphology in human fibroblasts. Nucleus (Austin, Tex.). 6: 408-16. PMID 26734724 DOI: 10.1080/19491034.2015.1095432  0.775
2015 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 of the United States of America. 112: 8002-7. PMID 26080430 DOI: 10.1073/Pnas.1505822112  0.825
2015 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 (Austin, Tex.). 6: 55-65. PMID 25738643 DOI: 10.1080/19491034.2014.1003745  0.795
2014 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: e375. PMID 25116795 DOI: 10.1038/Tp.2014.12  0.338
2012 Rajapakse I, Perlman MD, Martin PJ, Hansen JA, Kooperberg C. Multivariate detection of gene-gene interactions. Genetic Epidemiology. 36: 622-30. PMID 22782518 DOI: 10.1002/Gepi.21656  0.334
2012 Rajapakse I, Groudine M, Mesbahi M. What can systems theory of networks offer to biology? Plos Computational Biology. 8: e1002543. PMID 22761554 DOI: 10.1371/Journal.Pcbi.1002543  0.666
2011 Rajapakse I, Scalzo D, Groudine M. Losing control: cancer's catastrophic transition. Nucleus (Austin, Tex.). 2: 249-52. PMID 21941112 DOI: 10.4161/Nucl.2.4.16506  0.642
2011 Rajapakse I, Groudine M, Mesbahi M. Dynamics and control of state-dependent networks for probing genomic organization. Proceedings of the National Academy of Sciences of the United States of America. 108: 17257-62. PMID 21911407 DOI: 10.1073/Pnas.1113249108  0.692
2011 Rajapakse I, Groudine M. On emerging nuclear order. The Journal of Cell Biology. 192: 711-21. PMID 21383074 DOI: 10.1083/Jcb.201010129  0.693
2010 Rajapakse I, Scalzo D, Tapscott SJ, Kosak ST, Groudine M. Networking the nucleus. Molecular Systems Biology. 6: 395. PMID 20664641 DOI: 10.1038/Msb.2010.48  0.671
2009 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: 472-488. PMID 20640184 DOI: 10.1214/09-Sts287  0.34
2009 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 of the United States of America. 106: 6679-84. PMID 19276122 DOI: 10.1073/Pnas.0900986106  0.711
2009 Groudine MT, Rajapakse I, Scalzo D, Perlman M, Kooperberg CL, Kosak S. Dynamics of Genomic Organization. Blood. 114. DOI: 10.1182/Blood.V114.22.Sci-17.Sci-17  0.476
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