I. Rajapakse

Most-cited papers

Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates
Gregory Hannum, J. Guinney, Ling Zhao, Li Zhang +12 more
2012Molecules and Cells3,847 citations Open access
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Transcripts involved in calcium signaling and telencephalic neuronal fate are altered in induced pluripotent stem cells from bipolar disorder patients
Haiming Chen, C. DeLong, M. Bame, I. Rajapakse +3 more
2014Translational Psychiatry159 citations Open access
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On emerging nuclear order
I. Rajapakse, M. Groudine
2011Journal of Cell Biology136 citations Open access
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Functional organization of the human 4D Nucleome
Haiming Chen, Jie Chen, Lindsey A. Muir, Scott Ronquist +5 more
2015Proceedings of the National Academy of Sciences of the United States of America106 citations Open access
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The emergence of lineage-specific chromosomal topologies from coordinate gene regulation
I. Rajapakse, M. Perlman, David Scalzo, C. Kooperberg +2 more
2009Proceedings of the National Academy of Sciences of the United States of America101 citations Open access
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Spectral identification of topological domains
Jie Chen, A. Hero, I. Rajapakse
2016Bioinform.71 citations Open access
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Dynamics and control of state-dependent networks for probing genomic organization
I. Rajapakse, M. Groudine, M. Mesbahi
2011Proceedings of the National Academy of Sciences of the United States of America70 citations Open access
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Controllability of Hypergraphs
Can Chen, A. Surana, Anthony M. Bloch, I. Rajapakse
2020IEEE Transactions on Network Science and Engineering67 citations Open access
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A lipid-associated macrophage lineage rewires the spatial landscape of adipose tissue in early obesity
Cooper M. Stansbury, Gabrielle A. Dotson, H. Pugh, A. Rehemtulla +2 more
2023bioRxiv60 citations Open access
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Deciphering multi-way interactions in the human genome
Gabrielle A. Dotson, Can Chen, Stephen Lindsly, Anthony Cicalo +11 more
2021bioRxiv52 citations Open access
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Tensor Entropy for Uniform Hypergraphs
Can Chen, I. Rajapakse
2019IEEE Transactions on Network Science and Engineering48 citations Open access
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Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters
Lindsey A. Muir, K. Cho, L. Geletka, Nicki A. Baker +8 more
2022JCI Insight46 citations Open access
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Hypergraph Similarity Measures
Amit Surana, Can Chen, I. Rajapakse
2023IEEE Transactions on Network Science and Engineering41 citations
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Multilinear Control Systems Theory
Can Chen, A. Surana, A. Bloch, I. Rajapakse
2020SIAM Journal of Control and Optimization40 citations Open access
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Algorithm for cellular reprogramming
Scott Ronquist, G. Patterson, Markus A. Brown, Stephen Lindsly +6 more
2017Proceedings of the National Academy of Sciences of the United States of America40 citations Open access
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Multilinear Time Invariant System Theory
Can Chen, A. Surana, A. Bloch, I. Rajapakse
20192019 Proceedings of the Conference on Control and its Applications35 citations Open access
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What Can Systems Theory of Networks Offer to Biology?
I. Rajapakse, M. Groudine, M. Mesbahi
2012PLoS Comput. Biol.33 citations Open access
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Biomaterial scaffolds recruit an aggressive population of metastatic tumor cells in vivo
Grace G. Bushnell, Tejaswini P. Hardas, Rachel M. Hartfield, Yi-Ning Zhang +7 more
2019Cancer Research32 citations Open access
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Fast Incremental von Neumann Graph Entropy Computation: Theory, Algorithm, and Applications
Pin-Yu Chen, Ling-Fei Wu, Si-Jia Liu, I. Rajapakse
2018International Conference on Machine Learning31 citations
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Structures and Assumptions: Strategies to Harness Gene × Gene and Gene × Environment Interactions in GWAS
C. Kooperberg, M. LeBlanc, James Y. Dai, I. Rajapakse
2009Statistical Science30 citations Open access
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Nucleome Analysis Reveals Structure-function Relationships for Colon Cancer
L. Seaman, Haiming Chen, Markus A. Brown, Darawalee Wangsa +5 more
2017Molecular Cancer Research29 citations Open access
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Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming
Sijia Liu, Haiming Chen, Scott Ronquist, L. Seaman +9 more
2018iScience28 citations Open access
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Emergence of function from coordinated cells in a tissue
I. Rajapakse, S. Smale
2017Proceedings of the National Academy of Sciences of the United States of America28 citations Open access
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Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression
Rüdiger Braun, Scott Ronquist, Darawalee Wangsa, Haiming Chen +9 more
2019Neoplasia27 citations Open access
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Multivariate detection of gene-gene interactions
I. Rajapakse, M. Perlman, P. Martin, John A. Hansen +1 more
2012Genetic Epidemiology27 citations Open access
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The 4D Nucleome.
T. Ried, I. Rajapakse
2017Methods25 citations
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Networking the nucleus
I. Rajapakse, David Scalzo, S. Tapscott, S. Kosak +1 more
2010Molecular Systems Biology24 citations Open access
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SEWAL: an open-source platform for next-generation sequence analysis and visualization
J. Pitt, I. Rajapakse, A. Ferré-D'Amaré
2010Nucleic Acids Research22 citations Open access
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Automatic biomarker discovery and enrichment with BRAD
Joshua Pickard, Ram Prakash, Marc Andrew Choi, Natalie Oliven +6 more
2025Bioinform.20 citations
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Periodicity of nuclear morphology in human fibroblasts
L. Seaman, W. Meixner, John Snyder, I. Rajapakse
2015The Nucleus20 citations Open access
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Mathematics of the Genome
I. Rajapakse, S. Smale
2015Foundations of Computational Mathematics19 citations Open access
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A unified approach of detecting phase transition in time-varying complex networks
Mohamed Ridha Znaidi, J. Sia, Scott Ronquist, I. Rajapakse +2 more
2023Scientific Reports17 citations Open access
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4DNvestigator: time series genomic data analysis toolbox
Stephen Lindsly, Can Chen, Sijia Liu, Scott Ronquist +3 more
2021The Nucleus17 citations Open access
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KRONECKER PRODUCT OF TENSORS AND HYPERGRAPHS: STRUCTURE AND DYNAMICS
Joshua K. Pickard, Can Chen, Cooper M. Stansbury, Amit Surana +2 more
2023SIAM Journal on Matrix Analysis and Applications16 citations Open access
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Network dynamics of hypothalamic feeding neurons
P. Sweeney, Can Chen, I. Rajapakse, R. Cone
2021Proceedings of the National Academy of Sciences of the United States of America16 citations Open access
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Latent Heterogeneous Multilayer Community Detection
Hafiz Tiomoko Ali, Si-Jia Liu, Yasin Yılmaz, Romain Couillet +2 more
2018IEEE International Conference on Acoustics, Speech, and Signal Processing16 citations Open access
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HAT: Hypergraph analysis toolbox
Joshua K. Pickard, Can Chen, Rahmy Salman, Cooper M. Stansbury +4 more
2022PLoS Comput. Biol.15 citations Open access
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Observability of Hypergraphs
Joshua K. Pickard, Amit Surana, Anthony Bloch, I. Rajapakse
2023IEEE Conference on Decision and Control14 citations Open access
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Functional organization of the maternal and paternal human 4D Nucleome
Stephen Lindsly, Wenlong Jia, Haiming Chen, Sijia Liu +12 more
2020bioRxiv14 citations Open access
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The Pitchfork Bifurcation
I. Rajapakse, S. Smale
2016International Journal of Bifurcation and Chaos in Applied Sciences and Engineering13 citations Open access
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Dynamics of the Genome
I. Rajapakse, S. Smale
201513 citations
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RAILS: A Robust Adversarial Immune-Inspired Learning System
Ren Wang, Tianqi Chen, Stephen Lindsly, Cooper M. Stansbury +3 more
2020IEEE Access12 citations Open access
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Dynamic tensor time series modeling and analysis
A. Surana, G. Patterson, I. Rajapakse
2016IEEE Conference on Decision and Control11 citations
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ASK: Adversarial Soft k-Nearest Neighbor Attack and Defense
Ren Wang, Tianqi Chen, Philip Yao, Si-Jia Liu +2 more
2021IEEE Access10 citations Open access
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Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers
Haiming Chen, L. Seaman, Sijia Liu, T. Ried +1 more
2017The Nucleus10 citations Open access
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Genome Architecture Leads a Bifurcation in Cell Identity
Sijia Liu, H. Chen, Scott Ronquist, L. Seaman +9 more
2017bioRxiv10 citations Open access
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4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities
L. Seaman, I. Rajapakse
2018Bioinform.9 citations
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Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids
Haiming Chen, Nicholas Comment, Jie Chen, Scott Ronquist +3 more
2015The Nucleus9 citations Open access
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TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization
Markus A. Brown, Gabrielle A. Dotson, Scott Ronquist, Georg Emons +2 more
2021Neoplasia7 citations Open access
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Data-Driven Model Reduction for Multilinear Control Systems via Tensor Trains
Can Chen, A. Surana, A. Bloch, I. Rajapakse
20197 citations
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