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ArticlesPeer ReviewedFull Text
Digital twins for predictive oncology will be a paradigm shift for precision cancer care
Author / Creator:Hernandez-Boussard, Tina ; Macklin, Paul ; Greenspan, Emily J. ; Gryshuk, Amy L. ; Stahlberg, Eric ; Syeda-Mahmood, Tanveer ; Shmulevich, Ilya
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2021-12, Vol.27 (12), p.2065-2066
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On the Lyapunov Exponent of Monotone Boolean Networks
Author / Creator:Shmulevich, Ilya
Publisher:MDPI AG
Journal title:Mathematics (Basel), 2020-06, Vol.8 (6), p.1035
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Correction: Computational capabilities of a multicellular reservoir computing system
Author / Creator:Nikolić, Vladimir ; Echlin, Moriah ; Aguilar, Boris ; Shmulevich, Ilya
Publisher:United States: Public Library of Science
Journal title:PloS one, 2024-12, Vol.19 (12), p.e0315300
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Computational capabilities of a multicellular reservoir computing system
Author / Creator:Nikolić, Vladimir ; Echlin, Moriah ; Aguilar, Boris ; Shmulevich, Ilya
Publisher:United States: Public Library of Science
Journal title:PloS one, 2023-04, Vol.18 (4), p.e0282122
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Discovery of driver non-coding splice-site-creating mutations in cancer
Author / Creator:Cao, Song ; Zhou, Daniel Cui ; Oh, Clara ; Jayasinghe, Reyka G. ; Zhao, Yanyan ; Yoon, Christopher J. ; Wyczalkowski, Matthew A. ; Bailey, Matthew H. ; Tsou, Terrence ; Gao, Qingsong ; Malone, Andrew ; Reynolds, Sheila ; Shmulevich, Ilya ; Wendl, Michael C. ; Chen, Feng ; Ding, Li
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-11, Vol.11 (1), p.5573-5573, Article 5573
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Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model
Author / Creator:Echlin, Moriah ; Aguilar, Boris ; Shmulevich, Ilya
Publisher:Switzerland: MDPI AG
Journal title:Entropy (Basel, Switzerland), 2023-02, Vol.25 (2), p.319
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Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
Author / Creator:Gibbs, David L. ; Shmulevich, Ilya
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2017-06, Vol.13 (6), p.e1005591-e1005591
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Epigenetic profiling for the molecular classification of metastatic brain tumors
Author / Creator:Orozco, Javier I. J. ; Knijnenburg, Theo A. ; Manughian-Peter, Ayla O. ; Salomon, Matthew P. ; Barkhoudarian, Garni ; Jalas, John R. ; Wilmott, James S. ; Hothi, Parvinder ; Wang, Xiaowen ; Takasumi, Yuki ; Buckland, Michael E. ; Thompson, John F. ; Long, Georgina V. ; Cobbs, Charles S. ; Shmulevich, Ilya ; Kelly, Daniel F. ; Scolyer, Richard A. ; Hoon, Dave S. B. ; Marzese, Diego M.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-11, Vol.9 (1), p.4627-14, Article 4627
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CRI iAtlas: an interactive portal for immuno-oncology research [version 1; peer review: 3 approved]
Author / Creator:Eddy, James A ; Thorsson, Vésteinn ; Lamb, Andrew E ; Gibbs, David L ; Heimann, Carolina ; Yu, Jia Xin ; Chung, Verena ; Chae, Yooree ; Dang, Kristen ; Vincent, Benjamin G ; Shmulevich, Ilya ; Guinney, Justin
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2020, Vol.9, p.1028-1028
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ArticlesPeer ReviewedFull Text
Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression
Author / Creator:Turner, Kristen M. ; Sun, Youting ; Ji, Ping ; Granberg, Kirsi J. ; Bernard, Brady ; Hu, Limei ; Cogdell, David E. ; Zhou, Xinhui ; Yli-Harja, Olli ; Nykter, Matti ; Shmulevich, Ilya ; Yung, W. K. Alfred ; Fuller, Gregory N. ; Zhang, Wei
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2015-03, Vol.112 (11), p.3421-3426
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ArticlesPeer ReviewedFull Text
ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells
Author / Creator:Danziger, Samuel A. ; Gibbs, David L. ; Shmulevich, Ilya ; McConnell, Mark ; Trotter, Matthew W. B. ; Schmitz, Frank ; Reiss, David J. ; Ratushny, Alexander V.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2019-11, Vol.14 (11), p.e0224693-e0224693
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ArticlesPeer ReviewedFull Text
Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms
Author / Creator:Balleza, Enrique ; Alvarez-Buylla, Elena R. ; Chaos, Alvaro ; Kauffman, Stuart ; Shmulevich, Ilya ; Aldana, Maximino
Publisher:United States: Public Library of Science
Journal title:PloS one, 2008-06, Vol.3 (6), p.e2456-e2456
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ArticlesPeer ReviewedFull Text
Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions
Author / Creator:Guo, Fei ; Parker Kerrigan, Brittany C ; Yang, Da ; Hu, Limei ; Shmulevich, Ilya ; Sood, Anil K ; Xue, Fengxia ; Zhang, Wei
Publisher:England: BioMed Central Ltd
Journal title:Journal of hematology and oncology, 2014-03, Vol.7 (1), p.19-19, Article 19
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ArticlesPeer ReviewedFull Text
Eukaryotic Cells Are Dynamically Ordered or Critical but Not Chaotic
Author / Creator:Shmulevich, Ilya ; Kauffman, Stuart A. ; Aldana, Maximino ; Kadanoff, Leo P.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2005-09, Vol.102 (38), p.13439-13444
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ArticlesPeer ReviewedFull Text
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
Author / Creator:Poole, William ; Leinonen, Kalle ; Shmulevich, Ilya ; Knijnenburg, Theo A. ; Bernard, Brady
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2017-02, Vol.13 (2), p.e1005347-e1005347
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ArticlesPeer ReviewedFull Text
A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins
Author / Creator:L. Rocha, Heber ; Aguilar, Boris ; Getz, Michael ; Shmulevich, Ilya ; Macklin, Paul
Publisher:London: Nature Publishing Group UK
Journal title:NPJ systems biology and applications, 2024-12, Vol.10 (1), p.144-12, Article 144
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ArticlesPeer ReviewedFull Text
Gene expression dynamics in the macrophage exhibit criticality
Author / Creator:Nykter, Matti ; Price, Nathan D ; Aldana, Maximino ; Ramsey, Stephen A ; Kauffman, Stuart A ; Hood, Leroy E ; Yli-Harja, Olli ; Shmulevich, Ilya
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2008-02, Vol.105 (6), p.1897-1900
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ArticlesPeer ReviewedFull Text
Bright Field Microscopy as an Alternative to Whole Cell Fluorescence in Automated Analysis of Macrophage Images
Author / Creator:Selinummi, Jyrki ; Ruusuvuori, Pekka ; Podolsky, Irina ; Ozinsky, Adrian ; Gold, Elizabeth ; Yli-Harja, Olli ; Aderem, Alan ; Shmulevich, Ilya
Publisher:United States: Public Library of Science
Journal title:PloS one, 2009-10, Vol.4 (10), p.e7497-e7497
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ArticlesPeer ReviewedFull Text
Cell death as a trigger for morphogenesis
Author / Creator:Aguilar, Boris ; Ghaffarizadeh, Ahmadreza ; Johnson, Christopher D. ; Podgorski, Gregory J. ; Shmulevich, Ilya ; Flann, Nicholas S.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2018-03, Vol.13 (3), p.e0191089-e0191089
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ArticlesPeer ReviewedFull Text
Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters
Author / Creator:Echlin, Moriah ; Aguilar, Boris ; Notarangelo, Max ; Gibbs, David L. ; Shmulevich, Ilya
Publisher:Basel: MDPI AG
Journal title:Entropy (Basel, Switzerland), 2018-12, Vol.20 (12), p.954
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Showing 1 to 20 of 123 results

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Digital twins for predictive oncology will be a paradigm shift for precision cancer care

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On the Lyapunov Exponent of Monotone Boolean Networks

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Correction: Computational capabilities of a multicellular reservoir computing system

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Computational capabilities of a multicellular reservoir computing system

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Discovery of driver non-coding splice-site-creating mutations in cancer

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Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model

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Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle

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Epigenetic profiling for the molecular classification of metastatic brain tumors

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CRI iAtlas: an interactive portal for immuno-oncology research [version 1; peer review: 3 approved]

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Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

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ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells

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Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms

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Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions

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Eukaryotic Cells Are Dynamically Ordered or Critical but Not Chaotic

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Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

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A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins

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Gene expression dynamics in the macrophage exhibit criticality

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Bright Field Microscopy as an Alternative to Whole Cell Fluorescence in Automated Analysis of Macrophage Images

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Cell death as a trigger for morphogenesis

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Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters

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