On the Lyapunov Exponent of Monotone Boolean Networks ^† by Ilya Shmulevich

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Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. by David L Gibbs, Ilya Shmulevich

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Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model by Moriah Echlin, Boris Aguilar, Ilya Shmulevich

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Probabilistic inference of transcription factor binding from multiple data sources. by Harri Lähdesmäki, Alistair G Rust, Ilya Shmulevich

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Computational capabilities of a multicellular reservoir computing system by Vladimir Nikolić, Moriah Echlin, Boris Aguilar, Ilya Shmulevich

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Computational capabilities of a multicellular reservoir computing system. by Vladimir Nikolić, Moriah Echlin, Boris Aguilar, Ilya Shmulevich

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Increasing coverage of transcription factor position weight matrices through domain-level homology. by Brady Bernard, Vesteinn Thorsson, Hector Rovira, Ilya Shmulevich

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Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters by Moriah Echlin, Boris Aguilar, Max Notarangelo, David L. Gibbs, Ilya Shmulevich

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Probabilistic boolean networks predict transcription factor targets to induce transdifferentiation by Bahar Tercan, Boris Aguilar, Sui Huang, Edward R. Dougherty, Ilya Shmulevich

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Critical dynamics in genetic regulatory networks: examples from four kingdoms. by Enrique Balleza, Elena R Alvarez-Buylla, Alvaro Chaos, Stuart Kauffman, Ilya Shmulevich, Maximino Aldana

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Cell death as a trigger for morphogenesis. by Boris Aguilar, Ahmadreza Ghaffarizadeh, Christopher D Johnson, Gregory J Podgorski, Ilya Shmulevich, Nicholas S Flann

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Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma. by Yuexin Liu, Yan Sun, Russell Broaddus, Jinsong Liu, Anil K Sood, Ilya Shmulevich, Wei Zhang

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Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. by Jyrki Selinummi, Pekka Ruusuvuori, Irina Podolsky, Adrian Ozinsky, Elizabeth Gold, Olli Yli-Harja, Alan Aderem, Ilya Shmulevich

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CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data. by Ryan Bressler, Richard B Kreisberg, Brady Bernard, John E Niederhuber, Joseph G Vockley, Ilya Shmulevich, Theo A Knijnenburg

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SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery [version 2; peer review: 2 approved] by William Longabaugh, John Phan, Christopher J. Kemp, David Pot, Guangrong Qin, Bahar Tercan, Boris Aguilar, Taek-Kyun Kim, Ilya Shmulevich, Nyasha Chambwe

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ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. by Samuel A Danziger, David L Gibbs, Ilya Shmulevich, Mark McConnell, Matthew W B Trotter, Frank Schmitz, David J Reiss, Alexander V Ratushny

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Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis by Eliza J.R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga

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Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis by Eliza J.R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga

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A framework towards digital twins for type 2 diabetes by Yue Zhang, Guangrong Qin, Boris Aguilar, Noa Rappaport, Noa Rappaport, James T. Yurkovich, James T. Yurkovich, Lance Pflieger, Lance Pflieger, Sui Huang, Leroy Hood, Leroy Hood, Leroy Hood, Ilya Shmulevich

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CRI iAtlas: an interactive portal for immuno-oncology research [version 1; peer review: 2 approved] by James A. Eddy, Vésteinn Thorsson, Andrew E. Lamb, David L. Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, Yooree Chae, Kristen Dang, Benjamin G. Vincent, Ilya Shmulevich, Justin Guinney

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