ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data von Ravi, Sudharshan, Gunawan, Rudiyanto

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SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles von Papili Gao, Nan, Ud-Dean, S M Minhaz, Gandrillon, Olivier, Gunawan, Rudiyanto

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A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis von Groth, Theodore, Gunawan, Rudiyanto, Neelamegham, Sriram

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Assessment of network inference methods: how to cope with an underdetermined problem von Siegenthaler, Caroline, Gunawan, Rudiyanto

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Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection von Noh, Heeju, Shoemaker, Jason E, Gunawan, Rudiyanto

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Inferring gene targets of drugs and chemical compounds from gene expression profiles von Noh, Heeju, Gunawan, Rudiyanto

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Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process von Richard, Angélique, Boullu, Loïs, Herbach, Ulysse, Bonnafoux, Arnaud, Morin, Valérie, Vallin, Elodie, Guillemin, Anissa, Papili Gao, Nan, Gunawan, Rudiyanto, Cosette, Jérémie, Arnaud, Ophélie, Kupiec, Jean-Jacques, Espinasse, Thibault, Gonin-Giraud, Sandrine, Gandrillon, Olivier

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Clonal expansion of mitochondrial DNA deletions is a private mechanism of aging in long‐lived animals von Lakshmanan, Lakshmi Narayanan, Yee, Zhuangli, Ng, Li Fang, Gunawan, Rudiyanto, Halliwell, Barry, Gruber, Jan

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Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta von Teo, Emelyne, Ravi, Sudharshan, Barardo, Diogo, Kim, Hyung-Seok, Fong, Sheng, Cazenave-Gassiot, Amaury, Tan, Tsze Yin, Ching, Jianhong, Kovalik, Jean-Paul, Wenk, Markus R, Gunawan, Rudiyanto, Moore, Philip K, Halliwell, Barry, Tolwinski, Nicholas, Gruber, Jan

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Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations von Tam, Zhi Yang, Gruber, Jan, Halliwell, Barry, Gunawan, Rudiyanto

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DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks von Noh, Heeju, Hua, Ziyi, Chrysinas, Panagiotis, Shoemaker, Jason E, Gunawan, Rudiyanto

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Mathematical modeling of the role of mitochondrial fusion and fission in mitochondrial DNA maintenance von Tam, Zhi Yang, Gruber, Jan, Halliwell, Barry, Gunawan, Rudiyanto

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Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells von Parmentier, Romuald, Racine, Laëtitia, Moussy, Alice, Chantalat, Sophie, Sudharshan, Ravi, Papili Gao, Nan, Stockholm, Daniel, Corre, Guillaume, Fourel, Geneviève, Deleuze, Jean-François, Gunawan, Rudiyanto, Paldi, Andras

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Global parameter estimation methods for stochastic biochemical systems von Poovathingal, Suresh Kumar, Gunawan, Rudiyanto

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High resolution algorithms for multidimensional population balance equations von Gunawan, Rudiyanto, Fusman, Irene, Braatz, Richard D.

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Biological Networks von Gunawan, Rudiyanto, Bagheri, Neda

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Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method von Jia, Gengjie, Stephanopoulos, Gregory N., Gunawan, Rudiyanto

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Single-cell transcriptional uncertainty landscape of cell differentiation [version 1; peer review: 1 approved, 1 approved with reservations] von Gao, Nan Papili, Gandrillon, Olivier, Páldi, András, Herbach, Ulysse, Gunawan, Rudiyanto

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Single-cell transcriptional uncertainty landscape of cell differentiation [version 2; peer review: 2 approved] von Gao, Nan Papili, Gandrillon, Olivier, Páldi, András, Herbach, Ulysse, Gunawan, Rudiyanto

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Spherical Crystallization of Glycine from Monodisperse Microfluidic Emulsions von Toldy, Arpad I, Badruddoza, Abu Zayed M, Zheng, Lu, Hatton, T. Alan, Gunawan, Rudiyanto, Rajagopalan, Raj, Khan, Saif A

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