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Computational systems biology

Citations

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Cited by:

  1. Ariel L Rivas & Mark D Jankowski & Renata Piccinini & Gabriel Leitner & Daniel Schwarz & Kevin L Anderson & Jeanne M Fair & Almira L Hoogesteijn & Wilfried Wolter & Marcelo Chaffer & Shlomo Blum & Tom, 2013. "Feedback-Based, System-Level Properties of Vertebrate-Microbial Interactions," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-16, February.
  2. Leonard Schmiester & Yannik Schälte & Frank T Bergmann & Tacio Camba & Erika Dudkin & Janine Egert & Fabian Fröhlich & Lara Fuhrmann & Adrian L Hauber & Svenja Kemmer & Polina Lakrisenko & Carolin Loo, 2021. "PEtab—Interoperable specification of parameter estimation problems in systems biology," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-10, January.
  3. Matej Troják & David Šafránek & Lukrécia Mertová & Luboš Brim, 2020. "Executable biochemical space for specification and analysis of biochemical systems," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-24, September.
  4. Mika Gustafsson & Michael Hörnquist, 2010. "Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge," PLOS ONE, Public Library of Science, vol. 5(2), pages 1-8, February.
  5. Fabian Fröhlich & Barbara Kaltenbacher & Fabian J Theis & Jan Hasenauer, 2017. "Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-18, January.
  6. Niki Vermeulen, 2018. "The choreography of a new research field: Aggregation, circulation and oscillation," Environment and Planning A, , vol. 50(8), pages 1764-1784, November.
  7. Lucia, Umberto, 2012. "Irreversibility in biophysical and biochemical engineering," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(23), pages 5997-6007.
  8. Jacobo Ayensa-Jiménez & Marina Pérez-Aliacar & Teodora Randelovic & José Antonio Sanz-Herrera & Mohamed H. Doweidar & Manuel Doblaré, 2020. "Analysis of the Parametric Correlation in Mathematical Modeling of In Vitro Glioblastoma Evolution Using Copulas," Mathematics, MDPI, vol. 9(1), pages 1-22, December.
  9. Qing-Ju Jiao & Yan-Kai Zhang & Lu-Ning Li & Hong-Bin Shen, 2011. "BinTree Seeking: A Novel Approach to Mine Both Bi-Sparse and Cohesive Modules in Protein Interaction Networks," PLOS ONE, Public Library of Science, vol. 6(11), pages 1-12, November.
  10. Luca Cardelli & Rosa D Hernansaiz-Ballesteros & Neil Dalchau & Attila Csikász-Nagy, 2017. "Efficient Switches in Biology and Computer Science," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-16, January.
  11. Markus J. Buehler & Theodor Ackbarow, 2008. "Nanomechanical strength mechanisms of hierarchical biological materials and tissues," Computer Methods in Biomechanics and Biomedical Engineering, Taylor & Francis Journals, vol. 11(6), pages 595-607.
  12. Diego Fernández Slezak & Cecilia Suárez & Guillermo A Cecchi & Guillermo Marshall & Gustavo Stolovitzky, 2010. "When the Optimal Is Not the Best: Parameter Estimation in Complex Biological Models," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-10, October.
  13. Richard A Williams & Jon Timmis & Eva E Qwarnstrom, 2016. "Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-27, August.
  14. Tom C Freeman & Leon Goldovsky & Markus Brosch & Stijn van Dongen & Pierre Mazière & Russell J Grocock & Shiri Freilich & Janet Thornton & Anton J Enright, 2007. "Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data," PLOS Computational Biology, Public Library of Science, vol. 3(10), pages 1-11, October.
  15. Yuksel Bayraktar & Esme Isik & Ibrahim Isik & Ayfer Ozyilmaz & Metin Toprak & Fatma Kahraman Guloglu & Serdar Aydin, 2022. "Analyzing of Alzheimer’s Disease Based on Biomedical and Socio-Economic Approach Using Molecular Communication, Artificial Neural Network, and Random Forest Models," Sustainability, MDPI, vol. 14(13), pages 1-15, June.
  16. Matthew A Hibbs & Chad L Myers & Curtis Huttenhower & David C Hess & Kai Li & Amy A Caudy & Olga G Troyanskaya, 2009. "Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis," PLOS Computational Biology, Public Library of Science, vol. 5(3), pages 1-12, March.
  17. Joshua Russell-Buckland & Christopher P Barnes & Ilias Tachtsidis, 2019. "A Bayesian framework for the analysis of systems biology models of the brain," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-29, April.
  18. Christian L Barrett & Bernhard O Palsson, 2006. "Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach," PLOS Computational Biology, Public Library of Science, vol. 2(5), pages 1-10, May.
  19. Kansuporn Sriyudthsak & Fumihide Shiraishi & Masami Yokota Hirai, 2013. "Identification of a Metabolic Reaction Network from Time-Series Data of Metabolite Concentrations," PLOS ONE, Public Library of Science, vol. 8(1), pages 1-9, January.
  20. Luca Marchetti & Rosario Lombardo & Corrado Priami, 2017. "HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks," Complexity, Hindawi, vol. 2017, pages 1-12, December.
  21. Samuel Bandara & Johannes P Schlöder & Roland Eils & Hans Georg Bock & Tobias Meyer, 2009. "Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model," PLOS Computational Biology, Public Library of Science, vol. 5(11), pages 1-12, November.
  22. Joly, Marcel & Rondó, Patrícia H.C., 2017. "The future of computational biomedicine: Complex systems thinking," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 132(C), pages 1-27.
  23. Mark Read & Paul S. Andrews & Jon Timmis & Vipin Kumar, 2011. "Techniques for grounding agent-based simulations in the real domain: a case study in experimental autoimmune encephalomyelitis," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 18(1), pages 67-86, May.
  24. Gianluca D’Addese & Martina Casari & Roberto Serra & Marco Villani, 2021. "A Fast and Effective Method to Identify Relevant Sets of Variables in Complex Systems," Mathematics, MDPI, vol. 9(9), pages 1-27, April.
  25. Hütt, M.-Th. & Lüttge, U., 2005. "The interplay of synchronization and fluctuations reveals connectivity levels in networks of nonlinear oscillators," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 350(2), pages 207-226.
  26. Wenpin Hou & Takeyuki Tamura & Wai-Ki Ching & Tatsuya Akutsu, 2016. "Finding And Analyzing The Minimum Set Of Driver Nodes In Control Of Boolean Networks," Advances in Complex Systems (ACS), World Scientific Publishing Co. Pte. Ltd., vol. 19(03), pages 1-32, May.
  27. Héctor García Martín & Vinay Satish Kumar & Daniel Weaver & Amit Ghosh & Victor Chubukov & Aindrila Mukhopadhyay & Adam Arkin & Jay D Keasling, 2015. "A Method to Constrain Genome-Scale Models with 13C Labeling Data," PLOS Computational Biology, Public Library of Science, vol. 11(9), pages 1-34, September.
  28. Edward Bishop Smith & Yuan Hou, 2015. "Redundant Heterogeneity and Group Performance," Organization Science, INFORMS, vol. 26(1), pages 37-51, February.
  29. Ryan N Gutenkunst & Joshua J Waterfall & Fergal P Casey & Kevin S Brown & Christopher R Myers & James P Sethna, 2007. "Universally Sloppy Parameter Sensitivities in Systems Biology Models," PLOS Computational Biology, Public Library of Science, vol. 3(10), pages 1-8, October.
  30. Andrea Degasperi & Marc R Birtwistle & Natalia Volinsky & Jens Rauch & Walter Kolch & Boris N Kholodenko, 2014. "Evaluating Strategies to Normalise Biological Replicates of Western Blot Data," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-11, January.
  31. Alan A Cohen & Emmanuel Milot & Qing Li & Patrick Bergeron & Roxane Poirier & Francis Dusseault-Bélanger & Tamàs Fülöp & Maxime Leroux & Véronique Legault & E Jeffrey Metter & Linda P Fried & Luigi Fe, 2015. "Detection of a Novel, Integrative Aging Process Suggests Complex Physiological Integration," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-26, March.
  32. Armaghan W Naik & Joshua D Kangas & Christopher J Langmead & Robert F Murphy, 2013. "Efficient Modeling and Active Learning Discovery of Biological Responses," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-1, December.
  33. Ting Hu & Karoliina Oksanen & Weidong Zhang & Ed Randell & Andrew Furey & Guang Sun & Guangju Zhai, 2018. "An evolutionary learning and network approach to identifying key metabolites for osteoarthritis," PLOS Computational Biology, Public Library of Science, vol. 14(3), pages 1-18, March.
  34. Zandi-Mehran, Nazanin & Panahi, Shirin & Hosseini, Zahra & Hashemi Golpayegani, Seyed Mohammad Reza & Jafari, Sajad, 2020. "One dimensional map-based neuron model: A phase space interpretation," Chaos, Solitons & Fractals, Elsevier, vol. 132(C).
  35. Joep P J Schmitz & Jeroen A L Jeneson & Joep W M van Oorschot & Jeanine J Prompers & Klaas Nicolay & Peter A J Hilbers & Natal A W van Riel, 2012. "Prediction of Muscle Energy States at Low Metabolic Rates Requires Feedback Control of Mitochondrial Respiratory Chain Activity by Inorganic Phosphate," PLOS ONE, Public Library of Science, vol. 7(3), pages 1-14, March.
  36. Pier Luigi Sacco & Alex Arenas & Manlio De Domenico, 2022. "The resilience of the multirelational structure of geopolitical treaties is critically linked to past colonial world order and offshore fiscal havens," Papers 2203.00618, arXiv.org.
  37. Burton W Andrews & Tau-Mu Yi & Pablo A Iglesias, 2006. "Optimal Noise Filtering in the Chemotactic Response of Escherichia coli," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-12, November.
  38. Chandra, Yanto & Wilkinson, Ian F., 2017. "Firm internationalization from a network-centric complex-systems perspective," Journal of World Business, Elsevier, vol. 52(5), pages 691-701.
  39. Marco S Nobile & Paolo Cazzaniga & Daniela Besozzi & Dario Pescini & Giancarlo Mauri, 2014. "cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-20, March.
  40. Julia Gilhodes & Florence Dalenc & Jocelyn Gal & Christophe Zemmour & Eve Leconte & Jean Marie Boher & Thomas Filleron, 2020. "Comparison of Variable Selection Methods for Time-to-Event Data in High-Dimensional Settings," Post-Print hal-02934793, HAL.
  41. Yohei Murakami, 2014. "Bayesian Parameter Inference and Model Selection by Population Annealing in Systems Biology," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-15, August.
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