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From molecular to modular cell biology

Citations

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Cited by:

  1. Lazaros K Gallos & Fabricio Q Potiguar & José S Andrade Jr & Hernan A Makse, 2013. "IMDB Network Revisited: Unveiling Fractal and Modular Properties from a Typical Small-World Network," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-8, June.
  2. Andriani, Pierpaolo & Carignani, Giuseppe, 2014. "Modular exaptation: A missing link in the synthesis of artificial form," Research Policy, Elsevier, vol. 43(9), pages 1608-1620.
  3. T. Ochiai & J. C. Nacher, 2007. "Stochastic analysis of autoregulatory gene expression dynamics," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 14(4), pages 377-388, November.
  4. Robrecht Cannoodt & Joeri Ruyssinck & Jan Ramon & Katleen De Preter & Yvan Saeys, 2018. "IncGraph: Incremental graphlet counting for topology optimisation," PLOS ONE, Public Library of Science, vol. 13(4), pages 1-11, April.
  5. Margaritis Voliotis & Philipp Thomas & Ramon Grima & Clive G Bowsher, 2016. "Stochastic Simulation of Biomolecular Networks in Dynamic Environments," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-18, June.
  6. 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.
  7. Daniel Couch & Zhenning Yu & Jin Hyun Nam & Carter Allen & Paula S Ramos & Willian A da Silveira & Kelly J Hunt & Edward S Hazard & Gary Hardiman & Andrew Lawson & Dongjun Chung, 2019. "GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-19, July.
  8. Manfred Füllsack, 2011. "Firstness - As seen from the perspective of Complexity Research," E-LOGOS, Prague University of Economics and Business, vol. 2011(1), pages 1-19.
  9. Samrat Chatterjee & Dhiraj Kumar, 2011. "Unraveling the Design Principle for Motif Organization in Signaling Networks," PLOS ONE, Public Library of Science, vol. 6(12), pages 1-9, December.
  10. Anupam Saxena & Hod Lipson & Francisco J Valero-Cuevas, 2012. "Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation," PLOS Computational Biology, Public Library of Science, vol. 8(11), pages 1-17, November.
  11. Perc, Matjaž, 2010. "Growth and structure of Slovenia’s scientific collaboration network," Journal of Informetrics, Elsevier, vol. 4(4), pages 475-482.
  12. Krivonosov, Mikhail & Nazarenko, Tatiana & Bacalini, Maria Giulia & Vedunova, Maria & Franceschi, Claudio & Zaikin, Alexey & Ivanchenko, Mikhail, 2022. "Age-related trajectories of DNA methylation network markers: A parenclitic network approach to a family-based cohort of patients with Down Syndrome," Chaos, Solitons & Fractals, Elsevier, vol. 165(P2).
  13. Pilar García-Peñarrubia & Juan J Gálvez & Jesús Gálvez, 2011. "Spatio-Temporal Dependence of the Signaling Response in Immune-Receptor Trafficking Networks Regulated by Cell Density: A Theoretical Model," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-12, July.
  14. Nikolaos K. Voulgarakis, 2024. "Hierarchical Symmetry-Breaking Model for Stem Cell Differentiation," Mathematics, MDPI, vol. 12(9), pages 1-15, May.
  15. 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.
  16. Mahdieh Ghasemi & Maseud Rahgozar & Gholamreza Bidkhori & Ali Masoudi-Nejad, 2013. "C-element: A New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-12, September.
  17. Cai Gao & Xin Lan & Xiaoge Zhang & Yong Deng, 2013. "A Bio-Inspired Methodology of Identifying Influential Nodes in Complex Networks," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-11, June.
  18. Bogna J. Smug & Krzysztof Szczepaniak & Eduardo P. C. Rocha & Stanislaw Dunin-Horkawicz & Rafał J. Mostowy, 2023. "Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  19. N. Bourgeois & A. Giannakos & G. Lucarelli & I. Milis & V. T. Paschos & O. Pottié, 2012. "The max quasi-independent set problem," Journal of Combinatorial Optimization, Springer, vol. 23(1), pages 94-117, January.
  20. Saharnaz Dilmaghani & Matthias R Brust & Carlos H C Ribeiro & Emmanuel Kieffer & Grégoire Danoy & Pascal Bouvry, 2022. "From communities to protein complexes: A local community detection algorithm on PPI networks," PLOS ONE, Public Library of Science, vol. 17(1), pages 1-17, January.
  21. Yongli Li & Chong Wu & Zizheng Wang, 2015. "An information-theoretic approach for detecting communities in networks," Quality & Quantity: International Journal of Methodology, Springer, vol. 49(4), pages 1719-1733, July.
  22. Emre Guney & Baldo Oliva, 2014. "Analysis of the Robustness of Network-Based Disease-Gene Prioritization Methods Reveals Redundancy in the Human Interactome and Functional Diversity of Disease-Genes," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-11, April.
  23. Mark K Transtrum & Peng Qiu, 2016. "Bridging Mechanistic and Phenomenological Models of Complex Biological Systems," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-34, May.
  24. Alexander Veremyev & Oleg A. Prokopyev & Sergiy Butenko & Eduardo L. Pasiliao, 2016. "Exact MIP-based approaches for finding maximum quasi-cliques and dense subgraphs," Computational Optimization and Applications, Springer, vol. 64(1), pages 177-214, May.
  25. Andras Gyorgy, 2023. "Competition and evolutionary selection among core regulatory motifs in gene expression control," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  26. Sanjana Gupta & Robin E C Lee & James R Faeder, 2020. "Parallel Tempering with Lasso for model reduction in systems biology," PLOS Computational Biology, Public Library of Science, vol. 16(3), pages 1-22, March.
  27. Nicola Bellomo & Richard Bingham & Mark A.J. Chaplain & Giovanni Dosi & Guido Forni & Damian A. Knopoff & John Lowengrub & Reidun Twarock & Maria Enrica Virgillito, 2020. "A multi-scale model of virus pandemic: Heterogeneous interactive entities in a globally connected world," LEM Papers Series 2020/16, Laboratory of Economics and Management (LEM), Sant'Anna School of Advanced Studies, Pisa, Italy.
  28. Joshua S Weitz & Philip N Benfey & Ned S Wingreen, 2007. "Evolution, Interactions, and Biological Networks," PLOS Biology, Public Library of Science, vol. 5(1), pages 1-3, January.
  29. Alexander Rivkind & Hallel Schreier & Naama Brenner & Omri Barak, 2020. "Scale free topology as an effective feedback system," PLOS Computational Biology, Public Library of Science, vol. 16(5), pages 1-24, May.
  30. Cui, Xue-Mei & Yoon, Chang No & Youn, Hyejin & Lee, Sang Hoon & Jung, Jean S. & Han, Seung Kee, 2017. "Dynamic burstiness of word-occurrence and network modularity in textbook systems," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 487(C), pages 103-110.
  31. Qian Yu & Rui Tao & Shan Jiang, 2023. "Exploring the evolution of interdisciplinary citation network by the colored network motifs: the case of Perovskite Materials," Scientometrics, Springer;Akadémiai Kiadó, vol. 128(8), pages 4421-4446, August.
  32. Zheng Hong, 2019. "A novel individualized drug repositioning approach for predicting personalized candidate drugs for type 1 diabetes mellitus," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(5), pages 1-9, October.
  33. Anne Lopes & Sophie Sacquin-Mora & Viktoriya Dimitrova & Elodie Laine & Yann Ponty & Alessandra Carbone, 2013. "Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information," PLOS Computational Biology, Public Library of Science, vol. 9(12), pages 1-18, December.
  34. Simeon D. Castle & Michiel Stock & Thomas E. Gorochowski, 2024. "Engineering is evolution: a perspective on design processes to engineer biology," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  35. Bo Xu & Hongfei Lin & Yang Chen & Zhihao Yang & Hongfang Liu, 2013. "Protein Complex Identification by Integrating Protein-Protein Interaction Evidence from Multiple Sources," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.
  36. Tracy Chih-Ting Koubkova-Yu & Jung-Chi Chao & Jun-Yi Leu, 2018. "Heterologous Hsp90 promotes phenotypic diversity through network evolution," PLOS Biology, Public Library of Science, vol. 16(11), pages 1-29, November.
  37. Romualdo Pastor-Satorras & Eric Smith & Ricard V. Solé, 2002. "Evolving Protein Interaction Networks through Gene Duplication," Working Papers 02-02-008, Santa Fe Institute.
  38. Miguel Fribourg & Diomedes E Logothetis & Javier González-Maeso & Stuart C Sealfon & Belén Galocha-Iragüen & Fernando Las-Heras Andrés & Vladimir Brezina, 2017. "Elucidation of molecular kinetic schemes from macroscopic traces using system identification," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-34, February.
  39. Zhou, Qing & Benlic, Una & Wu, Qinghua, 2020. "An opposition-based memetic algorithm for the maximum quasi-clique problem," European Journal of Operational Research, Elsevier, vol. 286(1), pages 63-83.
  40. Krishnan, Arun & Tomita, Masaru & Giuliani, Alessandro, 2008. "Evolution of gene regulatory networks: Robustness as an emergent property of evolution," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(8), pages 2170-2186.
  41. Zhang, Yuerong & Marshall, Stephen & Manley, Ed, 2021. "Understanding the roles of rail stations: Insights from network approaches in the London metropolitan area," Journal of Transport Geography, Elsevier, vol. 94(C).
  42. Frederic Li Mow Chee & Bruno Beernaert & Billie G. C. Griffith & Alexander E. P. Loftus & Yatendra Kumar & Jimi C. Wills & Martin Lee & Jessica Valli & Ann P. Wheeler & J. Douglas Armstrong & Maddy Pa, 2023. "Mena regulates nesprin-2 to control actin–nuclear lamina associations, trans-nuclear membrane signalling and gene expression," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  43. Sun, Lanfang & Jiang, Lu & Li, Menghui & He, Dacheng, 2006. "Statistical analysis of gene regulatory networks reconstructed from gene expression data of lung cancer," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 370(2), pages 663-671.
  44. Haijia Shi & Lei Shi, 2014. "Identifying Emerging Motif in Growing Networks," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-12, June.
  45. Elena Kutumova & Ilya Akberdin & Ilya Kiselev & Ruslan Sharipov & Fedor Kolpakov, 2022. "Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example," Mathematics, MDPI, vol. 10(7), pages 1-20, April.
  46. Kuo-Ching Ying & Shih-Wei Lin, 2020. "Maximizing cohesion and separation for detecting protein functional modules in protein-protein interaction networks," PLOS ONE, Public Library of Science, vol. 15(10), pages 1-16, October.
  47. Scholtens, Denise & Miron, Alexander & M. Merchant, Faisal & Miller, Arden & L. Miron, Penelope & Dirk Iglehart, J. & Gentleman, Robert, 2004. "Analyzing factorial designed microarray experiments," Journal of Multivariate Analysis, Elsevier, vol. 90(1), pages 19-43, July.
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