Bow ties, metabolism and disease

Cited by (472)

Items 201–300 of 472

1. Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks
   Steffen Klamt, Oliver Hädicke, Axel von Kamp · 2014 · Modeling and simulation in science, engineering & technology
2. Profiling the transcription factor regulatory networks of human cell types
   Shihua Zhang, Dechao Tian, Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang · 2014 · Nucleic Acids Research
3. Metabolic determinants of enzyme evolution in a genome-scale bacterial metabolic network
   José Aguilar-Rodríguez, Andreas Wagner · 2018 · Genome Biology and Evolution
4. Planning the reconfiguration of grounded truss structures with truss climbing robots that carry truss elements
   Seung-kook Yun, David Alan Hjelle, Eric Schweikardt, Hod Lipson, Daniela L. Rus · 2009 · Proceedings - IEEE International Conference on Robotics and Automation/Proceedings
5. Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses
   Kiana Toufighi, Jae‐Seong Yang, Nuno Miguel Luis, Salvador Aznar Benitah, Ben Lehner, Luis G. Serrano, Christina Kiel · 2015 · PLoS Computational Biology
6. Modulation of hepatic copper-ATPase activity by insulin and glucagon involves protein kinase A (PKA) signaling pathway
   Elaine Hilário‐Souza, Martine Cuillel, Elisabeth Mintz, Peggy Charbonnier, Adalberto Ramón Vieyra, Doris Cassio, Jennifer Lowe · 2016 · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
7. A Conceptual Framework for Organismal Biology: Linking Theories, Models, and Data
   William E. Zamer, Samuel M. Scheiner · 2014 · Integrative and Comparative Biology
8. Parameter adaptations during phenotype transitions in progressive diseases
   Tiemann, Christian A, Vanlier, Joep, Hilbers, Peter AJ, van Riel, Natal AW · 2011 · BMC Systems Biology
9. Division of labour promotes the spread of information in colony emigrations by the ant Temnothorax rugatulus
   Gabriele Valentini, Naoki Masuda, Zachary Shaffer, Jake R. Hanson, Takao Sasaki, Sara Imari Walker, Theodore P. Pavlic, Stephen C. Pratt · 2020 · Proceedings of the Royal Society B Biological Sciences
10. Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs)
    Sang Ok Song, Anirikh Chakrabarti, Jeffrey D. Varner · 2010 · Biotechnology Journal
11. The reconstruction and analysis of tissue specific human metabolic networks
    Tong Hao, Hongwu Ma, Xueming Zhao, Igor Goryanin · 2011 · Molecular BioSystems
12. The Brain in Space
    Kenneth Knoblauch, Mária Ercsey-Ravasz, Henry Kennedy, Zoltán Toroczkai · 2016 · Research and perspectives in neurosciences
13. Molecular Communication: New Paradigm for Communication among Nanoscale Biological Machines
    Michael John Moore, Akihiro Enomoto, Tatsuya Suda, Tadashi Nakano, Yutaka Okaie · 2007 · Wiley eBooks
14. Identifying Functional Mechanisms of Gene and Protein Regulatory Networks in Response to a Broader Range of Environmental Stresses
    Chengwei Li, Bor‐Sen Chen · 2010 · Comparative and Functional Genomics
15. The Danaid Theory of Aging
    Maarten Jan Wensink, Alan Arthur Cohen · 2022 · Frontiers in Cell and Developmental Biology
16. Biomarkers of mitochondrial dysfunction and inflammaging in older adults and blood pressure variability
    Leonardo Bencivenga, Mathilde Strumia, Yves Rolland, Laurent O. Martinez, Philippe Cestac, Sophie Guyonnet, Sandrine Andrieu, Angelo Parini, Alexandre Lucas, Bruno J. Vellas et al. · 2022 · GeroScience
17. Increased Circulating Levels of Alpha-Ketoglutarate in Morbidly Obese Women with Non-Alcoholic Fatty Liver Disease
    Gemma Aragonès, Teresa Auguet, Alba Berlanga, Esther Guiu‐Jurado, Salomé Martínez, Sandra Armengol, Fàtima Sabench, Rosa Ras, Mercè Hernández, Carmen Aguilar et al. · 2016 · PLoS ONE
18. Universal hypotrochoidic law for random matrices with cyclic correlations
    Pau Vilimelis Aceituno, Tim Rogers, Henning Schomerus · 2019 · Physical review. E
19. Invisible Designers: Brain Evolution Through the Lens of Parasite Manipulation
    Marco Del Giudice · 2019 · The Quarterly Review of Biology
20. Socially-aware congestion control in ad-hoc networks: Current status and the way forward
    Hannan Bin Liaqat, Amjad Ali, Junaid Qadir, Ali Kashif Bashir, Muhammad Bilal, Fiaz Majeed · 2019 · Future Generation Computer Systems
21. Robustness and complexity
    Steven A. Frank · 2023 · Cell Systems
22. Human Nutrition and Genetic Variation
    Patrick J. Stover · 2007 · Food and Nutrition Bulletin
23. A robotically reconfigurable truss
    David Alan Hjelle, Hod Lipson · 2009
24. Pathway knockout and redundancy in metabolic networks
    Yong Ki Min, Xiaogang Jin, Ming Chen, Zhengzheng Pan, Ying Ge, Jie Chang · 2010 · Journal of Theoretical Biology
25. Functional models for large-scale gene regulation networks: realism and fiction
    Marco Cosentino Lagomarsino, B. Bassetti, Gastone Castellani, Daniel Remondini · 1900 · Molecular BioSystems
26. A unifying computational framework for stability and flexibility of arousal
    Christin Kosse, Denis Burdakov · 2014 · Frontiers in Systems Neuroscience
27. A Biorefinery approach towards development of renewable platform chemicals from sustainable biomass
    Gurunathan Baskar, R. Aiswarya, G. Maria Kalavathy, Ashok Pandey, Edgard Gnansounou, Jegannathan Kenthorai Raman, R. Praveen Kumar · 2019 · Elsevier eBooks
28. A Test of Highly Optimized Tolerance Reveals Fragile Cell-Cycle Mechanisms Are Molecular Targets in Clinical Cancer Trials
    Satyaprakash Nayak, Saniya Salim, Deyan Luan, Michael Zai, Jeffrey D. Varner · 2008 · PLoS ONE
29. Frank Beach Award Winner: The centrality of the hypothalamic-pituitary-adrenal axis in dealing with environmental change across temporal scales
    Ben Dantzer · 2023 · Hormones and Behavior
30. Pattern qualifications and examples of next-generation agile system-security strategies
    Rick Dove · 2010 · IEEE International Carnahan Conference on Security Technology (ICCST)
31. The hourglass effect in hierarchical dependency networks
    Kaeser Md. Sabrin, Constantine Dovrolis · 2017 · Network Science
32. A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli
    Anne Grimbs, David F. Klosik, Stefan Bornholdt, M.‐Th. Hütt · 2019 · PLoS Computational Biology
33. Degeneracy allows for both apparent homogeneity and diversification in populations
    James M. Whitacre, Sergei P. Atamas · 2012 · Biosystems
34. Inflamm-aging as a diverse and context-dependent process: From species and population differences to individual trajectories
    Maximilien Franck, Camille Daunizeau, Jacob E. Aronoff, Kamaryn Tanner, Benjamin C. Trumble, Claudio Franceschi, Johannes Hertel, Tamàs Fülöp, Maël Lemoine, Michael Gurven et al. · 2025 · Ageing Research Reviews
35. Trade‐off of dynamic fragility but not of robustness in metabolic pathways in silico
    Mark J. Quinton-Tulloch, Frank J. Bruggeman, Jacky L. Snoep, Hans Victor Westerhoff · 2012 · FEBS Journal
36. Predicting novel metabolic pathways through subgraph mining
    Aravind Sankar, Sayan Ranu, Karthik Raman · 2017 · Bioinformatics
37. Efficient representations of binarized health deficit data: the frailty index and beyond
    G. Pridham, K. Rockwood, A. Rutenberg · 2023 · GeroScience
38. Bioenergetics: the evolutionary basis of progressive kidney disease
    Robert L. Chevalier · 2023 · Physiological Reviews
39. Regularizing capacity of metabolic networks
    Carsten Marr, Mark Müller‐Linow, M.‐Th. Hütt · 2007 · Physical Review E
40. What is the role of the next generation of cognitive robotics?
    Shingo Shimoda, Lorenzo Jamone, Dimitri Ognibene, Takayuki Nagai, Alessandra Sciutti, Álvaro Costa‐García, Yohei Oseki, Tadahiro Taniguchi · 2021 · Advanced Robotics
41. Randomizing Genome-Scale Metabolic Networks
    Areejit Samal, Olivier Martin · 2011 · PLoS ONE
42. How Brain Arousal Mechanisms Work
    Donald W. Pfaff · 2018 · Cambridge University Press eBooks
43. FinO/ProQ-family proteins: an evolutionary perspective
    Zhen Liao, Alexandre Smirnov · 2023 · Bioscience Reports
44. Human growth from the cell to the organism: Saltations and integrative physiology
    Michelle Lampl · 2009 · Annals of Human Biology
45. How to Build a Biological Machine Using Engineering Materials and Methods
    Alex A. Ellery · 2020 · Biomimetics
46. An explanatory evo-devo model for the developmental hourglass
    Saamer Akhshabi, Shrutii Sarda, Constantine Dovrolis, Soojin V. Yi · 2014 · F1000Research
47. Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data
    Wei-Sheng Wu, Bor‐Sen Chen · 2007 · Bioinformatics and Biology Insights
48. Highly optimized tolerance and power laws in dense and sparse resource regimes
    M. Lisa Manning, Jean M. Carlson, John C. Doyle · 2005 · Physical Review E
49. Introducing Computational Systems Biology
    Andres Kriete, Roland Eils · 2006 · Elsevier eBooks
50. What does evolution make? Learning in living lineages and machines
    Benedikt Hartl, Michael G. Levin · 2025 · Trends in Genetics
51. Design principles of ciliary signaling
    Carolyn M. Ott, Jennifer Lippincott‐Schwartz · 2025 · Journal of Cell Science
52. Influence of bimanual exercise on muscle activation in post-stroke patients
    Matti Itkonen, Álvaro Costa, Hiroshi R. Yamasaki, Shotaro Okajima, Fady S.K. Alnajjar, Takatsune Kumada, Shingo Shimoda · 2019 · ROBOMECH Journal
53. The Motivational Architecture of Emotions
    Marco Del Giudice · 2024 · Oxford University Press eBooks
54. Local bow-tie structure of the web
    Yuji Fujita, Yuichi Kichikawa, Yoshi Fujiwara, Wataru Souma, Hiroshi Iyetomi · 2019 · Applied Network Science
55. The central role of peripheral nodes in directed network dynamics
    Edgar A. P. Wright, S. Y. Yoon, António Luis Ferreira, José F. F. Mendes, A. V. Goltsev · 2019 · Scientific Reports
56. Network Analysis for Economics and Finance: An Application to Firm Ownership
    Janina Engel, Michela Nardo, Michela Rancan · 2021 · Springer eBooks
57. Hybrid computational modeling methods for systems biology
    Daniel A. Cruz, Melissa Lambeth Kemp · 2021 · Progress in Biomedical Engineering
58. Versatile system cores as a conceptual basis for generality in cell and developmental biology
    Elisa Cristina De Proença Rodrigues Gallo, Stefano De Renzis, James A. Sharpe, Roberto Mayor, Jonas Hartmann · 2024 · Cell Systems
59. Identification of metabolomic profile related to adult Fontan pathophysiology
    Noriko Motoki, Hirohiko Motoki, Masafumi Utsumi, Shoko Yamazaki, Haruka Obinata, Kohta Takei, Satoshi Yasukochi · 2021 · IJC Heart & Vasculature
60. Reconstruction and Analysis of Human Liver-Specific Metabolic Network Based on CNHLPP Data
    Jing Zhao, Chao Geng, Lin Tao, Duanfeng Zhang, Ying Jiang, Kailin Tang, Ruixin Zhu, Hong Jun Yu, Weidong Zhang, Fuchu He et al. · 2010 · Journal of Proteome Research
61. Reconstruction and analysis of a genome-scale metabolic model for Eriocheir sinensis eyestalks
    Bin Wang, Qianji Ning, Tong Hao, Ailing Yu, Jinsheng Sun · 2015 · Molecular BioSystems
62. Understanding Regulation of Metabolism through Feasibility Analysis
    Emrah Nıkerel, Jan Berkhout, Fengyuan Hu, Bas Teusink, Marcel J. T. Reinders, Dick de Ridder · 2012 · PLoS ONE
63. Assessing the Dynamics and Complexity of Disease Pathogenicity Using 4-Dimensional Immunological Data
    A. Rivas, A. Hoogesteijn, A. Antoniades, Marios Tomazou, T. Buranda, D. Perkins, J. Fair, R. Durvasula, F. Fasina, G. Tegos et al. · 2019 · Frontiers in Immunology
64. Design patterns of biological cells
    Steven S. Andrews, H. Steven Wiley, Herbert M. Sauro · 2024 · BioEssays
65. A Computational Method for Reconstructing Gapless Metabolic Networks
    Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen · 2008 · Communications in computer and information science
66. Modeling of Molecular and Cellular Mechanisms Involved in Ca2+ Signal Encoding in Airway Myocytes
    Marko Marhl, Denis Noble, Étienne Roux · 2006 · Cell Biochemistry and Biophysics
67. Generation of Human-Like Movement from Symbolized Information
    Shotaro Okajima, Maxime Tournier, Fady S.K. Alnajjar, Mitsuhiro Hayashibe, Yasuhisa Hasegawa, Shingo Shimoda · 2018 · Frontiers in Neurorobotics
68. Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks
    Shalini Thakur Singh, Areejit Samal, Varun Giri, Sandeep Krishna, Nandula Raghuram, Sanjay Jain · 2013 · Physical Review E
69. Interampatteness – a generic property of biochemical networks
    Torbjörn E. M. Nordling, Elling W. Jacobsen · 2009 · IET Systems Biology
70. Ellipsoid-SLAM: enhancing dynamic scene understanding through ellipsoidal object representation and trajectory tracking
    Haowei Zhu, Suqin Bai, Jinlong Shi, Jiawen Lu, Xin Zuo, Shucheng Huang, Yao Xu · 2025 · The Visual Computer
71. Robust Physiological Metrics From Sparsely Sampled Networks
    Alan Arthur Cohen, Sébastien Leblanc, Xavier Roucou · 2021 · Frontiers in Physiology
72. Synthetic Biology Meets Machine Learning
    Brendan Fu‐Long Sieow, Ryan De Sotto, Zhi Ren Darren Seet, In Young Hwang, Matthew Wook Chang · 2022 · Methods in molecular biology
73. Bow-tie architectures in biological and artificial neural networks: Implications for network evolution and assay design
    Seth Hilliard, Karen Mosoyan, Sergio Branciamore, Grigoriy Gogoshin, Alvin Zhang, Diana L. Simons, Russell C. Rockne, Peter P. Lee, Andréi S. Rodin · 2023 · iScience
74. Patterns of Self-Organizing Agile Security for Resilient Network Situational Awareness and Sensemaking
    Rick Dove · 2011 · International Conference on Information Technology: New Generations
75. How MAP kinase modules function as robust, yet adaptable, circuits
    Tianhai Tian, Angus Silas Harding · 2014 · Cell Cycle
76. Intrinsic health as a foundation for a science of health
    Alan Arthur Cohen, Martin A. Picard, John Beard, Daniel W. Belsky, Julie Beth Herbstman, Christine L. Kuryla, Molei Liu, Nour Makarem, Daniel Malinsky, Sen Pei et al. · 2025 · Science Advances
77. Genomic Variation, Evolvability, and the Paradox of Mental Illness
    Camillo Thomas Gualtieri · 2021 · Frontiers in Psychiatry
78. MODELING OF HUMAN BAROREFLEX: CONSIDERATIONS ON THE SEIDEL–HERZEL MODEL
    Andrea Duggento, Nicola Toschi, Maria Guerrisi · 2012 · Fluctuation and Noise Letters
79. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function
    Olivier Martin, A. Krzywicki, Marcin Zagórski · 2016 · Physics of Life Reviews
80. Structural and Functional Analysis of Giant Strong Component of Bacillus thuringiensis Metabolic Network
    Dewu Ding, Y.R. Ding, L.N. Li, Y.J. Cai, Wenbo Xu · 2009 · Brazilian Journal of Microbiology
81. ARDesigner: A web-based system for allosteric RNA design
    Wenjie Shu, Ming Liu, Hebing Chen, Xiaochen Bo, Shengqi Wang · 2010 · Journal of Biotechnology
82. Early spatiotemporal-specific changes in intermediate signals are predictive of cytotoxic sensitivity to TNFα and co-treatments
    Lit‐Hsin Loo, Nicola Michelle Bougen-Zhukov, Wei-Ling Cecilia Tan · 2017 · Scientific Reports
83. Modular Organization and Emergence in Systems Biology
    M.‐Th. Hütt · 2019 · Springer eBooks
84. Robustness as a non‐localizable relational phenomenon
    José A. Fernández-León · 2013 · Biological reviews/Biological reviews of the Cambridge Philosophical Society
85. ‘Domino’ systems biology and the ‘A’ of ATP
    Malkhey Verma, Maksim V. Zakhartsev, Matthias Reuß, Hans Victor Westerhoff · 2012 · Biochimica et Biophysica Acta (BBA) - Bioenergetics
86. Gene regulatory network inference in long-lived C. elegans reveals modular properties that are predictive of novel aging genes
    Manusnan Suriyalaksh, C. Raimondi, Abraham Mains, A. Segonds-Pichon, Shahzabe Mukhtar, Sharlene Murdoch, R. Aldunate, F. Krueger, R. Guimerà, Simon R. Andrews et al. · 2021 · iScience
87. Expanded flux variability analysis on metabolic network of Escherichia coli
    Tong Chen, Zhengwei Xie, Qi Ouyang · 2009 · 中国科学通报：英文版
88. Metabolic flexibility of d -ribose producer strain of Bacillus pumilus under environmental perturbations
    Rajesh K. Srivastava, Soumen Kumar Maiti, Debasish Das, Prashant Madhusudan Bapat, Kritika Batta, Mani Bhushan, Pramod P. Wangikar · 2012 · Journal of Industrial Microbiology & Biotechnology
89. Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments
    Zitong Jerry Wang, Matt W. Thomson · 2022 · Cell Systems
90. Self-replicating probes are imminent – implications for SETI
    Alex A. Ellery · 2022 · International Journal of Astrobiology
91. Structural Efficiency of Percolated Landscapes in Flow Networks
    M. Ángeles Serrano, Paolo De Los Rios · 2008 · PLoS ONE
92. A Fluorimetric Readout Reporting the Kinetics of Nucleotide‐Induced Human Ribonucleotide Reductase Oligomerization
    Yuan Fu, Hongyu Lin, Somsinee Wisitpitthaya, William A. Blessing, Yimon Aye · 2014 · ChemBioChem
93. Identification of Major Signaling Pathways in Prion Disease Progression Using Network Analysis
    Khalique Newaz, Krishnamachari Sriram, Debajyoti Bera · 2015 · PLoS ONE
94. Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes
    Gaoyang Li, Huansheng Cao, Ying Xu · 2018 · Briefings in Bioinformatics
95. Complete Topological Mapping of a Cellular Protein Interactome Reveals Bow-Tie Motifs as Ubiquitous Connectors of Protein Complexes
    Kristoffer Niss, Cristina Gómez‐Casado, Jessica Xin Hjaltelin, Thorsten Joeris, William W. Agace, Kirstine Belling, Søren Brunak · 2020 · Cell Reports
96. Minimal Cut Sets and the Use of Failure Modes in Metabolic Networks
    Sangaalofa Tooki Clark, Wynand S. Verwoerd · 2012 · Metabolites
97. A power law distribution of metabolite abundance levels in mice regardless of the time and spatial scale of analysis
    Shumpei Sato, Makoto Horikawa, Takeshi Kondo, Tomohito Sato, Mitsutoshi Setou · 2018 · Scientific Reports
98. Are There Biomimetic Lessons from Genetic Regulatory Networks for Developing a Lunar Industrial Ecology?
    Alex A. Ellery · 2021 · Biomimetics
99. Network models in drug discovery and regenerative medicine
    David Alan Winkler · 2008 · Biotechnology annual review
100. Pervasive Flexibility in Living Technologies through Degeneracy-Based Design
     James M. Whitacre, Axel Bender · 2013 · Artificial Life