A genome‐scale computational study of the interplay between transcriptional regulation and metabolism

Cited by (253)

Items 101–200 of 253

1. Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
   José P. Faria, Ross Overbeek, Fang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry · 2013 · Briefings in Bioinformatics
2. Deciphering and designing microbial communities by genome-scale metabolic modelling
   Shengbo Wu, Zheping Qu, Danlei Chen, Hao Wu, Qinggele Caiyin, Jianjun Qiao · 2024 · Computational and Structural Biotechnology Journal
3. Multistability and oscillations in genetic control of metabolism
   Diego A. Oyarzún, Madalena Chaves, Marit Hoff-Hoffmeyer-Zlotnik · 2011 · Journal of Theoretical Biology
4. Maximum entropy decomposition of flux distribution at steady state to elementary modes
   Quanyu Zhao, Hiroyuki Kurata · 2009 · Journal of Bioscience and Bioengineering
5. Slave nodes and the controllability of metabolic networks
   DH Kim, Adilson E. Motter · 2009 · New Journal of Physics
6. Crosstalk between transcription and metabolism: how much enzyme is enough for a cell?
   Stefano Donati, Timur Sander, Hannes Link · 2017 · WIREs Systems Biology and Medicine
7. The Genome-Scale Integrated Networks in Microorganisms
   Tong Hao, Dan Wu, Lingxuan Zhao, Qian Wang, Edwin Wang, Jinsheng Sun · 2018 · Frontiers in Microbiology
8. Application of Metabolic Flux Analysis in Metabolic Engineering
   Sang Yup Lee, Jong Myoung Park, Tae Yong Kim · 2011 · Methods in enzymology on CD-ROM/Methods in enzymology
9. Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria
   Lore Cloots, Kathleen Marchal · 2011 · Current Opinion in Microbiology
10. Computational Approaches in Metabolic Engineering
    Jennifer L. Reed, Ryan S. Senger, Maciek R. Antoniewicz, Jamey D. Young · 2010 · BioMed Research International
11. Bioinformatics and systems biology
    Prahlad T. Ram, John M. Mendelsohn, Gordon Brent Mills · 2012 · Molecular Oncology
12. Bridging the gap between gene expression and metabolic phenotype via kinetic models
    Francisco G Vital-Lopez, Anders Wallqvist, Jaques Reifman A · 2013 · BMC Systems Biology
13. Genome-Scale Metabolic Models of Saccharomyces cerevisiae
    Intawat Nookaew, Roberto Olivares‐Hernández, Sakarindr Bhumiratana, Jens Nielsen · 2011 · Methods in molecular biology
14. Hybrid Physics-Informed Metabolic Cybergenetics: Process Rates Augmented with Machine-Learning Surrogates Informed by Flux Balance Analysis
    Sebastián Espinel‐Ríos, José L. Avalos‬ · 2024 · Industrial & Engineering Chemistry Research
15. Gobal optimization of hybrid kinetic/FBA models via outer-approximation
    Carlos Pozo, Antoni Miró, Gonzalo Guillén‐Gosálbez, Albert Sorribas B, Rui Alves, Laureano Jiménez · 2014 · Computers & Chemical Engineering
16. Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks
    Steffen Klamt, Oliver Hädicke, Axel von Kamp · 2014 · Modeling and simulation in science, engineering & technology
17. Regulatory dynamic enzyme-cost flux balance analysis: A unifying framework for constraint-based modeling
    Lin Liu, Alexander Bockmayr · 2020 · Journal of Theoretical Biology
18. A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism
    Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijović · 2021 · PLoS Computational Biology
19. Characterizing metabolic pathway diversification in the context of perturbation size
    Laurence Yang, Shyamsundhar Srinivasan, Radhakrishnan Mahadevan, W.R. Cluett · 2014 · Metabolic Engineering
20. Metabolic Network-Based Interpretation of Gene Expression Data Elucidates Human Cellular Metabolism
    Tomer Shlomi · 2009 · Biotechnology and Genetic Engineering Reviews
21. A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
    Fernando Cruz, José P. Faria, Miguel Rocha, Isabel Rocha, Óscar Dias · 2020 · Biochemical Society Transactions
22. Flux balance analysis of metabolic networks for efficient engineering of microbial cell factories
    Pramita Sen · 2022 · Biotechnology and Genetic Engineering Reviews
23. Phenotype prediction in regulated metabolic networks
    Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich · 2008 · BMC Systems Biology
24. Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis
    Quanyu Zhao, Hiroyuki Kurata · 2010 · Journal of Bioscience and Bioengineering
25. Identification of metabolic pathways using pathfinding approaches: a systematic review
    Zeyad Abd Algfoor, Mohd Shahrizal Sunar, Afnizanfaizal Abdullah, Hoshang Kolivand · 2016 · Briefings in Functional Genomics
26. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli
    Valentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde de Jong · 2011 · Journal of Theoretical Biology
27. Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella
    Jason McDermott, Hyunjin Yoon, Ernesto Satoshi Nakayasu, Thomas Metz, Daniel R. Hyduke, Afshan S. Kidwai, Bernhard Ørn Palsson, Joshua Adkins, Fred Heffron · 2011 · Frontiers in Microbiology
28. Modeling with a view to target identification in metabolic engineering: A critical evaluation of the available tools
    Jo Maertens, Peter A. Vanrolleghem · 2010 · Biotechnology Progress
29. Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
    Biju Joseph Ampattu, L. Hagmann, Chun-Guang Liang, M. Dittrich, A. Schlüter, J. Blom, E. Krol, A. Goesmann, A. Becker, T. Dandekar et al. · 2017 · BMC Genomics
30. A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information
    Paulo Vilaça, Isabel Rocha, Miguel Rocha · 2010 · Biosystems
31. An overview of bioinformatics methods for modeling biological pathways in yeast
    Jie Hou, Lipi R. Acharya, Dongxiao Zhu, Jianlin Jack Cheng · 2015 · Briefings in Functional Genomics
32. Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer’s disease
    Han Yu, Rachael Hageman Blair · 2019 · BMC Bioinformatics
33. MUFINS: multi-formalism interaction network simulator
    Huihai Wu, Axel von Kamp, Vytautas Leoncikas, Wataru Mori, Nilgun Sahin, Albert Gevorgyan, Catherine Linley, Marek Grabowski, Ahmad A. Mannan, Nicholas S. Stoy et al. · 2016 · npj Systems Biology and Applications
34. In silico cell factory design driven by comprehensive genome-scale metabolic models: development and challenges
    Jiangong Lu, Xinyu Bi, Yanfeng Liu, Xueqin Lv, Jianghua Li, Guocheng Du, Long Liu · 2022 · Systems Microbiology and Biomanufacturing
35. Gapsplit : efficient random sampling for non-convex constraint-based models
    Thomas C. Keaty, Paul A. Jensen · 2020 · Bioinformatics
36. Reconstruction and validation of a constraint‐based metabolic network model for bone marrow‐derived mesenchymal stem cells
    Hamideh Fouladiha, Sayed‐Amir Marashi, Mohammad Ali Shokrgozar · 2015 · Cell Proliferation
37. Towards the automated engineering of a synthetic genome
    Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo · 2009 · Molecular BioSystems
38. 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
39. Genome-scale reconstruction of a metabolic network for Gluconobacter oxydans 621H
    Xinsen Wu, Xiaoyang Wang, Wenyu Lu · 2014 · Biosystems
40. Visual Analysis of Overlapping Biological Networks
    David C. Y. Fung, Seok-Hee Hong, Dirk Koschützki A, Falk Schreiber, Kai Xu · 2009 · International Conference on Information Visualisation (IV)
41. Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
    Arup Kumar Bag, Sapan Mandloi, Saulius Jarmalavicius, Susmita Mondal, Krishna G. Kumar, Chhabinath Mandal, Peter Walden, Saikat Chakrabarti, Chitra Mandal · 2019 · PLoS Computational Biology
42. Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells
    Naroa Barrena, Luis V. Valcárcel, Danel Olaverri-Mendizabal, Iñigo Apaolaza, Francisco J. Planes · 2023 · npj Systems Biology and Applications
43. Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2
    Rafael Silva‐Rocha, Danilo R. Pérez-Pantoja, Vı́ctor de Lorenzo · 2012 · The ISME Journal
44. Optimality Principles in the Regulation of Metabolic Networks
    Jan Berkhout, Frank J. Bruggeman, Bas Teusink · 2012 · Metabolites
45. Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks
    Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay K. Nakhleh · 2013 · PLoS Computational Biology
46. Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches
    Georg Basler · 2015 · Methods in molecular biology
47. Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis
    Santhust Kumar, Saurabh Mahajan, Sanjay Jain · 2018 · PLoS ONE
48. Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs
    Christian Jungreuthmayer, David E. Ruckerbauer, Matthias Peter Gerstl, Michael Hanscho, Jürgen Zanghellini · 2015 · PLoS ONE
49. Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment
    Tracy J. Kuper, Mohammad Mazharul Islam, Shayn M. Peirce, Jason A. Papin, Roseanne M. Ford · 2024 · PLoS Computational Biology
50. Deep epistasis in human metabolism
    Marcin B. Imielinski, Calin A. Belta · 2010 · Chaos An Interdisciplinary Journal of Nonlinear Science
51. Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models
    Matteo Barberis, Robert G. Todd, Lucas van der Zee · 2016 · FEMS Yeast Research
52. Identifying, Characterizing, and Engineering a Phenolic Acid-Responsive Transcriptional Factor from Bacillus amyloliquefaciens
    Chenyi Li, Yuyang Zhou, Yusong Zou, Tian Jiang, Xinyu Gong, Yajun Yan · 2023 · ACS Synthetic Biology
53. Integrating scientific cultures
    Trey E. Ideker, Vineet Bafna, Thomas Lemberger · 2007 · Molecular Systems Biology
54. Prediction and integration of metabolite-protein interactions with genome-scale metabolic models
    Mahdis Habibpour, Zahra Razaghi‐Moghadam, Zoran Nikoloski · 2024 · Metabolic Engineering
55. Metabolic Systems Biology
    Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard Ørn Palsson · 2009 · Springer eBooks
56. A Lattice-Theoretic Framework for Metabolic Pathway Analysis
    Yaron Goldstein, Alexander Bockmayr · 2013 · Lecture notes in computer science
57. Uncovering Metabolic Objectives Pursued by Changes of Enzyme Levels
    Sabrina Hoffmann, Hermann−Georg Holzhütter · 2009 · Annals of the New York Academy of Sciences
58. TRIMER: Transcription Regulation Integrated with Metabolic Regulation
    Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian K. Blaby, Xiaoning Qian · 2021 · iScience
59. Integration of Metabolic Reactions and Gene Regulation
    Chen‐Hsiang Yeang · 2010 · Molecular Biotechnology
60. A Protocol for the Construction and Curation of Genome-Scale Integrated Metabolic and Regulatory Network Models
    Sriram Chandrasekaran · 2019 · Methods in molecular biology
61. Metabolic cell communication within tumour microenvironment: models, methods and perspectives
    Matteo Parri, Luigi Ippolito, Paolo Cirri, Matteo Ramazzotti, Paola Chiarugi · 2020 · Current Opinion in Biotechnology
62. A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acidmetabolism
    Idit Diamant, Yonina C. Eldar, Oleg Rokhlenko, Eytan Ruppin, Tomer Shlomi · 2009 · Molecular BioSystems
63. Challenges in Integrating Genetic Control in Plant and Crop Models
    Valentina Baldazzi, Nadia Bertin, Michel Génard, Hélène Gautier, Elsa Desnoues, Bénédicte Quilot‐Turion · 2015 · Springer eBooks
64. Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications
    Sanjeev Dahal, Jiao Zhao, Laurence Yang · 2020 · Biotechnology and Bioprocess Engineering
65. The future of genome‐scale modeling of yeast through integration of a transcriptional regulatory network
    Guodong Liu, Antonio Marras, Jens Nielsen · 2014 · Quantitative Biology
66. Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks
    Hanen Mhamdi, Jérémie Bourdon, Abdelhalim Larhlimi, Mourad Elloumi · 2020 · Informatics
67. Integrating Omics Data to Prioritize Target Genes in Pathogenic Bacteria
    Marisa Nicolás, Maiana de Oliveira Cerqueira e Costa, Pablo Ivan Pereira Ramos, Marcelo Trindade dos Santos, Ernesto Pérez‐Rueda, Marcelo Adrian Marti, Darío Fernández Do Porto, Adrian Gustavo Turjanski · 2020 · Computational biology
68. Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation
    José P. Faria, James J. Davis, Janaka N. Edirisinghe, Ronald C. Taylor, Pamela B. Weisenhorn, Robert Olson, Rick L. Stevens, Miguel Rocha, Isabel Rocha, Aaron A. Best et al. · 2016 · Frontiers in Microbiology
69. OPTIMAL METABOLIC REGULATION USING A CONSTRAINT-BASED MODEL
    William J. Riehl, Daniel Segrè · 2008 · International Conference on Genome Informatics (GIW)
70. Metabolomic Systems Biology of Protozoan Parasites
    Rainer Breitling A, Barbara M. Bakker, Michael Peter Barrett, Saskia Decuypere, Jean‐Claude Dujardin · 2012 · Springer eBooks
71. A review of advances in integrating gene regulatory networks and metabolic networks for designing strain optimization
    Ridho Ananda, Kauthar Mohd Daud, Suhaila Zainudin · 2024 · Journal of King Saud University - Computer and Information Sciences
72. Quantitative modeling of human metabolism: A call for a community effort
    María Masid, Vassily Hatzimanikatis A · 2021 · Current Opinion in Systems Biology
73. Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models
    Paul A. Jensen · 2017 · Methods in molecular biology
74. Genome-Scale Network Modeling
    Sang Yup Lee, Seung Bum Sohn, Hyun Uk Kim, Jong Myoung Park, Tae Yong Kim, Jeffrey D. Orth, Bernhard Ørn Palsson · 2012 · Springer eBooks
75. Analysis of a genetic-metabolic oscillator with piecewise linear models
    Madalena Chaves A, Diego A. Oyarzún, Jean‐Luc Gouzé · 2018 · Journal of Theoretical Biology
76. A computational method using differential gene expression to predict altered metabolism of multicellular organisms
    Lvxing Zhu, Haoran Zheng, Xinying Hu, Yang Xu · 2017 · Molecular BioSystems
77. cysA, cysP, and rpoS mutations increase the power density in P. aeruginosa microbial fuel cells: Performing enhancement based on metabolic flux analysis
    Juan Diego Mejía, Cindy Stephany Rojas, Laura Avellaneda-Franco, David Alejandro Urbina Gómez, Beatriz Helena Correa Arias, Nubia Velasco, Maria Teresa Cortes Montañez, Martha J. Vives, Andrés Fernando González Barrios · 2013 · Advances in Bioscience and Biotechnology
78. Network Dynamics as an Interface between Modeling and Experiment in Systems Biology
    James Smith, M.‐Th. Hütt · 2010
79. Protein Interaction Networks and Their Statistical Analysis
    Waqar Ali, Charlotte Mary Deane, Gesine Reinert · 2011
80. Development and applications of genome-scale metabolic network models
    Jinyi Qian, Chao Ye · 2024 · Advances in applied microbiology
81. Technologies for whole‐cell modeling: Genome‐wide reconstruction of a cell in silico
    Kazunari Kaizu, Koichi Takahashi · 2023 · Development Growth & Differentiation
82. Network Medicine: New Paradigm in the -Omics Era
    Nancy Lan Guo · 2011 · Anatomy & Physiology
83. Construction and analysis of an integrated biological network of Escherichia coli
    Zhitao Mao, Teng Huang, Qianqian Yuan, Hongwu Ma · 2021 · Systems Microbiology and Biomanufacturing
84. Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline
    Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian K. Blaby, Xiaoning Qian · 2022 · STAR Protocols
85. Metabolomics using Fourier transform mass spectrometry
    Christophe Junot, François Fenaille · 2019 · Elsevier eBooks
86. Controlling the Outcome of the Toll-Like Receptor Signaling Pathways
    Guilhem Richard, Calin A. Belta, A. Agung Julius, Salomon Amar · 2012 · PLoS ONE
87. Correction: The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes
    Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Johannes Geiselmann, Hidde de Jong · 2010 · PLoS Computational Biology
88. Non-Equilibrium Hyperbolic Transport in Transcriptional Regulation
    Enrique Hernandez Lemus, María D. Correa-Rodríguez · 2011 · PLoS ONE
89. [Genomics in medicine].
    Ruth Ruiz-Esparza Garrido, Miguel Ángel Velázquez-Flores, Diego Julio Arenas-Aranda, Fabio Salamanca-Gómez · 2014 · PubMed
90. Identifying model error in metabolic flux analysis – a generalized least squares approach
    Stanislav Sokolenko, Marco Quattrociocchi, Marc Gordon Aucoin · 2016 · BMC Systems Biology
91. Multiomic Data Integration and Analysis via Model-Driven Approaches
    Igor Marín de Mas · 2018 · Comprehensive analytical chemistry
92. Identifying Enzyme Knockout Strategies on Multiple Enzyme Associations
    Bin Song, I. Esra, Nirmalya Bandyopadhyay, Sanjay Ranka, Tamer Kahveci · 2011 · InTech eBooks
93. In Silico Approaches to Metabolic Engineering
    Abinaya Badri, Aparajitha Srinivasan, Karthik Raman · 2016 · Elsevier eBooks
94. Constraint-based analysis of substructures of metabolic networks
    Sayed‐Amir Marashi · 2011 · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver
95. ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization
    Gustavo Tamasco · 2022
96. Predicting Phenotype from Genotype Through Reconstruction and Integrative Modeling of Metabolic and Regulatory Networks
    Sriram Chandrasekaran · 2014 · Springer eBooks
97. A systems biology approach towards oral cancer using computational tools and techniques
    Yadav Keerti Kumar, Anil Kumar, Ajay Kumar Singh · 2022 · Chemometrics and Intelligent Laboratory Systems
98. Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models
    Mahdi Jalili, Martin Scharm, Olaf Wolkenhauer A, Ali Salehzadeh‐Yazdi · 2023 · npj Systems Biology and Applications
99. Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data
    Deqing Gu, Xingxing Jian, Cheng Zhang, Qiang Hua · 2016 · IEEE Transactions on Computational Biology and Bioinformatics
100. Evolutionary dynamics of metabolic adaptation
     Milan J. A. Hoek · 2008 · Utrecht University Repository (Utrecht University)