A Whole-Cell Computational Model Predicts Phenotype from Genotype
Karr, Jonathan R., Sanghvi, Jayodita C., Macklin, Derek N., Gutschow, Miriam V., Jacobs, Jared M., Bolival, Benjamin, Assad-Garcia, Nacyra, Glass, John I. +1 more·2012·Cell
Cited by (1,292)
Items 801–900 of 1,292
- Collaborative explanation, explanatory roles, and scientific explaining in practiceAlan C. Love · 2015 · Studies in History and Philosophy of Science Part A
- Integrating multi‐scale knowledge on cardiac development into a computational model of ventricular trabeculationBouke A. de Boer, Jean‐François Le Garrec, Vincent M. Christoffels · 2014 · WIREs Systems Biology and Medicine
- Hybrid Simulations of Heterogeneous Biochemical Models in SBMLHui-Ju Katherine Chiang, François Fages, Jie Hong Roland Jiang, Sylvain Soliman · 2015 · ACM Transactions on Modeling and Computer Simulation
- Engineering microbial chemical factories using metabolic modelsDebolina Sarkar, Costas D. Maranas · 2019 · BMC Chemical Engineering
- A compiler for biological networks on silicon chipsKyle Medley, Jonathan J. Y. Teo, Sung Sik Woo, Joseph Hellerstein, Rahul Sarpeshkar, Herbert M. Sauro · 2020 · PLoS Computational Biology
- Romance of the three domains: how cladistics transformed the classification of cellular organismsChi-Chun Ho, Susanna K. P. Lau, Patrick C. Y. Woo · 2013 · Protein & Cell
- Designing Cell-Targeted Therapeutic Proteins Reveals the Interplay between Domain Connectivity and Cell BindingAvi Robinson-Mosher, Jan‐Hung Chen, Jeffrey C. Way · 2014 · Biophysical Journal
- The Demise of the GeneStuart A. Newman · 2013 · Capitalism Nature Socialism
- Logic modeling and the ridiculome under the rugMichael L. Blinov, Ion I. Moraru · 2012 · BMC Biology
- Dynamic Flux Balance Analysis Models in SBMLMatthias König, Leandro H. Watanabe, Jan Grzegorzewski, C. Myers · 2018 · bioRxiv
- The genome design suite: enabling massive in-silico experiments to design genomesOliver Chalkley, Oliver Purcell, Claire Suzanne Grierson, Lucia Marucci · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Ultra-weak protein-protein interactions can modulate proteome-wide searching and bindingJennifer L. Hofmann, Akshay J. Maheshwari, Alp M. Sunol, Drew Endy, Roseanna N. Zia · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome-scale metabolic modelling in antimicrobial pharmacology: Present and futureJianjun Tao, Yu-Wei Lin, Lingyuxiu Zhong, Yan Zhu, Xinpeng Yao, Michael Aichem, Falk Schreiber, Jinxin Zhao, Jian Li · 2025 · Advanced Drug Delivery Reviews
- Viruses in multi-scale ocean models: challenges and opportunitiesDavid Talmy, Cristina Howard‐Varona, Damien Eveillard, Markus W. Covert, Matthew B. Sullivan · 2025 · Frontiers in Marine Science
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunitiesHuasen Jiang, Xiaoyu Huang, Xiangpeng Bi, Wenjian Ma, Haibo Ni, Zhiqiang Wei, Pin Sun, Henggui Zhang, Shugang Zhang · 2026 · Briefings in Bioinformatics
- Metabolic Objectives and Trade-Offs: Inference and ApplicationsDa-Wei Lin, Saanjh Khattar, Sriram Chandrasekaran · 2025 · Metabolites
- A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populationsMarco Vanoni, Pasquale J Palumbo, Federico Papa, Stefano Busti, Laura Gotti, Meike Tessa Wortel, Bas Teusink, Ivan Orlandi, Alex Pessina, Cristina Airoldi et al. · 2025 · PLoS Computational Biology
- Information-Theoretic Analysis of the Dynamics of an Executable Biological ModelAvital Sadot, Septimia Sârbu, Juha Kesseli · 2013 · PLoS ONE
- Systems Biology Approaches to Enzyme Kinetics: Analyzing Network Models of Drug MetabolismNnenna A. Finn, Melissa Lambeth Kemp · 2014 · Methods in molecular biology
- FPGA Implementation of Different Stochastic Biochemical Reactions Involved in a CellBarman Mandal Soma, Acharya Moumita, Basu Samik · 2021 · International Symposium on VLSI Design and Test (VDAT)
- Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartmentsXue Na Yang, Zhitao Mao, Jianfeng Huang, Ruoyu Wang, Huaming Dong, Yanfei Zhang, Hongwu Ma · 2023 · Synthetic and Systems Biotechnology
- Digital entrepreneurship from cellular data: How omics afford the emergence of a new wave of digital ventures in healthHannes Rothe, Katharina Barbara Lauer, Callum Talbot-Cooper, Daniel Juan Sivizaca Conde · 2023 · Electronic Markets
- Technologies for whole‐cell modeling: Genome‐wide reconstruction of a cell in silicoKazunari Kaizu, Koichi Takahashi · 2023 · Development Growth & Differentiation
- A computational spatial whole-Cell model for hepatitis B viral infection and drug interactionsZhaleh Ghaemi, Oluwadara Nafiu, Emad Tajkhorshid, Martin Gruebele, Jianming Hu · 2023 · Scientific Reports
- Dynamic metabolic models in context: biomass backtrackingKatja Tummler, Clemens Kühn, Edda Klipp · 2015 · Integrative Biology
- Grand Challenges in Synthetic Biology to be AccomplishedPengcheng Fu · 2013 · Frontiers in Bioengineering and Biotechnology
- Dynamic Modeling of Metabolic and Gene Regulatory Systems toward Developing Virtual MicrobesHiroyuki Kurata, Kazuhiro Maeda, Yu Matsuoka · 2013 · JOURNAL OF CHEMICAL ENGINEERING OF JAPAN
- Contextualization Procedure and Modeling of Monocyte Specific TLR SignalingMaike Kathrin Aurich, Ines Thiele · 2012 · PLoS ONE
- SS-mPMG and SS-GA: Tools for Finding Pathways and Dynamic Simulation of Metabolic NetworksTetsuo Katsuragi, Naoaki Ono, Keiichi Yasumoto, Md. Altaf‐Ul‐Amin, Masami Yokota Hirai, Kansuporn Sriyudthsak, Yuji Sawada, Yui Yamashita, Yukako Chiba, Hitoshi Onouchi et al. · 2013 · Plant and Cell Physiology
- The Notion of Scientific Knowledge in BiologySilvia Morante, Giancarlo C. Rossi · 2016 · Science & Education
- Selection on Network Dynamics Drives Differential Rates of Protein Domain EvolutionBrian K. Mannakee, Ryan N. Gutenkunst · 2016 · PLoS Genetics
- Systems Biology Tools for MethylotrophsMarina Kalyuzhnaya, Song Yang, David A. C. Beck · 2015 · Springer protocols handbooks/Springer protocols
- Neurodegenerative Disease Conditions and Genomic Treatment for Better HealthRavindra V. Badhe, Dharmesh R. Chejara, Pradeep Kumar, Yahya Essop Choonara, Viness Pillay · 2018 · Springer eBooks
- A network-based zoning for parallel whole-cell simulationB.N. Das, Abhijeet Patil, Pralay Mitra · 2018 · Bioinformatics
- Enhancing Metabolic Models with Genome-Scale Experimental DataKristian Lund Jensen, Steinn Guðmundsson, Markus J. Herrgård · 2018 · RNA technologies
- Delving deeper: Relating the behaviour of a metabolic system to the properties of its components using symbolic metabolic control analysisCarl D. Christensen, Jan‐Hendrik S. Hofmeyr, Johann M. Rohwer · 2018 · PLoS ONE
- Biocomputers: Problems They Solve, State of the Art, and ProspectsPavel M. Gotovtsev, Д. А. Кириллова, Raif G. Vasilov · 2020 · Nanotechnologies in Russia
- Unsupervised logic-based mechanism inference for network-driven biological processesMartina Prugger, Lukas Daniel Einkemmer, Samantha P. Beik, Perry T. Wasdin, Leonard A. Harris, Carlos F. Lopez · 2021 · PLoS Computational Biology
- Systems Biology Approaches to Enzyme KineticsNnenna A. Finn, Andrew D. Raddatz, Melissa Lambeth Kemp · 2021 · Methods in molecular biology
- Data-driven network models for genetic circuits from time-series data with incomplete measurementsEnoch Yeung, Jongmin Kim, Ye Yuan, Jorge M. Gonçalves, Richard M. Murray · 2021 · Journal of The Royal Society Interface
- Ensemble Methods for Identifying RNA Operons and Regulons in the Clock Network of Neurospora CrassaAhmad Al-Omari, James William Griffith, Ashley Scruse, Robert W. Robinson, H.-B. Schüttler, Jonathan Arnold · 2022 · IEEE Access
- Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary MetabolitesMarc Griesemer, Ali Navid · 2023 · Microorganisms
- Resource Allocation Principles and Minimal Cell DesignDavid Hidalgo, José Utrilla · 2019 · Springer eBooks
- The Axes of Life: A Roadmap for Understanding Dynamic Multiscale SystemsSriram Chandrasekaran, Nicole Danos, Uduak Z. George, Jin-Ping Han, Gerald Quon, Rolf Müller, Yinphan Tsang, Charles W. Wolgemuth · 2021 · Integrative and Comparative Biology
- The Neal Amundson era. Rapid evolution of chemical engineering scienceDoraiswami Ramkrishna · 2013 · AIChE Journal
- Social networks to biological networks: systems biology of Mycobacterium tuberculosisRohit Vashisht, Anshu Bhardwaj, Samir Kumar Brahmachari · 2013 · Molecular BioSystems
- The “computable egg”: Myth or useful concept?Kilian Biasuz, Bruno Leggio, Emmanuel Faure, Patrick Lemaire · 2018 · Current Opinion in Systems Biology
- In Silico Prediction of Drug Side EffectsMichael J. Keiser · 2015 · Methods and principles in medicinal chemistry
- Whole-Colony Modeling of Escherichia coliChristopher John Skalnik, Eran Agmon, Ryan K. Spangler, Lee Talman, Jerry H. Morrison, Shayn M. Peirce, Markus W. Covert · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Mapping, Modeling, and Reprogramming Cell-Fate Decision-Making SystemsLucy Ham, Taylor E. Woodward, Megan A. Coomer, Michael P. H. Stumpf · 2025 · Annual Review of Biomedical Data Science
- The convergence of AI-driven engineering biology and emerging technologies advancing globally networked autonomous biofoundriesRyan R. Cochrane, Leandro Vieira dos Santos, Yizhi Cai · 2026 · Current Opinion in Biotechnology
- Reconstruction of Metabolic–Protein Interaction Integrated Network of Eriocheir sinensis and Analysis of Ecdysone SynthesisTong Hao, Zhentao Song, Mingzhi Zhang · 2024 · Genes
- From FAIR to CURE: guidelines for computational models of biological systemsHerbert M. Sauro, E. Agmon, M. Blinov, John H. Gennari, Joseph L. Hellerstein, Adel Heydarabadipour, Bartholomew E. Jardine, E. May, D. Nickerson, Lucian P. Smith et al. · 2026 · npj Systems Biology and Applications
- Signaling pathways in contextFriedemann Uschner, Edda Klipp · 2019 · Current Opinion in Biotechnology
- Data integration strategies for whole-cell modelingKatja Tummler, Edda Klipp · 2024 · FEMS Yeast Research
- Black-box Brain Experiments, Causal Mathematical Logic, and the Thermodynamics of IntelligenceSergio Pissanetzky, Felix Lanzalaco · 2013 · Journal of Artificial General Intelligence
- Genomics 3.0: Big-data in Precision MedicineAsoke K. Talukder · 2015 · Lecture notes in computer science
- Systems Biology and Metabolic Modeling of C1-MetabolismIlya R. Akberdin, Merlin Thompson, Marina Kalyuzhnaya · 2018 · Springer eBooks
- Toward a Logic of the Organism: A Process Philosophical ConsiderationSpyridon A. Koutroufinis · 2021 · Entropy
- Microbial Growth DynamicsNicolai S. Panikov · 2019 · Elsevier eBooks
- Bacillus subtilisSystems Biology: Applications of -Omics Techniques to the Study of Endospore FormationAshley R. Bate, Richard Bonneau, Patrick Eichenberger · 2016 · ASM Press eBooks
- Current Challenges in Modeling Cellular MetabolismNikolaus Sonnenschein, Kai H. Zhuang, Daniel Machado, Markus J. Herrgard · 2016 · Frontiers research topics
- Simulation of diffusion using a modular cell dynamic simulation systemChristoph Leberecht, Florian Heinke, Dirk Labudde · 2017 · In Silico Biology
- Simulating heterogeneous populations using Boolean modelsBrian C. Ross, Mayla R. Boguslav, Holly Weeks · 2018 · BMC Systems Biology
- Symmetry at the Cellular MesoscaleDavid S. Goodsell · 2019 · Symmetry
- New Genomic Information Systems (GenISs): Species Delimitation and IDentificationSambriddhi Mainali, Max Garzón, Fredy A. Colorado · 2020 · Lecture notes in computer science
- BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpointVincent Henry, Fatiha Saïs, Olivier Inizan · 2020 · BMC Bioinformatics
- Overview: Standards for Modeling in Systems MedicineAndreas Dräger, Dagmar Waltemath · 2020 · Elsevier eBooks
- Culturing pluripotent stem cells: State of the art, challenges and future opportunitiesAntonella La Regina, Elisa Pedone, Lucia Marucci · 2021 · Current Opinion in Systems Biology
- In silico model-based inference: an emerging approach for inverse problems in engineering better medicinesDavid J. Klinke, Marc R. Birtwistle · 2015 · Current Opinion in Chemical Engineering
- Analysis and design of molecular machinesClaudio Angione, Jole Costanza, Giovanni Carapezza, Píetro Lió, Giuseppe Nicosia · 2015 · Theoretical Computer Science
- Simulations of Living Cell Origins Using a Cellular Automata ModelTakeshi Ishida · 2014 · Origins of Life and Evolution of Biospheres
- From Pangenome to Panphenome and BackMarco Galardini, Alessio Mengoni, Stéfano Mocali · 2014 · Methods in molecular biology
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems BiologyLucia Marucci, Matteo Barberis, Jonathan R. Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan A. Hoffmann, Sophie Landon, Elibio Leopoldo Rech et al. · 2020 · Frontiers in Bioengineering and Biotechnology
- Back to the Future: Reintegrating Biology to Understand How Past Eco-evolutionary Change Can Predict Future OutcomesCynthia L. Thompson, Marina Alberti, Sahas Barve, Fabia Ursula Battistuzzi, Jeana L. Drake, Guilherme Casas Goncalves, Lynn Govaert, Charlyn Partridge, Ya Jun Yang · 2021 · Integrative and Comparative Biology
- Synthetic research tools as alternatives to animal modelsKara Rosania · 2013 · Lab Animal
- Gene-centric constraint of metabolic modelsNick Fyson, Min Kyung Kim, Desmond S. Lun, Caroline Colijn · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Designing Minimal Genomes Using Whole-Cell ModelsJoshua Rees, Oliver Chalkley, Sophie Landon · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and DataP.J. Gawthrop, Michael Pan, Edmund J. Crampin · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving LabsLauren M. Sanders, Jason H. Yang, Ryan T. Scott, A. Qutub, Héctor García Martín, D. Berrios, Jaden J. A. Hastings, J. Rask, Graham Mackintosh, Adrienne L. Hoarfrost et al. · 2021 · arXiv.org
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive ModelsTatsuya Sakaguchi, Yuta Irifune, Rui Kamada, Kazuyasu Sakaguchi · 2025 · International Journal of Molecular Sciences
- Revisiting the blueprint for an interpretable virtual cellAngela Ruohao Wu · 2026 · Nature Reviews Genetics
- Heterogeneity of bacterial host-pathogen interactions across biological scalesJuan Alfonso Redondo, Niharika Purkait, Pawel Paszek · 2026 · mSystems
- Towards the construction of a virtual yeastLiujia Qian, Zizhuo Zhou, Peijie Zhou, Zhen Dong, Xudong Zhang, Zhenwu Dai, Zhangyang Gao, Siqi Sun, Kevin R. Roy, Shuaiyao Wang et al. · 2026 · Nature
- Invariance and optimality in the regulation of an enzymeEd Reznik, Stefan T. Yohe, Daniel Segrè · 2013 · Biology Direct
- Single-cell systems analysis: decision geometry in outliersAbrahams, Lianne · 2021 · Bioinformatics
- A Systematic Review of Second Language Acquisition from the Perspective of Complex Dynamic System TheorySoheil Behdarvandirad · 2024 · Theory and Practice of Second Language Acquisition
- Theory and design in the biotechnical age: A schematic understanding of Bio Design and Synthetic Biology practiceMartyn Dade‐Robertson, Meng Zhang · 2024 · The Design Journal
- Digital Twins in BiomanufacturingMichelangelo Canzoneri, Marc Horner, Prith Banerjee · 2024 · Springer eBooks
- Rational design of organelle compartments in cellsClaudio Angione, Giovanni Carapezza, Jole Costanza · 2012 · EMBnet journal
- The Role of Single-Cell Analyses in Understanding Cell Lineage CommitmentTyler M. Gibson, C. A. Gersbach · 2013 · Biotechnology Journal
- Space-induced bifurcation in repression-based transcriptional circuitsAmanda Lo Van, Hédi Antoine Soula, Hugues Berry · 2014 · BMC Systems Biology
- The MYpop toolbox: Putting yeast stress responses in cellular context on single cell and population scalesThomas W. Spiesser, Clemens Kühn, Marcus Krantz · 2016 · Biotechnology Journal
- Spatially explicit individual-based modelling of insect-plant interactions: effects of level of detail in Queensland fruit fly models2015 · International Congress on Modelling and Simulation (MODSIM)
- Trans-algorithmic nature of learning in biological systemsYury P. Shimansky · 2018 · Biological Cybernetics
- Synthetic Animal: Trends in Animal Breeding and GeneticsAbolfazl Bahrami, Najafi Ali · 2019 · Insights in Biology and Medicine
- Construction of Microbial Cell Factories by Systems and Synthetic BiotechnologyYaokang Wu, Yang Mo Gu, Rongzhen Tian, Guocheng Du, Jian Chen, Long Liu · 2019 · Springer eBooks
- Artificial Intelligence in Biological ModellingFrançois Fages · 2020 · Springer eBooks
- Minimal Genome Design Algorithms Using Whole-Cell ModelsJoshua Rees-Garbutt, Oliver Chalkley, Claire Grierson · 2020 · Methods in molecular biology
- Modeling the activity of the dopamine signaling pathway by combination of analog electrical circuit and mathematical approachesA.V. Shumilov, Pavel M. Gotovtsev · 2021 · Heliyon