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
DOI 10.1016/j.cell.2012.05.044

Cited by (1,292)

Items 1,101–1,200 of 1,292

  1. Genoma, microbioma y epigenoma humano. Una visión contemporánea de la tríada ecológica. The Genome, the microbiome, and the human epigenome. A contemporary view of the ecological triad.
    Agustín Zerón · 2014
  2. Stochastic Simulation of Multiscale Reaction-Diffusion Models via First Exit Times
    Lina Meinecke · 2016 · Uppsala University Publications (Uppsala University)
  3. THE FUTURE OF GENOME-BASED MEDICINE
    Quaid Morris, Steven E. Brenner, Jennifer Listgarten · 2012 · Pacific Symposium on Biocomputing (PSB)
  4. Tapping the Wealth of Microbial Data in High-Throughput Metabolic Model Reconstruction
    Ric Colasanti, Janaka N. Edirisinghe, Tahmineh Khazaei, José P. Faria, Samuel M. D. Seaver, Fangfang Xia, Christopher S. Henry · 2014 · Methods in molecular biology
  5. DREAMTools: a Python package for scoring collaborative challenges (version 1; referees: awaiting peer review)
    Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce Hoff et al. · 2015
  6. Deterministic simulations of large-scale models of cellular processes accelerated on Graphics Processing Units
    Andrea Tangherloni, Paolo Cazzaniga, Marco Salvatore Nobile · 2015 · BOA (University of Milano-Bicocca)
  7. Simulation technology and its application in Systems Biology
    Akira Funahashi, Noriko F. Hiroi · 2016 · Folia Pharmacologica Japonica
  8. Systems modeling and network inference for genetic and epigenetic regulation of gene expression
    Haifeng Chen · 2016
  9. Bioinformatics Challenges and Potentialities in Studying Extreme Environments
    Claudio Angione, Píetro Lió, Sandra Pucciarelli, Başarbatu Can, Maxwell Conway, Marina Lotti, Habib Bokhari, Alessio Mancini, Osman Uğur Sezerman, Andrea Telatin · 2016 · Lecture notes in computer science
  10. Molecular programming and microsystems.
    Alexandre Baccouche, Teruo Fujii, Yannick Rondelez · 2015
  11. Efficient sampling in stochastic biological models
    Rory Donovan-Maiye · 2016 · D-Scholarship@Pitt (University of Pittsburgh)
  12. Computational challenges in modeling and simulating living matter
    Alexandre C. Sena, Dı́lson Silva, Leandro A. J. Marzulo · 2016 · AIP conference proceedings
  13. Network Analysis and Modeling in Systems Biology
    Gabriel Bosque Chacón · 2017
  14. Model analysis and parameter estimation in biochemical reaction networks = Biokémiai reakcióhálózatok analízise és paramétereinek becslése
    Attila Gábor · 2017 · REAL-PhD (Hungarian Academy of Sciences)
  15. Metabolic modeling to understand and redesign microbial systems
    Ruben G. A. van Heck · 2017
  16. Cells as Machines: Towards Deciphering Biochemical Programs in the Cell
    Inria Paris-Rocquencourt · 2014
  17. A Foundational Framework for Step-by-step Model Construction
    Mikhail Barash, Ion Petre · 2017 · Fundamenta Informaticae
  18. Action potentials as indicators of metabolic perturbations for temporal proteomic analysis
    Aditya Reddy Kolli · 2014 · Journal of International Crisis and Risk Communication Research
  19. Study of Cells in the Steady‐State Growth Space
    Sten Erm, Kristo Abner, Andrus Seiman, Kaarel Adamberg, Raivo Vilu · 2017 · Wiley eBooks
  20. Die Ursprünge des Lebendigen
    Aleksandar Janjic · 2017 · Springer eBooks
  21. Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
    Tjerko Kamminga · 2017
  22. Identificação in silico de ncRNAs no organismo modelo Halobacterium salinarum NRC-1
    Marcos Abraão de Souza Fonseca · 2017
  23. A comprehensive stochastic computational model of HIV infection from DNA integration to viral burst
    Jayodita C. Sanghvi, Don Mai, Adam P. Arkin · 2017 · arXiv (Cornell University)
  24. Gene Expression for Simulation of Biological Tissue
    Sadyk Sayfullin, Fedor Akhmetov, Manuel Mazzara, Ruslan Mustafin, Victor Rivera · 2018 · International Conference on Advanced Information Networking and Applications Workshops (WAINA)
  25. Modeling and analyzing the kinetic of conjugative plasmids
    Antonio Prestes García · 2017
  26. Integrative understanding of transcription in animal cell mode
    L Gerardo Rico, Verónica Verónica · 2016 · TDX (Tesis Doctorals en Xarxa)
  27. Hierarchical evolutive systems, fuzzy categories and the living single cell
    Alejandro Mesón, C. Manuel Carlevaro, Fernando Vericat · 2018 · arXiv (Cornell University)
  28. Generation of Molecular Models and Pathways
    Amel Bekkar, Julien Dorier, Isaac Crespo · 2018
  29. Assembly Rules of the Microbiome
    Roie Levy · 2015 · ResearchWorks at the University of Washington (University of Washington)
  30. Metabolic Models: From DNA to Physiology (and Back)
    Márcio Argollo de Menezes · 2018 · Computational biology
  31. A Framework for Predicting Design Failures in Engineered Genetic Codes
    Bea Yu, Matthew Murphy, Peter A. Carr · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Initiation rites in molecular biology
    Paul E. Schavemaker · 2018 · University of Groningen research database (University of Groningen / Centre for Information Technology)
  33. Nitric Oxide Stress as a Metabolic Flux
    Mark P. Brynildsen · 2018 · Advances in microbial physiology/Advances in Microbial Physiology
  34. Subcellular Time Series Modeling of Heterogeneous Cell Protrusion
    Yeesock Kim, Hee June Choi, Kwonmoo Lee · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Interactive functional networks in microbiota
    Bastian Hornung · 2018
  36. Mathematical models in the human cardiovascular system. Approaches to the description of 0.1 Hz oscillations of heart rate variability and the magistral blood flow
    Andrey A. Grinevich · 2019 · Regional blood circulation and microcirculation
  37. Constitutive Activation of BCR Explains Dysfunctional Signaling in Chronic Lymphocytic Leukemia
    Carly G.K. Ziegler, Joel Kim, Kelly Piersanti, Alon Oyler‐Yaniv, Kimon V. Argyropoulos, Marcel R.M. van den Brink, Maria Lia Palomba, Nihal Altan‐Bonnet, Grégoire Y Altan-Bonnet · 2019 · SSRN Electronic Journal
  38. Dynamic optimization of metabolic networks coupled with gene expression
    Steffen Waldherr, Diego A. Oyarzún, Alexander Bockmayr · 2013 · arXiv (Cornell University)
  39. Systems-Based Mechanisms of Aging
    Carole J. Proctor, Amy E. Morgan, Mark T. Mc Auley · 2019 · Elsevier eBooks
  40. Ursprung und Evolution des Lebendigen
    Aleksandar Janjic · 2019 · Astrobiologie - die Suche nach außerirdischem Leben
  41. Systembiologie als Nexus zwischen Genen und Gesundheit?
    Regine Kollek · 2012 · TATuP Zeitschrift für Technikfolgenabschätzung in Theorie und Praxis
  42. Modelling heterogeneous intracellular networks at the cellular scale
    Ann C. Babtie · 2019 · Current Opinion in Systems Biology
  43. Pan-organ model integration of metabolic and regulatory processes in type 1 diabetes
    Marouen Ben Guebila, Ines Thiele · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  44. Development of a framework for whole-cell model creation
    Frederico Chaves Carvalho, Paulo Eduardo Ambrósio · 2018
  45. Prediction of Cellular Burden with Host–Circuit Models
    Evangelos-Marios Nikolados, Andrea Y. Weiße, Diego A. Oyarzún · 2021 · Methods in molecular biology
  46. Systems Immunology
    Brian A. Kidd, Joel T. Dudley · 2015 · Elsevier eBooks
  47. A CRISPR-Cas-Inspired Mechanism for Detecting Hardware Trojans in FPGA Devices
    Dillon Staub, Rashmi Jha, David Kapp · 2020 · arXiv (Cornell University)
  48. Structuring spreadsheets with ObjTables enables data quality control, reuse, and integration
    Jonathan R. Karr, Wolfram Liebermeister, Arthur P. Goldberg, John A. P. Sekar, Bilal Shaikh · 2020 · arXiv (Cornell University)
  49. Bond Graphs Unify Stoichiometric Analysis and Thermodynamics
    P.J. Gawthrop · 2020 · arXiv (Cornell University)
  50. Understanding metabolic behaviour in whole-cell model output
    Sophie Landon, Oliver Chalkley, Gus Breese, Claire Suzanne Grierson, Lucia Marucci · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Analog Electronic Circuits to Model Cooperativity in Hill Process
    Maria Waqas, Muhammad Khurram, Suhaiza Hasan · 2020 · Mehran University Research Journal of Engineering and Technology
  52. FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research
    Katherine S. Scheuer, Bret M. Hanlon, Jerdon W. Dresel, Erik D. Nolan, John C. Davis, Laurence Loewe · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Neural differentiation dynamics controlled by multiple feedback loop motifs in a comprehensive molecular interaction network
    Tsuyoshi Iwasaki, Ryo Takiguchi, Takumi Hiraiwa, Takahiro Yamada, Kazuto Yamazaki, Noriko F. Hiroi, Akira Funahashi · 2019 · Research Square
  54. A Possible Artificial Intelligence Ecosystem Avatar: the Moorea case (IDEA)
    Jean‐Pierre Barriot, Neil Davies, Benoît Stoll · 2021 · arXiv (Cornell University)
  55. Reconstruction of a Bacterial Genome from DNA Cassettes
    USDOE, Christopher Dupont, John Glass, Laura Sheahan, Shibu Yooseph, Lisa Zeigler Allen, Mathangi Thiagarajan, Andrew Ellis Allen, Robert Friedman, J. Venter · 2011
  56. Revisiting Cybernetic Laws via Optimal Control Theory
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  57. Centralizing data to unlock whole-cell models
    Yin Hoon Chew, Jonathan R. Karr · 2021 · Current Opinion in Systems Biology
  58. Improving cyanobacteria productivity: From theory to assay
    Kiyan Shabestary · 2020 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
  59. Optimierung des Rekonstruktions-Tools TSNI für genregulatorische Netzwerke mittels Parallelisierung und ein Vergleich mit Time Delay ARACNE
    Marco Schäfer, Christian Jetschni, Chong Wang · 2019 · Wissenschaftliche Beiträge / Technische Hochschule Wildau
  60. The 2017 Whole-Cell Modeling Summer School
    Jonathan R. Karr, María Lluch‐Senar, Luis Serrano · 2017 · Zenodo (CERN European Organization for Nuclear Research)
  61. The Hybrid Cybernetic Model (HCM)
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  62. Engineering Transcriptional Control and Synthetic Gene Circuits in Cell Free systems
    Sukanya Iyer · 2012
  63. Cell, Minimal
    Rosario Gil · 2021 · Encyclopedia of Astrobiology
  64. Searching for Essential Genes in the Cancer Genome
    Mikhail A. Pyatnitskiy, Dmitry S. Karpov, Sergei A. Moshkovskii · 2018 · Biochemistry (Moscow) Supplement Series B Biomedical Chemistry
  65. The evolving microbial taxonomy
    Huijue Jia · 2022 · Elsevier eBooks
  66. FRONT MATTER
    Pete E. Lestrel · 2013
  67. Relationships between Models of Genetic Regulatory Networks with Emphasis on Discrete State Stochastic Models
    Randip Pal · 2019 · IGI Global eBooks
  68. Cell, Minimal
    Rosario Gil · 2014 · Encyclopedia of Astrobiology
  69. Die funktionelle Analyse von Genomen
    Paul M. Selzer, Richard J. Marhöfer, Oliver Koch · 2018 · Springer eBooks
  70. EMBnet.journal 18 Suppl. B
    EMBnet journal · 2012 · EMBnet journal
  71. Faculty Opinions recommendation of Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.
    Sarah Anne Harris · 2017 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  72. Faculty Opinions recommendation of A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.
    Jens Nielsen · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  73. Pathway Modeling
    Pablo Carbonell · 2019 · Learning materials in biosciences
  74. Model-driven design of Mycoplasma as a vaccine chassis
    Erika Gaspari · 2021
  75. Cell, Minimal
    Rosario Gil · 2015 · Encyclopedia of Astrobiology
  76. Mathematical Models in Biotechnology
    Ryan A. Tasseff, Jeffrey D. Varner · 2016 · Elsevier eBooks
  77. 'Whole-cell' computer model
    2012 · Nature
  78. Faculty Opinions recommendation of Toward Community Standards and Software for Whole-Cell Modeling.
    Herbert M. Sauro · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  79. Faculty Opinions recommendation of Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.
    Balázs Papp · 2017 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  80. FORMAÇÃO DE PADRÕES ESPACIAIS NA DINÂMICA DE POPULAÇÕES
    EDUARDO HENRIQUE FILIZZOLA COLOMBO · 2014
  81. ProFuMCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell
    B.N. Das, Pralay Mitra · 2022 · Journal of Molecular Modeling
  82. A Spatial Whole-Cell Model for Hepatitis B Viral Infection and Drug Interactions
    Zhaleh Ghaemi, Oluwadara Nafiu, Emad Tajkhorshid, Martin Gruebele, Jianming Hu · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  83. Modeling Approaches to Microbial Metabolism
    Andreas Kremling · 2022 · Methods in molecular biology
  84. Early Development of Cybernetic Models
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  85. Nonlinear Analysis of Cybernetic Models
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  86. Toward Modeling of Metabolic Networks
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  87. Index
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  88. Preface
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018
  89. Enzymatic Adaptation
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  90. Introduction
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  91. The Lumped Hybrid Cybernetic Model (L-HCM)
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  92. Designable Dynamical Systems for the Generalized Landau Scenario and the Nonlinear Complexification of Periodic Orbits
    R. Herrero, Jordi Farjas, Francese Pi · 2021 · UPCommons institutional repository (Universitat Politècnica de Catalunya)
  93. Metabolic Modeling Landscape
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  94. Predicting Dynamic Behavior of Mutant Strains with L-HCM
    Doraiswami Ramkrishna, Hyun‐Seob Song · 2018 · Cambridge University Press eBooks
  95. Nanoinformatics approaches for information extraction and text mining in nanomedical research texts
    Diana de la Iglesia Jimenez · 2014
  96. Proteomic and genomic data mining with applications in plant science
    Hong Luo · 2023
  97. Cell, Minimal
    Rosario Gil · 2023 · Encyclopedia of Astrobiology
  98. Integrative Modeling of Jcvi-Syn3a Nucleoids with a Modular Approach
    David S. Goodsell, Ludovic Autin · 2023 · SSRN Electronic Journal
  99. Perspective Chapter: Genomics, Proteomics, and System Biology of Insecticides Resistance in Insects
    Rabbiah Manzoor Malik, Sahar Fazal, Narjis Khatoon · 2023 · IntechOpen eBooks
  100. GPU Acceleration of a Conjugate Exponential Model for Cancer Tissue Heterogeneity
    Anik Chaudhuri, Anwoy Kumar Mohanty, Manoranjan Satpathy · 2024 · ACM Transactions on Computing for Healthcare