Bernhard Palsson
#28,094
Most Influential Person Now
American biologist and Professor of Bioengineering at the University of California, San Diego
Bernhard Palsson's AcademicInfluence.com Rankings
Bernhard Palssonengineering Degrees
Engineering
#569
World Rank
#938
Historical Rank
#251
USA Rank
Bioengineering
#3
World Rank
#3
Historical Rank
#2
USA Rank
Bernhard Palssonbiology Degrees
Biology
#1244
World Rank
#2116
Historical Rank
#639
USA Rank
Systems Biology
#3
World Rank
#3
Historical Rank
#2
USA Rank
Evolutionary Biology
#32
World Rank
#45
Historical Rank
#21
USA Rank
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Engineering Biology
Why Is Bernhard Palsson Influential?
(Suggest an Edit or Addition)According to Wikipedia, Bernhard Ørn Palsson is the Galletti Professor of Bioengineering and an adjunct professor of Medicine at the University of California, San Diego. Education Palsson received his PhD from the University of Wisconsin–Madison in 1984 under the supervision of Edwin N. Lightfoot.
Bernhard Palsson's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- What is flux balance analysis? (2010) (3055)
- Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking (2016) (2091)
- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 (2007) (1723)
- A protocol for generating a high-quality genome-scale metabolic reconstruction (2010) (1487)
- A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007) (1452)
- Global reconstruction of the human metabolic network based on genomic and bibliomic data (2007) (1389)
- Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. (2003) (1106)
- Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 (1994) (1054)
- Genome-scale models of microbial cells: evaluating the consequences of constraints (2004) (1049)
- Cancer cell lines (1999) (1044)
- An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) (2003) (1034)
- In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data (2001) (991)
- A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 (2011) (982)
- A community-driven global reconstruction of human metabolism (2013) (974)
- The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. (2000) (955)
- Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use (1994) (954)
- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox (2007) (880)
- Reconstruction of biochemical networks in microorganisms (2009) (864)
- Systems Biology: Properties of Reconstructed Networks (2006) (852)
- Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth (2002) (847)
- Applications of genome-scale metabolic reconstructions (2009) (826)
- Integrating high-throughput and computational data elucidates bacterial networks (2004) (819)
- COBRApy: COnstraints-Based Reconstruction and Analysis for Python (2013) (781)
- The model organism as a system: integrating 'omics' data sets (2006) (781)
- Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods (2012) (722)
- The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line (2011) (721)
- Constraint-based models predict metabolic and associated cellular functions (2014) (709)
- Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. (2000) (698)
- Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. (2004) (681)
- Network-based prediction of human tissue-specific metabolism (2008) (652)
- BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2015) (614)
- A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008) (601)
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 (2019) (596)
- Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models (2010) (586)
- The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli (2008) (575)
- BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010) (567)
- Using Genome-scale Models to Predict Biological Capabilities (2015) (546)
- The evolution of molecular biology into systems biology (2004) (537)
- The biomass objective function. (2010) (537)
- Context-Specific Metabolic Networks Are Consistent with Experiments (2008) (522)
- Reconstruction of cellular signalling networks and analysis of their properties (2005) (520)
- Connecting extracellular metabolomic measurements to intracellular flux states in yeast (2009) (451)
- Regulation of gene expression in flux balance models of metabolism. (2001) (439)
- Genome-scale microbial in silico models: the constraints-based approach. (2003) (424)
- Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction (2013) (423)
- Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post‐genomic Era (1999) (407)
- Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data* (2007) (404)
- Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype* (1999) (401)
- Metabolic modelling of microbes: the flux-balance approach. (2002) (394)
- Comparison of network-based pathway analysis methods. (2004) (389)
- Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network (2003) (387)
- Towards multidimensional genome annotation (2006) (376)
- Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale (2006) (365)
- In silico design and adaptive evolution of Escherichia coli for production of lactic acid. (2005) (361)
- Metabolic pathways in the post-genome era. (2003) (361)
- Internal Model Control: extension to nonlinear system (1986) (360)
- Effects of ammonia and lactate on hybridoma growth, metabolism, and antibody production (1992) (357)
- Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome (2013) (352)
- Genome-Scale Metabolic Model of Helicobacter pylori 26695 (2002) (351)
- Metabolic modeling of microbial strains in silico. (2001) (336)
- Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli (2013) (335)
- Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli * 210 (2002) (334)
- The challenges of in silico biology (2000) (331)
- Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism (2018) (319)
- Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli (2003) (318)
- Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates (1993) (317)
- Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling (2006) (313)
- Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes (2004) (311)
- iML1515, a knowledgebase that computes Escherichia coli traits (2017) (304)
- Internal model control. VI: Extension to nonlinear systems (1986) (303)
- Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions (2000) (296)
- Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism (2011) (295)
- Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis (2012) (294)
- Systems approach to refining genome annotation (2006) (289)
- Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. (2005) (286)
- Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets (2007) (280)
- Microbial laboratory evolution in the era of genome-scale science (2011) (274)
- Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015) (270)
- Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli (2006) (262)
- The transcription unit architecture of the Escherichia coli genome (2009) (261)
- In silico method for modelling metabolism and gene product expression at genome scale (2012) (260)
- Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation (2005) (253)
- Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants (2005) (250)
- Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri (2006) (248)
- Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions (2010) (247)
- Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. (1993) (245)
- Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. (2000) (245)
- Ion Mobility Derived Collision Cross Sections to Support Metabolomics Applications (2014) (245)
- Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. (2006) (245)
- Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns (1993) (242)
- Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments (2013) (241)
- Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. (2000) (240)
- Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. (1992) (239)
- Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures. (1998) (239)
- Use of Randomized Sampling for Analysis of Metabolic Networks* (2009) (238)
- A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory (2008) (232)
- Large-scale in silico modeling of metabolic interactions between cell types in the human brain (2010) (231)
- Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. (2004) (229)
- What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira (2016) (221)
- Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution (2012) (220)
- Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. (2010) (220)
- The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. (2019) (219)
- MS/MS networking guided analysis of molecule and gene cluster families (2013) (219)
- MEMOTE for standardized genome-scale metabolic model testing (2020) (214)
- Ion Mobility-Derived Collision Cross Section As an Additional Measure for Lipid Fingerprinting and Identification (2014) (212)
- Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. (2010) (210)
- Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli (2014) (209)
- Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. (2004) (205)
- Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances (1999) (203)
- Elimination of thermodynamically infeasible loops in steady-state metabolic models. (2011) (201)
- Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium (2014) (198)
- Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion. (1997) (196)
- Optimizing genome-scale network reconstructions (2014) (196)
- Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model (2010) (196)
- RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media (2010) (193)
- Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations (2009) (193)
- High‐density algal photobioreactors using light‐emitting diodes (1994) (192)
- Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. (2008) (190)
- Biochemical production capabilities of escherichia coli (1993) (189)
- Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization (2009) (187)
- A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. (2016) (186)
- Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity (2016) (185)
- A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action (2019) (184)
- Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes* (2006) (182)
- The underlying pathway structure of biochemical reaction networks. (1998) (182)
- Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima (2009) (182)
- Formulating genome-scale kinetic models in the post-genome era (2008) (182)
- Constraints-based models: regulation of gene expression reduces the steady-state solution space. (2003) (181)
- Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network (2008) (179)
- Analysis of omics data with genome-scale models of metabolism. (2013) (178)
- Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli (2008) (176)
- Recon3D enables a three-dimensional view of gene variation in human metabolism (2018) (174)
- MECHANISM OF RELEASE FROM PELLETS COATED WITH AN ETHYLCELLULOSE-BASED FILM (1990) (174)
- A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology (2011) (171)
- Effect of medium osmolarity on hybridoma growth, metabolism, and antibody production. (1991) (171)
- Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. (2001) (170)
- Large-scale Expansion of Human Stem and Progenitor Cells From Bone Marrow Mononuclear Cells in Continuous Perfusion Cultures (1993) (169)
- Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. (2014) (167)
- Growth, Metabolic, and Antibody Production Kinetics of Hybridoma Cell Culture: 2. Effects of Serum Concentration, Dissolved Oxygen Concentration, and Medium pH in a Batch Reactor (1991) (165)
- Next-generation genome-scale models for metabolic engineering. (2015) (165)
- Proteomic analysis of Chinese hamster ovary cells. (2012) (165)
- Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. (2003) (163)
- Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data* (2004) (162)
- Systematizing the generation of missing metabolic knowledge (2010) (161)
- Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model. (1989) (161)
- Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction (2009) (160)
- Reconstruction of microbial transcriptional regulatory networks. (2004) (160)
- Extreme pathway analysis of human red blood cell metabolism. (2002) (157)
- Candidate Metabolic Network States in Human Mitochondria (2005) (157)
- Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. (2014) (155)
- Chemical Decomposition of Glutamine in Cell Culture Media: Effect of Media Type, pH, and Serum Concentration (1990) (155)
- High‐density photoautotrophic algal cultures: Design, construction, and operation of a novel photobioreactor system (1991) (155)
- Engineering synergy in biotechnology. (2014) (151)
- An atlas of human metabolism (2020) (151)
- Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. (2004) (151)
- Characterizing the metabolic phenotype: A phenotype phase plane analysis (2002) (149)
- A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 (2010) (149)
- Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. (2004) (148)
- Systems Biology: Constraint-based Reconstruction and Analysis (2015) (148)
- Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. (2017) (147)
- A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 (2011) (146)
- A road map for the development of community systems (CoSy) biology (2012) (146)
- Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism. (1992) (145)
- Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, l-1,2-Propanediol (2010) (145)
- The challenges of integrating multi-omic data sets. (2010) (144)
- Extreme pathway lengths and reaction participation in genome-scale metabolic networks. (2002) (142)
- Human Cell Culture (1999) (142)
- Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation (2012) (142)
- Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor. (2012) (139)
- Extreme pathways and Kirchhoff's second law. (2002) (138)
- Robustness Analysis of the Escherichiacoli Metabolic Network (2000) (138)
- SBML Level 3: an extensible format for the exchange and reuse of biological models (2020) (137)
- The COMBREX Project: Design, Methodology, and Initial Results (2013) (137)
- Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. (2002) (135)
- Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations (2014) (135)
- Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene (2010) (135)
- The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. (2004) (134)
- Retroviral infection is limited by Brownian motion. (1996) (133)
- Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles (2006) (132)
- Multi-omic data integration enables discovery of hidden biological regularities (2016) (130)
- Towards genome-scale signalling-network reconstructions (2010) (128)
- Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures. (1993) (127)
- Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. (2017) (126)
- Reconciling gene expression data with known genome-scale regulatory network structures. (2003) (124)
- Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling (2012) (124)
- Systems biology as a foundation for genome-scale synthetic biology. (2006) (124)
- Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model (2003) (124)
- BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree (2019) (123)
- Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. (2015) (121)
- Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. (2010) (120)
- Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage (2012) (117)
- Using the reconstructed genome‐scale human metabolic network to study physiology and pathology (2012) (117)
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models (2018) (117)
- Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli (2013) (116)
- GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data (2013) (116)
- Network Context and Selection in the Evolution to Enzyme Specificity (2012) (116)
- Immobilization of Escherichia coli RNA Polymerase and Location of Binding Sites by Use of Chromatin Immunoprecipitation and Microarrays (2005) (116)
- High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli. (2018) (115)
- Symmetry of initial cell divisions among primitive hematopoietic progenitors is independent of ontogenic age and regulatory molecules. (1999) (114)
- Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers. (1996) (114)
- Expansion of Human Bone Marrow Progenitor Cells in a High Cell Density Continuous Perfusion System (1993) (113)
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression (2017) (109)
- Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. (2004) (109)
- Biomass as a source of chemical feedstocks: an economic evaluation. (1981) (107)
- The Escherichia coli transcriptome mostly consists of independently regulated modules (2019) (107)
- Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance (2018) (106)
- Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems (2006) (105)
- Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states (2014) (105)
- An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228 (2011) (104)
- Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects. (1995) (103)
- Moloney murine leukemia virus-derived retroviral vectors decay intracellularly with a half-life in the range of 5.5 to 7.5 hours (1997) (103)
- Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics (2017) (103)
- Reconstructing organisms in silico: genome-scale models and their emerging applications (2020) (102)
- Systems Biology: Simulation of Dynamic Network States (2011) (102)
- How will bioinformatics influence metabolic engineering? (1998) (100)
- In silico biology through “omics” (2002) (99)
- Dynamic simulation of the human red blood cell metabolic network (2001) (99)
- Metabolic dynamics in the human red cell. Part III--Metabolic reaction rates. (1990) (99)
- Genome-Scale Analysis of the Uses of the Escherichia coli Genome: Model-Driven Analysis of Heterogeneous Data Sets (2003) (98)
- Effects of Dissolved Oxygen on Hybridoma Cell Growth, Metabolism, and Antibody Production Kinetics in Continuous Culture (1990) (98)
- The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. (2005) (97)
- Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments (2016) (97)
- The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. (2003) (96)
- In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling (2011) (96)
- The PurR regulon in Escherichia coli K-12 MG1655 (2011) (95)
- Rapid medium perfusion rate significantly increases the productivity and longevity of human bone marrow cultures. (1991) (94)
- Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. (2016) (94)
- Metabolic systems biology (2009) (94)
- Biomarkers defining the metabolic age of red blood cells during cold storage. (2016) (94)
- Biomarkers defining the metabolic age of red blood cells during cold storage. (2016) (94)
- High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities (2019) (92)
- Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods. (1992) (92)
- Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli (2007) (91)
- Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. (2015) (91)
- Mathematical modelling of dynamics and control in metabolic networks. I. On Michaelis-Menten kinetics. (1984) (90)
- Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association (2013) (90)
- Properties of metabolic networks: structure versus function. (2005) (88)
- Adaptive laboratory evolution of a genome-reduced Escherichia coli (2019) (88)
- The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function (2019) (88)
- Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes (2016) (88)
- Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes (2016) (88)
- A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. (2011) (88)
- Deciphering the transcriptional regulatory logic of amino acid metabolism. (2011) (87)
- Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? (2003) (87)
- Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale (2014) (87)
- iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states (2011) (87)
- Immobilization can improve the stability of hybridoma antibody productivity in serum‐free media (1990) (87)
- k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. (2005) (87)
- Sharing and community curation of mass spectrometry data with GNPS (2016) (87)
- Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. (2016) (85)
- Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum (2004) (85)
- Structural and operational complexity of the Geobacter sulfurreducens genome. (2010) (84)
- Growth, Metabolic, And Antibody Production Kinetics Of Hybridoma Cell Culture: 1. Analysis Of Data From Controlled Batch Reactors (1991) (84)
- Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina (2014) (84)
- Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol (2014) (83)
- Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom (2016) (83)
- Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis (2016) (83)
- Model-driven discovery of underground metabolic functions in Escherichia coli (2015) (82)
- Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism (2017) (82)
- Predicting gene essentiality using genome-scale in silico models. (2008) (82)
- Reconstructing metabolic flux vectors from extreme pathways: defining the α-spectrum (2003) (81)
- Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. (2003) (80)
- Network-based analysis of metabolic regulation in the human red blood cell. (2003) (79)
- Systems Biology: Transcriptional Regulatory Networks (2006) (79)
- Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS) (2011) (79)
- Production of monoclonal antibody using free‐suspended and immobilized hybridoma cells: Effect of serum (1991) (79)
- The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions (2011) (78)
- Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits (2018) (77)
- Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. (2016) (76)
- Expa: a Program for Calculating Extreme Pathways in Biochemical Reaction Networks (2005) (76)
- Exploiting Adaptive Laboratory Evolution of Streptomyces clavuligerus for Antibiotic Discovery and Overproduction (2012) (75)
- Citrate metabolism in red blood cells stored in additive solution‐3 (2017) (73)
- Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities (2017) (73)
- Antigen receptor repertoire profiling from RNA-seq data (72)
- Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces (2020) (71)
- Loss of antibody productivity during long-term cultivation of a hybridoma cell line in low serum and serum-free media. (1990) (71)
- Review: Tissue engineering: Reconstitution of human hematopoiesis ex vivo (1993) (71)
- Metabolic analysis of adaptive evolution for in silico‐designed lactate‐producing strains (2006) (71)
- UPLC-UV-MSE analysis for quantification and identification of major carotenoid and chlorophyll species in algae (2012) (70)
- Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom (2019) (70)
- Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. (2006) (69)
- Parametric sensitivity of stoichiometric flux balance models applied to wild‐type Escherichia coli metabolism (1995) (69)
- Redefining fundamental concepts of transcription initiation in bacteria (2020) (68)
- ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation (2018) (68)
- Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20 (2003) (68)
- Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli (2015) (67)
- A genome-scale, constraint-based approach to systems biology of human metabolism. (2007) (67)
- Two-dimensional annotation of genomes (2004) (66)
- Improving Collaboration by Standardization Efforts in Systems Biology (2014) (66)
- Metabolic Characterization of Escherichia coli Strains Adapted to Growth on Lactate (2007) (65)
- The physico-chemical factors that govern retrovirus-mediated gene transfer. (1997) (65)
- Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies (2017) (65)
- The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models (2013) (65)
- Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types. (2006) (65)
- The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models (2013) (65)
- High‐throughput laser‐mediated in situ cell purification with high purity and yield (2004) (64)
- Computing the functional proteome: recent progress and future prospects for genome-scale models. (2015) (64)
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- Systems Biology: E. coli Core Metabolic Network (2006) (0)
- Fundamental Network Properties (2015) (0)
- Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the <named-content content-type='genus-species'>Streptomyces clavuligerus</named-content> Genome (2021) (0)
- Methods, compositions, and devices for culturing cells (1990) (0)
- Systems Biology: Dynamic simulation: the basic procedure (2011) (0)
- Systems Biology: References (2011) (0)
- Metabolomic Characterization of Escherichia coli K-12 Adaptation to Glycerol (2007) (0)
- Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments Metabolic regulation can be predicted in genome-scale models modifications on metabolic regulation (2017) (0)
- Systems Biology: Coupling pathways (2011) (0)
- Systems Biology: Properties of Solution Spaces (2006) (0)
- An Outline on Ion Signaling (2021) (0)
- The reconstruction of the genome‐scale transcriptional regulatory network in e. coli (2008) (0)
- Determination of the Multiple Binding Modes between Transcription Factor ArgR and Genomic DNA using ChIP-exo (2015) (0)
- Methods, compositions and devices to develop cells. (1990) (0)
- Homing and Self-Renewal of Hematopoietic Stem Cells (2000) (0)
- Catalytic potential and disturbance rejection of glycolytic kinases in the human red blood cell (2017) (0)
- Systems Biology: Bibliography (2006) (0)
- Systems Biology: Basic concepts (2011) (0)
- Systems Biology: CAPABILITIES OF RECONSTRUCTED NETWORKS (2006) (0)
- Systems Biology: Regulation as elementary phenomena (2011) (0)
- SB-O2 Phenotypic and metabolic properties of experimentally evolved microbial cells(Section XI Systems Biotechnology/Metabolic Engineering) (2009) (0)
- Systems Biology: Building networks (2011) (0)
- Next-Gen 3 : Sequencing, Modeling, and Advanced Biofuels - Final Technical Report (2017) (0)
- MEMOTE for standardized genome-scale metabolic model testing (2020) (0)
- Engineering CHO cells for the production of "Hard-To-Produce" proteins (2018) (0)
- genome sulfurreducens Geobacter Structural and operational complexity of the Material (2010) (0)
- Systems Biology: The Left Null Space of S (2006) (0)
- Abstracts for talks The construction of an integrated metabolic and transcriptional regulatory network (2005) (0)
- Human cell culture volume 6: Human embryonic stem cells (2007) (0)
- Visualization and creation of biochemical networks with Escher (2017) (0)
- Toward a Proteome-Complete Computational Model of the Human Red Blood Cell (2018) (0)
- New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher (2016) (0)
- ErythroDB: A multi‐omic visual knowledge base for the human red blood cell (2018) (0)
- Systems Biology: Orders of magnitude (2011) (0)
- Biological determinants of photobioreactor design. 1st Quarterly report, September 1, 1993--November 30, 1993 (1994) (0)
- Network Reconstruction: The Concept (2015) (0)
- Systems Biology: Open systems (2011) (0)
- Systems Biology: The Row and Column Spaces of S (2006) (0)
- A systems biology approach for human metabolism in health and disease (2010) (0)
- T of AMMONIA and GLUTAMINE in CELL CULTURE MEDIA by GAS SENSING (2005) (0)
- 8th Key Symposium: Translational and systems medicine (2012) (0)
- Genome-Scale Models and the Genetic Basis for E. coli Adaptation (2009) (0)
- Systems Biology: Chemical reactions (2011) (0)
- The effects of fatty acids on hybridoma growth metabolism and cell composition (1989) (0)
- Systems Biology: Homework problems (2011) (0)
- Systems Biology: Regulated enzymes (2011) (0)
- Analysis of experimental evolution of Escherichia Coli based on flux profiling (2008) (0)
- Systems Biology: Enzyme kinetics (2011) (0)
- MATHEMATICAL REPRESENTATION OF RECONSTRUCTED NETWORKS (2006) (0)
- Systems Biology: Fundamental Subspaces of S (2006) (0)
- Systems Biology: Metabolic Networks (2006) (0)
- Bioinformatics for bioengineers (2007) (0)
- Metabolic homeostasis and growth in abiotic cells (2022) (0)
- Letter to the Editor (2004) (0)
- Replating of bioreactor expanded human bone marrow results in extended growth of primitive and mature cells (2004) (0)
- Bioreactor for growth and attitude of mammalian cells (1996) (0)
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models (2018) (0)
- Dataset on economic analysis of mass production of algae in LED-based photobioreactors (2018) (0)
- Systems Biology: Hemoglobin (2011) (0)
- Biological determinants of photobioreactor design. 6th Quarterly report, October 1994--December 1994 (1995) (0)
- Biomarkers de fi ning the metabolic age of red blood cells during cold storage (2016) (0)
- A WhiteBox Machine Learning Approach for Revealing Antibiotic Mechanisms of Action Graphical (2019) (0)
- Systems Biology: Environmental Parameters (2015) (0)
- Development of a novel assay techniques for migration studies of loosely adherent cells (1999) (0)
- Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification (2018) (0)
- THERAPEUTC COMPOUNDS IN A GENETICALLY DEFINED SETTING (2017) (0)
- Clinical-scale laser-based scanning and processing of live cells: selective photothermal killing of fluorescent tumor targets for autologous stem cell transplantation (2001) (0)
- supplementation with hematopoietic growth factors In vitro myelopoiesis stimulated by rapid medium exchange and (2011) (0)
- Unravelling why some people have drug side effects (2016) (0)
- Comprar Embryonic Stem Cells | Masters, John R. | 9781402059827 | Springer (2007) (0)
- Regulatory perturbations of ribosome allocation optimize the growth proteome with a trade-off in adaptation capacity (2021) (0)
- Network Reconstruction: The Process (2015) (0)
- Metabolic Network Experimentation and Modeling 90 Metabolic Engineering of Light and Dark Biochemical Pathways in Wild-Type and Mutant Synechocystis PCC 6803 Strains for Maximal , 24-Hour Production of Hydrogen Gas (2006) (0)
- Systems Biology: BIOLOGICAL CHARACTERISTICS (2011) (0)
- Systems Biology: Signaling Networks (2006) (0)
- The OME Framework for genome-scale systems biology (2014) (0)
- Global Rebalancing of Cel lular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution Graphical (2016) (0)
- A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli (2021) (0)
- Gene Expression Profiling and the Use of Genome-Scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content (cid:1) (2009) (0)
- Biomanufacturing of melatonin is now possible (2023) (0)
- Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes (2020) (0)
- Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media (2014) (0)
- Adaptive Evolution of a Minimal Organism With a Synthetic Genome (2022) (0)
- Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks (2023) (0)
- Prediction of intracellular metabolic states from extracellular metabolomic data (2014) (0)
- Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins (2022) (0)
- Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli (2021) (0)
- Metastructures of Genomes (2015) (0)
- , Robert Escherichia coli Genes in Assessment of Conditionally Essential Experimental and Computational (2006) (0)
- Genome-scale models can compute proteome allocation (2016) (0)
- Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media (2020) (0)
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 (2019) (0)
- Biomarkers de fi ning the metabolic age of red blood cells during cold storage (2016) (0)
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