Publications
Year of Publication: 2018

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Frontiers in Genetics. 9 .
2018.

Systems biology as an emerging paradigm in transfusion medicine.. BMC Syst Biol. 12(1):31. .
2018.



Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.. Metab Eng. 47:73-82. .
2018.


Quantitative -omic data empowers bottom-up systems biology. Current Opinion in Biotechnology. 51:130-136. .
2018.

Recon3D enables a three-dimensional view of gene variation in human metabolism.. Nat Biotechnol. .
2018.

ssbio: A Python Framework for Structural Systems Biology. Bioinformatics. .
2018.

Modeling the multi-scale mechanisms of macromolecular resource allocation. Current Opinion in Microbiology. 45:8-15. .
2018.

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.. PLoS Comput Biol. 14(1):e1005895. .
2018.

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.. Nucleic Acids Res. .
2018.
Year of Publication: 2017

Metabolic Models of Protein Allocation Call for the Kinetome.. Cell Syst. 5(6):538-541. .
2017.

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli.. Proc Natl Acad Sci U S A. .
2017.

Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function.. Cell Host Microbe. .
2017.

Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution.. Microb Cell Fact. 16(1):204. .
2017.

iML1515, a knowledgebase that computes Escherichia coli traits.. Nat Biotechnol. 35(10):904-908. .
2017.

A Padawan Programmer’s Guide to Developing Software Libraries. Cell Systems. .
2017.


Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences. 377121391183:201705524. .
2017.


Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.. Proc Natl Acad Sci U S A. .
2017.

Mannose and fructose metabolism in red blood cells during cold storage in SAGM.. Transfusion. .
2017.

Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. 2017 IEEE Conference on Control Technology and Applications (CCTA). .
2017.

Underground metabolism: network-level perspective and biotechnological potential. Current Opinion in Biotechnology. 49:108-114. .
2017.




Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.. Appl Environ Microbiol. .
2017.

Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression.. Bioinformatics. .
2017.

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.. PLoS Comput Biol. 13(3):e1005424. .
2017.


A Model for Designing Adaptive Laboratory Evolution Experiments.. Appl Environ Microbiol. .
2017.




Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.. Sci Rep. 7:41241. .
2017.

Year of Publication: 2016

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.. Proc Natl Acad Sci U S A. 113(51):E8344-E8353. .
2016.


A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.. Cell Syst. 3(5):434-443.e8. .
2016.

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.. Metab Eng. 39:141-150. .
2016.

The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiological Research. 194:47-52. .
2016.

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.. Sci Rep. 7:40863. .
2016.

Citrate metabolism in red blood cells stored in additive solution-3.. Transfusion. 57(2):325-336. .
2016.

Multi-omic data integration enables discovery of hidden biological regularities.. Nat Commun. 7:13091. .
2016.


solveME: fast and reliable solution of nonlinear ME models.. BMC Bioinformatics. 17(1):391. .
2016.

A Phaeodactylum tricornutum literature database for interactive annotation of content. Algal Research. 18:241-243. .
2016.



ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. bioRxiv. .
2016.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.. Nat Biotechnol. 34(8):828-837. .
2016.

Metabolic fate of adenine in red blood cells during storage in SAGM solution.. Transfusion. .
2016.


A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.. PLoS Comput Biol. 12(7):e1005039. .
2016.

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.. PLoS Comput Biol. 12(6):e1004998. .
2016.


Evaluation of rate law approximations in bottom-up kinetic models of metabolism.. BMC Syst Biol. 10(1):40. .
2016.


Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.. PLoS One. 11(5):e0155038. .
2016.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.. Cell Syst. 2(4):260-71. .
2016.

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Metabolic Engineering Communications. 3 .
2016.

Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.. PLoS One. 11(3):e0151130. .
2016.

Systems biology of the structural proteome.. BMC Syst Biol. 10(1):26. .
2016.



What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis. 10(2):e0004403. .
2016.

Solving puzzles with missing pieces: The power of systems biology. Proceedings of the IEEE. 104(1) .
2016.


BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.. Nucleic Acids Res. .
2016.
Year of Publication: 2015


A logical data representation framework for electricity-driven bioproduction processes.. Biotechnol Adv. 33(6 Pt 1):736-44. .
2015.

Networks of energetic and metabolic interactions define dynamics in microbial communities.. Proc Natl Acad Sci U S A. .
2015.

Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Scientific Reports. doi:10.1038/srep16025 .
2015.

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.. BMC Syst Biol. 9(1):68. .
2015.


Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 11(10):831. .
2015.

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems. 1:283-292. .
2015.



Engineering of oleaginous organisms for lipid production.. Curr Opin Biotechnol. 36:32-39. .
2015.

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.. PLoS Comput Biol. 11(8):e1004321. .
2015.

Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.. Appl Environ Microbiol. 81(16):5477-85. .
2015.

Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.. Integr Biol (Camb). 7(8):869-82. .
2015.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.. Proc Natl Acad Sci U S A. .
2015.


Computing the functional proteome: recent progress and future prospects for genome-scale models.. Curr Opin Biotechnol. 34C:125-134. .
2015.

Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.. Biotechnol J. 10(7):939-49. .
2015.

Next-generation genome-scale models for metabolic engineering.. Curr Opin Biotechnol. 35C:23-29. .
2015.

A streamlined ribosome profiling protocol for the characterization of microorganisms.. Biotechniques. 58(6):329-32. .
2015.

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.. Bioinformatics. .
2015.

How to set up collaborations between academia and industrial biotech companies.. Nat Biotechnol. 33(3):237-40. .
2015.


Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis.. Nat Commun. 6:7101. .
2015.

Prediction of intracellular metabolic states from extracellular metabolomic data.. Metabolomics. 11(3):603-619. .
2015.

Unraveling interactions in microbial communities - from co-cultures to microbiomes.. J Microbiol. 53(5):295-305. .
2015.

Using Genome-scale Models to Predict Biological Capabilities.. Cell. 161(5):971-987. .
2015.

Decoding the jargon of bottom-up metabolic systems biology.. Bioessays. .
2015.

The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.. Nucleic Acids Res. .
2015.

Multidimensional Analytical Approach Based on UHPLC-UV-Ion Mobility-MS for the Screening of Natural Pigments.. Anal Chem. 87(5):2593-9. .
2015.

A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites. Metabolomics. 10.1007/s11306-015-0790-y .
2015.

Model-driven discovery of underground metabolic functions in Escherichia coli.. Proc Natl Acad Sci U S A. .
2015.
Year of Publication: 2014

Optimizing genome-scale network reconstructions.. Nat Biotechnol. 32(5):447-452. .
2014.




Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol.. Nat Commun. 5:3233. .
2014.

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.. BMC Biol. 12(1):4. .
2014.


Constraint-based models predict metabolic and associated cellular functions.. Nat Rev Genet. 15(2):107-20. .
2014.

Engineering synergy in biotechnology.. Nat Chem Biol. 10(5):319-22. .
2014.

Ion mobility derived collision cross sections to support metabolomics applications.. Anal Chem. 86(8):3985-93. .
2014.

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens.. PLoS Comput Biol. 10(4):e1003575. .
2014.

Determining the control circuitry of redox metabolism at the genome-scale.. PLoS Genet. 10(4):e1004264. .
2014.

Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.. Microb Cell Fact. 13(1):3. .
2014.

Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.
Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.. Sci Rep. 4:3925. .
2014.


Improving collaboration by standardization efforts in systems biology.. Front Bioeng Biotechnol. 2:61. .
2014.



Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.. BMC Syst Biol. 8(1):110. .
2014.


Systems glycobiology for glycoengineering.. Curr Opin Biotechnol. 30C:218-224. .
2014.


A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.. PLoS Comput Biol. 10(9):e1003837. .
2014.



A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.. Genome Announc. 2(4) .
2014.


Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice.. PLoS One. 9(7):e102319. .
2014.

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.. Mol Syst Biol. 10(7):737. .
2014.

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.. Metab Eng. 25C:140-158. .
2014.

From random mutagenesis to systems biology in metabolic engineering of mammalian cells. Pharmaceutical Bioprocessing. 2 .
2014.


Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media. Metabolomics. 10(10.1007/s11306-014-0686-2) .
2014.
Year of Publication: 2013

Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways.. Drug Metab Dispos. .
2013.

COBRApy: COnstraints-Based Reconstruction and Analysis for Python.. BMC Syst Biol. 7(1):74. .
2013.


Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli.. Science. 340(6137):1220-3. .
2013.

MS/MS networking guided analysis of molecule and gene cluster families.. Proc Natl Acad Sci U S A. 110(28):E2611-20. .
2013.

The genome organization of Thermotoga maritima reflects its lifestyle.. PLoS Genet. 9(4):e1003485. .
2013.

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. Mol Syst Biol. 9:661. .
2013.



A community-driven global reconstruction of human metabolism.. Nat Biotechnol. .
2013.

The microbiome extends to subepidermal compartments of normal skin.. Nat Commun. 4:1431. .
2013.

Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant.. FEMS Microbiol Lett. 342(1):62-9. .
2013.




Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.. Microb Cell Fact. 12(1):118. .
2013.

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.. Curr Top Microbiol Immunol. 363:21-41. .
2013.

Sulfide-driven microbial electrosynthesis.. Environ Sci Technol. 47(1):568-573. .
2013.

Analysis of omics data with genome-scale models of metabolism.. Mol Biosyst. 9(2):167-74. .
2013.

Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.. Appl Microbiol Biotechnol. 97(6):2395-403. .
2013.

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.. Biochem J. 449(2):427-35. .
2013.


TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.. PLoS One. 8(12):e82238. .
2013.



Path2Models: large-scale generation of computational models from biochemical pathway maps.. BMC Syst Biol. 7:116. .
2013.


Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.. Biotechnol Adv. 32(2):255-268. .
2013.


Antibacterial mechanisms identified through structural systems pharmacology.. BMC Syst Biol. 7(1):102. .
2013.


Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.. Mol Syst Biol. 9:693. .
2013.

The COMBREX project: design, methodology, and initial results.. PLoS Biol. 11(8):e1001638. .
2013.

Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap. Industrial Biotechnology. 9(4):236-246. .
2013.

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.. Front Microbiol. 4:244. .
2013.

The systems biology simulation core algorithm.. BMC Syst Biol. 7:55. .
2013.
Year of Publication: 2012
Systems biology of stored blood cells: can it help to extend the expiration date? J Proteomics. 76 Spec No.:163-7. .
2012.
Proteomic analysis of Chinese hamster ovary cells.. J Proteome Res. 11(11):5265-76. .
2012.
Network context and selection in the evolution to enzyme specificity.. Science. 337(6098):1101-4. .
2012.
In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 3:929. .
2012.
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.. Int J Antimicrob Agents. .
2012.
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.. Mol Syst Biol. 8:558. .
2012.
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.. BMC Syst Biol. 6(1):30. .
2012.
Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.. J Chromatogr B Analyt Technol Biomed Life Sci. 898:111-20. .
2012.
Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.. PLoS One. 7(3):e33727. .
2012.
A road map for the development of community systems (CoSy) biology.. Nat Rev Microbiol. 10(5):366-72. .
2012.
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.. Proc Natl Acad Sci U S A. 109(7):2678-83. .
2012.
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.. Nat Rev Microbiol. 10(4):291-305. .
2012.
Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling.. BMC Syst Biol. 6:9. .
2012.
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.. BMC Genomics. 13(1):679. .
2012.
Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate.. Microbiology. 158(Pt 12):2946-57. .
2012.
Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.. PLoS One. 7(9):e45635. .
2012.
UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae.. Anal Bioanal Chem. 404(10):3145-54. .
2012.
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.. J Bacteriol. 194(5):1145-57. .
2012.
Using the reconstructed genome-scale human metabolic network to study physiology and pathology.. J Intern Med. 271(2):131-41. .
2012.
MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH.. Pac Symp Biocomput. 17:283-286. .
2012.
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).. Anal Bioanal Chem. 402(3):1183-98. .
2012.
A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.. J Theor Biol. 292:71-7. .
2012.
Year of Publication: 2011
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.. Nat Protoc. 6(9):1290-307. .
2011.
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.. Mol Syst Biol. 7:518. .
2011.
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.. Nat Biotechnol. 29(8):735-41. .
2011.
Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509. .
2011.
Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.. J Biol Chem. 286(36):31522-31. .
2011.
Technologies and approaches to elucidate and model the virulence program of salmonella.. Front Microbiol. 2:121. .
2011.
The PurR regulon in Escherichia coli K-12 MG1655.. Nucleic Acids Res. 39(15):6456-64. .
2011.
Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.. J Biol Chem. 286(26):23150-9. .
2011.
Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering.. Curr Opin Biotechnol. 22(4):590-4. .
2011.
The role of cellular objectives and selective pressures in metabolic pathway evolution.. Curr Opin Biotechnol. 22(4):595-600. .
2011.
An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.. J Bacteriol. 193(7):1710-7. .
2011.
Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53. .
2011.
Adaptive Laboratory Evolution. Microbe. .
2011.
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.. BMC Syst Biol. 5:180. .
2011.
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.. BMC Syst Biol. 5:155. .
2011.
Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.. PLoS One. 6(10):e26172. .
2011.
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.. BMC Syst Biol. 5:163. .
2011.
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.. Mol Syst Biol. 7:535. .
2011.
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.. BMC Syst Biol. 5:8. .
2011.
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.. Nat Rev Microbiol. 9(1):39-50. .
2011.
Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis.. Nucleic Acids Res. 39(5):1656-65. .
2011.
Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nat Chem Biol. 8(1):65-71. .
2011.
Year of Publication: 2010
Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA.. FEMS microbiology letters. 310(1):62-8. .
2010.
Structural and operational complexity of the Geobacter sulfurreducens genome.. Genome research. 20(9):1304-11. .
2010.
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422. .
2010.
Systematizing the generation of missing metabolic knowledge.. Biotechnology and bioengineering. 107(3):403-12. .
2010.
Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.. Applied and environmental microbiology. 76(19):6529-40. .
2010.
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20500-5. .
2010.
Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9. .
2010.
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.. PLoS genetics. 6(11):e1001186. .
2010.
The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9. .
2010.
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.. Biophysical journal. 98(10):2072-81. .
2010.
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86. .
2010.
What is flux balance analysis? Nature biotechnology. 28(3):245-8. .
2010.
The biomass objective function.. Current opinion in microbiology. 13(3):344-9. .
2010.
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.. Applied and environmental microbiology. 76(13):4158-68. .
2010.
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.. Molecular systems biology. 6:390. .
2010.
Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85. .
2010.
Large-scale in silico modeling of metabolic interactions between cell types in the human brain.. Nature biotechnology. 28(12):1279-85. .
2010.
Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361. .
2010.
Towards genome-scale signalling network reconstructions.. Nature reviews. Genetics. 11(4):297-307. .
2010.
Drug off-target effects predicted using structural analysis in the context of a metabolic network model.. PLoS computational biology. 6(9):e1000938. .
2010.
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.. BMC bioinformatics. 11:213. .
2010.
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.. BMC systems biology. 4:140. .
2010.
A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121. .
2010.
Year of Publication: 2009
Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3. .
2009.
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.. Science (New York, N.Y.). 325(5947):1544-9. .
2009.
The transcription unit architecture of the Escherichia coli genome.. Nature biotechnology. 27(11):1043-9. .
2009.
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology. 5(3):e1000312. .
2009.
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.. Journal of bacteriology. 191(11):3437-44. .
2009.
Functional states of the genome-scale Escherichia coli transcriptional regulatory system.. PLoS computational biology. 5(6):e1000403. .
2009.
Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44. .
2009.
Genome-scale network analysis of imprinted human metabolic genes.. Epigenetics : official journal of the DNA Methylation Society. 4(1):43-6. .
2009.
Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61. .
2009.
Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology. 5(2):e1000292. .
2009.
Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43. .
2009.
Metabolic systems biology.. FEBS letters. 583(24):3900-4. .
2009.
Central role of the cell in microbial ecology.. Microbiology and molecular biology reviews : MMBR. 73(4):712-29. .
2009.
Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. Molecular cell. 35(3):255-6. .
2009.
Probing the basis for genotype-phenotype relationships.. Nature methods. 6(8):565-6. .
2009.
Metabolic network analysis integrated with transcript verification for sequenced genomes.. Nature methods. 6(8):589-92. .
2009.
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.. BMC systems biology. 3:38. .
2009.
Applications of genome-scale metabolic reconstructions.. Molecular systems biology. 5:320. .
2009.
Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37. .
2009.
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.. BMC systems biology. 3:30. .
2009.
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.. BMC systems biology. 3:44. .
2009.
Year of Publication: 2008
Network-based prediction of human tissue-specific metabolism.. Nature biotechnology. 26(9):1003-10. .
2008.
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.. Applied microbiology and biotechnology. 80(5):849-62. .
2008.
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.. Nature biotechnology. 26(10):1155-60. .
2008.
Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082. .
2008.
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67. .
2008.
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.. Genome research. 18(6):900-10. .
2008.
Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli.. Journal of bacteriology. 190(14):5087-94. .
2008.
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.. Proceedings of the National Academy of Sciences of the United States of America. 105(49):19462-7. .
2008.
Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain.. Applied and environmental microbiology. 74(24):7561-9. .
2008.
Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.. Methods in molecular biology (Clifton, N.J.). 439:131-45. .
2008.
Predicting gene essentiality using genome-scale in silico models.. Methods in molecular biology (Clifton, N.J.). 416:433-57. .
2008.
Top-down analysis of temporal hierarchy in biochemical reaction networks.. PLoS computational biology. 4(9):e1000177. .
2008.
Three factors underlying incorrect in silico predictions of essential metabolic genes.. BMC systems biology. 2:14. .
2008.
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.. BMC systems biology. 2:79. .
2008.
Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology. 4:171. .
2008.
Year of Publication: 2007
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.. The Journal of biological chemistry. 282(39):28791-9. .
2007.
A genome-scale, constraint-based approach to systems biology of human metabolism.. Molecular bioSystems. 3(9):598-603. .
2007.
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.. PLoS computational biology. 3(10):1887-95. .
2007.
Systematic condition-dependent annotation of metabolic genes.. Genome research. 17(11):1626-33. .
2007.
Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.. Biochemistry. 46(19):5722-31. .
2007.
Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.. Molecular genetics and metabolism. 91(1):15-22. .
2007.
Metabolic characterization of Escherichia coli strains adapted to growth on lactate.. Applied and environmental microbiology. 73(14):4639-47. .
2007.
Building the power house: recent advances in mitochondrial studies through proteomics and systems biology.. American journal of physiology. Cell physiology. 292(1):C164-77. .
2007.
Global reconstruction of the human metabolic network based on genomic and bibliomic data.. Proceedings of the National Academy of Sciences of the United States of America. 104(6):1777-82. .
2007.
Microbial regulatory and metabolic networks.. Current opinion in biotechnology. 18(4):360-4. .
2007.
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.. Nature protocols. 2(3):727-38. .
2007.
Estimation of the number of extreme pathways for metabolic networks.. BMC bioinformatics. 8(1):363. .
2007.