Publications
Year of Publication: 2019

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.. PLoS Comput Biol. 15(1):e1006644. .
2019.

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. Nucleic Acids Research. .
2019.

Pseudogene repair driven by selection pressure applied in experimental evolution.. Nat Microbiol. .
2019.
Year of Publication: 2018

Dataset on economic analysis of mass production of algae in LED-based photobioreactors.. Data Brief. 22:137-139. .
2018.

Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nature Communications. 9 .
2018.

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nature Communications. 9 .
2018.

Reframing gene essentiality in terms of adaptive flexibility.. BMC Syst Biol. 12(1):143. .
2018.



Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris. Science of The Total Environment. 654:275-283. .
2018.

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proceedings of the National Academy of Sciences. .
2018.

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology. .
2018.

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends in Biochemical Sciences. .
2018.

Identification of growth-coupled production strains considering protein costs and kinetic variability. Metabolic Engineering Communications. 7:e00080. .
2018.

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7 .
2018.


Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences. .
2018.

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.. Nucleic Acids Res. .
2018.

Escher-FBA: a web application for interactive flux balance analysis. BMC Systems Biology. .
2018.

Basics of genome-scale metabolic modeling and applications on C1-utilization.. FEMS Microbiol Lett. .
2018.

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.. Nat Commun. 9(1):3771. .
2018.

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.. Nat Commun. 9(1):3796. .
2018.

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.. Nucleic Acids Res. .
2018.

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.. PLoS Comput Biol. 14(8):e1006356. .
2018.


Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Frontiers in Microbiology. .
2018.

Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution.. Biochem J. 475(13):2225-2240. .
2018.

COBRAme: A computational framework for genome-scale models of metabolism and gene expression.. PLoS Comput Biol. 14(7):e1006302. .
2018.

Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions.. Appl Environ Microbiol. .
2018.


Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.. Biophys J. 114(11):2691-2702. .
2018.


ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.. PLoS One. 13(5):e0197272. .
2018.


The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9 .
2018.

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

High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli.. ACS Synth Biol. 7(4):1085-1094. .
2018.


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

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

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


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

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

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

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


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


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.


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.

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.

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


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


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



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

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

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

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

Year of Publication: 2015


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

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


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

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

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

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

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

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.

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.


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.


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.

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


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

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