| Solving puzzles with missing pieces: The power of systems biology |
J.T. Yurkovich; B.O. Palsson |
2016 |
| A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. |
N. Mih; E. Brunk; A. Bordbar; B.O. Palsson |
2016 |
| Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes. |
A. Bordbar; P.I. Johansson; G. Paglia; S.J. Harrison; K. Wichuk; M. Magnúsdóttir; S. Valgeirsdottir; M. Gybel-Brask; S.R. Ostrowski; S. Palsson; O. Rolfsson; O.E. Sigurjónsson; M.B. Hansen; S. Gudmundsson; B.O. Palsson |
2016 |
| Construction and Evaluation of an Organic Anion Transporter 1 (OAT1)-Centered Metabolic Network. |
H.C. Liu; N. Jamshidi; Y. Chen; S.A. Eraly; S.Yee Cho; V. Bhatnagar; W. Wu; K.T. Bush; R. Abagyan; B.O. Palsson; S.K. Nigam |
2016 |
| Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution. |
H. Mundhada; J.M. Seoane; K. Schneider; A. Koza; H.B. Christensen; T. Klein; P.V. Phaneuf; M. Herrgard; A.M. Feist; A.T. Nielsen |
2016 |
| Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. |
E.J. O'Brien; J. Utrilla; B.O. Palsson |
2016 |
| ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions |
H. Latif; S. Federowicz; A. Ebrahim; J. Tarasova; R. Szubin; J. Utrilla; K. Zengler; B.O. Palsson |
2016 |
| Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. |
D. Ma; L. Yang; R.M.T. Fleming; I. Thiele; B.O. Palsson; M.A. Saunders |
2016 |
| Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow. |
A. Golabgir; J.M. Gutierrez; H. Hefzi; S. Li; B.O. Palsson; C. Herwig; N.E. Lewis |
2016 |
| BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. |
Z.A. King; J. Lu; A. Dräger; P. Miller; S. Federowicz; J.A. Lerman; A. Ebrahim; B.O. Palsson; N.E. Lewis |
2016 |
| Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling. |
J.M. Gutierrez; N.E. Lewis |
2015 |
| SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. |
A. Dräger; D.C. Zielinski; R. Keller; M. Rall; J. Eichner; B.O. Palsson; A. Zell |
2015 |
| The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli. |
S. Cho; Y.B. Cho; T.Jin Kang; S.Chang Kim; B. Palsson; B.K. Cho |
2015 |
| Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. |
R.K. Aziz; V.L. Khaw; J.M. Monk; E. Brunk; R. Lewis; S.I. Loh; A. Mishra; A.A. Nagle; C. Satyanarayana; S. Dhakshinamoorthy; M. Luche; D.B. Kitchen; K.A. Andrews; B.Ø. Palsson; P. Charusanti |
2015 |
| Multidimensional Analytical Approach Based on UHPLC-UV-Ion Mobility-MS for the Screening of Natural Pigments. |
T. Pacini; W. Fu; S. Gudmundsson; E. Chiaravalle; S. Brynjolfson; B.O. Palsson; G. Astarita; G. Paglia |
2015 |
| Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. |
Z.A. King; A. Dräger; A. Ebrahim; N. Sonnenschein; N.E. Lewis; B.O. Palsson |
2015 |
| Next-generation genome-scale models for metabolic engineering. |
Z.A. King; C.J. Lloyd; A.M. Feist; B.O. Palsson |
2015 |
| Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. |
S.Woo Seo; D. Kim; R. Szubin; B.O. Palsson |
2015 |
| Computing the functional proteome: recent progress and future prospects for genome-scale models. |
E.J. O'Brien; B.O. Palsson |
2015 |
| Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. |
L. Yang; J. Tan; E.J. O'Brien; J.M. Monk; D. Kim; H.J. Li; P. Charusanti; A. Ebrahim; C.J. Lloyd; J.T. Yurkovich; B. Du; A. Dräger; A. Thomas; Y. Sun; M.A. Saunders; B.O. Palsson |
2015 |
| Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. |
S.Woo Seo; D. Kim; E.J. O'Brien; R. Szubin; B.O. Palsson |
2015 |
| Model-driven discovery of underground metabolic functions in Escherichia coli. |
G.I. Guzman; J. Utrilla; S. Nurk; E. Brunk; J.M. Monk; A. Ebrahim; B.O. Palsson; A.M. Feist |
2015 |
| A Markov chain model for N-linked protein glycosylation - towards a low-parameter tool for model-driven glycoengineering. |
P.N. Spahn; A.H. Hansen; H.G. Hansen; J. Arnsdorf; H.F. Kildegaard; N.E. Lewis |
2015 |
| CONDENSED VERSION--Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis |
D.C. Zielinski; F.V. Filipp; A. Bordbar; K. Jensen; J.W. Smith; M.J. Herrgard; M.L. Mo; B.Ø. Palsson |
2015 |
| Engineering of oleaginous organisms for lipid production. |
J. Levering; J. Broddrick; K. Zengler |
2015 |
| Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network. |
H. Latif; M. Sahin; J. Tarasova; Y. Tarasova; V.A. Portnoy; J. Nogales; K. Zengler |
2015 |
| A streamlined ribosome profiling protocol for the characterization of microorganisms. |
H. Latif; R. Szubin; J. Tan; E. Brunk; A. Lechner; K. Zengler; B.O. Palsson |
2015 |
| Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. |
A. Islam; K. Zengler; E.A. Edwards; R. Mahadevan; G. Stephanopoulos |
2015 |
| JSBML 1.0: providing a smorgasbord of options to encode systems biology models. |
N. Rodriguez; A. Thomas; L. Watanabe; I.Y. Vazirabad; V. Kofia; H.F. Gómez; F. Mittag; J. Matthes; J. Rudolph; F. Wrzodek; E. Netz; A. Diamantikos; J. Eichner; R. Keller; C. Wrzodek; S. Fröhlich; N.E. Lewis; C.J. Myers; N. Le Novère; B.Ø. Palsson; M. Hucka; A. Dräger |
2015 |
| Unraveling interactions in microbial communities - from co-cultures to microbiomes. |
J. Tan; C. Zuniga; K. Zengler |
2015 |