| 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 |
| Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media |
D.M. McCloskey; J. Utrilla; R.K. Naviaux; B.O. Palsson; A.M. Feist |
2014 |
| Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis. |
N. Rohatgi; T.Kragh Nielsen; S.Petersen Bjørn; I. Axelsson; G. Paglia; B.Gunnar Voldborg; B.O. Palsson; O. Rolfsson |
2014 |
| A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks. |
H. Nam; M. Campodonico; A. Bordbar; D.R. Hyduke; S. Kim; D.C. Zielinski; B.O. Palsson |
2014 |
| Engineering synergy in biotechnology. |
J. Nielsen; M. Fussenegger; J. Keasling; S.Y. Lee; J.C. Liao; K. Prather; B. Palsson |
2014 |
| Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. |
J.K. Liu; E.J.O. Brien; J.A. Lerman; K. Zengler; B.O. Palsson; A.M. Feist |
2014 |
| Optimizing genome-scale network reconstructions. |
J. Monk; J. Nogales; B.O. Palsson |
2014 |
| Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. |
S.Woo Seo; D. Kim; H. Latif; E.J. O'Brien; R. Szubin; B.O. Palsson |
2014 |
| Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens. |
A.M. Feist; H. Nagarajan; A.E. Rotaru; P.L. Tremblay; T. Zhang; K.P. Nevin; D.R. Lovley; K. Zengler |
2014 |
| From random mutagenesis to systems biology in metabolic engineering of mammalian cells |
H. Hefzi; N.E. Lewis |
2014 |
| Systems glycobiology for glycoengineering. |
P.N. Spahn; N.E. Lewis |
2014 |
| Ion mobility derived collision cross sections to support metabolomics applications. |
G. Paglia; J.P. Williams; L. Menikarachchi; W. Thompson; R. Tyldesley-Worster; S. Halldórsson; O. Rolfsson; A. Moseley; D. Grant; J. Langridge; B.O. Palsson; G. Astarita |
2014 |
| Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates. |
G. Paglia; O.E. Sigurjónsson; O. Rolfsson; M.Bagge Hansen; S. Brynjólfsson; S. Gudmundsson; B.O. Palsson |
2014 |
| Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds. |
H.Marcus Geertz-Hansen; N. Blom; A.M. Feist; S. Brunak; T.Nordahl Petersen |
2014 |
| A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933. |
H. Latif; H.J. Li; P. Charusanti; B.Ø. Palsson; R.K. Aziz |
2014 |
| Determining the control circuitry of redox metabolism at the genome-scale. |
S. Federowicz; D. Kim; A. Ebrahim; J. Lerman; H. Nagarajan; B.K. Cho; K. Zengler; B. Palsson |
2014 |
| Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. |
M.A. Campodonico; B.A. Andrews; J.A. Asenjo; B.O. Palsson; A.M. Feist |
2014 |
| Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. |
K.K. Cheng; B.S. Lee; T. Masuda; T. Ito; K. Ikeda; A. Hirayama; L. Deng; J. Dong; K. Shimizu; T. Soga; M. Tomita; B.O. Palsson; M. Robert |
2014 |
| Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations. |
T.E. Sandberg; M. Pedersen; R.A. LaCroix; A. Ebrahim; M. Bonde; M.J. Herrgard; B.O. Palsson; M. Sommer; A.M. Feist |
2014 |