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Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS.

Cell Syst. 2016 May 19. pii: S2405-4712(16)30112-0. doi: 10.1016/j.cels.2016.04.004. [Epub ahead of print]


Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.

Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K.

PLoS One. 2016 May 6;11(5):e0155038. doi: 10.1371/journal.pone.0155038. eCollection 2016.


Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.

Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO.

Cell Syst. 2015 Oct 28;1(4):283-92. doi: 10.1016/j.cels.2015.10.003. Epub 2015 Oct 28.


Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.

Cell Syst. 2016 Apr 27;2(4):260-71. doi: 10.1016/j.cels.2016.04.003. Epub 2016 Apr 27.


Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale.

McCloskey D, Young JD, Xu S, Palsson BO, Feist AM.

Anal Chem. 2016 Apr 5;88(7):3844-52. doi: 10.1021/acs.analchem.5b04914. Epub 2016 Mar 24.


Systems biology of the structural proteome.

Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO.

BMC Syst Biol. 2016 Mar 11;10:26. doi: 10.1186/s12918-016-0271-6.


Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.

Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO.

PLoS One. 2016 Mar 10;11(3):e0151130. doi: 10.1371/journal.pone.0151130. eCollection 2016.


Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow.

Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE.

Biotechnol Adv. 2016 Mar 3. pii: S0734-9750(16)30018-0. doi: 10.1016/j.biotechadv.2016.02.011. [Epub ahead of print] Review.


Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes.

Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnusdottir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S, Rolfsson O, Sigurjónsson OE, Hansen MB, Gudmundsson S, Palsson BO.

Transfusion. 2016 Apr;56(4):852-62. doi: 10.1111/trf.13460. Epub 2016 Jan 8.


MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications.

McCloskey D, Young JD, Xu S, Palsson BO, Feist AM.

Anal Chem. 2016 Jan 19;88(2):1362-70. doi: 10.1021/acs.analchem.5b03887. Epub 2015 Dec 24.


Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations.

Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO, Charusanti P.

Sci Rep. 2015 Nov 4;5:16025. doi: 10.1038/srep16025.


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

King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.

Nucleic Acids Res. 2016 Jan 4;44(D1):D515-22. doi: 10.1093/nar/gkv1049. Epub 2015 Oct 17.


Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.

Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.

BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9.


Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P.

Front Microbiol. 2015 Sep 23;6:958. doi: 10.3389/fmicb.2015.00958. eCollection 2015.


Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004321. doi: 10.1371/journal.pcbi.1004321. eCollection 2015 Aug.


Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.

Seo SW, Kim D, Szubin R, Palsson BO.

Cell Rep. 2015 Aug 25;12(8):1289-99. doi: 10.1016/j.celrep.2015.07.043. Epub 2015 Aug 13.


Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson BO.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10810-5. doi: 10.1073/pnas.1501384112. Epub 2015 Aug 10.


Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.

Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO.

Nat Commun. 2015 Aug 10;6:7970. doi: 10.1038/ncomms8970.


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

Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.

Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.

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