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Items: 1 to 20 of 26


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.


High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling.

Rollin JA, Martin del Campo J, Myung S, Sun F, You C, Bakovic A, Castro R, Chandrayan SK, Wu CH, Adams MW, Senger RS, Zhang YH.

Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):4964-9. doi: 10.1073/pnas.1417719112. Epub 2015 Apr 6.


A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories.

Fisher AK, Freedman BG, Bevan DR, Senger RS.

Comput Struct Biotechnol J. 2014 Sep 3;11(18):91-9. doi: 10.1016/j.csbj.2014.08.010. eCollection 2014 Aug. Review.


Near-real-time analysis of the phenotypic responses of Escherichia coli to 1-butanol exposure using Raman Spectroscopy.

Zu TN, Athamneh AI, Wallace RS, Collakova E, Senger RS.

J Bacteriol. 2014 Dec;196(23):3983-91. doi: 10.1128/JB.01590-14. Epub 2014 Aug 25.


Transport of magnesium by a bacterial Nramp-related gene.

Shin JH, Wakeman CA, Goodson JR, Rodionov DA, Freedman BG, Senger RS, Winkler WC.

PLoS Genet. 2014 Jun 26;10(6):e1004429. doi: 10.1371/journal.pgen.1004429. eCollection 2014 Jun.


Designing novel cellulase systems through agent-based modeling and global sensitivity analysis.

Apte AA, Senger RS, Fong SS.

Bioengineered. 2014 Jul-Aug;5(4):243-53. doi: 10.4161/bioe.29160. Epub 2014 May 15.


Phenotypic profiling of antibiotic response signatures in Escherichia coli using Raman spectroscopy.

Athamneh AI, Alajlouni RA, Wallace RS, Seleem MN, Senger RS.

Antimicrob Agents Chemother. 2014;58(3):1302-14. doi: 10.1128/AAC.02098-13. Epub 2013 Dec 2.


Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints.

Yen JY, Nazem-Bokaee H, Freedman BG, Athamneh AI, Senger RS.

Biotechnol J. 2013 May;8(5):581-94. doi: 10.1002/biot.201200234. Epub 2013 Apr 11.


Resolving cell composition through simple measurements, genome-scale modeling, and a genetic algorithm.

Senger RS, Nazem-Bokaee H.

Methods Mol Biol. 2013;985:85-101. doi: 10.1007/978-1-62703-299-5_5.


Peptide-guided surface-enhanced Raman scattering probes for localized cell composition analysis.

Athamneh AI, Senger RS.

Appl Environ Microbiol. 2012 Nov;78(21):7805-8. doi: 10.1128/AEM.02000-12. Epub 2012 Aug 24.


Are we ready for genome-scale modeling in plants?

Collakova E, Yen JY, Senger RS.

Plant Sci. 2012 Aug;191-192:53-70. doi: 10.1016/j.plantsci.2012.04.010. Epub 2012 May 3. Review.


Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.

McAnulty MJ, Yen JY, Freedman BG, Senger RS.

BMC Syst Biol. 2012 May 14;6:42. doi: 10.1186/1752-0509-6-42.


Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052.

Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND.

BMC Syst Biol. 2011 Aug 16;5:130. doi: 10.1186/1752-0509-5-130.


Biofuel production improvement with genome-scale models: The role of cell composition.

Senger RS.

Biotechnol J. 2010 Jul;5(7):671-85. doi: 10.1002/biot.201000007. Review.


Computational approaches in metabolic engineering.

Reed JL, Senger RS, Antoniewicz MR, Young JD.

J Biomed Biotechnol. 2010;2010:207414. doi: 10.1155/2010/207414. Epub 2011 Apr 7. No abstract available.


Microarray-based gene expression analysis as a process characterization tool to establish comparability of complex biological products: scale-up of a whole-cell immunotherapy product.

Wang M, Senger RS, Paredes C, Banik GG, Lin A, Papoutsakis ET.

Biotechnol Bioeng. 2009 Nov 1;104(4):796-808. doi: 10.1002/bit.22441.


Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis.

Senger RS, Papoutsakis ET.

Biotechnol Bioeng. 2008 Dec 1;101(5):1036-52. doi: 10.1002/bit.22010.


The transcriptional program underlying the physiology of clostridial sporulation.

Jones SW, Paredes CJ, Tracy B, Cheng N, Sillers R, Senger RS, Papoutsakis ET.

Genome Biol. 2008;9(7):R114. doi: 10.1186/gb-2008-9-7-r114. Epub 2008 Jul 16.


Prediction of N-linked glycan branching patterns using artificial neural networks.

Senger RS, Karim MN.

Math Biosci. 2008 Jan;211(1):89-104. Epub 2007 Oct 30.

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