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Items: 1 to 20 of 27


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.


Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.

Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM.

BMC Syst Biol. 2014 Sep 18;8:110. doi: 10.1186/s12918-014-0110-6.


Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.

Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25.


Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.

O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ.

Mol Syst Biol. 2013 Oct 1;9:693. doi: 10.1038/msb.2013.52.


COBRApy: COnstraints-Based Reconstruction and Analysis for Python.

Ebrahim A, Lerman JA, Palsson BO, Hyduke DR.

BMC Syst Biol. 2013 Aug 8;7:74. doi: 10.1186/1752-0509-7-74.


The genome organization of Thermotoga maritima reflects its lifestyle.

Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K.

PLoS Genet. 2013 Apr;9(4):e1003485. doi: 10.1371/journal.pgen.1003485. Epub 2013 Apr 25.


Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant.

Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P.

FEMS Microbiol Lett. 2013 May;342(1):62-9. doi: 10.1111/1574-6968.12109. Epub 2013 Mar 15.


Network context and selection in the evolution to enzyme specificity.

Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO.

Science. 2012 Aug 31;337(6098):1101-4. doi: 10.1126/science.1216861.


Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.

Ho Sui SJ, Lo R, Fernandes AR, Caulfield MD, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FS.

Int J Antimicrob Agents. 2012 Sep;40(3):246-51. doi: 10.1016/j.ijantimicag.2012.05.009. Epub 2012 Jul 20.


In silico method for modelling metabolism and gene product expression at genome scale.

Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO.

Nat Commun. 2012 Jul 3;3:929. doi: 10.1038/ncomms1928.


An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO.

BMC Syst Biol. 2011 Oct 13;5:163. doi: 10.1186/1752-0509-5-163.


A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ.

Mol Syst Biol. 2011 Oct 11;7:535. doi: 10.1038/msb.2011.65.


Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.

Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ.

Mol Syst Biol. 2010 Jul;6:390. doi: 10.1038/msb.2010.47.


Reliability of radiographic parameters in neuromuscular scoliosis.

Gupta MC, Wijesekera S, Sossan A, Martin L, Vogel LC, Boakes JL, Lerman JA, McDonald CM, Betz RR.

Spine (Phila Pa 1976). 2007 Mar 15;32(6):691-5.


Assessment of children with brachial plexus birth palsy using the Pediatric Outcomes Data Collection Instrument.

Huffman GR, Bagley AM, James MA, Lerman JA, Rab G.

J Pediatr Orthop. 2005 May-Jun;25(3):400-4.


Spinal arthrodesis for scoliosis in Down syndrome.

Lerman JA, Emans JB, Hall JE, Karlin LI.

J Pediatr Orthop. 2003 Mar-Apr;23(2):159-61.


Open versus closed halo rings: comparison of fixation strengths.

Lerman JA, Haynes RJ.

Spine (Phila Pa 1976). 2001 Oct 1;26(19):2102-4.

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