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Results: 18

1.

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO.

Mol Syst Biol. 2014 Jul 1;10:737. doi: 10.15252/msb.20145243.

PMID:
24987116
[PubMed - in process]
Free Article
2.

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K.

PLoS Comput Biol. 2014 Apr 24;10(4):e1003575. doi: 10.1371/journal.pcbi.1003575. eCollection 2014 Apr.

PMID:
24762737
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Determining the control circuitry of redox metabolism at the genome-scale.

Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B.

PLoS Genet. 2014 Apr 3;10(4):e1004264. doi: 10.1371/journal.pgen.1004264. eCollection 2014 Apr.

PMID:
24699140
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism.

Embree M, Qiu Y, Shieu W, Nagarajan H, O'Neil R, Lovley D, Zengler K.

Appl Environ Microbiol. 2014 May;80(9):2918-27. doi: 10.1128/AEM.03916-13. Epub 2014 Feb 28.

PMID:
24584254
[PubMed - in process]
Free PMC Article
5.

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.

Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K.

Microb Cell Fact. 2013 Nov 25;12:118. doi: 10.1186/1475-2859-12-118.

PMID:
24274140
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.

Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.

Nat Commun. 2013;4:2809. doi: 10.1038/ncomms3809.

PMID:
24264237
[PubMed - indexed for MEDLINE]
7.

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.

Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K.

ISME J. 2014 Apr;8(4):757-67. doi: 10.1038/ismej.2013.187. Epub 2013 Oct 24.

PMID:
24152715
[PubMed - indexed for MEDLINE]
8.

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.

Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO.

Nat Biotechnol. 2013 Aug;31(8):759-65. doi: 10.1038/nbt.2624. Epub 2013 Jul 21.

PMID:
23873082
[PubMed - indexed for MEDLINE]
9.

MS/MS networking guided analysis of molecule and gene cluster families.

Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):E2611-20. doi: 10.1073/pnas.1303471110. Epub 2013 Jun 24.

PMID:
23798442
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23637642
[PubMed - in process]
Free PMC Article
11.

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.

Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K.

Nat Commun. 2013;4:1755. doi: 10.1038/ncomms2743.

PMID:
23612296
[PubMed - indexed for MEDLINE]
12.

The microbiome extends to subepidermal compartments of normal skin.

Nakatsuji T, Chiang HI, Jiang SB, Nagarajan H, Zengler K, Gallo RL.

Nat Commun. 2013;4:1431. doi: 10.1038/ncomms2441.

PMID:
23385576
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Proteomic analysis of Chinese hamster ovary cells.

Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson BO, Zhang H, Betenbaugh M.

J Proteome Res. 2012 Nov 2;11(11):5265-76. doi: 10.1021/pr300476w. Epub 2012 Oct 5.

PMID:
22971049
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.

Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ.

PLoS Genet. 2012;8(8):e1002867. doi: 10.1371/journal.pgen.1002867. Epub 2012 Aug 9.

PMID:
22912590
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.

Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO.

PLoS One. 2012;7(3):e33727. doi: 10.1371/journal.pone.0033727. Epub 2012 Mar 21.

PMID:
22470465
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Lewis NE, Nagarajan H, Palsson BO.

Nat Rev Microbiol. 2012 Feb 27;10(4):291-305. doi: 10.1038/nrmicro2737. Review.

PMID:
22367118
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.

Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J.

Nat Biotechnol. 2011 Jul 31;29(8):735-41. doi: 10.1038/nbt.1932.

PMID:
21804562
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.

Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL.

PLoS One. 2010 Jun 8;5(6):e10922. doi: 10.1371/journal.pone.0010922.

PMID:
20544019
[PubMed - indexed for MEDLINE]
Free PMC Article

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