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Results: 1 to 20 of 57

1.

PE-Assembler: de novo assembler using short paired-end reads.

Ariyaratne PN, Sung WK.

Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626. Epub 2010 Dec 12.

PMID:
21149345
[PubMed - indexed for MEDLINE]
Free Article
2.

Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.

Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BØ.

PLoS Genet. 2010 Nov 4;6(11):e1001186. doi: 10.1371/journal.pgen.1001186.

PMID:
21079674
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes.

Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y.

PLoS One. 2010 Sep 24;5(9):e12651. doi: 10.1371/journal.pone.0012651.

PMID:
20885980
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.

Tsai IJ, Otto TD, Berriman M.

Genome Biol. 2010;11(4):R41. doi: 10.1186/gb-2010-11-4-r41. Epub 2010 Apr 13.

PMID:
20388197
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Metabolic engineering for the production of shikimic acid in an evolved Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system.

Escalante A, Calderón R, Valdivia A, de Anda R, Hernández G, Ramírez OT, Gosset G, Bolívar F.

Microb Cell Fact. 2010 Apr 12;9:21. doi: 10.1186/1475-2859-9-21.

PMID:
20385022
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A practical approach to RT-qPCR-Publishing data that conform to the MIQE guidelines.

Taylor S, Wakem M, Dijkman G, Alsarraj M, Nguyen M.

Methods. 2010 Apr;50(4):S1-5. doi: 10.1016/j.ymeth.2010.01.005.

PMID:
20215014
[PubMed - indexed for MEDLINE]
7.

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.

Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BØ.

Genome Biol. 2009;10(10):R118. doi: 10.1186/gb-2009-10-10-r118. Epub 2009 Oct 22.

PMID:
19849850
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation.

Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolívar F.

PLoS One. 2009 Oct 19;4(10):e7466. doi: 10.1371/journal.pone.0007466.

PMID:
19838295
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.

Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R.

Bioinformatics. 2009 Oct 1;25(19):2607-8. doi: 10.1093/bioinformatics/btp450. Epub 2009 Aug 3.

PMID:
19654119
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.

Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19.

PMID:
19542151
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Reordering contigs of draft genomes using the Mauve aligner.

Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT.

Bioinformatics. 2009 Aug 15;25(16):2071-3. doi: 10.1093/bioinformatics/btp356. Epub 2009 Jun 10.

PMID:
19515959
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

PMID:
19261174
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT.

Clin Chem. 2009 Apr;55(4):611-22. doi: 10.1373/clinchem.2008.112797. Epub 2009 Feb 26.

PMID:
19246619
[PubMed - indexed for MEDLINE]
Free Article
14.

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E.

PLoS Genet. 2009 Jan;5(1):e1000344. doi: 10.1371/journal.pgen.1000344. Epub 2009 Jan 23.

PMID:
19165319
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.

Rodriguez SM, Panjikar S, Van Belle K, Wyns L, Messens J, Loris R.

Protein Sci. 2008 Apr;17(4):681-90. doi: 10.1110/ps.073420708. Epub 2008 Feb 27.

PMID:
18305191
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Coutilization of glucose and glycerol enhances the production of aromatic compounds in an Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system.

Martínez K, de Anda R, Hernández G, Escalante A, Gosset G, Ramírez OT, Bolívar FG.

Microb Cell Fact. 2008 Jan 22;7:1. doi: 10.1186/1475-2859-7-1.

PMID:
18211716
[PubMed]
Free PMC Article
17.

The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal.

Deana A, Celesnik H, Belasco JG.

Nature. 2008 Jan 17;451(7176):355-8. doi: 10.1038/nature06475.

PMID:
18202662
[PubMed - indexed for MEDLINE]
18.

New insights into the role of sigma factor RpoS as revealed in escherichia coli strains lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system.

Flores N, Escalante A, de Anda R, Báez-Viveros JL, Merino E, Franco B, Georgellis D, Gosset G, Bolívar F.

J Mol Microbiol Biotechnol. 2008;14(4):176-92. Epub 2007 Oct 15.

PMID:
17938565
[PubMed - indexed for MEDLINE]
19.

An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.

Herring CD, Palsson BØ.

BMC Genomics. 2007 Aug 14;8:274.

PMID:
17697331
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Growth recovery on glucose under aerobic conditions of an Escherichia coli strain carrying a phosphoenolpyruvate:carbohydrate phosphotransferase system deletion by inactivating arcA and overexpressing the genes coding for glucokinase and galactose permease.

Flores N, Leal L, Sigala JC, de Anda R, Escalante A, Martínez A, Ramírez OT, Gosset G, Bolivar F.

J Mol Microbiol Biotechnol. 2007;13(1-3):105-16.

PMID:
17693718
[PubMed - indexed for MEDLINE]

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