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Items: 1 to 20 of 34

1.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

2.

A survey of metabolic databases emphasizing the MetaCyc family.

Karp PD, Caspi R.

Arch Toxicol. 2011 Sep;85(9):1015-33. doi: 10.1007/s00204-011-0705-2. Epub 2011 Apr 27. Review.

3.

Web tools for predictive toxicology model building.

Jeliazkova N.

Expert Opin Drug Metab Toxicol. 2012 Jul;8(7):791-801. doi: 10.1517/17425255.2012.685158. Epub 2012 May 12. Review.

PMID:
22577953
4.

Workflow based framework for life science informatics.

Tiwari A, Sekhar AK.

Comput Biol Chem. 2007 Oct;31(5-6):305-19. Epub 2007 Aug 19. Review.

PMID:
17931570
5.

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M.

Brief Bioinform. 2014 Jan;15(1):123-35. doi: 10.1093/bib/bbs058. Epub 2012 Nov 19. Review.

6.

A brief review of software tools for pangenomics.

Xiao J, Zhang Z, Wu J, Yu J.

Genomics Proteomics Bioinformatics. 2015 Feb;13(1):73-6. doi: 10.1016/j.gpb.2015.01.007. Epub 2015 Feb 23. Review.

7.

In silico Reconstruction of the Metabolic and Pathogenic Potential of Bacterial Genomes Using Subsystems.

McNeil LK, Aziz RK.

Genome Dyn. 2009;6:21-34. doi: 10.1159/000235760. Epub 2009 Aug 19. Review.

PMID:
19696491
8.

A global approach to analysis and interpretation of metabolic data for plant natural product discovery.

Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES.

Nat Prod Rep. 2013 Apr;30(4):565-83. doi: 10.1039/c3np20111b. Review.

9.

(Post-)genomics approaches in fungal research.

Aguilar-Pontes MV, de Vries RP, Zhou M.

Brief Funct Genomics. 2014 Nov;13(6):424-39. doi: 10.1093/bfgp/elu028. Epub 2014 Jul 17. Review.

PMID:
25037051
10.

An integrated computational pipeline and database to support whole-genome sequence annotation.

Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE.

Genome Biol. 2002;3(12):RESEARCH0081. Epub 2002 Dec 23. Review.

11.

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology.

Fondi M, Liò P.

Microbiol Res. 2015 Feb;171:52-64. doi: 10.1016/j.micres.2015.01.003. Epub 2015 Jan 7. Review.

12.

What we can learn about Escherichia coli through application of Gene Ontology.

Hu JC, Karp PD, Keseler IM, Krummenacker M, Siegele DA.

Trends Microbiol. 2009 Jul;17(7):269-78. doi: 10.1016/j.tim.2009.04.004. Epub 2009 Jul 1. Review.

13.

Collaborative software for traditional and translational research.

Berman AE, Barnett WK, Mooney SD.

Hum Genomics. 2012 Sep 25;6:21. doi: 10.1186/1479-7364-6-21. Review.

14.

Updating and curating metabolic pathways of TB.

Slayden RA, Jackson M, Zucker J, Ramirez MV, Dawson CC, Crew R, Sampson NS, Thomas ST, Jamshidi N, Sisk P, Caspi R, Crick DC, McNeil MR, Pavelka MS, Niederweis M, Siroy A, Dona V, McFadden J, Boshoff H, Lew JM.

Tuberculosis (Edinb). 2013 Jan;93(1):47-59. doi: 10.1016/j.tube.2012.11.001. Epub 2013 Feb 1. Review.

15.

Ten years of pan-genome analyses.

Vernikos G, Medini D, Riley DR, Tettelin H.

Curr Opin Microbiol. 2015 Feb;23:148-54. doi: 10.1016/j.mib.2014.11.016. Epub 2014 Dec 5. Review.

PMID:
25483351
16.

Informatics and clinical genome sequencing: opening the black box.

Moorthie S, Hall A, Wright CF.

Genet Med. 2013 Mar;15(3):165-71. doi: 10.1038/gim.2012.116. Epub 2012 Sep 13. Review.

PMID:
22975759
17.

Recent advances in the reconstruction of metabolic models and integration of omics data.

Saha R, Chowdhury A, Maranas CD.

Curr Opin Biotechnol. 2014 Oct;29:39-45. doi: 10.1016/j.copbio.2014.02.011. Epub 2014 Mar 12. Review.

PMID:
24632194
18.

Microbial virus genome annotation-mustering the troops to fight the sequence onslaught.

Brister JR, Le Mercier P, Hu JC.

Virology. 2012 Dec 20;434(2):175-80. doi: 10.1016/j.virol.2012.09.027. Epub 2012 Oct 18. Review.

19.

Improving collaboration by standardization efforts in systems biology.

Dräger A, Palsson BØ.

Front Bioeng Biotechnol. 2014 Dec 8;2:61. doi: 10.3389/fbioe.2014.00061. eCollection 2014. Review.

20.

The challenge of constructing, classifying, and representing metabolic pathways.

Caspi R, Dreher K, Karp PD.

FEMS Microbiol Lett. 2013 Aug;345(2):85-93. doi: 10.1111/1574-6968.12194. Epub 2013 Jun 27. Review.

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