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Items: 17

1.

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.

Faria JP, Davis JJ, Edirisinghe JN, Taylor RC, Weisenhorn P, Olson RD, Stevens RL, Rocha M, Rocha I, Best AA, DeJongh M, Tintle NL, Parrello B, Overbeek R, Henry CS.

Front Microbiol. 2016 Nov 24;7:1819.

2.

IDENTIFICATION AND ANALYSIS OF BACTERIAL GENOMIC METABOLIC SIGNATURES.

Bowerman N, Tintle N, Dejongh M, Best AA.

Pac Symp Biocomput. 2016;22:3-14.

3.

A Bayesian Framework for the Classification of Microbial Gene Activity States.

Disselkoen C, Greco B, Cook K, Koch K, Lerebours R, Viss C, Cape J, Held E, Ashenafi Y, Fischer K, Acosta A, Cunningham M, Best AA, DeJongh M, Tintle N.

Front Microbiol. 2016 Aug 9;7:1191. doi: 10.3389/fmicb.2016.01191.

4.

Cautions about the reliability of pairwise gene correlations based on expression data.

Powers S, DeJongh M, Best AA, Tintle NL.

Front Microbiol. 2015 Jun 26;6:650. doi: 10.3389/fmicb.2015.00650.

5.

Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.

Devoid S, Overbeek R, DeJongh M, Vonstein V, Best AA, Henry C.

Methods Mol Biol. 2013;985:17-45. doi: 10.1007/978-1-62703-299-5_2.

PMID:
23417797
6.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.

Tintle NL, Sitarik A, Boerema B, Young K, Best AA, Dejongh M.

BMC Bioinformatics. 2012 Aug 8;13:193. doi: 10.1186/1471-2105-13-193.

7.

CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.

DeJongh M, Bockstege B, Frybarger P, Hazekamp N, Kammeraad J, McGeehan T.

Bioinformatics. 2012 Mar 15;28(6):891-2. doi: 10.1093/bioinformatics/btr719.

8.

Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.

Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA.

J Bacteriol. 2011 Jul;193(13):3228-40. doi: 10.1128/JB.00350-11.

9.

Connecting genotype to phenotype in the era of high-throughput sequencing.

Henry CS, Overbeek R, Xia F, Best AA, Glass E, Gilbert J, Larsen P, Edwards R, Disz T, Meyer F, Vonstein V, Dejongh M, Bartels D, Desai N, D'Souza M, Devoid S, Keegan KP, Olson R, Wilke A, Wilkening J, Stevens RL.

Biochim Biophys Acta. 2011 Oct;1810(10):967-77. doi: 10.1016/j.bbagen.2011.03.010. Review.

PMID:
21421023
10.

High-throughput generation, optimization and analysis of genome-scale metabolic models.

Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL.

Nat Biotechnol. 2010 Sep;28(9):977-82. doi: 10.1038/nbt.1672.

PMID:
20802497
11.

Gene set analyses for interpreting microarray experiments on prokaryotic organisms.

Tintle NL, Best AA, DeJongh M, Van Bruggen D, Heffron F, Porwollik S, Taylor RC.

BMC Bioinformatics. 2008 Nov 5;9:469. doi: 10.1186/1471-2105-9-469.

12.

The RAST Server: rapid annotations using subsystems technology.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.

BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.

13.

Toward the automated generation of genome-scale metabolic networks in the SEED.

DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A.

BMC Bioinformatics. 2007 Apr 26;8:139.

14.

Linking molecular function and biological process terms in the ontology for gene expression data analysis.

Dejongh M, Van Dort P, Ramsay B.

Conf Proc IEEE Eng Med Biol Soc. 2004;4:2984-6.

PMID:
17270905
15.

An evaluation of ontology exchange languages for bioinformatics.

McEntire R, Karp P, Abernethy N, Benton D, Helt G, DeJongh M, Kent R, Kosky A, Lewis S, Hodnett D, Neumann E, Olken F, Pathak D, Tarczy-Hornoch P, Toldo L, Topaloglou T.

Proc Int Conf Intell Syst Mol Biol. 2000;8:239-50.

PMID:
10977085
16.

RedSoar--a system for red blood cell antibody identification.

Johnson KA, Johnson TR, Smith JW Jr, DeJongh M, Fischer O, Amra NK, Bayazitoglu A.

Proc Annu Symp Comput Appl Med Care. 1991:664-8.

17.
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