Doing G - Search Results

1

Correcting for experiment-specific variability in expression compendia can remove underlying signals.

Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Lee AJ, et al. Among authors: doing g. Gigascience. 2020 Nov 3;9(11):giaa117. doi: 10.1093/gigascience/giaa117. Gigascience. 2020. PMID: 33140829 Free PMC article.

2

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

Tan J, Doing G, Lewis KA, Price CE, Chen KM, Cady KC, Perchuk B, Laub MT, Hogan DA, Greene CS. Tan J, et al. Among authors: doing g. Cell Syst. 2017 Jul 26;5(1):63-71.e6. doi: 10.1016/j.cels.2017.06.003. Epub 2017 Jul 12. Cell Syst. 2017. PMID: 28711280 Free PMC article.

3

Using genome-wide expression compendia to study microorganisms.

Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Lee AJ, et al. Among authors: doing g. Comput Struct Biotechnol J. 2022 Aug 10;20:4315-4324. doi: 10.1016/j.csbj.2022.08.012. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 36016717 Free PMC article. Review.

4

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.

Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. Chen KM, et al. Among authors: doing g. BioData Min. 2018 Jul 3;11:14. doi: 10.1186/s13040-018-0175-7. eCollection 2018. BioData Min. 2018. PMID: 29988723 Free PMC article.

5

SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses.

Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS. Lee AJ, et al. Among authors: doing g. Genomics Proteomics Bioinformatics. 2022 Oct;20(5):912-927. doi: 10.1016/j.gpb.2022.09.011. Epub 2022 Oct 7. Genomics Proteomics Bioinformatics. 2022. PMID: 36216026 Free PMC article.

6

A Multimodal Strategy Used by a Large c-di-GMP Network.

Dahlstrom KM, Collins AJ, Doing G, Taroni JN, Gauvin TJ, Greene CS, Hogan DA, O'Toole GA. Dahlstrom KM, et al. Among authors: doing g. J Bacteriol. 2018 Mar 26;200(8):e00703-17. doi: 10.1128/JB.00703-17. Print 2018 Apr 15. J Bacteriol. 2018. PMID: 29311282 Free PMC article.

7

CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies.

Neff SL, Hampton TH, Puerner C, Cengher L, Doing G, Lee AJ, Koeppen K, Cheung AL, Hogan DA, Cramer RA, Stanton BA. Neff SL, et al. Among authors: doing g. Sci Data. 2022 Jun 16;9(1):343. doi: 10.1038/s41597-022-01431-1. Sci Data. 2022. PMID: 35710652 Free PMC article.

8

Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics.

Doing G, Koeppen K, Occipinti P, Harty CE, Hogan DA. Doing G, et al. PLoS Genet. 2020 Aug 19;16(8):e1008783. doi: 10.1371/journal.pgen.1008783. eCollection 2020 Aug. PLoS Genet. 2020. PMID: 32813693 Free PMC article.

9

Ethanol Stimulates Trehalose Production through a SpoT-DksA-AlgU-Dependent Pathway in Pseudomonas aeruginosa.

Harty CE, Martins D, Doing G, Mould DL, Clay ME, Occhipinti P, Nguyen D, Hogan DA. Harty CE, et al. Among authors: doing g. J Bacteriol. 2019 May 22;201(12):e00794-18. doi: 10.1128/JB.00794-18. Print 2019 Jun 15. J Bacteriol. 2019. PMID: 30936375 Free PMC article.

A network analysis using a model, eADAGE, built from publicly available P. aeruginosa transcriptome data sets (J. Tan, G. Doing, K. A. Lewis, C. E. Price, et al., Cell Syst 5:63-71, 2017, https://doi.org/10.1016/j.cels.2017.06.003) provided strong support for our mo …

A network analysis using a model, eADAGE, built from publicly available P. aeruginosa transcriptome data sets (J. Tan, G. Doing …

10

Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed.

Doing G, Perron GG, Jude BA. Doing G, et al. Genome Announc. 2018 Jan 4;6(1):e01428-17. doi: 10.1128/genomeA.01428-17. Genome Announc. 2018. PMID: 29301892 Free PMC article.

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