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Published in mSphere, 2025
This paper demonstrates a method for targeted transcriptional profiling of low biomass samples.
Recommended citation: Doing G, Shanbhag P, Bell I, Cassidy S, Motakis E, Aiken E, Oh J, Adams MD. 2024. TEAL-seq: Targeted Expression Analysis Sequencing. bioRxiv 2024.11.26.625462. http://academicpages.github.io/TEAL-seq.pdf
Published in mSystems, 2024
This is a tool for the re-analysis of public gene expression datasets.
Recommended citation: Taub L, Hampton TH, Sarkar S, Doing G, Neff SL, Finger CE, Ferreira Fukutani K, Stanton BA.2024.E.PathDash, pathway activation analysis of publicly available pathogen gene expression data. mSystems9:e01030-24.https://doi.org/10.1128/msystems.01030-24 http://academicpages.github.io/taub-et-al-2024-e-pathdash-pathway-activation-analysis-of-publicly-available-pathogen-gene-expression-data.pdf
Published in Microbiology Spectrum, 2024
This paper looks at P. aeruginosa gene expression in ex vivo sputum.
Recommended citation: Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum. Microbiol Spectr. 2024 Apr 2;12(4):e0315723. doi: 10.1128/spectrum.03157-23. Epub 2024 Feb 22. PMID: 38385740; PMCID: PMC10986534. http://academicpages.github.io/neff_and_doing-et-al-2024-pseudomonas-aeruginosa-transcriptome-analysis-of-metal-restriction-in-ex-vivo-cystic-fibrosis-sputum.pdf
Published in mSystems, 2023
This paper is about compendia of microbial gene expression.
Recommended citation: Doing G, Lee AJ, Neff SL, Reiter T, Holt JD, Stanton BA, Greene CS, Hogan DA. Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia. mSystems. 2023 Feb 23;8(1):e0034122. doi: 10.1128/msystems.00341-22. Epub 2022 Dec 21. PubMed [citation] PMID: 36541761, PMCID: PMC9948711 http://academicpages.github.io/Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia.pdf
Published in mSystems, 2023
This paper is about PAO1 and PA14 transcriptomics.
Recommended citation: Lee AJ, Doing G, Neff SL, Reiter T, Hogan DA, Greene CS. Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14. mSystems. 2023 Feb 23;8(1):e0034222. doi: 10.1128/msystems.00342-22. Epub 2022 Dec 21. PubMed [citation] PMID: 36541762, PMCID: PMC9948736 http://academicpages.github.io/Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14.pdf
Published in Genomics Proteomics Bioinformatics, 2022
This paper is about simulating gene expression data.
Recommended citation: Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS. SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genomics Proteomics Bioinformatics. 2022 Oct;20(5):912-927. doi: 10.1016/j.gpb.2022.09.011. Epub 2022 Oct 7. PubMed [citation] PMID: 36216026, PMCID: PMC10025681 http://academicpages.github.io/SOPHIE_ Generative Neural Networks Separate Common and Specific Transcriptional Responses.pdf
Published in Computational and Structural Biotechnology, 2022
This is a review.
Recommended citation: Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Using genome-wide expression compendia to study microorganisms. Comput Struct Biotechnol J. 2022 Aug 10;20:4315-4324. doi: 10.1016/j.csbj.2022.08.012. eCollection 2022. Review. PubMed [citation] PMID: 36016717, PMCID: PMC9396250 http://academicpages.github.io/Using genome-wide expression compendia to study microorganisms.pdf
Published in Scientific Data, 2022
This paper is about development of an app for re-analysis of public data.
Recommended citation: Neff SL, Hampton TH, Puerner C, Cengher L, Doing G, Lee AJ, Koeppen K, Cheung AL, Hogan DA, Cramer RA, Stanton BA. CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. Sci Data. 2022 Jun 16;9(1):343. doi: 10.1038/s41597-022-01431-1. PubMed [citation] PMID: 35710652, PMCID: PMC9203545 http://academicpages.github.io/CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies.pdf
Published in Gigascience, 2020
This paper is about gene expression compendia.
Recommended citation: Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 2020 Nov 3;9(11). pii: giaa117. doi: 10.1093/gigascience/giaa117. PubMed [citation] PMID: 33140829, PMCID: PMC7607552 http://academicpages.github.io/giaa117.pdf
Published in PLoS Genetics, 2020
This paper is about co-culture and dual-seq transcriptomics.
Recommended citation: Doing G, Koeppen K, Occipinti P, Harty CE, Hogan DA. Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics. PLoS Genet. 2020 Aug 19;16(8):e1008783. doi: 10.1371/journal.pgen.1008783. eCollection 2020 Aug. PubMed [citation] PMID: 32813693, PMCID: PMC7480860 http://academicpages.github.io/Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans_ An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics.pdf
Published in Journal of Bacteriology, 2019
This paper is about the P. aeruginosa response to ethanol.
Recommended citation: Harty CE, Martins D, Doing G, Mould DL, Clay ME, Occhipinti P, Nguyen D, Hogan DA. Ethanol Stimulates Trehalose Production through a SpoT-DksA-AlgU-Dependent Pathway in Pseudomonas aeruginosa. J Bacteriol. 2019 May 22;201(12). pii: e00794-18. doi: 10.1128/JB.00794-18. Print 2019 Jun 15. PubMed [citation] PMID: 30936375, PMCID: PMC6531624 http://academicpages.github.io/Ethanol Stimulates Trehalose Production through a SpoT-DksA-AlgU-Dependent Pathway in Pseudomonas aeruginosa.pdf
Published in BioData Mining, 2018
This paper is about gene set and pathway enrichment analysis.
Recommended citation: Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Min. 2018 Jul 3;11:14. doi: 10.1186/s13040-018-0175-7. eCollection 2018. PubMed [citation] PMID: 29988723, PMCID: PMC6029133 http://academicpages.github.io/PathCORE-T_ identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.pdf
Published in Journal of Bacteriology, 2018
This paper is about Pseudomonas DGC-PDE interactions.
Recommended citation: Dahlstrom KM, Collins AJ, Doing G, Taroni JN, Gauvin TJ, Greene CS, Hogan DA, O'Toole GA. A Multimodal Strategy Used by a Large c-di-GMP Network. J Bacteriol. 2018 Mar 26;200(8). pii: e00703-17. doi: 10.1128/JB.00703-17. Print 2018 Apr 15. PubMed [citation] PMID: 29311282, PMCID: PMC5869470 http://academicpages.github.io/files/A Multimodal Strategy Used by a Large c-di-GMP Network.pdf
Published in Genome Announcements, 2018
This paper is about strains from the BJB collection.
Recommended citation: Bettina AM, Doing G, O'Brien K, Perron GG, Jude BA. Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed. Genome Announc. 2018 Jan 18;6(3). pii: e01426-17. doi: 10.1128/genomeA.01426-17. PubMed [citation] PMID: 29348334, PMCID: PMC5773719 http://academicpages.github.io/files/Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed.pdf
Published in Genome Announcements, 2018
This paper is about strain BJB302.
Recommended citation: Doing G, Perron GG, Jude BA. Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed. Genome Announc. 2018 Jan 4;6(1). pii:PMCID: PMC5754501 e01428-17. doi: 10.1128/genomeA.01428-17. PubMed [citation] PMID: 29301892, http://academicpages.github.io/files/Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed.pdf
Published in Cell Systems, 2017
This paper is about eADAGE.
Recommended citation: Tan J, Doing G, Lewis KA, Price CE, Chen KM, Cady KC, Perchuk B, Laub MT, Hogan DA, Greene CS. Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. Cell Syst. 2017 Jul 26;5(1):63-71.e6. doi: 10.1016/j.cels.2017.06.003. Epub 2017 Jul 12. PubMed [citation] PMID: 28711280, PMCID: PMC5532071 http://academicpages.github.io/files/Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.pdf