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
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,
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
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
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
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
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
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
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
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
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
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
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
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.
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
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.
Talk at Bard College, Annandale-on-Hudson, NY
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Talk at M2P2, Fairlee, VT
Talk at NEMPET, Blue Mountain Lake, NY
Talk at Dartmouth College, Hanover, NH
Talk at Bard College, Annandale-on-Hudson, NY
Talk at Dartmouth College, Hanover, NH
Talk at The Jackson Laboratory for Genomic Medicine, Farmington, CT
Talk at Dartmouth College, Hanover, NH
Talk at Thomas Jefferson High School, Alexandria, VA
Talk at The Jackson Laboratory for Genomic Medicine, Farmington, CT
Talk at University of Connecticut, Farmington, CT
Talk at Bard College, Annandale-on-Hudson, NY
Talk at Union College, Schenectady, NY
Talk at The Jackson Laboratory for Genomic Medicine, Farmington, CT
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Talk at CT State Northwestern, Winstead, CT
Talk at Lake Arrowhead Microbial Genomics, Lake Arrowhead, CA
Talk at New England Biolabs, Ipswitch, MA
Talk at Duke Microbiome Center, Durham, NC
Talk at Northeast and CT Valley ASM, Worcester, MA
Talk at Yale University, New Haven, CT