| Unsupervised extraction of stable expression signatures from public compendia with an ensemble of neural networks J Tan, G Doing, KA Lewis, CE Price, KM Chen, KC Cady, B Perchuk, ... Cell systems 5 (1), 63-71. e6, 2017 | 82 | 2017 |
| A multimodal strategy used by a large c-di-GMP network KM Dahlstrom, AJ Collins, G Doing, JN Taroni, TJ Gauvin, CS Greene, ... Journal of bacteriology 200 (8), 10.1128/jb. 00703-17, 2018 | 57 | 2018 |
| Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual … G Doing, K Koeppen, P Occipinti, CE Harty, DA Hogan PLoS genetics 16 (8), e1008783, 2020 | 33 | 2020 |
| Ethanol stimulates trehalose production through a SpoT-DksA-AlgU-dependent pathway in Pseudomonas aeruginosa CE Harty, D Martins, G Doing, DL Mould, ME Clay, P Occhipinti, ... Journal of Bacteriology 201 (12), 10.1128/jb. 00794-18, 2019 | 19 | 2019 |
| Correcting for experiment-specific variability in expression compendia can remove underlying signals AJ Lee, YS Park, G Doing, DA Hogan, CS Greene GigaScience 9 (11), giaa117, 2020 | 18 | 2020 |
| PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia KM Chen, J Tan, GP Way, G Doing, DA Hogan, CS Greene BioData Mining 11, 1-20, 2018 | 15 | 2018 |
| Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed G Doing, GG Perron, BA Jude Genome Announcements 6 (1), 10.1128/genomea. 01428-17, 2018 | 9 | 2018 |
| Compendium-wide analysis of Pseudomonas aeruginosa core and accessory genes reveals transcriptional patterns across strains PAO1 and PA14 AJ Lee, G Doing, SL Neff, T Reiter, DA Hogan, CS Greene MSystems 8 (1), e00342-22, 2023 | 8 | 2023 |
| Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia G Doing, AJ Lee, SL Neff, T Reiter, JD Holt, BA Stanton, CS Greene, ... Msystems 8 (1), e00341-22, 2023 | 7 | 2023 |
| CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies SL Neff, TH Hampton, C Puerner, L Cengher, G Doing, AJ Lee, ... Scientific Data 9 (1), 343, 2022 | 7 | 2022 |
| Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed AM Bettina, G Doing, K O’Brien, GG Perron, BA Jude Genome Announcements 6 (3), 10.1128/genomea. 01426-17, 2018 | 4 | 2018 |
| Unsupervised extraction of stable expression signatures from public compendia with eADAGE J Tan, G Doing, KA Lewis, CE Price, KM Chen, KC Cady, B Perchuk, ... | 4 | 2016 |
| Unsupervised extraction of functional gene expression signatures in the bacterial pathogen Pseudomonas aeruginosa with eADAGE J Tan, G Doing, KA Lewis, CE Price, KM Chen, KC Cady, B Perchuk, ... bioRxiv, 078659, 2016 | 3 | 2016 |
| SOPHIE: generative neural networks separate common and specific transcriptional responses AJ Lee, DL Mould, J Crawford, D Hu, RK Powers, G Doing, JC Costello, ... Genomics, Proteomics and Bioinformatics 20 (5), 912-927, 2022 | 2 | 2022 |
| Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum SL Neff, G Doing, T Reiter, TH Hampton, CS Greene, DA Hogan Microbiology Spectrum, e03157-23, 2024 | 1 | 2024 |
| Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns AJ Lee, G Doing, SL Neff, T Reiter, DA Hogan, CS Greene bioRxiv, 2022.04. 14.488429, 2022 | 1 | 2022 |
| Generative neural networks separate common and specific transcriptional responses AJ Lee, DL Mould, J Crawford, D Hu, RK Powers, G Doing, JC Costello, ... bioRxiv, 2021.05. 24.445440, 2021 | 1 | 2021 |
| System-wide automatic extraction of functional signatures in Pseudomonas aeruginosa with eADAGE J Tan, G Doing, KA Lewis, CE Price, KM Chen, KC Cady, B Perchuk, ... Cell Systems, 2016 | 1 | 2016 |
| E. PathDash, pathway activation analysis of public cystic fibrosis pathogen gene expression data L Taub, TH Hampton, S Sarkar, G Doing, SL Neff, CE Finger, KF Fukutani, ... bioRxiv, 2024.04. 10.588749, 2024 | | 2024 |
| Analysis of Pseudomonas aeruginosa transcription in an ex vivo cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus SL Neff, G Doing, T Reiter, TH Hampton, CS Greene, DA Hogan bioRxiv, 2023 | | 2023 |
