| The molecular architecture of engulfment during Bacillus subtilis sporulation K Khanna, J Lopez-Garrido, Z Zhao, R Watanabe, Y Yuan, J Sugie, ... Elife 8, e45257, 2019 | 46 | 2019 |
| Machine learning of all Mycobacterium tuberculosis H37Rv RNA-seq data reveals a structured interplay between metabolism, stress response, and infection R Yoo, K Rychel, S Poudel, T Al-Bulushi, Y Yuan, S Chauhan, ... MSphere 7 (2), e00033-22, 2022 | 33 | 2022 |
| Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius SM Chauhan, S Poudel, K Rychel, C Lamoureux, R Yoo, T Al Bulushi, ... Frontiers in Microbiology 12, 753521, 2021 | 26 | 2021 |
| Pan-genome analysis of transcriptional regulation in six Salmonella enterica serovar typhimurium strains reveals their different regulatory structures Y Yuan, Y Seif, K Rychel, R Yoo, S Chauhan, S Poudel, T Al-Bulushi, ... Msystems 7 (6), e00467-22, 2022 | 13 | 2022 |
| Machine learning of all Mycobacterium tuberculosis H37Rv RNA-seq data reveals a structured interplay between metabolism, stress response, and infection. MSphere. 2022; 7 (2 … R Yoo, K Rychel, S Poudel, T Al-Bulushi, Y Yuan, S Chauhan DOI 10, 00033-22, 0 | 7 | |
| Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains Y Yuan, Y Seif, K Rychel, R Yoo, S Chauhan, S Poudel, T Al-bulushi, ... bioRxiv, 2022.01. 11.475931, 2022 | 5 | 2022 |
| iModulonMiner and PyModulon: software for unsupervised mining of gene expression compendia AV Sastry, Y Yuan, S Poudel, K Rychel, R Yoo, CR Lamoureux, G Li, ... PLOS Computational Biology 20 (10), e1012546, 2024 | 2 | 2024 |
| Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942 Y Yuan, T Al Bulushi, AV Sastry, C Sancar, R Szubin, SS Golden, ... Proceedings of the National Academy of Sciences 121 (38), e2410492121, 2024 | 1 | 2024 |
| iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets EA Catoiu, J Krishnan, G Li, XA Lou, K Rychel, Y Yuan, H Bajpe, A Patel, ... Nucleic Acids Research 53 (D1), D99-D106, 2025 | | 2025 |