iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning K Rychel, K Decker, AV Sastry, PV Phaneuf, S Poudel, BO Palsson Nucleic acids research 49 (D1), D112-D120, 2021 | 85 | 2021 |
Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response S Poudel, H Tsunemoto, Y Seif, AV Sastry, R Szubin, S Xu, H Machado, ... Proceedings of the National Academy of Sciences 117 (29), 17228-17239, 2020 | 70 | 2020 |
Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration A Anand, KE Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ... Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019 | 64 | 2019 |
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions ES Kavvas, Y Seif, JT Yurkovich, C Norsigian, S Poudel, WW Greenwald, ... BMC systems biology 12, 1-15, 2018 | 59 | 2018 |
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types Y Seif, JM Monk, N Mih, H Tsunemoto, S Poudel, C Zuniga, J Broddrick, ... PLoS computational biology 15 (1), e1006644, 2019 | 56 | 2019 |
Optimal dimensionality selection for independent component analysis of transcriptomic data JL McConn, CR Lamoureux, S Poudel, BO Palsson, AV Sastry BMC bioinformatics 22, 1-13, 2021 | 40 | 2021 |
Independent component analysis recovers consistent regulatory signals from disparate datasets AV Sastry, A Hu, D Heckmann, S Poudel, E Kavvas, BO Palsson PLoS computational biology 17 (2), e1008647, 2021 | 38 | 2021 |
Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks AV Sastry, S Poudel, K Rychel, R Yoo, CR Lamoureux, S Chauhan, ... BioRxiv, 2021.07. 01.450581, 2021 | 34 | 2021 |
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 | 30 | 2022 |
Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens A Rajput, Y Seif, KS Choudhary, C Dalldorf, S Poudel, JM Monk, ... Msystems 6 (1), 10.1128/msystems. 00981-20, 2021 | 29 | 2021 |
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 | 23 | 2021 |
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics D Choe, R Szubin, S Poudel, A Sastry, Y Song, Y Lee, S Cho, B Palsson, ... PLoS genetics 17 (9), e1009821, 2021 | 23 | 2021 |
Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease NJ Gao, MM Al-Bassam, S Poudel, JM Wozniak, DJ Gonzalez, J Olson, ... Frontiers in microbiology 10, 1967, 2019 | 21 | 2019 |
Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories A Fait, Y Seif, K Mikkelsen, S Poudel, JM Wells, BO Palsson, H Ingmer Proceedings of the National Academy of Sciences 119 (30), e2118262119, 2022 | 17 | 2022 |
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media S Poudel, H Tsunemoto, M Meehan, R Szubin, CA Olson, A Lamsa, Y Seif, ... Scientific data 6 (1), 43, 2019 | 14 | 2019 |
Machine learning of bacterial transcriptomes reveals responses underlying differential antibiotic susceptibility AV Sastry, N Dillon, A Anand, S Poudel, Y Hefner, S Xu, R Szubin, ... Msphere 6 (4), 10.1128/msphere. 00443-21, 2021 | 13 | 2021 |
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media A Rajput, S Poudel, H Tsunemoto, M Meehan, R Szubin, CA Olson, ... Scientific data 6 (1), 322, 2019 | 12 | 2019 |
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 | 10 | 2022 |
Experimental evolution reveals unifying systems-level adaptations but diversity in driving genotypes ES Kavvas, CP Long, A Sastry, S Poudel, MR Antoniewicz, Y Ding, ... Msystems 7 (6), e00165-22, 2022 | 10 | 2022 |
Mathematical models to study the biology of pathogens and the infectious diseases they cause JB Xavier, JM Monk, S Poudel, CJ Norsigian, AV Sastry, C Liao, J Bento, ... Iscience 25 (4), 2022 | 10 | 2022 |