Saugat Poudel
Title
Cited by
Cited by
Year
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), 1-15, 2018
292018
Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration
A Anand, K Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ...
Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019
252019
Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators and role in key physiological responses
S Poudel, H Tsunemoto, Y Seif, AV Sastry, R Szubin, S Xu, H Machado, ...
Proceedings of the National Academy of Sciences, 2020
202020
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
182019
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
82021
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), 1-6, 2019
82019
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), 1-7, 2019
82019
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
52021
Matrix factorization recovers consistent regulatory signals from disparate datasets
AV Sastry, A Hu, D Heckmann, S Poudel, E Kavvas, BO Palsson
bioRxiv, 2020
42020
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
42019
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), e00981-20, 2021
22021
Optimal dimensionality selection for independent component analysis of transcriptomic data
JL McConn, CR Lamoureux, S Poudel, BO Palsson, AV Sastry
bioRxiv, 2021
12021
Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions
N Dillon, H Tsunemoto, S Poudel, MJ Meehan, Y Seif, R Szubin, ...
bioRxiv, 2020
12020
Decomposition of transcriptional responses provides insights into differential antibiotic susceptibility
A Sastry, N Dillon, S Poudel, Y Hefner, S Xu, R Szubin, A Feist, V Nizet, ...
bioRxiv, 2020
12020
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), e00443-21, 2021
2021
Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection
R Yoo, K Rychel, S Poudel, T Al-bulushi, Y Yuan, S Chauhan, ...
2021
RiboRid: a Low Cost, Advanced, and Ultra-efficient Method to Remove Ribosomal RNA for Bacterial Transcriptomics
C Donghui, R SZUBIN, S POUDEL, A SASTRY, S Yoseb, LEE Yongjae, ...
한국생물공학회 학술대회, 599-599, 2021
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, ...
bioRxiv, 2021
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, ...
bioRxiv, 2021
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
2021
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