Følg
Saugat Poudel
Saugat Poudel
Senior Data Scientist, Palmona Pathogenomics
Verificeret mail på ucsd.edu
Titel
Citeret af
Citeret af
År
Expansion of the Gene Ontology knowledgebase and resources
S Carbon, H Dietze, SE Lewis, CJ Mungall, MC Munoz-Torres, S Basu, ...
Nucleic acids research 45 (D1), 2017
2102017
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
622021
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
612020
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
572019
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
532018
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
492019
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
342021
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
332021
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
262021
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
222021
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
212022
Machine learning uncovers a data-driven transcriptional regulatory network for the crenarchaeal thermoacidophile Sulfolobus acidocaldarius
SM Chauhan, S Poudel, BO Palsson
Frontiers in Microbiology 12, 753521, 2021
192021
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, 476691, 2019
152019
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
152019
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
122022
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
122021
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
122019
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
102021
Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens. mSystems 6: e00981-20
A Rajput, Y Seif, KS Choudhary, C Dalldorf, S Poudel, JM Monk, ...
92021
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
62022
Systemet kan ikke foretage handlingen nu. Prøv igen senere.
Artikler 1–20