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Saugat Poudel - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 
Area:
Microbiology, Systems Biology
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21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains. Msystems. e0048022. PMID 36321827 DOI: 10.1128/msystems.00480-22  0.793
2022 Yuan Y, Seif Y, Rychel K, Yoo R, Chauhan S, Poudel S, Al-Bulushi T, Palsson BO, Sastry AV. Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures. Msystems. e0046722. PMID 36317888 DOI: 10.1128/msystems.00467-22  0.814
2022 Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. Msystems. e0016522. PMID 36226969 DOI: 10.1128/msystems.00165-22  0.789
2022 Fait A, Seif Y, Mikkelsen K, Poudel S, Wells JM, Palsson BO, Ingmer H. Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. Proceedings of the National Academy of Sciences of the United States of America. 119: e2118262119. PMID 35858453 DOI: 10.1073/pnas.2118262119  0.785
2022 Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJR, Baliga NS, Stoeger T, Ruffin F, Richardson RAK, Gao CA, et al. Mathematical models to study the biology of pathogens and the infectious diseases they cause. Iscience. 25: 104079. PMID 35359802 DOI: 10.1016/j.isci.2022.104079  0.752
2022 Yoo R, Rychel K, Poudel S, Al-Bulushi T, Yuan Y, Chauhan S, Lamoureux C, Palsson BO, Sastry A. Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. Msphere. e0003322. PMID 35306876 DOI: 10.1128/msphere.00033-22  0.765
2021 McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV. Optimal dimensionality selection for independent component analysis of transcriptomic data. Bmc Bioinformatics. 22: 584. PMID 34879815 DOI: 10.1186/s12859-021-04497-7  0.724
2021 Chauhan SM, Poudel S, Rychel K, Lamoureux C, Yoo R, Al Bulushi T, Yuan Y, Palsson BO, Sastry AV. Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile . Frontiers in Microbiology. 12: 753521. PMID 34777307 DOI: 10.3389/fmicb.2021.753521  0.75
2021 Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK. RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics. Plos Genetics. 17: e1009821. PMID 34570751 DOI: 10.1371/journal.pgen.1009821  0.701
2021 Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B. Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. Msphere. 6: e0044321. PMID 34431696 DOI: 10.1128/mSphere.00443-21  0.777
2021 Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO. Independent component analysis recovers consistent regulatory signals from disparate datasets. Plos Computational Biology. 17: e1008647. PMID 33529205 DOI: 10.1371/journal.pcbi.1008647  0.791
2021 Rajput A, Seif Y, Choudhary KS, Dalldorf C, Poudel S, Monk JM, Palsson BO. Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. Msystems. 6. PMID 33500331 DOI: 10.1128/mSystems.00981-20  0.804
2021 Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, et al. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 10. PMID 33420779 DOI: 10.1093/gigascience/giaa156  0.756
2020 Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Research. PMID 33045728 DOI: 10.1093/nar/gkaa810  0.798
2020 Poudel S, Tsunemoto H, Seif Y, Sastry AV, Szubin R, Xu S, Machado H, Olson CA, Anand A, Pogliano J, Nizet V, Palsson BO. Revealing 29 sets of independently modulated genes in , their regulators, and role in key physiological response. Proceedings of the National Academy of Sciences of the United States of America. PMID 32616573 DOI: 10.1073/Pnas.2008413117  0.76
2019 Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, et al. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Scientific Data. 6: 322. PMID 31848353 DOI: 10.1038/S41597-019-0331-Z  0.776
2019 Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proceedings of the National Academy of Sciences of the United States of America. PMID 31767748 DOI: 10.1073/Pnas.1909987116  0.733
2019 Gao NJ, Al-Bassam MM, Poudel S, Wozniak JM, Gonzalez DJ, Olson J, Zengler K, Nizet V, Valderrama JA. Functional and Proteomic Analysis of Virulence Upon Loss of Its Native Cas9 Nuclease. Frontiers in Microbiology. 10: 1967. PMID 31507572 DOI: 10.3389/Fmicb.2019.01967  0.768
2019 Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, et al. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Scientific Data. 6: 43. PMID 31028276 DOI: 10.1038/S41597-019-0051-4  0.767
2019 Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. Plos Computational Biology. 15: e1006644. PMID 30625152 DOI: 10.1371/Journal.Pcbi.1006644  0.764
2018 Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. Bmc Systems Biology. 12: 25. PMID 29499714 DOI: 10.1186/S12918-018-0557-Y  0.735
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