Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
11 papers
Recent·Most cited
Y. Hirose, S. Poudel, A. V. Sastry, R. Szubin, D. C. Zielinski, H. G. Lim, N. D. Menon, H. Bergsten, S. Uchiyama, T. Hanada, S. Kawabata, B. O. Palsson, V. Nizet
The paper identifies carbon sources that regulate hemolytic toxin expression in Streptococcus pyogenes using transcriptome-wide independent component analysis.
bioRxiv · Aug 4, 2022Microbiology
S. Poudel, Y. Hefner, R. Szubin, A. V. Sastry, Y. Gao, V. Nizet, B. O. Palsson
This paper uses ICA to modularize the TRN of S. aureus USA300 and combines it with a metabolic model to show coordination between CcpA and CodY in regulating carbon and amino acid metabolism.
bioRxiv · May 25, 2022Microbiology
P. V. Phaneuf, D. C. Zielinski, J. T. Yurkovich, J. Johnsen, R. Szubin, L. Yang, S. H. Kim, S. Schulz, M. Wu, C. Dalldorf, E. Ozdemir, B. O. Palsson, A. Feist
This paper presents a data-driven workflow to design microbial strains using aggregated ALE mutational data, revealing gene-centric mutations that significantly alter cellular states.
bioRxiv · Jul 19, 2021Bioengineering
S. Poudel, H. Tsunemoto, Y. Seif, A. V. Sastry, R. Szubin, S. Xu, H. Machado, C. Olson, A. Anand, J. Pogliano, V. Nizet, B. Palsson
This paper identifies 29 independently modulated gene sets in S. aureus using ICA, linking them to regulators and physiological responses.
Proceedings of the National Academy of Sciences · Jul 2, 2020Peer-reviewedMicrobiology
H. Machado, Y. Seif, G. Sakoulas, C. A. Olson, R. Szubin, B. Palsson, V. Nizet, A. M. Feist
This study identifies media-specific mutational mechanisms of vancomycin resistance in S. aureus using adaptive laboratory evolution and sequencing.
bioRxiv · Jun 7, 2020Microbiology
N. A. Dillon, Y. Seif, H. Tsunemoto, S. Poudel, M. Meehan, R. Szubin, C. Olson, A. Rajput, G. Alarcon, A. Lamsa, A. Vrbanac, J. Sugie, S. Dahesh, J. Monk, P. Dorrestein, , V. Nizet
This study examines how MDR A. baumannii responds to azithromycin in different growth conditions using multiple analytical techniques.
bioRxiv · May 19, 2020 · PreprintMicrobiology
A. Rajput, S. Poudel, H. Tsunemoto, M. Meehan, R. Szubin, C. Olson, Y. Seif, A. Lamsa, N. Dillon, A. Vrbanac, J. Sugie, S. Dahesh, J. Monk, P. Dorrestein, J. Pogliano, , B. O. Palsson
The paper examines vancomycin's effect on HA-MRSA USA100 strains using bacteriological and physiological media through growth curves, RNA sequencing, and exo-metabolomics.
bioRxiv · May 6, 2020 · PreprintMicrobiology
A. V. Sastry, N. Dillon, S. Poudel, Y. Hefner, S. Xu, R. Szubin, A. Feist, V. Nizet, B. Palsson
The paper investigates how media composition affects antibiotic susceptibility in E. coli using transcriptomics and machine learning, identifying key regulators and shifts in respiration and iron availability.
bioRxiv · May 4, 2020 · PreprintMicrobiology
Y. Seif, S. Poudel, H. Tsunemoto, R. Szubin, M. J. Meehan, C. Olson, A. Rajput, G. Alarcon, A. Lamsa, N. Dillon, A. Vrbanac, J. Sugie, S. Daesh, J. Monk, P. Dorrestein, , V. Nizet
This study investigates how nafcillin affects HA-MRSA D592 in different media types, revealing media-dependent antibiotic activity through multi-dimensional analysis.
bioRxiv · Apr 30, 2020 · PreprintMicrobiology
I. A. Rodionova, Y. Gao, A. V. Sastry, J. Monk, n. wong, R. Szubin, H. Lim, Z. Zhang, M. H. Saier, B. O. Palsson
This paper identifies PtrR as a dual activator/repressor in E. coli that regulates putrescine stress response and glutamate utilization through transcriptional control of multiple genes.
bioRxiv · Apr 27, 2020 · PreprintMicrobiology
B. Du, C. A. Olson, A. V. Sastry, X. Fang, P. V. Phaneuf, K. Chen, M. Wu, R. Szubin, S. Xu, Y. Gao, Y. Hefner, A. M. Feist, B. O. Palsson
This study evolves E. coli under acid stress and identifies genetic and expression changes that enhance acid tolerance.
bioRxiv · Jun 4, 2019Microbiology