| Revealing oxidative pentose metabolism in new Pseudomonas putida isolates |
Park, M. R., Gauttam, R., Fong, B., Chen, Y., Lim, H. G., Feist, A. M., Mukhopadhyay, A., Petzold, C. J., Simmons, B. A., & Singer, S. W. |
2023 |
| Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance |
Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO.
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2023 |
| A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century |
Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C |
2023 |
| Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways |
Mattei, G., Gan, Z., Ramazzotti, M., Palsson, B.O., Zielinski, D.C.
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2023 |
| Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks |
Catoiu EA, Phaneuf P, Monk J, Palsson BO |
2023 |
| Modeling Red Blood Cell Metabolism in the Omics Era |
Key A, Haiman Z, Palsson BO, D’Alessandro A.
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2023 |
| The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets |
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2023 |
| Functional annotation of enzyme-encoding genes using deep learning with transformer layers |
Kim GB, Kim JY, Lee JA, Norsigian CJ, Palsson BO, Lee SY
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2023 |
| Metabolic homeostasis and growth in abiotic cells |
Akbari A, Palsson BO |
2023 |
| High-resolution temporal profiling of E. coli transcriptional response |
Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J.
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2023 |
| Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
Shin J, Rychel K, Palsson BO. |
2023 |
| Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species |
Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO
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2023 |
| E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding |
Rodionova IA, Hosseinnia A, Kim S, Goodacre N, Zhang L, Zhang Z, Palsson B, Uetz P, Babu M, Saier MH Jr. |
2023 |
| Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators |
Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO |
2022 |
| Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures |
Yuan Y, Seif Y, Rychel K, Yoo R, Chauhan S, Poudel S, Al-Bulushi T, Palsson BO, Sastry AV |
2022 |
| Synthetic 3'-UTR valves for optimal metabolic flux control in Escherichia coli |
Choe D, Kim K, Kang M, Lee SG, Cho S, Palsson B, Cho BK |
2022 |
| Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains |
Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO |
2022 |
| System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus |
Hwang S, Lee N, Choe D, Lee Y, Kim W, Kim JH, Kim G, Kim H, Ahn NH, Lee BH, Palsson BO, Cho BK |
2022 |
| An unexpected role for leucyl aminopeptidase in UV tolerance revealed by a genome-wide fitness assessment in a model cyanobacterium |
Weiss EL, Fang M, Taton A, Szubin R, Palsson BØ, Mitchell BG, Golden SS |
2022 |
| Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity |
Hidalgo D, Martínez-Ortiz CA, Palsson BO, Jiménez JI, Utrilla J. |
2022 |
| Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes |
Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO |
2022 |
| Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power |
Norsigian CJ, Danhof HA, Brand CK, Midani FS, Broddrick JT, Savidge TC, Britton RA, Palsson BO, Spinler JK, Monk JM |
2022 |
| A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli |
Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH Jr, Palsson BO |
2022 |
| Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network |
Lim HG, Rychel K, Sastry AV, Bentley GJ, Mueller J, Schindel HS, Larsen PE, Laible PD, Guss AM, Niu W, Johnson CW, Beckham GT, Feist AM, Palsson BO |
2022 |
| Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets |
Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO. |
2022 |
| Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli |
Yang L, Malla S, Özdemir E, Kim SH, Lennen R, Christensen HB, Christensen U, Munro LJ, Herrgård MJ, Kell DB, Palsson BO |
2022 |
| Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity |
Anand A, Patel A, Chen K, Olson CA, Phaneuf PV, Lamoureux C, Hefner Y, Szubin R, Feist AM, Palsson BO |
2022 |
| Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories |
Fait, A., Seif, Y., Mikkelsen, K., Poudel, S., Wells, J. M., Palsson, B. O., & Ingmer, H. |
2022 |
| Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity |
Hyun JC, Monk JM, Palsson BO |
2022 |
| Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism |
Akbari A, Palsson BO |
2022 |