| A multi-scale expression and regulation knowledge base for Escherichia coli |
Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO
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2023 |
| 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 |
| Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa |
Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO |
2022 |
| Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism |
Broddrick JT, Ware MA, Jallet D, Palsson BO, Peers G |
2022 |
| Minireview: Engineering evolution to reconfigure phenotypic traits in microbes for biotechnological applications Add to Default shortcuts |
Kangsan Kim, Minjeong Kang, Sang-Hyeok Cho, Eojin Yoo, Ui-Gi Kim, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho |
2022 |
| Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information |
Lee Y, Lee N, Hwang S, Kim W, Cho S, Palsson BO, Cho BK |
2022 |
| High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917 |
van 't Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA |
2022 |
| Is the kinetome conserved? |
Palsson BO, Yurkovich JT |
2022 |
| Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing |
Choe D, Kim U, Hwang S, Seo SW, Kim D, Cho S, Palsson B, Cho BK |
2022 |
| Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection |
Yoo R, Rychel K, Poudel S, Al-Bulushi T, Yuan Y, Chauhan S, Lamoureux C, Palsson BO, Sastry A. |
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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |