| Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species |
Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO
|
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 |
| Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins |
Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V |
2023 |
| Empowering drug off-target discovery with metabolic and structural analysis |
Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI |
2023 |
| Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC |
Gao Y, Poudel S, Seif Y, Shen Z, Palsson BO |
2023 |
| Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family |
Akanksha Rajput, Siddharth M. Chauhan, Omkar S. Mohite, Jason C. Hyun, Omid Ardalani, Leonie J. Jahn, Morten OA. Sommer, Bernhard O. Palsson
|
2023 |
| Adaptive Evolution of a Minimal Organism with a Synthetic Genome |
Sandberg, T.E., Wise, K.S., Dalldorf, C., Szubin, R., Feist, A.M., Glass, J.I., Palsson, B.O.
|
2023 |
| Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess |
Kumaraswamy M, Coady A, Szubin R, Martin TCS, Palsson B, Nizet V, Monk JM |
2023 |
| Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome |
Hyun, J.C., Palsson, B.O.
|
2023 |
| Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli |
Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW, Palsson BO, Kim D |
2023 |
| Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection |
Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO
|
2023 |
| Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling |
Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D |
2023 |
| Recent advances in non-model bacterial chassis construction |
Hwang S, Joung C, Kim W, Palsson B, Cho B-K
|
2023 |
| 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 |
| 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 |
| 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 |
| 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 |
| Is the kinetome conserved? |
Palsson BO, Yurkovich JT |
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 |
| 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 |
| 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 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 |