| 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 reveals general and specific tolerance mechanisms for commodity chemicals |
Lennen RM, Lim HG, Jensen K, Mohammed ET, Phaneuf PV, Noh MH, Malla S, Börner RA, Chekina K, Özdemir E, Bonde I, Koza A, Maury J, Pedersen LE, Schöning LY, Sonnenschein N, Palsson BO, Nielsen AT, Sommer MOA, Herrgård MJ, Feist AM |
2023 |
| 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
|
2023 |
| 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 |
| 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 |