| Trade-off between resistance and persistence in high cell density cultures |
Beulig F, Bafna-Rührer J, Jensen PE, Kim SH, Patel A, Kandasamy V, Steffen C, Decker K, Zielinski D, Yang L, Özdemir E, Sudarsan S, Palsson B.
|
2025 |
| Regulatory orchestration of FK506 biosynthesis in Streptomyces tsukubaensisNRRL 18488 revealed through systematic analysis |
Lee N, Kim W, Kim JH, Lee Y, Hwang S, Kim G, Kim H, Dan Q, Schmidt M, Yoon YJ, Cho S, Palsson B, Keasling JD, Cho BK.
|
2025 |
| CRISPRi screening reveals E. coli's anaerobic-like respiratory adaptations to gentamicin: membrane depolarization by CpxR |
Choe D, Lee E, Song Y, Kim SC, Jeong KJ, Palsson B, Cho B-K, Cho S.
|
2025 |
| Evolution-guided tolerance engineering of Pseudomonas putida KT2440 for production of the aviation fuel precursor isoprenol |
Lim HG, Srinivasan A, Menchavez R, Yunus IS, Noh MH, White M, Chen Y, Gin JW, Palsson BO, Lee TS, Petzold CJ, Eng T, Mukhopadhyay A, Feist AM
|
2025 |
| Pangenome mining of the Streptomyces genus redefines species' biosynthetic potential |
Mohite OS, Jørgensen TS, Booth TJ, Charusanti P, Phaneuf PV, Weber T, Palsson BO
|
2025 |
| Metabolic growth-coupling strategies for in vivo enzyme selection systems |
Alter TB, Pieters PA, Lloyd CJ, Feist AM, Özdemir E, Palsson BO, Zielinski DC
|
2025 |
| Machine learning uncovers the transcriptional regulatory network for the production host Streptomyces albidoflavus |
Jönsson M, Sigrist R, Gren T, Semenov Petrov M, Marcussen NEJ, Svetlova A, Charusanti P, Gockel P, Palsson BO, Yang L, Özdemir E.
|
2025 |
| RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell |
Haiman ZB, Key A, D'Alessandro A, Palsson BO.
|
2025 |
| Extracellular respiration is a latent energy metabolism in Escherichia coli. |
Kundu BB, Krishnan J, Szubin R, Patel A, Palsson BO, Zielinski DC, Ajo-Franklin CM.
|
2025 |
| Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction |
Poudel S, Hyun J, Hefner Y, Monk J, Nizet V, Palsson BO.
|
2025 |
| A live bacteria enzyme assay for identification of human disease mutations and drug screening |
Choe D, Palsson BO.
|
2025 |
| Rapid identification of key antibiotic resistance genes in E. coli using high-resolution genome-scale CRISPRi screening |
Donghui Choe, Eunju Lee, Kangsan Kim, Soonkyu Hwang, Ki Jun Jeong, Bernhard O. Palsson, Byung-Kwan Cho, and Suhyung Cho
|
2025 |
| Multi-scale reactor designs extend the physical limits of CO2 fixation |
Amir Akbari, Bernhard O. Palsson
|
2025 |
| Bottom-up parameterization of enzyme rate constants: Reconciling inconsistent data |
Daniel C. Zielinski, Marta R.A. Matos, James E. de Bree, Kevin Glass, Nikolaus Sonnenschein, Bernhard O. Palsson
|
2024 |
| Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298 |
Champie A, Lachance J-C, Sastry A, Matteau D, Lloyd CJ, Grenier F, Lamoureux CR, Jeanneau S, Feist AM, Jacques P-É, Palsson BO, Rodrigue S.
|
2024 |
| BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets |
Nuhamunada M, Mohite OS, Phaneuf PV, Palsson BO, Weber T.
|
2024 |
| iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. |
Sastry AV, Yuan Y, Poudel S, Rychel K, Yoo R, Lamoureux CR, Li G, Burrows JT, Chauhan S, Haiman ZB, Al Bulushi T, Seif Y, Palsson BO, Zielinski DC.
|
2024 |
| Escherichia coli non-coding regulatory regions are highly conserved |
Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC.
|
2024 |
| iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets |
Catoiu EA, Krishnan J, Li G, Lou XA, Rychel K, Yuan Y, Bajpe H, Patel A, Choe D, Shin J, Burrows J, Phaneuf PV, Zielinski DC, Palsson BO.
|
2024 |
| Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering |
Shin J, Zielinski DC, Palsson BO.
|
2024 |
| Diversity of transcriptional regulatory adaptation in E. coli |
Dalldorf C, Hefner Y, Szubin R, Johnsen J, Mohamed E, Li G, Krishnan J, Feist AM, Palsson BO, Zielinski DC
|
2024 |
| The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions |
Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO.
|
2024 |
| PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining |
Sun B, Pashkova L, Pieters PA, Harke AS, Mohite OS, Santos A, Zielinski DC, Palsson BO, Phaneuf PV
|
2024 |
| Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution |
Lee, S.M., Le, H.T., Taizhanova, A., Nong, L.K., Park, J.Y., Lee, E.J., Palsson, B.O., Kim, D.
|
2024 |
| Proteome allocation is linked to transcriptional regulation through a modularized transcriptome |
Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO.
|
2024 |
| Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase. |
Lim HG, Gao Y, Rychel K, Lamoureux C, Lou XA, Palsson BO.
|
2024 |
| Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. |
Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V.
|
2024 |
| A treasure trove of 1034 actinomycete genomes |
Jørgensen TS, Mohite OS, Sterndorff EB, Alvarez-Arevalo M, Blin K, Booth TJ, Charusanti P, Faurdal D, Hansen TØ, Nuhamunada M, Mourched AS, Palsson BØ, Weber T.
|
2024 |
| Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species |
Chauhan SM, Ardalani O, Hyun JC, Monk JM, Phaneuf PV, Palsson BO.
|
2024 |
| A data-driven approach for timescale decomposition of biochemical reaction networks |
Akbari A, Haiman ZB, Palsson BO
|
2024 |