| 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 |
| Microbial production of creatine using growth-coupled selection systems |
Li J, Krarup SR, Pieters P, Alter TB, Jacottin P, Johnsen J, Mohamed ET, Harris T, Ahonen L, Adhikari KB, Palsson BO, Feist AM, Yang L.
|
2025 |
| Longitudinal big biological data in the AI era |
Mardinoglu A, Turkez H, Shong M, Srinivasulu VP, Nielsen J, Palsson BO, Hood L, Uhlen M.
|
2025 |
| Reframing the role of the objective function in its proper context for metabolic network modeling |
Islam MM, Shao W, Batavia M, Ford RM, Palsson BO, Nielsen J, Maranas CD, Lee SY, Papin JA.
|
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 |
| Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli |
Rychel K, Chen K, Catoiu EA, Olson E, Sandberg TE, Gao Y, Xu S, Hefner Y, Szubin R, Patel A, Feist AM, 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 |
| QSProteome: a community-driven interactive platform for large-scale exploration and evaluation of predicted protein complex structures |
Catoiu EA, Kambo D, Rodriguez B, Vear K, Wang Z, Akpata J, Shah J, Ayoub R, Hofmann M, Ananda K, Tantry A, Gupta I, Anwyl R, Faucher C, Nichols J, Ton B, Marchal LO, Palsson BO
|
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 |
| Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning |
Kim K, Choe D, Kim SC, Yim SS, Jeong KJ, Palsson B, Cho S, Cho BK.
|
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 |
| PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data |
Krishnan KJ, Hefner Y, Szubin R, Monk J, Pride DT, Palsson B.
|
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 |
| 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 |
| 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 |