| 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 |
| 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 |
| Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits |
Ardalani O, Phaneuf PV, Mohite OS, Nielsen LK, Palsson BO.
|
2024 |
| Inferred regulons are consistent with regulator binding sequences in E. coli. |
Qiu S, Wan X, Liang Y, Lamoureux CR, Akbari A, Palsson BO, Zielinski DC.
|
2024 |
| Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes. |
Nemkov T, Stephenson D, Earley EJ, Keele GR, Hay A, Key A, Haiman ZB, Erickson C, Dzieciatkowska M, Reisz JA, Moore A, Stone M, Deng X, Kleinman S, Spitalnik SL, Hod EA, Hudson KE, Hansen KC, Palsson BO, Churchill GA, Roubinian N, Norris PJ, Busch MP, Zimring JC, Page GP, D'Alessandro A.
|
2024 |
| Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440 |
Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT
|
2024 |
| Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing |
Phaneuf PV, Kim SH, Rychel K, Rode C, Beulig F, Palsson BO, Yang L
|
2024 |
| Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning |
Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO.
|
2024 |
| Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules |
Shin J, Zielinski DC, Palsson BO
|
2024 |
| Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses |
Zhao J, Chen K, Palsson BO, Yang L.
|
2024 |
| Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters |
Lee Y, Choe D, Palsson BO, Cho BK.
|
2024 |
| Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment |
Choe D, Olson CA, Szubin R, Yang H, Sung J, Feist AM, Palsson BO
|
2024 |
| Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatusPCC 7942 |
Yuan Y, Al Bulushi T, Sastry AV, Sancar C, Szubin R, Golden SS, Palsson BO.
|
2024 |
| Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology |
Kim K, Choe D, Cho S, Palsson B, Cho BK.
|
2024 |
| Genome-scale models in human metabologenomics |
Mardinoglu A, Palsson BØ
|
2024 |
| Serial adaptive laboratory evolution enhances mixed carbon metabolic capacity of Escherichia coli |
Kim K, Choe D, Kang M, Cho SH, Cho S, Jeong KJ, Palsson B, Cho BK
|
2024 |
| CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli |
Rodionova IA, Lim HG, Gao Y, Rodionov DA, Hutchison Y, Szubin R, Dalldorf C, Monk J, Palsson BO
|
2024 |