| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits |
Ardalani O, Phaneuf PV, Mohite OS, Nielsen LK, Palsson BO.
|
2024 |
| A data-driven approach for timescale decomposition of biochemical reaction networks |
Akbari A, Haiman ZB, Palsson BO
|
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 |
| 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 |
| 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 |
| 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 |
| Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules |
Shin J, Zielinski DC, Palsson BO
|
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 |
| 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 |
| Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses |
Zhao J, Chen K, Palsson BO, Yang L.
|
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 |
| 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 |
| Genome-scale models in human metabologenomics |
Mardinoglu A, Palsson BØ
|
2024 |
| Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology |
Kim K, Choe D, Cho S, 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 |