Publication Title | Authors | Publication Year Sort ascending |
---|---|---|
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 |
Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology | Kim K, Choe D, Cho S, Palsson B, Cho BK. |
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 |
Grand Challenges at the Interface of Engineering and Medicine | Subramaniam S, Akay M, Anastasio MA, Bailey V, Boas D, Bonato P, Chilkoti A, Cochran JR, Colvin V, Desai TA, Duncan JS, Epstein FH, Fraley S, Giachelli C, Grande-Allen KJ, Green J, Guo XE, Hilton IB, Humphrey JD, Johnson CR, Karniadakis G, King MR, Kirsch RF, Kumar S, Laurencin CT, Li S, Lieber RL, Lovell N, Mali P, Margulies SS, Meaney DF, Ogle B, Palsson B, A Peppas N, Perreault EJ, Rabbitt R, Setton LA, Shea LD, Shroff SG, Shung K, Tolias AS, van der Meulen MCH, Varghese S, Vunjak-Novakovic G, White JA, Winslow R, Zhang J, Zhang K, Zukoski C, Miller MI. |
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 |
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 data-driven approach for timescale decomposition of biochemical reaction networks | Akbari A, Haiman ZB, 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 |
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 |
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 |
Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses | Zhao J, Chen K, Palsson BO, Yang L. |
2024 |
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 |
Revealing oxidative pentose metabolism in new Pseudomonas putida isolates | Park, M. R., Gauttam, R., Fong, B., Chen, Y., Lim, H. G., Feist, A. M., Mukhopadhyay, A., Petzold, C. J., Simmons, B. A., & Singer, S. W. |
2023 |
Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance | Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO. |
2023 |
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century | Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C |
2023 |
Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways | Mattei, G., Gan, Z., Ramazzotti, M., Palsson, B.O., Zielinski, D.C. |
2023 |
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks | Catoiu EA, Phaneuf P, Monk J, Palsson BO |
2023 |
Modeling Red Blood Cell Metabolism in the Omics Era | Key A, Haiman Z, Palsson BO, D’Alessandro A. |
2023 |
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets | 2023 | |
Functional annotation of enzyme-encoding genes using deep learning with transformer layers | Kim GB, Kim JY, Lee JA, Norsigian CJ, Palsson BO, Lee SY |
2023 |
Metabolic homeostasis and growth in abiotic cells | Akbari A, Palsson BO |
2023 |
High-resolution temporal profiling of E. coli transcriptional response | Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J. |
2023 |
Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome | Shin J, Rychel K, Palsson BO. |
2023 |
Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species | Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO |
2023 |
E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding | Rodionova IA, Hosseinnia A, Kim S, Goodacre N, Zhang L, Zhang Z, Palsson B, Uetz P, Babu M, Saier MH Jr. |
2023 |