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