| Escherichia coli non-coding regulatory regions are highly conserved |
Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC.
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2024 |
| Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering |
Shin J, Zielinski DC, Palsson BO.
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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.
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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.
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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.
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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.
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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.
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2024 |
| A data-driven approach for timescale decomposition of biochemical reaction networks |
Akbari A, Haiman ZB, Palsson BO
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2024 |
| Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits |
Ardalani O, Phaneuf PV, Mohite OS, Nielsen LK, Palsson BO.
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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.
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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.
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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
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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
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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.
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2024 |
| Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules |
Shin J, Zielinski DC, Palsson BO
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2024 |
| Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses |
Zhao J, Chen K, Palsson BO, Yang L.
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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
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2024 |
| Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology |
Kim K, Choe D, Cho S, Palsson B, Cho BK.
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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
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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.
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2024 |
| Bottom-up parameterization of enzyme rate constants: Reconciling inconsistent data |
Daniel C. Zielinski, Marta R.A. Matos, James E. de Bree, Kevin Glass, Nikolaus Sonnenschein, Bernhard O. Palsson
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2024 |
| BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets |
Nuhamunada M, Mohite OS, Phaneuf PV, Palsson BO, Weber T.
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2024 |
| 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
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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.
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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
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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 |
| Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins |
Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V |
2023 |