Publication Title | Authors | Publication Year Sort ascending |
---|---|---|
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 |
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 |
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 |
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. |
2024 |
Escherichia coli non-coding regulatory regions are highly conserved | Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC. |
2024 |
Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering | Shin J, Zielinski DC, Palsson BO. |
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 |
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 |
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 |
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 |
Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family | Akanksha Rajput, Siddharth M. Chauhan, Omkar S. Mohite, Jason C. Hyun, Omid Ardalani, Leonie J. Jahn, Morten OA. Sommer, Bernhard O. Palsson |
2023 |
Adaptive Evolution of a Minimal Organism with a Synthetic Genome | Sandberg, T.E., Wise, K.S., Dalldorf, C., Szubin, R., Feist, A.M., Glass, J.I., Palsson, B.O. |
2023 |
Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess | Kumaraswamy M, Coady A, Szubin R, Martin TCS, Palsson B, Nizet V, Monk JM |
2023 |
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome | Hyun, J.C., Palsson, B.O. |
2023 |
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 |