Publication Title | Authors | Publication Year Sort ascending |
---|---|---|
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 |
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 |
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 |
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes | Hirose Y, Zielinski DC, Poudel S, Rychel K, Baker JL, Toya Y, Yamaguchi M, Heinken A, Thiele I, Kawabata S, Palsson BO, Nizet V. |
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 |
Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298 | Champie A, Lachance J-C, Sastry A, Matteau D, Lloyd CJ, Grenier F, Lamoureux CR, Jeanneau S, Feist AM, Jacques P-É, Palsson BO, Rodrigue S. |
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 |
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. | Sastry AV, Yuan Y, Poudel S, Rychel K, Yoo R, Lamoureux CR, Li G, Burrows JT, Chauhan S, Haiman ZB, Al Bulushi T, Seif Y, Palsson BO, Zielinski DC. |
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 |
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets | Catoiu EA, Krishnan J, Li G, Lou XA, Rychel K, Yuan Y, Bajpe H, Patel A, Choe D, Shin J, Burrows J, Phaneuf PV, Zielinski DC, Palsson BO. |
2024 |
Escherichia coli non-coding regulatory regions are highly conserved | Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC. |
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 |
Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering | Shin J, 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 |
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 |
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 |
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 |
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 |
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 |