Publication Title | Authors | Publication Year Sort ascending |
---|---|---|
Machine learning uncovers the transcriptional regulatory network for the production host Streptomyces albidoflavus | Jönsson M, Sigrist R, Gren T, Semenov Petrov M, Marcussen NEJ, Svetlova A, Charusanti P, Gockel P, Palsson BO, Yang L, Özdemir E. |
2025 |
RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell | Haiman ZB, Key A, D'Alessandro A, Palsson BO. |
2025 |
Extracellular respiration is a latent energy metabolism in Escherichia coli. | Kundu BB, Krishnan J, Szubin R, Patel A, Palsson BO, Zielinski DC, Ajo-Franklin CM. |
2025 |
Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction | Poudel S, Hyun J, Hefner Y, Monk J, Nizet V, Palsson BO. |
2025 |
A live bacteria enzyme assay for identification of human disease mutations and drug screening | Choe D, Palsson BO. |
2025 |
Rapid identification of key antibiotic resistance genes in E. coli using high-resolution genome-scale CRISPRi screening | Donghui Choe, Eunju Lee, Kangsan Kim, Soonkyu Hwang, Ki Jun Jeong, Bernhard O. Palsson, Byung-Kwan Cho, and Suhyung Cho |
2025 |
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 |
Metabolic growth-coupling strategies for in vivo enzyme selection systems | Alter TB, Pieters PA, Lloyd CJ, Feist AM, Özdemir E, Palsson BO, Zielinski DC |
2025 |
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 |
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 |
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 |
Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules | Shin J, Zielinski DC, Palsson BO |
2024 |
Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses | Zhao J, Chen K, Palsson BO, Yang L. |
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 |
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 |
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 |
Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology | Kim K, Choe D, Cho S, Palsson B, Cho BK. |
2024 |
Genome-scale models in human metabologenomics | Mardinoglu A, Palsson BØ |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Escherichia coli non-coding regulatory regions are highly conserved | Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC. |
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 |
Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering | Shin J, Zielinski DC, Palsson BO. |
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 |