| 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 |
| 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 |
| 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 |
| 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 |
| Empowering drug off-target discovery with metabolic and structural analysis |
Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI |
2023 |
| Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC |
Gao Y, Poudel S, Seif Y, Shen Z, Palsson BO |
2023 |
| 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 |