MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics |
Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO |
2021 |
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data |
Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM |
2021 |
Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications |
Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO |
2021 |
Optimal dimensionality selection for independent component analysis of transcriptomic data |
McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV |
2021 |
Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture |
Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK |
2021 |
Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome. |
Hwang S, Lee N, Choe D, Lee Y, Kim W, Jeong Y, Cho S, Palsson BO, Cho BK |
2021 |
Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters |
Lee N, Choi M, Kim W, Hwang S, Lee Y, Kim JH, Kim G, Kim H, Cho S, Kim SC, Palsson B, Jang KS, Cho BK |
2021 |
The quantitative metabolome is shaped by abiotic constraints |
Akbari A, Yurkovich JT, Zielinski DC, Palsson BO |
2021 |
Streptomyces as Microbial Chassis for Heterologous Protein Expression |
Hwang S, Lee Y, Kim JH, Kim G, Kim H, Kim W, Cho S, Palsson BO, Cho BK |
2021 |
Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus |
Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM |
2021 |
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth |
Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO |
2021 |
Genome-scale metabolic modeling reveals key features of a minimal gene set |
Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. |
2021 |
Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli |
Rodionova IA, Gao Y, Sastry A, Hefner Y, Lim HG, Rodionov DA, Saier MH Jr, Palsson BO
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2021 |
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo |
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2021 |
Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media |
Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Pogliano J, Nizet V, Feist AM, Palsson BO |
2021 |
Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility |
Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B |
2021 |
Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes |
Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK |
2021 |
Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution |
Lim HG, Eng T, Banerjee D, Alarcon G, Lau AK, Park M-R, Simmons BA, Palsson BO, Singer SW, Mukhopadhyay A, Feist AM |
2021 |
Transcriptome and translatome profiles of Streptomyces species in different growth phases. |
Kim W, Hwang S, Lee N, Lee Y, Cho S, Palsson B, Cho BK. |
2020 |
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers |
Heckmann D, Campeau A, Lloyd CJ, et al. |
2020 |
Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis |
Hwang S, Lee N, Cho S, Palsson B, Cho BK
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2020 |
Reconstructing organisms in silico: genome-scale models and their emerging applications |
Fang X, Lloyd CJ, Palsson BO |
2020 |
Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus |
Lee N, Kim W, Chung J, Lee Y, Cho S, Jang KS, Kim SC, Palsson B, Cho BK |
2020 |
Multiplex secretome engineering enhances recombinant protein production and purity |
Kol S, Ley D, Wulff T, et al. |
2020 |
The Bitome: digitized genomic features reveal fundamental genome organization |
Lamoureux CR, Choudhary KS, King ZA, Sandberg TE, Gao Y, Sastry AV, Phaneuf PV, Choe D, Cho BK, Palsson BO. |
2020 |
Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters |
Lee N, Kim W, Hwang S, Lee Y, Cho S, Palsson B, Cho BK |
2020 |
Adaptations of Escherichia Coli Strains to Oxidative Stress Are Reflected in Properties of Their Structural Proteomes |
Mih N, Monk JM, Fang X, et al. |
2020 |
Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution |
Lim, H.G., Fong, B., Alacon, G., Magrudeniya, H.D., Eng, T., Szubin, R., Olson, C.A., Palsson, B.O., Gladden, J.M., Simmons, B.A., Mukhopadhyay, Singer, S.W., Feist, A.M., |
2020 |
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens |
Hyun JC, Kavvas ES, Monk JM, Palsson BO |
2020 |
Microbial Synthesis of Human-Hormone Melatonin at Gram Scales |
Luo H, Schneider K, Christensen U, Lei Y, Herrgard M, Palsson BØ |
2020 |