Publication Title Authors Publication Year Sort ascending
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

2021
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo 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
 

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