Publication Title Authors Publication Year Sort ascending
Recent advances in non-model bacterial chassis construction

Hwang S, Joung C, Kim W, Palsson B, Cho B-K

2023
Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Anand A, Patel A, Chen K, Olson CA, Phaneuf PV, Lamoureux C, Hefner Y, Szubin R, Feist AM, Palsson BO

2022
Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories

Fait, A., Seif, Y., Mikkelsen, K., Poudel, S., Wells, J. M., Palsson, B. O., & Ingmer, H.

2022
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

Hyun JC, Monk JM, Palsson BO

2022
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism

Akbari A, Palsson BO

2022
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO

2022
Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism

Broddrick JT, Ware MA, Jallet D, Palsson BO, Peers G

2022
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information

Lee Y, Lee N, Hwang S, Kim W, Cho S, Palsson BO, Cho BK

2022
Minireview: Engineering evolution to reconfigure phenotypic traits in microbes for biotechnological applications Add to Default shortcuts

Kangsan Kim, Minjeong Kang, Sang-Hyeok Cho, Eojin Yoo, Ui-Gi Kim, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho

2022
Is the kinetome conserved?

Palsson BO, Yurkovich JT

2022
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

van 't Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA

2022
Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection

Yoo R, Rychel K, Poudel S, Al-Bulushi T, Yuan Y, Chauhan S, Lamoureux C, Palsson BO, Sastry A.

2022
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing

Choe D, Kim U, Hwang S, Seo SW, Kim D, Cho S, Palsson B, Cho BK

2022
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO

2022
Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

Yuan Y, Seif Y, Rychel K, Yoo R, Chauhan S, Poudel S, Al-Bulushi T, Palsson BO, Sastry AV

2022
Synthetic 3'-UTR valves for optimal metabolic flux control in Escherichia coli

Choe D, Kim K, Kang M, Lee SG, Cho S, Palsson B, Cho BK

2022
Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains

Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO

2022
System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus

Hwang S, Lee N, Choe D, Lee Y, Kim W, Kim JH, Kim G, Kim H, Ahn NH, Lee BH, Palsson BO, Cho BK

2022
An unexpected role for leucyl aminopeptidase in UV tolerance revealed by a genome-wide fitness assessment in a model cyanobacterium

Weiss EL, Fang M, Taton A, Szubin R, Palsson BØ, Mitchell BG, Golden SS

2022
Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity

Hidalgo D, Martínez-Ortiz CA, Palsson BO, Jiménez JI, Utrilla J.

2022
Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes

Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO

2022
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power

Norsigian CJ, Danhof HA, Brand CK, Midani FS, Broddrick JT, Savidge TC, Britton RA, Palsson BO, Spinler JK, Monk JM

2022
A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH Jr, Palsson BO

2022
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Lim HG, Rychel K, Sastry AV, Bentley GJ, Mueller J, Schindel HS, Larsen PE, Laible PD, Guss AM, Niu W, Johnson CW, Beckham GT, Feist AM, Palsson BO

2022
Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO.

2022
Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli

Yang L, Malla S, Özdemir E, Kim SH, Lennen R, Christensen HB, Christensen U, Munro LJ, Herrgård MJ, Kell DB, Palsson BO

2022
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