Publication Title Authors Publication Year Sort ascending
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

Catoiu EA, Phaneuf P, Monk J, Palsson BO

2023
Modeling Red Blood Cell Metabolism in the Omics Era

Key A, Haiman Z, Palsson BO, D’Alessandro A.

2023
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
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
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