Publication Title Authors Publication Year Sort ascending
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets 2023
Metabolic homeostasis and growth in abiotic cells

Akbari A, Palsson BO

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
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
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

Hyun, J.C., Palsson, B.O.

2023
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW, Palsson BO, Kim D

2023
Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection

Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO

2023
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling

Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D

2023
Recent advances in non-model bacterial chassis construction

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

2023
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals

Lennen RM, Lim HG, Jensen K, Mohammed ET, Phaneuf PV, Noh MH, Malla S, Börner RA, Chekina K, Özdemir E, Bonde I, Koza A, Maury J, Pedersen LE, Schöning LY, Sonnenschein N, Palsson BO, Nielsen AT, Sommer MOA, Herrgård MJ, Feist AM

2023
A multi-scale expression and regulation knowledge base for Escherichia coli

Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO

2023
Revealing oxidative pentose metabolism in new Pseudomonas putida isolates

Park, M. R., Gauttam, R., Fong, B., Chen, Y., Lim, H. G., Feist, A. M., Mukhopadhyay, A., Petzold, C. J., Simmons, B. A., & Singer, S. W.

2023
Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO.

2023
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C

2023
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
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