Publication Title Authors Publication Year Sort ascending
Genome-scale models in human metabologenomics

Mardinoglu A, Palsson BØ

2024
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
Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways

Mattei, G., Gan, Z., Ramazzotti, M., Palsson, B.O., Zielinski, D.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
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
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 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