| 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.
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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.
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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
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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 |
| 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 |