| 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
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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
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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
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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.
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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.
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2023 |
| The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets |
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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.
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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
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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 |
| 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 |