| 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 |
| Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli |
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2021 |
| Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo |
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2021 |
| Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media |
Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Pogliano J, Nizet V, Feist AM, Palsson BO |
2021 |
| Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility |
Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B |
2021 |
| Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes |
Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK |
2021 |
| Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution |
Lim HG, Eng T, Banerjee D, Alarcon G, Lau AK, Park M-R, Simmons BA, Palsson BO, Singer SW, Mukhopadhyay A, Feist AM |
2021 |
| Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types |
Chen K, Anand A, Olson C, Sandberg TE, Gao Y, Mih N, Palsson BO |
2021 |
| Path to improving the life cycle and quality of genome-scale models of metabolism |
Seif Y, Palsson BØ |
2021 |
| Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens |
Rajput A, Seif Y, Choudhary KS, Dalldorf C, Poudel S, Monk JM, Palsson BO. |
2021 |
| RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics |
Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK |
2021 |
| Independent component analysis recovers consistent regulatory signals from disparate datasets |
Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO |
2021 |
| Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius |
Chauhan SM, Poudel S, Rychel K, Lamoureux C, Yoo R, Al Bulushi T, Yuan Y, Palsson BO, Sastry AV. |
2021 |
| Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus |
Wilken SE, Monk JM, Leggieri PA, Lawson CE, Lankiewicz TS, Seppälä S, Daum CG, Jenkins J, Lipzen AM, Mondo SJ, Barry KW, Grigoriev IV, Henske JK, Theodorou MK, Palsson BO, Petzold LR, O'Malley MA. |
2021 |
| proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms |
Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO |
2021 |
| MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics |
Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO |
2021 |
| Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data |
Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM |
2021 |
| Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications |
Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO |
2021 |
| Optimal dimensionality selection for independent component analysis of transcriptomic data |
McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV |
2021 |
| Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture |
Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK |
2021 |
| Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome. |
Hwang S, Lee N, Choe D, Lee Y, Kim W, Jeong Y, Cho S, Palsson BO, Cho BK |
2021 |