| 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 |
| 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 |
| Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters |
Lee N, Choi M, Kim W, Hwang S, Lee Y, Kim JH, Kim G, Kim H, Cho S, Kim SC, Palsson B, Jang KS, Cho BK |
2021 |
| The quantitative metabolome is shaped by abiotic constraints |
Akbari A, Yurkovich JT, Zielinski DC, Palsson BO |
2021 |
| Streptomyces as Microbial Chassis for Heterologous Protein Expression |
Hwang S, Lee Y, Kim JH, Kim G, Kim H, Kim W, Cho S, Palsson BO, Cho BK |
2021 |
| Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus |
Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM |
2021 |
| Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth |
Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO |
2021 |
| Genome-scale metabolic modeling reveals key features of a minimal gene set |
Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. |
2021 |
| 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 |