| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis | Hwang S, Lee N, Cho S, Palsson B, Cho BK |
2020 |
| Reconstructing organisms in silico: genome-scale models and their emerging applications | Fang X, Lloyd CJ, Palsson BO |
2020 |
| Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus | Lee N, Kim W, Chung J, Lee Y, Cho S, Jang KS, Kim SC, Palsson B, Cho BK |
2020 |
| Multiplex secretome engineering enhances recombinant protein production and purity | Kol S, Ley D, Wulff T, et al. |
2020 |
| The Bitome: digitized genomic features reveal fundamental genome organization | Lamoureux CR, Choudhary KS, King ZA, Sandberg TE, Gao Y, Sastry AV, Phaneuf PV, Choe D, Cho BK, Palsson BO. |
2020 |
| Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters | Lee N, Kim W, Hwang S, Lee Y, Cho S, Palsson B, Cho BK |
2020 |
| Adaptations of Escherichia Coli Strains to Oxidative Stress Are Reflected in Properties of Their Structural Proteomes | Mih N, Monk JM, Fang X, et al. |
2020 |
| Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution | Lim, H.G., Fong, B., Alacon, G., Magrudeniya, H.D., Eng, T., Szubin, R., Olson, C.A., Palsson, B.O., Gladden, J.M., Simmons, B.A., Mukhopadhyay, Singer, S.W., Feist, A.M., |
2020 |
| Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens | Hyun JC, Kavvas ES, Monk JM, Palsson BO |
2020 |
| Microbial Synthesis of Human-Hormone Melatonin at Gram Scales | Luo H, Schneider K, Christensen U, Lei Y, Herrgard M, Palsson BØ |
2020 |
| Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity | Fang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, Sanders JG, Panitchpakdi M, Carpenter C, Jarmusch AK, Neill J, Miralles A, Dulai P, Singh S, Tsai M, Swafford AD, Smarr L, Boyle DL, Palsson BO, Chang JT, Dorrestein PC, Sandborn WJ, Knight R, Boland BS. |
2020 |
| Metabolic and genetic basis for auxotrophies in Gram-negative species | Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO |
2020 |
| Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains | Kim W, Lee N, Hwang S, et al. |
2020 |
| Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi | Shiratsubaki IS, Fang X, Souza ROO, Palsson BO, Silber AM, Siqueira-Neto JL. |
2020 |
| MEMOTE for standardized genome-scale metabolic model testing | Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. |
2020 |
| Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response | Poudel S, Tsunemoto H, Seif Y, et al. |
2020 |
| Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence | Norsigian, C.J., Danhof, H.A., Brand, C.K. et al. |
2020 |
| Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion | Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE |
2020 |
| Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models | Dahal S, Yurkovich JT, Xu H, Palsson BO |
2020 |
| iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning | Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO |
2020 |
| Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli | Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ |
2020 |
| Redefining fundamental concepts of transcription initiation in bacteria | Mejía-Almonte C, Busby SJW, Wade JT, et al. |
2020 |
| Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships | Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO |
2020 |
| Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus | Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM |
2020 |
| Independent component analysis of E. coli's transcriptome reveals thecellular processes that respond to heterologous gene expression | Tan, J., Sastry, A.V., Fremming, K.S., Bjørn, S.P., Hoffmeyer, A., Seo, S.,Voldborg, Bjø.G., Palsson, B.O. |
2020 |
| Scalable computation of intracellular metabolite concentrations | Akbari, A. and Palsson, B.O. |
2020 |
| STATR: A simple analysis pipeline of Ribo-Seq in bacteria | Choe D, Palsson B, Cho BK. |
2020 |
| Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces | Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho BK |
2020 |
| High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies | Broddrick Jared T., Szubin Richard, Norsigian Charles J., Monk Jonathan M., Palsson Bernhard O., Parenteau Mary N. |
2020 |
| An atlas of human metabolism | Robinson JL, Kocabaş P, Wang H, Cholley PE, Cook D, Nilsson A, Anton M, Ferreira R, Domenzain I, Billa V, Limeta A, Hedin A, Gustafsson J, Kerkhoven EJ, Svensson LT, Palsson BO, Mardinoglu A, Hansson L, Uhlén M, Nielsen J. |
2020 |