| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome | Hwang S, Lee N, Jeong Y, Lee Y, Kim W, Cho S, Palsson BO, Cho BK |
2019 |
| Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration | Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO |
2019 |
| The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function | S. Ghatak; Z.A. King; A. Sastry; B.O. Palsson |
2019 |
| Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism | Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA |
2019 |
| Expanding the uses of genome‐scale models with protein structures | Mih N and Palsson BO |
2019 |
| Pseudogene repair driven by selection pressure applied in experimental evolution. | A. Anand; C.A. Olson; L. Yang; A.V. Sastry; E. Catoiu; K.Sonal Choudhary; P.V. Phaneuf; T.E. Sandberg; S. Xu; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2019 |
| Synthetic Biology Tools for Novel Secondary Metabolite Discovery in Streptomyces | Lee N, Hwang S, Lee Y, Cho S, Palsson B, Cho BK |
2019 |
| The Escherichia coli transcriptome mostly consists of independently regulated modules | Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO |
2019 |
| A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. | Y. Seif; J.M. Monk; N. Mih; H. Tsunemoto; S. Poudel; C. Zuniga; J. Broddrick; K. Zengler; B.O. Palsson |
2019 |
| Cellular responses to reactive oxygen species are predicted from molecular mechanisms | Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, |
2019 |
| Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli | Du B, Yang L, Lloyd CJ, Fang X, Palsson BO |
2019 |
| Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in Trauma: A New Research Paradigm | Henriksen HH, McGarrity S, SigurÐardóttir RS, Nemkov T, D'Alessandro A, Palsson BO, Stensballe J, Wade CE, Rolfsson Ó, Johansson PI |
2019 |
| BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree | Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z |
2019 |
| Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates | Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM |
2019 |
| Minimal cells, maximal knowledge | Lachance JC, Rodrigue S, Palsson BO |
2019 |
| The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology | Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM |
2019 |
| Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment | Rosas-Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF |
2019 |
| Systems Biology and Pangenome of Salmonella O-Antigens | Seif Y, Monk JM, Machado H, Palsson BO. |
2019 |
| Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media | Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J. |
2019 |
| A defined minimal medium for systems analyses of Staphylococcus aureus reveals strain-specific metabolic requirements | Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. |
2019 |
| Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection | Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB |
2019 |