| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| BOFdata: Generating biomass objective functions for genome-scale metabolic models from experimental data | Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, |
2019 |
| High-quality genome-scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities | Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO |
2019 |
| 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 |