| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| Enzyme promiscuity shapes adaptation to novel growth substrates | Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, |
2019 |
| The genetic basis for adaptation of model-designed syntrophic co-cultures | Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM |
2019 |
| Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum | Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, |
2019 |
| Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom | Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE |
2019 |
| Adaptive laboratory evolution of a genome-reduced Escherichia coli | D. Choe; J.Hyoung Lee; M. Yoo; S. Hwang; B.Hyun Sung; S. Cho; B. Palsson; S.Chang Kim; B.K. Cho |
2019 |
| A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action | Yang, J.H., Wright, S.N., Hamblin, M., McCloskey, D., Alcantar, M.A., Schrubbers, L., Lopatkin, A.J., Satish, S., Nili, A., Palsson, B.O., Walker, G.C., Collins, J.J |
2019 |
| Adaptive laboratory evolution of Escherichia coli under acid stress | Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Hefner Y, Feist AM, Palsson BO |
2019 |
| Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. | L. Heirendt; S. Arreckx; T. Pfau; S.N. Mendoza; A. Richelle; A. Heinken; H.S. Haraldsdóttir; J. Wachowiak; S.M. Keating; V. Vlasov; S. Magnusdóttir; C.Yu Ng; G. Preciat; A. Žagare; S.H.J. Chan; M.K. Aurich; C.M. Clancy; J. Modamio; J.T. Sauls; A. Noronha; A. Bordbar; B. Cousins; D.C.El Assal; L.V. Valcarcel; I. Apaolaza; S. Ghaderi; M. Ahookhosh; M. Ben Guebila; A. Kostromins; N. Sompairac; H.M. Le; D. Ma; Y. Sun; L. Wang; J.T. Yurkovich; M.A.P. Oliveira; P.T. Vuong; L.P.El Assal; I. Kuperstein; A. Zinovyev; S. Hinton; W.A. Bryant; F.J.Aragón Artacho; F.J. Planes; E. Stalidzans; A. Maass; S. Vempala; M. Hucka; M.A. Saunders; C.D. Maranas; N.E. Lewis; T. Sauter; B.Ø. Palsson; I. Thiele; R.M.T. Fleming |
2019 |
| Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media | Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon |
2019 |
| OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states | Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO |
2019 |
| 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 |
| Escher-FBA: a web application for interactive flux balance analysis | E. Rowe; B.O. Palsson; Z.A. King |
2018 |
| High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli. | S. Cho; D. Choe; E. Lee; S.Chang Kim; B. Palsson; B.K. Cho |
2018 |
| Basics of genome-scale metabolic modeling and applications on C1-utilization. | I. Kabimoldayev; A.Duc Nguyen; L. Yang; S. Park; E.Yeol Lee; D. Kim |
2018 |
| iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE | C.J. Norsigian; E. Kavvas; Y. Seif; B.O. Palsson; J.M. Monk |
2018 |
| Reframing gene essentiality in terms of adaptive flexibility. | G.I. Guzman; C.A. Olson; Y. Hefner; P.V. Phaneuf; E. Catoiu; L.B. Crepaldi; L.Goldschmid Micas; B.O. Palsson; A.M. Feist |
2018 |
| Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. | Y. Seif; E. Kavvas; J.C. Lachance; J.T. Yurkovich; S.P. Nuccio; X. Fang; E. Catoiu; M. Raffatellu; B.O. Palsson; J.M. Monk |
2018 |
| Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. | T. Strucko; K. Zirngibl; F. Pereira; E. Kafkia; E.T. Mohamed; M. Rettel; F. Stein; A.M. Feist; P. Jouhten; K.Raosaheb Patil; J. Forster |
2018 |
| ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. | P.V. Phaneuf; D. Gosting; B.O. Palsson; A.M. Feist |
2018 |
| Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. | D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Systems biology as an emerging paradigm in transfusion medicine. | J.T. Yurkovich; A. Bordbar; O.E. Sigurjónsson; B.O. Palsson |
2018 |
| Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates | D. Heckmann; D.C. Zielinski; B.O. Palsson |
2018 |
| Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions. | D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. | E.S. Kavvas; Y. Seif; J.T. Yurkovich; C. Norsigian; S. Poudel; W.W. Greenwald; S. Ghatak; B.O. Palsson; J.M. Monk |
2018 |