| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| 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 |
| 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 |