Publication Title Authors Publication Year Sort ascending
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,
Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, Chen K,
Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO.

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
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO

2019
Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution

Kang M, Kim K, Choe D, Cho S, Kim SC, Palsson B, Cho BK

2019
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO

2019
Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U,
Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ,
Palsson BO

2019
The Transcription Unit Architecture of Streptomyces lividans TK24

Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK

2019
Enzyme promiscuity shapes adaptation to novel growth substrates

Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA,
Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM

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, 
Dupont CL, Mitchell BG, Palsson BO, Allen AE

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
Identification of growth-coupled production strains considering protein costs and kinetic variability

H.V. Dinh; Z.A. King; B.O. Palsson; A.M. Feist

2018