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
Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ

2020
Redefining fundamental concepts of transcription initiation in bacteria

Mejía-Almonte C, Busby SJW, Wade JT, et al.

2020
Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships

Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO

2020
Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus

Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM

2020
Independent component analysis of E. coli's transcriptome reveals thecellular processes that respond to heterologous gene expression

Tan, J., Sastry, A.V., Fremming, K.S., Bjørn, S.P., Hoffmeyer, A., Seo, S.,Voldborg, Bjø.G., Palsson, B.O.

2020
Scalable computation of intracellular metabolite concentrations

Akbari, A. and Palsson, B.O.

2020
STATR: A simple analysis pipeline of Ribo-Seq in bacteria

Choe D, Palsson B, Cho BK.

2020
Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces

Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho BK

2020
High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

Broddrick Jared T., Szubin Richard, Norsigian Charles J., Monk Jonathan M., Palsson Bernhard O., Parenteau Mary N.

2020
An atlas of human metabolism

Robinson JL, Kocabaş P, Wang H, Cholley PE, Cook D, Nilsson A, Anton M, Ferreira R, Domenzain I, Billa V, Limeta A, Hedin A, Gustafsson J, Kerkhoven EJ,  Svensson LT, Palsson BO, Mardinoglu A, Hansson L, Uhlén M, Nielsen J.

2020
Impact of insertion sequences on convergent evolution of Shigella species

Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE

2020
Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

Rychel, K., Sastry, A.V. & Palsson, B.O.

2020
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. 

2020
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

Phaneuf PV, Yurkovich JT, Heckmann D, et al.

2020
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Zielinski, D.C.; Patel, A.; Palsson, B.O. 

2020
Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis

Minasov G, Lam MR, Rosas Lemus M, Sławek J, Woinska M, Shabalin IG, Shuvalova  L, Palsson BØ, Godzik A, Minor W, Satchell KJF

2020
Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes

Sandberg TE, Szubin R, Phaneuf PV, Palsson BO

2020
DeepTFactor: A deep learning-based tool for the prediction of transcription factors

Kim, G.B., Gao, Y., Palsson, B.O., Lee, S.Y.

2020
Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA

Sales MJ, Sakoulas G, Szubin R, Palsson B, Arias C, Singh KV, Murray BE, Monk JM

2020
System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces

Lee Y, Lee N, Hwang S, et al.

2020
A biochemically-interpretable machine learning classifier for microbial GWAS

Kavvas ES, Yang L, Monk JM, Heckmann D, Palsson BO

2020