Publication Title Authors Publication Year
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
SBML Level 3: an extensible format for the exchange and reuse of biological models

Keating SM, Waltemath D, König M, et al.

 2020
Transcriptome and translatome profiles of Streptomyces species in different growth phases.

Kim W, Hwang S, Lee N, Lee Y, Cho S, Palsson B, Cho BK.

 2020
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Heckmann D, Campeau A, Lloyd CJ, et al.

 2020
Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis

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

 2020
Reconstructing organisms in silico: genome-scale models and their emerging applications

Fang X, Lloyd CJ, Palsson BO

 2020
Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus

Lee N, Kim W, Chung J, Lee Y, Cho S, Jang KS, Kim SC, Palsson B, Cho BK

 2020
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
Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters

Lee N, Kim W, Hwang S, Lee Y, Cho S, Palsson B, Cho BK

 2020
Adaptations of Escherichia Coli Strains to Oxidative Stress Are Reflected in Properties of Their Structural Proteomes

Mih N, Monk JM, Fang X, et al.

 2020
Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution

Lim, H.G., Fong, B., Alacon, G., Magrudeniya, H.D., Eng, T., Szubin, R., Olson, C.A., Palsson, B.O., Gladden, J.M., Simmons, B.A., Mukhopadhyay, Singer, S.W., Feist, A.M., 

 2020
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