Publication Title Authors Publication Year Sort ascending
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK

2021
Independent component analysis recovers consistent regulatory signals from disparate datasets

Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO

2021
Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius

Chauhan SM, Poudel S, Rychel K, Lamoureux C, Yoo R, Al Bulushi T, Yuan Y, Palsson BO, Sastry AV.

2021
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
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