Publication Title Authors Publication Year Sort ascending
Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology

Kim K, Choe D, Cho S, Palsson B, Cho BK.

2024
Genome-scale models in human metabologenomics

Mardinoglu A, Palsson BØ

2024
Serial adaptive laboratory evolution enhances mixed carbon metabolic capacity of Escherichia coli

Kim K, Choe D, Kang M, Cho SH, Cho S, Jeong KJ, Palsson B, Cho BK

2024
CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli

Rodionova IA, Lim HG, Gao Y, Rodionov DA, Hutchison Y, Szubin R, Dalldorf C, Monk J, Palsson BO

2024
Grand Challenges at the Interface of Engineering and Medicine

Subramaniam S, Akay M, Anastasio MA, Bailey V, Boas D, Bonato P, Chilkoti A, Cochran JR, Colvin V, Desai TA, Duncan JS, Epstein FH, Fraley S, Giachelli C, Grande-Allen KJ, Green J, Guo XE, Hilton IB, Humphrey JD, Johnson CR, Karniadakis G, King MR, Kirsch RF, Kumar S, Laurencin CT, Li S, Lieber RL, Lovell N, Mali P, Margulies SS, Meaney DF, Ogle B, Palsson B, A Peppas N, Perreault EJ, Rabbitt R, Setton LA, Shea LD, Shroff SG, Shung K, Tolias AS, van der Meulen MCH, Varghese S, Vunjak-Novakovic G, White JA, Winslow R, Zhang J, Zhang K, Zukoski C, Miller MI.

2024
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes

Hirose Y, Zielinski DC, Poudel S, Rychel K, Baker JL, Toya Y, Yamaguchi M, Heinken A, Thiele I, Kawabata S, Palsson BO, Nizet V.

2024
Bottom-up parameterization of enzyme rate constants: Reconciling inconsistent data

Daniel C. Zielinski, Marta R.A. Matos, James E. de Bree, Kevin Glass, Nikolaus Sonnenschein, Bernhard O. Palsson

2024
Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

Champie A, Lachance J-C, Sastry A, Matteau D, Lloyd CJ, Grenier F, Lamoureux CR, Jeanneau S, Feist AM, Jacques P-É, Palsson BO, Rodrigue S.

2024
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

Nuhamunada M, Mohite OS, Phaneuf PV, Palsson BO, Weber T.

2024
Escherichia coli non-coding regulatory regions are highly conserved

Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC.

2024
Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering

Shin J, Zielinski DC, Palsson BO.

2024
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO.

2024
Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution

Lee, S.M., Le, H.T., Taizhanova, A., Nong, L.K., Park, J.Y., Lee, E.J., Palsson, B.O., Kim, D.

2024
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO.

2024
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii.

Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V.

2024
A treasure trove of 1034 actinomycete genomes

Jørgensen TS, Mohite OS, Sterndorff EB, Alvarez-Arevalo M, Blin K, Booth TJ, Charusanti P, Faurdal D, Hansen TØ, Nuhamunada M, Mourched AS, Palsson BØ, Weber T.

2024
A data-driven approach for timescale decomposition of biochemical reaction networks

Akbari A, Haiman ZB, Palsson BO

2024
Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Ardalani O, Phaneuf PV, Mohite OS, Nielsen LK, Palsson BO.

2024
Inferred regulons are consistent with regulator binding sequences in E. coli.

Qiu S, Wan X, Liang Y, Lamoureux CR, Akbari A, Palsson BO, Zielinski DC.

2024
Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes.

Nemkov T, Stephenson D, Earley EJ, Keele GR, Hay A, Key A, Haiman ZB, Erickson C, Dzieciatkowska M, Reisz JA, Moore A, Stone M, Deng X, Kleinman S, Spitalnik SL, Hod EA, Hudson KE, Hansen KC, Palsson BO, Churchill GA, Roubinian N, Norris PJ, Busch MP, Zimring JC, Page GP, D'Alessandro A.

2024
Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT

2024
Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing

Phaneuf PV, Kim SH, Rychel K, Rode C, Beulig F, Palsson BO, Yang L

2024
Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning

Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO.

2024
Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules

Shin J, Zielinski DC, Palsson BO

2024
Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses

Zhao J, Chen K, Palsson BO, Yang L.

2024
Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters

Lee Y, Choe D, Palsson BO, Cho BK.

2024
Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment

Choe D, Olson CA, Szubin R, Yang H, Sung J, Feist AM, Palsson BO

2024
Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatusPCC 7942

Yuan Y, Al Bulushi T, Sastry AV, Sancar C, Szubin R, Golden SS, Palsson BO.

2024
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling

Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D

2023
Recent advances in non-model bacterial chassis construction

Hwang S, Joung C, Kim W, Palsson B, Cho B-K

2023