Publication Title Authors Publication Year Sort ascending
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
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.

Sastry AV, Yuan Y, Poudel S, Rychel K, Yoo R, Lamoureux CR, Li G, Burrows JT, Chauhan S, Haiman ZB, Al Bulushi T, Seif Y, Palsson BO, Zielinski DC.

2024
Escherichia coli non-coding regulatory regions are highly conserved

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

2024
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets

Catoiu EA, Krishnan J, Li G, Lou XA, Rychel K, Yuan Y, Bajpe H, Patel A, Choe D, Shin J, Burrows J, Phaneuf PV, Zielinski DC, Palsson BO.

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

Shin J, Zielinski DC, Palsson BO.

2024
Diversity of transcriptional regulatory adaptation in E. coli

Dalldorf C, Hefner Y, Szubin R, Johnsen J, Mohamed E, Li G, Krishnan J, Feist AM, Palsson BO, Zielinski DC

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
PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining

Sun B, Pashkova L, Pieters PA, Harke AS, Mohite OS, Santos A, Zielinski DC, Palsson BO, Phaneuf PV

2024
E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding

Rodionova IA, Hosseinnia A, Kim S, Goodacre N, Zhang L, Zhang Z, Palsson B, Uetz P, Babu M, Saier MH Jr.

2023
Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V

2023
Empowering drug off-target discovery with metabolic and structural analysis

Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI

2023
Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC

Gao Y, Poudel S, Seif Y, Shen Z, Palsson BO

2023
Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family

Akanksha Rajput, Siddharth M. Chauhan, Omkar S. Mohite, Jason C. Hyun, Omid Ardalani, Leonie J. Jahn, Morten OA. Sommer, Bernhard O. Palsson

2023
Adaptive Evolution of a Minimal Organism with a Synthetic Genome

Sandberg, T.E., Wise, K.S., Dalldorf, C., Szubin, R., Feist, A.M., Glass, J.I., Palsson, B.O.

2023
Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Kumaraswamy M, Coady A, Szubin R, Martin TCS, Palsson B, Nizet V, Monk JM

2023
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

Hyun, J.C., Palsson, B.O.

2023
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW, Palsson BO, Kim D

2023
Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection

Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO

2023
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
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals

Lennen RM, Lim HG, Jensen K, Mohammed ET, Phaneuf PV, Noh MH, Malla S, Börner RA, Chekina K, Özdemir E, Bonde I, Koza A, Maury J, Pedersen LE, Schöning LY, Sonnenschein N, Palsson BO, Nielsen AT, Sommer MOA, Herrgård MJ, Feist AM

2023
A multi-scale expression and regulation knowledge base for Escherichia coli

Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO

2023
Revealing oxidative pentose metabolism in new Pseudomonas putida isolates

Park, M. R., Gauttam, R., Fong, B., Chen, Y., Lim, H. G., Feist, A. M., Mukhopadhyay, A., Petzold, C. J., Simmons, B. A., & Singer, S. W.

2023
Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO.

2023
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C

2023
Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways

Mattei, G., Gan, Z., Ramazzotti, M., Palsson, B.O., Zielinski, D.C.

2023