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 |