Publications per year
Publications per year
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2024
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets
Nuhamunada, M., Mohite, O. S., Phaneuf, P. V., Palsson, B. O. & Weber, T., 2024, In: Nucleic Acids Research. 52, 10, p. 5478-5495Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile6 Downloads (Pure) -
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, D. C., Jahn, L., Sommer, M., Phaneuf, P. & Palsson, B. O., 2024, (Accepted/In press) In: mSystems. e0125723.Research output: Contribution to journal › Journal article › Research › peer-review
Open Access -
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, E. T. T., Phaneuf, P. V., Anand, A., Olson, C. A., Park, J. H., Sastry, A. V., Yang, L., Feist, A. M. & Palsson, B. O., 2023, In: Cell Reports. 42, 9, 21 p., 113105.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile37 Downloads (Pure) -
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals
Lennen, R. M., Lim, H. G., Jensen, K., Mohammed, E. T., Phaneuf, P. V., Noh, M. H., Malla, S., Börner, R. A., Chekina, K., Özdemir, E., Bonde, I., Koza, A., Maury, J., Pedersen, L. E., Schöning, L. Y., Sonnenschein, N., Palsson, B. O., Nielsen, A. T., Sommer, M. O. A. & Herrgård, M. J. & 1 others, , 2023, In: Metabolic Engineering. 76, p. 179-192 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile131 Downloads (Pure) -
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks
Catoiu, E. A., Phaneuf, P., Monk, J. & Palsson, B. O., 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 15, e2218835120.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile31 Downloads (Pure) -
2021
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data
Phaneuf, P. V., Zielinski, D. C., Yurkovich, J. T., Johnsen, J., Szubin, R., Yang, L., Kim, S. H., Schulz, S., Wu, M., Dalldorf, C., Ozdemir, E., Lennen, R. M., Palsson, B. O. & Feist, A. M., 2021, In: ACS Synthetic Biology. 10, 12, p. 3379–3395 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile211 Downloads (Pure) -
IModulonDB: A knowledgebase of microbial transcriptional regulation derived from machine learning
Rychel, K., Decker, K., Sastry, A. V., Phaneuf, P. V., Poudel, S. & Palsson, B. O., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D112-D120Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile147 Downloads (Pure)