| Increased production of L-serine in Escherichia coli through adaptive laboratory evolution H Mundhada, JM Seoane, K Schneider, A Koza, HB Christensen, T Klein, ... Metabolic engineering 39, 141-150, 2017 | 154 | 2017 |
| ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation PV Phaneuf, D Gosting, BO Palsson, AM Feist Nucleic acids research 47 (D1), D1164-D1171, 2019 | 114 | 2019 |
| Cellular responses to reactive oxygen species are predicted from molecular mechanisms L Yang, N Mih, A Anand, JH Park, J Tan, JT Yurkovich, JM Monk, CJ Lloyd, ... Proceedings of the National Academy of Sciences 116 (28), 14368-14373, 2019 | 103 | 2019 |
| iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning K Rychel, K Decker, AV Sastry, PV Phaneuf, S Poudel, BO Palsson Nucleic acids research 49 (D1), D112-D120, 2021 | 89 | 2021 |
| Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers D Heckmann, A Campeau, CJ Lloyd, PV Phaneuf, Y Hefner, ... Proceedings of the National Academy of Sciences 117 (37), 23182-23190, 2020 | 76 | 2020 |
| Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration A Anand, KE Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ... Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019 | 66 | 2019 |
| Adaptive laboratory evolution of Escherichia coli under acid stress B Du, CA Olson, AV Sastry, X Fang, PV Phaneuf, K Chen, M Wu, R Szubin, ... Microbiology 166 (2), 141-148, 2020 | 44 | 2020 |
| Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals RM Lennen, HG Lim, K Jensen, ET Mohammed, PV Phaneuf, MH Noh, ... Metabolic Engineering 76, 179-192, 2023 | 40 | 2023 |
| The genetic basis for adaptation of model-designed syntrophic co-cultures CJ Lloyd, ZA King, TE Sandberg, Y Hefner, CA Olson, PV Phaneuf, ... PLoS computational biology 15 (3), e1006213, 2019 | 27 | 2019 |
| Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity PV Phaneuf, JT Yurkovich, D Heckmann, M Wu, TE Sandberg, ZA King, ... BMC genomics 21, 1-16, 2020 | 25 | 2020 |
| Pseudogene repair driven by selection pressure applied in experimental evolution A Anand, CA Olson, L Yang, AV Sastry, E Catoiu, KS Choudhary, ... Nature microbiology 4 (3), 386-389, 2019 | 24 | 2019 |
| Reframing gene essentiality in terms of adaptive flexibility GI Guzmán, CA Olson, Y Hefner, PV Phaneuf, E Catoiu, LB Crepaldi, ... BMC systems biology 12, 1-20, 2018 | 17 | 2018 |
| Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks EA Catoiu, P Phaneuf, J Monk, BO Palsson Proceedings of the National Academy of Sciences 120 (15), e2218835120, 2023 | 16 | 2023 |
| The Bitome: digitized genomic features reveal fundamental genome organization CR Lamoureux, KS Choudhary, ZA King, TE Sandberg, Y Gao, AV Sastry, ... Nucleic Acids Research 48 (18), 10157-10163, 2020 | 16 | 2020 |
| Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity A Anand, A Patel, K Chen, CA Olson, PV Phaneuf, C Lamoureux, ... Nature communications 13 (1), 3682, 2022 | 15 | 2022 |
| Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes TE Sandberg, R Szubin, PV Phaneuf, BO Palsson Nature ecology & evolution 4 (10), 1402-1409, 2020 | 15 | 2020 |
| Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data PV Phaneuf, DC Zielinski, JT Yurkovich, J Johnsen, R Szubin, L Yang, ... ACS Synthetic Biology 10 (12), 3379-3395, 2021 | 13* | 2021 |
| Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance K Rychel, J Tan, A Patel, C Lamoureux, Y Hefner, R Szubin, J Johnsen, ... Cell reports 42 (9), 2023 | 12 | 2023 |
| BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets M Nuhamunada, OS Mohite, PV Phaneuf, BO Palsson, T Weber Nucleic Acids Research 52 (10), 5478-5495, 2024 | 9 | 2024 |
| Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning J Josephs-Spaulding, A Rajput, Y Hefner, R Szubin, A Balasubramanian, ... Msystems 9 (3), e01257-23, 2024 | 6 | 2024 |
Adam FeistUC San Diego (UCSD) / Technical University of Denmark (DTU)Email verificata su ucsd.edu
