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Patrick Phaneuf
Patrick Phaneuf
Center for Biosustainability Denmark Technical University
Verified email at biosustain.dtu.dk
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Cited by
Year
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
1462017
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
1112019
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
1012019
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
822021
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
742020
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
612019
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
402020
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
382023
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
272019
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
252020
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
232019
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
172018
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
162023
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
162020
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
152020
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
132022
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
112023
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
72024
Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
K Rychel, J Tan, A Patel, C Lamoureux, Y Hefner, R Szubin, J Johnsen, ...
bioRxiv, 2022.12. 20.521246, 2022
52022
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