Patrick Phaneuf
Patrick Phaneuf
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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
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
Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration
A Anand, K Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ...
Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 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
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
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), 143, 2018
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
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
Gapless, unambiguous genome sequence for Escherichia coli C, a workhorse of industrial biology
JE Pekar, P Phaneuf, R Szubin, B Palsson, A Feist, JM Monk
Microbiology Resource Announcements 7 (13), 2018
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
Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance
J Tan, CA Olson, JH Park, AV Sastry, P Phaneuf, L Yang, R Szubin, ...
bioRxiv, 749887, 2019
Model-driven design and evolution of non-trivial synthetic syntrophic pairs
CJ Lloyd, ZA King, TE Sandberg, Y Hefner, CA Olson, PV Phaneuf, ...
BioRxiv, 327270, 2018
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), 1-16, 2020
Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes
TE Sandberg, R Szubin, PV Phaneuf, BO Palsson
Nature Ecology & Evolution, 1-8, 2020
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning
K Rychel, K Decker, AV Sastry, PV Phaneuf, S Poudel, BO Palsson
bioRxiv, 2020
ALE Analytics: A Software Pipeline and Web Platform for the Analysis of Microbial Genomic Data from Adaptive Laboratory Evolution Experiments
PV Phaneuf
UC San Diego, 2016
255 Assignment 2, Fall 2015
P Phaneuf, D Yen, S Grady
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