Academic lineage
- Nathan E Lewis
- Ron Milo - Postdoctoral Associate
- Bernhard Ø Palsson - Ph.D. student
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks
- Edward Alexander Catoiu, Patrick Phaneuf, Jonathan Monk, …, Patrick Phaneuf, Jonathan Monk, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.2218835120
Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity
- Amitesh Anand, Arjun Patel, Ke Chen, …, Richard Szubin, Adam M Feist, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-022-30877-5
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data
- Patrick V Phaneuf, Daniel C Zielinski, James T Yurkovich, …, Rebecca M Lennen, Bernhard O Palsson, Adam M Feist
- ACS Synth Biol, 10.1021/acssynbio.1c00337
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning
- Kevin Rychel, Katherine Decker, Anand V Sastry, Patrick V Phaneuf, Saugat Poudel, Bernhard O Palsson
- Nucleic Acids Res, 10.1093/nar/gkaa810
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
- David Heckmann, Anaamika Campeau, Colton J Lloyd, …, Adam M Feist, David J Gonzalez, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.2001562117
Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes
- Troy E Sandberg, Richard Szubin, Patrick V Phaneuf, Bernhard O Palsson
- Nat Ecol Evol, 10.1038/s41559-020-1271-x
Cellular responses to reactive oxygen species are predicted from molecular mechanisms
- Laurence Yang, Nathan Mih, Amitesh Anand, …, Ying Hefner, Adam M Feist, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.1905039116
The genetic basis for adaptation of model-designed syntrophic co-cultures
- Colton J Lloyd, Zachary A King, Troy E Sandberg, …, Gregory Humphrey, Rob Knight, Adam M Feist
- PLoS Comput Biol, 10.1371/journal.pcbi.1006213
Reframing gene essentiality in terms of adaptive flexibility
- Gabriela I Guzmán, Connor A Olson, Ying Hefner, …, Lucas Goldschmidt Micas, Bernhard O Palsson, Adam M Feist
- None, 10.1186/s12918-018-0653-z
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation
- Patrick V Phaneuf, Dennis Gosting, Bernhard O Palsson, Adam M Feist
- Nucleic Acids Res, 10.1093/nar/gky983