P. Phaneuf

发表

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

B. Palsson, A. Feist, C. Lloyd, 2020, Proceedings of the National Academy of Sciences.

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Adam M. Feist, Patrick V. Phaneuf, B. Palsson, 2019, Proceedings of the National Academy of Sciences.

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.

Adam M. Feist, Adam M Feist, Markus J. Herrgård, 2017, Metabolic engineering.

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Adam M. Feist, Jared T. Broddrick, Jonathan M. Monk, 2019, Proceedings of the National Academy of Sciences.

The Bitome: digitized genomic features reveal fundamental genome organization

Zachary A. King, Anand V. Sastry, Troy E. Sandberg, 2020, Nucleic acids research.

Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2019, bioRxiv.

Synthetic Cross-Phyla Gene Replacement and Evolutionary Assimilation of Major Enzymes

Troy E. Sandberg, B. Palsson, R. Szubin, 2020, Nature Ecology & Evolution.

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

Adam M. Feist, Zachary A. King, James T. Yurkovich, 2020, BMC Genomics.

Adaptive laboratory evolution of Escherichia coli under acid stress

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2019, bioRxiv.

The genetic basis for adaptation of model-designed syntrophic co-cultures

Edward J. O'Brien, Adam M. Feist, Rob Knight, 2019, PLoS Comput. Biol..

Pseudogene repair driven by selection pressure applied in experimental evolution

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2019, Nature Microbiology.

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

Bernhard O Palsson, Saugat Poudel, Anand V. Sastry, 2020, bioRxiv.

Model-driven design and evolution of non-trivial synthetic syntrophic pairs

Edward J. O'Brien, Adam M. Feist, Zachary A. King, 2018, bioRxiv.

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

Adam M. Feist, Zachary A. King, James T. Yurkovich, 2020, BMC Genomics.

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation

Adam M. Feist, Bernhard O. Palsson, Patrick V. Phaneuf, 2018, bioRxiv.

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Adam M. Feist, Connor A. Olson, A. Feist, 2022, Nature Communications.

Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

Adam M. Feist, Daniel C. Zielinski, James T. Yurkovich, 2021, ACS synthetic biology.

Reframing gene essentiality in terms of adaptive flexibility

Adam M. Feist, Bernhard O. Palsson, L. B. Crepaldi, 2018, BMC Systems Biology.

ALE Analytics: A Software Pipeline and Web Platform for the Analysis of Microbial Genomic Data from Adaptive Laboratory Evolution Experiments

Patrick Victor Phaneuf, P. Phaneuf, 2016 .

Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals.

Adam M. Feist, Markus J. Herrgård, Ida Bonde, 2023, Metabolic engineering.

Cellular responses to reactive oxygen species can be predicted on multiple biological scales from molecular mechanisms

Justin Tan, Donghyuk Kim, Richard Szubin, 2017 .

ALE Variant Analysis scripts and data v0.1.0

P. Phaneuf, 2020 .

Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2022, bioRxiv.

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2019, Proceedings of the National Academy of Sciences.

Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli

Jonathan M. Monk, P. Phaneuf, E. Catoiu, 2022, bioRxiv.

Pseudogene repair driven by selection pressure applied in experimental evolution

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2019, Nature Microbiology.

BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

T. Weber, P. Phaneuf, Omkar S Mohite, 2023, bioRxiv.

Reconstructing the Transcriptional Regulatory Network of Probiotic L. reuteri is Enabled by Transcriptomics and Machine Learning

Daniel C. Zielinski, M. Sommer, D. Zielinski, 2023, bioRxiv.

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

P. Phaneuf, Omid Ardalani, Omkar S. Mohite, 2023, bioRxiv.

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

Adam M. Feist, Jonathan M. Monk, B. Palsson, 2018, Microbiology Resource Announcements.

Multi-scale model of the proteomic and metabolic consequences of reactive oxygen species

Adam M. Feist, Jared T. Broddrick, Jonathan M. Monk, 2017, bioRxiv.

Genomic insights into Lactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

P. Phaneuf, Siddharth M. Chauhan, Omid Ardalani, 2023, bioRxiv.

Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.

Adam M. Feist, Anand V. Sastry, Connor A. Olson, 2023, Cell Reports.