Patrick V. Phaneuf

Four-species Aspergillus pan-GWAS reveals rare genome expansion in pathogenicity and contraction in domestication

This study performs pan-GWAS across four Aspergillus species to show that pathogenicity involves rare genome expansion while industrial strains show rare genome contraction.

A Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis

The paper uses pangenome analysis of Escherichia coli to reveal the genetic basis of metabolic reactions and their evolutionary dynamics.

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining

PanKB is a microbial pangenome knowledgebase that integrates pangenomic data and literature to support research and biotechnological applications.

ProteusAI: An Open-Source and User-Friendly Platform for Machine Learning-Guided Protein Design and Engineering

ProteusAI is an open-source platform that streamlines ML-guided protein design and engineering, improving proteins and enzymes efficiently within the DBTL cycle.

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

The paper reconstructs pangenomes of Lactobacillaceae to generate metabolic models for 26 species, enabling species-specific metabolic trait predictions.

The Pangenome of Escherichia coli

The paper analyzes the pangenome of Escherichia coli using 2,377 genomes to define accessory genes and rare genomic variation across phylogroups.

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

BGCFlow is a systematic workflow for analyzing biosynthetic gene clusters across large genomic datasets, demonstrating improved dereplication and comparative analysis of RiPPs in Saccharopolyspora genomes.

Pangenome mining of the Streptomyces genus redefines their biosynthetic potential

The paper analyzes 2,371 Streptomyces genomes to refine biosynthetic gene cluster (BGC) diversity using MASH-clusters and reveals conserved genomic structures suggesting vertical inheritance.

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

This paper uses transcriptomics and machine learning to reconstruct the transcriptional regulatory network of L. reuteri, identifying key regulatory signals and metabolic pathways.

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

The paper analyzes the alleleome of the Lactobacillaceae family's core pangenome to understand strain diversity and identify phylogroup-specific variants.

Using the E. coli Alleleome in Strain Design

This study combines ALE and WT variants to explore sequence solutions for industrial tolerance in E. coli, finding that WT variants can provide greater benefits and help identify feasible genome design variables.

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

The paper uses adaptive laboratory evolution and transcriptomic analysis to identify six mechanisms of paraquat tolerance in E. coli.

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

The paper evolves ETS variants in E. coli and finds they all optimize growth rate and proteome allocation, with conserved aero-type strategies except for ETS-4H.

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

iModulonDB provides a knowledgebase of microbial transcriptional regulation derived from machine learning, offering curated gene sets and their activity levels across three bacterial species.

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

The paper estimates in vivo enzyme turnover numbers (kcats) in E. coli using metabolic specialist strains and shows their stability and predictive power over in vitro kcats.

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

This study uses adaptive laboratory evolution to generate E. coli strains with increased superoxide stress tolerance and identifies genetic and transcriptomic mechanisms underlying this adaptation.

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

This paper designs and evolves synthetic syntrophic E. coli pairs using a novel algorithm, revealing metabolic changes that enhance community fitness and guide co-culture optimization.

ALEdb 1.0: A Database of Mutations from Adaptive Laboratory Evolution

ALEdb 1.0 is a database of mutations from adaptive laboratory evolution experiments, providing structured access to over 11,000 mutations across multiple organisms.

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

The paper develops a quantitative framework to predict ROS stress responses in E. coli across molecular, network, and genetic levels.