J. C. Xavier

Self-generating autocatalytic networks: structural results, algorithms, and their relevance to evolutionary processes

This paper presents new structural and algorithmic results for autocatalytic reaction networks, focusing on complex catalysis and minimal RAF sets.

The structure of autocatalytic networks, with application to early biochemistry

This paper extends RAF theory to analyze autocatalytic networks in archaeal and bacterial metabolism, introducing new algorithms for visualizing and understanding early biochemistry structures.

Gene duplications trace mitochondria to the onset of eukaryote complexity

The paper identifies gene duplication events in the last eukaryote common ancestor (LECA) that suggest mitochondrial gene transfer preceded the onset of eukaryotic complexity.

Autocatalytic chemical networks preceded proteins and RNA in evolution

The paper identifies autocatalytic networks in ancient microbial metabolism, showing small-molecule catalysis preceded polymers in biochemical evolution.

Count does not recover major events of gene flux in real biological data

The paper tests Count's ability to detect mass gene transfer events and finds it biases towards uniform distribution rather than sporadic acquisition and differential loss.