Biology subjects

John, B.

Publications and source records attributed to John, B..

2 recordsLinked to original sources

bioRxiv2023

Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication

Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.

evolutionary biology↗

bioRxiv2021

Effective expression analysis using gene interaction matrices and convolutional neural networks

Artificial intelligence recently experienced a renaissance with the advancement of convolutional neural networks (CNNs). CNNs require spatially meaningful matrices (e.g., image data) with recurring patterns, limiting its applicability to high-throughput omics data. We present GIM, a simple, CNN-ready framework for omics data to detect both individual and network-level entities of biological importance. Using gene expression data, we show that GIM-CNNs can outperform comparable neural networks in performance and their design facilitates network-level interpretability. GIM-CNNs provide a means to discover novel disease-relevant factors beyond individual genes and their expression, factors that are likely missed by standard differential gene expression approaches.

bioinformatics↗