D. Vitkup

Functional optimization in distinct tissues and conditions constrains the rate of protein evolution

The paper shows that protein evolution rates are inversely related to functional optimality and expression levels across multiple organisms and tissues.

Cancer tissue of origin constrains the growth and metabolism of metastases

This study shows that cancer tissue-of-origin influences the metabolism and growth preferences of both primary and metastatic tumors.

Multiple macroecological laws do characterize various aspects of microbiota dynamics

The paper clarifies that macroecological laws describe microbiota dynamics with specific scaling exponents and shows these relationships are not due to external factors but internal dynamics.

Ability of the misfolding avoidance hypothesis to explain protein evolutionary rates in the light of empirical evidence

This study evaluates the misfolding avoidance hypothesis by analyzing protein stability and aggregation data in E. coli and H. sapiens, finding no strong correlation between evolutionary rates and protein stability.

Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited

This study shows that cancer cells rely on environmental lipids for proliferation under conditions of limited electron acceptors, such as hypoxia or mitochondrial inhibition.

Macroecological dynamics of gut microbiota

The paper identifies scaling relationships in gut microbiota dynamics across humans and mice, showing similarities to ecological and economic systems and revealing effects of diet and environment.

Molecular function limits divergent protein evolution on planetary timescales

The paper examines how molecular function constrains protein divergence over time, finding that sequence and structural similarities stabilize after ~1-2 billion years of evolution.

Quantifying spatiotemporal dynamics and noise in absolute microbiota abundances using replicate sampling

The paper introduces DIVERS, a method to quantify spatiotemporal dynamics and noise in microbiota abundances using replicate sampling and spike-in sequencing, applied to the human gut microbiome.

Avoidance of toxic misfolding and protein stability do not explain the sequence constraints of highly expressed proteins

The paper re-analyzes proteome-scale stability data and finds no correlation between protein stability and abundance, challenging the misfolding avoidance hypothesis.