The evolutionary origin of orphan genes

D Tautz, T Domazet-Lošo - Nature Reviews Genetics, 2011 - nature.com
Gene evolution has long been thought to be primarily driven by duplication and
rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes …

An integrated view of protein evolution

C Pál, B Papp, MJ Lercher - Nature reviews genetics, 2006 - nature.com
Why do proteins evolve at different rates? Advances in systems biology and genomics have
facilitated a move from studying individual proteins to characterizing global cellular factors …

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

J Zrimec, CS Börlin, F Buric, AS Muhammad… - Nature …, 2020 - nature.com
Understanding the genetic regulatory code governing gene expression is an important
challenge in molecular biology. However, how individual coding and non-coding regions of …

A benchmark of gene expression tissue-specificity metrics

N Kryuchkova-Mostacci… - Briefings in …, 2017 - academic.oup.com
One of the major properties of genes is their expression pattern. Notably, genes are often
classified as tissue specific or housekeeping. This property is of interest to molecular …

The quantitative proteome of a human cell line

M Beck, A Schmidt, J Malmstroem… - Molecular systems …, 2011 - embopress.org
The generation of mathematical models of biological processes, the simulation of these
processes under different conditions, and the comparison and integration of multiple data …

Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus

FS Barreto, ET Watson, TG Lima, CS Willett… - Nature ecology & …, 2018 - nature.com
The copepod Tigriopus californicus shows extensive population divergence and is
becoming a model for understanding allopatric differentiation and the early stages of …

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution

DA Drummond, CO Wilke - Cell, 2008 - cell.com
Strikingly consistent correlations between rates of coding-sequence evolution and gene
expression levels are apparent across taxa, but the biological causes behind the selective …

Why highly expressed proteins evolve slowly

DA Drummond, JD Bloom, C Adami… - Proceedings of the …, 2005 - National Acad Sciences
Much recent work has explored molecular and population-genetic constraints on the rate of
protein sequence evolution. The best predictor of evolutionary rate is expression level, for …

Global proteome analysis of the NCI-60 cell line panel

AM Gholami, H Hahne, Z Wu, FJ Auer, C Meng… - Cell reports, 2013 - cell.com
The NCI-60 cell line collection is a very widely used panel for the study of cellular
mechanisms of cancer in general and in vitro drug action in particular. It is a model system …

A single determinant dominates the rate of yeast protein evolution

DA Drummond, A Raval, CO Wilke - Molecular biology and …, 2006 - academic.oup.com
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities
in common use, but what determines evolutionary rates has remained unclear. Here, we …