Computational approaches to species phylogeny inference and gene tree reconciliation

L Nakhleh - Trends in ecology & evolution, 2013 - cell.com
An intricate relation exists between gene trees and species phylogenies, due to evolutionary
processes that act on the genes within and across the branches of the species phylogeny …

Evolution of intrinsic disorder in eukaryotic proteins

JB Ahrens, J Nunez-Castilla… - Cellular and Molecular …, 2017 - Springer
Conformational flexibility conferred though regions of intrinsic structural disorder allows
proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered …

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

YI Wolf, PS Novichkov, GP Karev… - Proceedings of the …, 2009 - National Acad Sciences
The evolutionary rates of protein-coding genes in an organism span, approximately, 3
orders of magnitude and show a universal, approximately log-normal distribution in a broad …

Origins of P450 diversity

H Sezutsu, G Le Goff… - … Transactions of the …, 2013 - royalsocietypublishing.org
The P450 enzymes maintain a conserved P450 fold despite a considerable variation in
sequence. The P450 family even includes proteins that lack the single conserved cysteine …

Toward a general model for the evolutionary dynamics of gene duplicates

A Konrad, AI Teufel, JA Grahnen… - Genome biology and …, 2011 - academic.oup.com
Gene duplication is an important process in the functional divergence of genes and
genomes. Several processes have been described that lead to duplicate gene retention …

Inference of ancient polyploidy from genomic data

H Chen, A Zwaenepoel - Polyploidy: Methods and protocols, 2023 - Springer
Whole-genome sequence data have revealed that numerous eukaryotic organisms derive
from distant polyploid ancestors, even when these same organisms are genetically and …

Extracting functional trends from whole genome duplication events using comparative genomics

RA Hermansen, TR Hvidsten, SR Sandve… - Biological procedures …, 2016 - Springer
Background The number of species with completed genomes, including those with evidence
for recent whole genome duplication events has exploded. The recently sequenced Atlantic …

Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species

T Hughes, DA Liberles - Journal of molecular evolution, 2008 - Springer
A clustering of all protein coding genes from the complete genomes of five tetrapod species
into gene families shows a clear deviation from the expected power-law distribution of gene …

Identification of abdominal aortic aneurysm subtypes based on mechanosensitive genes

C Sheng, Q Zeng, W Huang, M Liao, P Yang - Plos one, 2024 - journals.plos.org
Background Rupture of abdominal aortic aneurysm (rAAA) is a fatal event in the elderly.
Elevated blood pressure and weakening of vessel wall strength are major risk factors for this …

The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications

S Huang, H Tian, Z Chen, T Yu, A Xu - BMC evolutionary biology, 2010 - Springer
Background The vertebrate tetraspanin family has many features which make it suitable for
preserving the imprint of ancient sequence evolution and amenable for phylogenomic …