Comparative transcriptomics in human and mouse

A Breschi, TR Gingeras, R Guigó - Nature Reviews Genetics, 2017 - nature.com
Cross-species comparisons of genomes, transcriptomes and gene regulation are now
feasible at unprecedented resolution and throughput, enabling the comparison of human …

Evolutionary dynamics of coding and non-coding transcriptomes

A Necsulea, H Kaessmann - Nature Reviews Genetics, 2014 - nature.com
Gene expression changes may underlie much of phenotypic evolution. The development of
high-throughput RNA sequencing protocols has opened the door to unprecedented large …

SARS-CoV-2 receptors and entry genes are expressed in the human olfactory neuroepithelium and brain

L Fodoulian, J Tuberosa, D Rossier, M Boillat, C Kan… - Iscience, 2020 - cell.com
Reports indicate an association between COVID-19 and anosmia, as well as the presence
of SARS-CoV-2 virions in the olfactory bulb. To test whether the olfactory neuroepithelium …

The evolution of gene expression levels in mammalian organs

D Brawand, M Soumillon, A Necsulea, P Julien… - Nature, 2011 - nature.com
Abstract Changes in gene expression are thought to underlie many of the phenotypic
differences between species. However, large-scale analyses of gene expression evolution …

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

M Lechner, S Findeiß, L Steiner, M Marz, PF Stadler… - BMC …, 2011 - Springer
Background Orthology analysis is an important part of data analysis in many areas of
bioinformatics such as comparative genomics and molecular phylogenetics. The ever …

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

K Schroder, KM Irvine, MS Taylor… - Proceedings of the …, 2012 - National Acad Sciences
Evolutionary change in gene expression is generally considered to be a major driver of
phenotypic differences between species. We investigated innate immune diversification by …

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts

MP Hoeppner, A Lundquist, M Pirun, JRS Meadows… - PloS one, 2014 - journals.plos.org
The domestic dog, Canis familiaris, is a well-established model system for mapping trait and
disease loci. While the original draft sequence was of good quality, gaps were abundant …

Phylogenetic and functional assessment of orthologs inference projects and methods

AM Altenhoff, C Dessimoz - PLoS computational biology, 2009 - journals.plos.org
Accurate genome-wide identification of orthologs is a central problem in comparative
genomics, a fact reflected by the numerous orthology identification projects developed in …

Computational methods for Gene Orthology inference

DM Kristensen, YI Wolf, AR Mushegian… - Briefings in …, 2011 - academic.oup.com
Accurate inference of orthologous genes is a pre-requisite for most comparative genomics
studies, and is also important for functional annotation of new genomes. Identification of …

Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution

RM Davidson, M Gowda, G Moghe, H Lin… - The Plant …, 2012 - Wiley Online Library
The Poaceae family, also known as the grasses, includes agronomically important cereal
crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown …