Detection of aberrant gene expression events in RNA sequencing data

VA Yépez, C Mertes, MF Müller, D Klaproth-Andrade… - Nature protocols, 2021 - nature.com
RNA sequencing (RNA-seq) has emerged as a powerful approach to discover disease-
causing gene regulatory defects in individuals affected by genetically undiagnosed rare …

Reviving the transcriptome studies: an insight into the emergence of single-molecule transcriptome sequencing

B Wang, V Kumar, A Olson, D Ware - Frontiers in genetics, 2019 - frontiersin.org
Advances in transcriptomics have provided an exceptional opportunity to study functional
implications of the genetic variability. Technologies such as RNA-Seq have emerged as …

A multi-tissue atlas of regulatory variants in cattle

S Liu, Y Gao, O Canela-Xandri, S Wang, Y Yu, W Cai… - Nature …, 2022 - nature.com
Abstract Characterization of genetic regulatory variants acting on livestock gene expression
is essential for interpreting the molecular mechanisms underlying traits of economic value …

The GTEx Consortium atlas of genetic regulatory effects across human tissues

GTEx Consortium - Science, 2020 - science.org
The Genotype-Tissue Expression (GTEx) project was established to characterize genetic
effects on the transcriptome across human tissues and to link these regulatory mechanisms …

The impact of sex on gene expression across human tissues

M Oliva, M Muñoz-Aguirre, S Kim-Hellmuth, V Wucher… - Science, 2020 - science.org
INTRODUCTION Many complex human phenotypes, including diseases, exhibit sex-
differentiated characteristics. These sex differences have been variously attributed to …

A compendium of genetic regulatory effects across pig tissues

J Teng, Y Gao, H Yin, Z Bai, S Liu, H Zeng… - Nature …, 2024 - nature.com
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been
established to develop a public resource of genetic regulatory variants in livestock, which is …

Pervasive chromosomal instability and karyotype order in tumour evolution

TBK Watkins, EL Lim, M Petkovic, S Elizalde… - Nature, 2020 - nature.com
Chromosomal instability in cancer consists of dynamic changes to the number and structure
of chromosomes,. The resulting diversity in somatic copy number alterations (SCNAs) may …

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

OM de Goede, DC Nachun, NM Ferraro… - Cell, 2021 - cell.com
Long non-coding RNA (lncRNA) genes have well-established and important impacts on
molecular and cellular functions. However, among the thousands of lncRNA genes, it is still …

WhatsHap: fast and accurate read-based phasing

M Martin, M Patterson, S Garg, SO Fischer, N Pisanti… - BioRxiv, 2016 - biorxiv.org
Read-based phasing allows to reconstruct the haplotype structure of a sample purely from
sequencing reads. While phasing is a required step for answering questions about …

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

SE Castel, A Cervera, P Mohammadi, F Aguet… - Nature …, 2018 - nature.com
Coding variants represent many of the strongest associations between genotype and
phenotype; however, they exhibit inter-individual differences in effect, termed 'variable …