Nanopore native RNA sequencing of a human poly (A) transcriptome
High-throughput complementary DNA sequencing technologies have advanced our
understanding of transcriptome complexity and regulation. However, these methods lose …
understanding of transcriptome complexity and regulation. However, these methods lose …
The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes
G Magris, I Jurman, A Fornasiero, E Paparelli… - Nature …, 2021 - nature.com
In order to elucidate the still controversial processes that originated European wine grapes
from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all …
from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all …
Is it time to change the reference genome?
The use of the human reference genome has shaped methods and data across modern
genomics. This has offered many benefits while creating a few constraints. In the following …
genomics. This has offered many benefits while creating a few constraints. In the following …
Perspectives on allele-specific expression
Diploidy has profound implications for population genetics and susceptibility to genetic
diseases. Although two copies are present for most genes in the human genome, they are …
diseases. Although two copies are present for most genes in the human genome, they are …
Transcriptomic response to heat stress among ecologically divergent populations of redband trout
SR Narum, NR Campbell - BMC genomics, 2015 - Springer
Background As ectothermic organisms have evolved to differing aquatic climates, the
molecular basis of thermal adaptation is a key area of research. In this study, we tested for …
molecular basis of thermal adaptation is a key area of research. In this study, we tested for …
Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster
J Chen, V Nolte, C Schlötterer - PLoS genetics, 2015 - journals.plos.org
The regulatory architecture of gene expression remains an area of active research. Here, we
studied how the interplay of genetic and environmental variation affects gene expression by …
studied how the interplay of genetic and environmental variation affects gene expression by …
Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression
Vitis vinifera is an economically important crop and a useful model in which to study
chromatin dynamics. In contrast to the small and relatively simple genome of Arabidopsis …
chromatin dynamics. In contrast to the small and relatively simple genome of Arabidopsis …
ASEQ: fast allele-specific studies from next-generation sequencing data
Background Single base level information from next-generation sequencing (NGS) allows
for the quantitative assessment of biological phenomena such as mosaicism or allele …
for the quantitative assessment of biological phenomena such as mosaicism or allele …
Personalized and graph genomes reveal missing signal in epigenomic data
Background Epigenomic studies that use next generation sequencing experiments typically
rely on the alignment of reads to a reference sequence. However, because of genetic …
rely on the alignment of reads to a reference sequence. However, because of genetic …
IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing
Allele-specific expression (ASE) is a fundamental problem in studying gene regulation and
diploid transcriptome profiles, with two key challenges:(i) haplotyping and (ii) estimation of …
diploid transcriptome profiles, with two key challenges:(i) haplotyping and (ii) estimation of …