Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2
The COVID-19 outbreak has become a global health risk, and understanding the response
of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host …
of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host …
Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
F Finotello, C Mayer, C Plattner, G Laschober… - Genome medicine, 2019 - Springer
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from
bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor …
bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor …
DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
Background Nanopore long-read sequencing technology greatly expands the capacity of
long-range, single-molecule DNA-modification detection. A growing number of analytical …
long-range, single-molecule DNA-modification detection. A growing number of analytical …
[HTML][HTML] Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection
Divergence of gene function is a hallmark of evolution, but assessing functional divergence
over deep time is not trivial. The few alleles available for cross-species studies often fail to …
over deep time is not trivial. The few alleles available for cross-species studies often fail to …
[HTML][HTML] Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
J Huddleston, J Hadfield, TR Sibley, J Lee… - Journal of open …, 2021 - ncbi.nlm.nih.gov
The analysis of human pathogens requires a diverse collection of bioinformatics tools.
These tools include standard genomic and phylogenetic software and custom software …
These tools include standard genomic and phylogenetic software and custom software …
Metagenomic next-generation sequencing of nasopharyngeal specimens collected from confirmed and suspect COVID-19 patients
HH Mostafa, JA Fissel, B Fanelli, Y Bergman… - MBio, 2020 - Am Soc Microbiol
Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for
emerging pathogen detection directly from clinical specimens. In contrast to targeted …
emerging pathogen detection directly from clinical specimens. In contrast to targeted …
RAD capture (Rapture): flexible and efficient sequence-based genotyping
Massively parallel sequencing has revolutionized many areas of biology, but sequencing
large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many …
large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many …
[HTML][HTML] Anatomy promotes neutral coexistence of strains in the human skin microbiome
What enables strains of the same species to coexist in a microbiome? Here, we investigate
whether host anatomy can explain strain co-residence of Cutibacterium acnes, the most …
whether host anatomy can explain strain co-residence of Cutibacterium acnes, the most …
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach
We developed an in vivo library-on-library methodology to simultaneously assess single
guide RNA (sgRNA) activity across∼ 1,400 genomic loci. Assaying across multiple human …
guide RNA (sgRNA) activity across∼ 1,400 genomic loci. Assaying across multiple human …
Rapid gene isolation in barley and wheat by mutant chromosome sequencing
J Sánchez-Martín, B Steuernagel, S Ghosh, G Herren… - Genome biology, 2016 - Springer
Identification of causal mutations in barley and wheat is hampered by their large genomes
and suppressed recombination. To overcome these obstacles, we have developed …
and suppressed recombination. To overcome these obstacles, we have developed …