Computational and analytical challenges in single-cell transcriptomics
The development of high-throughput RNA sequencing (RNA-seq) at the single-cell level has
already led to profound new discoveries in biology, ranging from the identification of novel …
already led to profound new discoveries in biology, ranging from the identification of novel …
Design and computational analysis of single-cell RNA-sequencing experiments
R Bacher, C Kendziorski - Genome biology, 2016 - Springer
Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows
us to address scientific questions that eluded examination just a few years ago. With the …
us to address scientific questions that eluded examination just a few years ago. With the …
A human pluripotent stem cell-based platform to study SARS-CoV-2 tropism and model virus infection in human cells and organoids
SARS-CoV-2 has caused the COVID-19 pandemic. There is an urgent need for
physiological models to study SARS-CoV-2 infection using human disease-relevant cells …
physiological models to study SARS-CoV-2 infection using human disease-relevant cells …
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice
SH Lee, SY Cho, Y Yoon, C Park, J Sohn… - Nature …, 2021 - nature.com
The gut microbiome can influence the development of tumours and the efficacy of cancer
therapeutics,,,–; however, the multi-omics characteristics of antitumour bacterial strains have …
therapeutics,,,–; however, the multi-omics characteristics of antitumour bacterial strains have …
Genetic compensation triggered by mutant mRNA degradation
Genetic robustness, or the ability of an organism to maintain fitness in the presence of
harmful mutations, can be achieved via protein feedback loops. Previous work has …
harmful mutations, can be achieved via protein feedback loops. Previous work has …
Pluripotent stem cell-derived epithelium misidentified as brain microvascular endothelium requires ETS factors to acquire vascular fate
Cells derived from pluripotent sources in vitro must resemble those found in vivo as closely
as possible at both transcriptional and functional levels in order to be a useful tool for …
as possible at both transcriptional and functional levels in order to be a useful tool for …
Cellular senescence drives age-dependent hepatic steatosis
The incidence of non-alcoholic fatty liver disease (NAFLD) increases with age. Cellular
senescence refers to a state of irreversible cell-cycle arrest combined with the secretion of …
senescence refers to a state of irreversible cell-cycle arrest combined with the secretion of …
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are
increasingly used in high-throughput sequencing experiments. Through a UMI, identical …
increasingly used in high-throughput sequencing experiments. Through a UMI, identical …
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
Background As high-throughput sequencing platforms produce longer and longer reads,
sequences generated from short inserts, such as those obtained from fossil and degraded …
sequences generated from short inserts, such as those obtained from fossil and degraded …
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts
D Karagkouni, MD Paraskevopoulou… - Nucleic acids …, 2020 - academic.oup.com
Abstract DIANA-LncBase v3. 0 (www. microrna. gr/LncBase) is a reference repository with
experimentally supported miRNA targets on non-coding transcripts. Its third version provides …
experimentally supported miRNA targets on non-coding transcripts. Its third version provides …