High-Throughput Sequencing Technologies

Reuter, Jason; Spacek, Damek V.; Snyder, M

doi:10.1016/j.molcel.2015.05.004

Cited by 1,117 publications

(757 citation statements)

References 114 publications

(113 reference statements)

Supporting

Mentioning

746

Contrasting

Unclassified

Order By: Relevance

“…15 As these techniques are fundamentally optimized for the quantification of nucleic acids, gene expression profiling has traditionally focused on measuring the abundance and regulation of mRNA at the transcriptional level. However, gene expression is also extensively regulated at the translational level, meaning that mRNA abundance alone does not fully present the expressional status.…”

Section: Introductionmentioning

confidence: 99%

Knockdown of BC200 RNA expression reduces cell migration and invasion by destabilizing mRNA for calcium-binding protein S100A11

et al. 2017

View full text Add to dashboard Cite

Although BC200 RNA is best known as a neuron-specific non-coding RNA, it is overexpressed in various cancer cells. BC200 RNA was recently shown to contribute to metastasis in several cancer cell lines, but the underlying mechanism was not understood in detail. To examine this mechanism, we knocked down BC200 RNA in cancer cells, which overexpress the RNA, and examined cell motility, profiling of ribosome footprints, and the correlation between cell motility changes and genes exhibiting altered ribosome profiles. We found that BC200 RNA knockdown reduced cell migration and invasion, suggesting that BC200 RNA promotes cell motility. Our ribosome profiling analysis identified 29 genes whose ribosomal occupations were altered more than 2-fold by BC200 RNA knockdown. Many (> 30%) of them were directly or indirectly related to cancer progression. Among them, we focused on S100A11 (which showed a reduced ribosome footprint) because its expression was previously shown to increase cellular motility. S100A11 was decreased at both the mRNA and protein levels following knockdown of BC200 RNA. An actinomycin-chase experiment showed that BC200 RNA knockdown significantly decreased the stability of the S100A11 mRNA without changing its transcription rate, suggesting that the downregulation of S100A11 was mainly caused by destabilization of its mRNA. Finally, we showed that the BC200 RNAknockdown-induced decrease in cell motility was mainly mediated by S100A11. Together, our results show that BC200 RNA promotes cell motility by stabilizing S100A11 transcripts.

show abstract

Section: Introductionmentioning

confidence: 99%

Knockdown of BC200 RNA expression reduces cell migration and invasion by destabilizing mRNA for calcium-binding protein S100A11

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Bioinformatics is going through a transition driven by the ongoing developments of high throughput sequencing [1,2]. To cope with the surge of sequencing data, the bioinformatics community is under pressure to produce faster and more efficient algorithms.…”

Section: Introductionmentioning

confidence: 99%

Analytic Combinatorics for Computing Seeding Probabilities

Filion

2018

Algorithms

View full text Add to dashboard Cite

Seeding heuristics are the most widely used strategies to speed up sequence alignment in bioinformatics. Such strategies are most successful if they are calibrated, so that the speed-versus-accuracy trade-off can be properly tuned. In the widely used case of read mapping, it has been so far impossible to predict the success rate of competing seeding strategies for lack of a theoretical framework. Here, we present an approach to estimate such quantities based on the theory of analytic combinatorics. The strategy is to specify a combinatorial construction of reads where the seeding heuristic fails, translate this specification into a generating function using formal rules, and finally extract the probabilities of interest from the singularities of the generating function. The generating function can also be used to set up a simple recurrence to compute the probabilities with greater precision. We use this approach to construct simple estimators of the success rate of the seeding heuristic under different types of sequencing errors, and we show that the estimates are accurate in practical situations. More generally, this work shows novel strategies based on analytic combinatorics to compute probabilities of interest in bioinformatics.

show abstract

“…Illumina has come up with the latest NextSeq 500 that has only two-channel SBS technology that requires only two images to determine all four base calls. This reduces the image capturing time, number of cycle, cost of sequencing and time required for data processing, while delivering high quality and accuracy [22].…”

Section: Sequencing By Synthesis (Sbs)mentioning

confidence: 99%