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Poly(a) selection introduces bias and undue noise in direct RNA-sequencing
BackgroundGenome-wide RNA-sequencing technologies are increasingly critical to a wide variety of diagnostic and research applications. RNA-seq users...
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TILLING by Sequencing
The Targeting Induced Local Lesions In Genome (TILLING) is emerging as a preferred technique of reverse genetics. The use of next generation...
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Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender
Droplet-based single-cell assays, including single-cell RNA sequencing (scRNA-seq), single-nucleus RNA sequencing (snRNA-seq) and cellular indexing...
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Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
BackgroundDirect RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene...
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Mitochondrial DNA Sequencing and Heteroplasmy Quantification by Next Generation Sequencing
Over the last 10 years, next generation sequencing (NGS) became the gold standard for both diagnosis and discovery of new disease genes responsible...
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VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells
Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential...
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Application of Single-Cell Sequencing on Stem Cell Research
The variation and heterogeneity within cells are the fundamental features of stem cells. Each tissue has a resident stem cell niche compartmentalized...
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The chemistry of next-generation sequencing
The first large genome fully sequenced by next-generation sequencing (NGS) was that of a bacteriophage using sequencing by synthesis (SBS) as a...
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Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis
Many important biological facts have been found as single-cell RNA sequencing (scRNA-seq) technology has advanced. With the use of this technology,...
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Effect of genomic and cellular environments on gene expression noise
BackgroundIndividual cells from isogenic populations often display large cell-to-cell differences in gene expression. This “noise” in expression...
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16S rRNA Amplicon Sequencing
The 16S rRNA amplicon sequencing technique is a microbiome analysis where different samples are analyzed at the same time using multiplexing. The...
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Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA
Bisulfite sequencing (BS-seq) to detect 5-methylcytosine (5mC) is limited by lengthy reaction times, severe DNA damage, overestimation of 5mC level...
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DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing
BackgroundNanopore sequencing allows selective sequencing, the ability to programmatically reject unwanted reads in a sample. Selective sequencing...
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Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed...
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Single Cell RNA-Sequencing in Arabidopsis Root Tissues
Droplet-based single-cell RNA-sequencing (scRNA-seq)Single-cell RNA-sequencing (scRNA-seq) empowers transcriptomicTranscriptomics profiling with an...
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RNA Sequencing (RNA-seq)
RNA sequencing (or popularly known as RNA-seq) or whole transcriptome shortgun sequencing (WTSS) is a useful next-generation sequencing (NGS)...
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LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis
Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert...
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Identification of Closely Related Polymorphisms with Striga Resistance Using Next Generation Sequencing
Molecular markers are powerful tools to enhance speed of breeding. Recent advances of sequencing technology allow us to identify most polymorphisms...
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scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data
BackgroundSystematic description of library quality and sequencing performance of single-cell RNA sequencing (scRNA-seq) data is imperative for...
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Revolution of the Next-Generation Sequencing and Its Application in Phytobacterial Diseases: Unraveling the Culprits
The genome-sequencing revolution advances exponentially with a rich and diverse history and application. Next-generation sequencing (NGS) has vastly...