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Application of Deep Sequencing in Phage Display
This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the...
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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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DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection
Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and...
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Global detection of human variants and isoforms by deep proteome sequencing
An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically...
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Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses
Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding...
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Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
BackgroundClinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel...
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Deep sequencing unveils altered cardiac miRNome in congenital heart disease
AbstractCongenital heart disease (CHD) surges from fetal cardiac dysmorphogenesis and chiefly contributes to perinatal morbidity and cardiovascular...
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Improving protein domain classification for third-generation sequencing reads using deep learning
BackgroundWith the development of third-generation sequencing (TGS) technologies, people are able to obtain DNA sequences with lengths from 10s to...
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Deep Sc-RNA sequencing decoding the molecular dynamic architecture of the human retina
The human retina serves as a light detector and signals transmission tissue. Advanced insights into retinal disease mechanisms and therapeutic...
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Systematic characterization of immunoglobulin loci and deep sequencing of the expressed repertoire in the Atlantic cod (Gadus morhua)
BackgroundThe Atlantic cod is a prolific species in the Atlantic, despite its inconsistent specific antibody response. It presents a peculiar case...
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Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics
Advances in bioanalytical technologies are constantly expanding our insights into complex ecosystems. Here, we highlight strategies and applications...
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Cytosine base editors (CBEs) for inducing targeted DNA base editing in Nicotiana benthamiana
BackgroundThe base editors can introduce point mutations accurately without causing double-stranded DNA breaks or requiring donor DNA templates....
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Targeted Insertion in Nicotiana benthamiana Genomes via Protoplast Regeneration
Insertion of a specific sequence in a targeted region for precise editing is still a major challenge in plants. Current protocols rely on inefficient...
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Targeted A-to-G base editing of chloroplast DNA in plants
Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120–130) genes
1 , including those for essential components in photosystems I and II and the...
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NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the...
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Mitochondrial point heteroplasmy: insights from deep-sequencing of human replicate samples
BackgroundHuman mitochondrial heteroplasmy is an extensively investigated phenomenon in the context of medical diagnostics, forensic identification...
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CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato
CRISPR/Cas9 technology has become the most efficient method for genome editing in many plant species, including important industrial crops such as...
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Genome-wide identification of drought-responsive microRNAs and their target genes in Chinese jujube by deep sequencing
BackgroundMicroRNAs (miRNAs) are about 21 snucleotide (nt) long, non-coding RNAs that play an important role in plant abiotic stress responses....
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Multi-Knock—a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants
Plant genomes are characterized by large and complex gene families that often result in similar and partially overlap** functions. This genetic...
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Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development
Numerous toxins threaten humans, but specific antidotes are unavailable for most of them. Although CRISPR screening has aided the discovery of the...
