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Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs
BackgroundIdentifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying...
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PCR-Based Assembly of Gene Sequences by Thermodynamically Balanced Inside-Out (TBIO) Gene Synthesis
The ability to enzymatically assemble DNA oligonucleotides into longer DNA duplexes in a process known as gene synthesis has wide-ranging...
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Reporter gene assays and chromatin-level assays define substantially non-overlap** sets of enhancer sequences
BackgroundTranscriptional enhancers are essential for gene regulation, but how these regulatory elements are best defined remains a significant...
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A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences
Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary...
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Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
BackgroundDuring evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than...
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dCas9-based gene editing for cleavage-free genomic knock-in of long sequences
Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA...
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Gene Expression in Eukaryotes
Eukaryotes are multicellular organisms and thus have a complex process of gene regulation. In eukaryotes, the gene sequences are not continuous to...
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Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences
BackgroundMore than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a...
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Clustering Sequences into OTUs
This chapter describes and illustrates taxonomic classification of the representative sequences and clustering of OTUs. First it introduces some...
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Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences
BackgroundSmall nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most...
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Genetic analyses of rabies virus glycoprotein and nucleoprotein gene sequences reveal the emergence of multiple lineages in animals in Arkhangai province, a central region of Mongolia
Genetic characterizations of rabies viruses circulating in carnivore and non-carnivore animals were investigated for the first time in Arkhangai...
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Pig pangenome graph reveals functional features of non-reference sequences
BackgroundThe reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic...
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Genetics and evolutionary insights from Solanaceae genome sequences
The availability of genome sequence resources and genomic information enables the functional characterization of genes in crop plants. These genes...
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Phylogeny of the Dipus sagitta Species Complex by Nuclear Gene Sequences
The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was...
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Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories
BackgroundIn nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid...
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Deep generative design of RNA family sequences
RNA engineering has immense potential to drive innovation in biotechnology and medicine. Despite its importance, a versatile platform for the...
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Using Gene Editing Strategies for Wheat Improvement
Despite wheat’s global importance, it has trailed behind the other major cereals regarding genomic tools and resources as well as gene...
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Application of Repetitive Sequences in Fish Cell Depletion as a Target for the CRISPR/Cas9 System
Specific cell depletion is a common means to study the physiological function of cell lineages and tissue regeneration. However, 100% depletion is...
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Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes
Adenine base editors (ABEs) and cytosine base editors (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation of double...
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MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems
The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/ ) is an open-access data...