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Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation
G-quadruplexes (G4s) regulate DNA replication and gene transcription, and are enriched in promoters without fully appreciated functional relevance....
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Genetic Transformation of Candida auris via Homology-Directed Repair Using a Standard Lithium Acetate Protocol
Reverse genetics is a particularly powerful tool in non-model organisms with known whole-genome sequences enabling the characterization of gene and,...
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Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives
BackgroundAlthough plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic...
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Development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of Hemileia vastatrix in coffee plantations
Coffee leaf rust (CLR) caused by Hemileia vastatrix is a devastating worldwide disease. Early monitoring is crucial for controlling CLR quickly and...
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Primer extension refractory PCR: an efficient and reliable genome walking method
Genome walking, a molecular technique for obtaining unknown flanking genomic sequences from a known genomic sequence, has been broadly applied to...
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DNA sequence features underlying large-scale duplications and deletions in human
Copy number variants (CNVs) may cover up to 12% of the whole genome and have substantial impact on phenotypes. We used 5867 duplications and 33,181...
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Establishment of a visual gene knockout system based on CRISPR/Cas9 for the rare actinomycete Nonomuraea gerenzanensis
ObjectivesTo develop a modified CRISPR/Cas9 system with the β-glucuronidase (GusA) reporter and a dual sgRNA cassette for Nonomuraea gerenzanensis ( N...
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MTG-Link: leveraging barcode information from linked-reads to assemble specific loci
BackgroundLocal assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of...
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Codon usage pattern of the ancestor of green plants revealed through Rhodophyta
Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern...
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Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae
Eukaryotic genomes contain many duplicated genes closely located with each other, such as the hexose transporter ( HXT ) genes in Saccharomyces...
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Straglr: discovering and genoty** tandem repeat expansions using whole genome long-read sequences
Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over...
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Construction of a linkage map flanking the I locus controlling dominant white bulb color and analysis of differentially expressed genes between dominant white and red bulbs in onion (Allium cepa L.)
White bulb colors of onion ( Allium cepa L.) are determined by the C and I loci which control the so-called recessive and dominant white bulb colors,...
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Engineering SH2 Domains with Tailored Specificities and Affinities
The Src Homology 2 (SH2) domain is an emerging biotechnology with applications in basic science, drug discovery, and even diagnostics. The SH2...
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Application of Integrated Computational Approaches in Prediction of Plant Virus Encoded miRNAs and Their Targeted Plant Genes
This chapter presents a comprehensive approach to predict novel miRNAs encoded by plant viruses and identify their target plant genes, through...
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Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis
BackgroundCentromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division....
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Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences
Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is...
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Regulatory mechanism for the human glioblastoma cell-specific expression of the human GD1c/GT1a/GQ1b synthase (hST8Sia V) gene
In this study we observed that human GD1c/GT1a/GQ1b synthase (hST8Sia V) is particularly expressed in human glioblastoma cells. To address the...
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Detection of Transposition Events from Next-Generation Sequencing Data
Detection of transposition events of a transposon from short reads of next-generation sequencing (NGS) is challenging because transposons are...
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The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery
JTE-607 is an anticancer and anti-inflammatory compound and its active form, compound 2, directly binds to and inhibits CPSF73, the endonuclease for...
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Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108
BackgroundStructural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However,...
