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Article
Open AccessMassively targeted evaluation of therapeutic CRISPR off-targets in cells
Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential for advancing RGN-based gene therapies. Here we report SURRO-seq for simultaneously ev...
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Article
Open AccessEnhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning
The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRN...
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Article
Open AccessNovel circRNA discovery in sheep shows evidence of high backsplice junction conservation
Circular RNAs (circRNAs) are covalently closed circular non-coding RNAs. Due to their structure, circRNAs are more stable and have longer half-lives than linear RNAs making them good candidates for disease bio...
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Article
Open AccessCRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Recent experimental efforts of CRISPR-Cas9 systems have shown that off-target binding and cleavage are a concern for the system and that this is highly dependent on the selected guide RNA (gRNA) design. Comput...
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Article
Open AccessStructured RNAs and synteny regions in the pig genome
Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammal...
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Article
Open AccessAnalyses of pig genomes provide insight into porcine demography and evolution
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and...
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Article
Open AccessProfiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
MicroRNAs (miRNAs) are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level...
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Chapter
Elucidation of Ligand-Field Theory. Reformulation and Revival by Density Functional Theory
Constrained by the use of an “average-of-configuration” computation, Kohn-Sham-DFT allows identification of the complete set of dq states of the ligand field plus repulsion model, LFR. A one-to-one correspondence...
