Abstract: The disclosure provides methods and related kits, reagents, and systems for selectively deaminating unmethylated cytosine residues in nucleic acid molecules. In some embodiments, the methods and related kits, reagents, and systems are applied for methods of detecting and/or mapping methylated cytosine residues in nucleic acids. The nucleic can be RNA or DNA. Some embodiments include contacting the polynucleic acid with a bacterial cytosine deaminase, for example DddA or SsdA, or functional fragments or derivatives thereof. Representative DddA and SsdA have sequences set forth in SEQ ID NOS:1 and 2, respectively. The bacterial cytosine deaminases of the disclosure are sensitive to methylation and, thus, deaminate only unmethylated cytosines to provide a cytosine to uracil conversion. The conversion can be detected as a C•G-to-T•A transitions in subsequent sequencing analysis.

Abstract: Disclosed are methods and related compositions for genomic editing. In one aspect, methods of editing double stranded DNA (dsDNA) use first and second editing complexes specific for first and second target sequences on the sense and antisense strands of the dsDNA molecule, respectively. Each editing complex comprises an extended guide RNA associated with a fusion editor protein, which comprises a functional nickase domain and a functional reverse transcriptase domain. The respective guide RNAs guide their associated fusion editor proteins to the dsDNA, which implement single stranded breaks on opposite strands of the dsDNA. The respective reverse transcriptase domains generate 3? overhangs. Repair of the dsDNA excises the portion of dsDNA disposed between the two single-stranded breaks. A variety of configurations and applications of the method are disclosed, providing flexible, facile, efficient, and precise methods to impose genetic manipulations.

Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes.

Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.

Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.

Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.

Abstract: The present invention provides methods for multiplex assembly of oligonucleotides.

Abstract: Methods of genome sequencing of a fetus are provided herein. In some embodiments, such methods include steps of predicting inheritance or transmission of an allele from one or more maternal-only heterozygous sites from a maternal genomic sequence to a fetal genome sequence; and predicting inheritance or transmission of an allele from one or more paternal-only heterozygous sites from a paternal genomic sequence to a fetal genome sequence. In some embodiments, the methods may also include predicting transmission of one or more genomic variants at one or more heterozygous sites that are present on both a maternal genomic sequence and a paternal genomic sequence. According to these embodiments, the paternal genomic sequence and the maternal genomic sequence are derived from a biological sample containing DNA. According to other embodiments, the sequencing methods may include a step of predicting de novo mutations in a fetal genomic sequence.

Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.