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  • recognition
  • Hairpin polyamides are typically composed of pyrrole and imidazole rings and can be engineered, using simple recognition rules ( 16 ), to target specific 6-12 base pair (bp) sequences ( Fig. 1 A and Fig. S1 A and B ) ( 15 , 16 ). (pnas.org)
  • microbiome
  • Using fecal samples from the LifeLines DEEP cohort, they have profiled the gut microbiome of 893 participants by 16s ribosomal RNA sequencing and identified novel cross-sectional associations between several bacterial taxa and cardiometabolic phenotypes such as the body mass index and blood lipid levels. (ahajournals.org)
  • Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. (stanford.edu)
  • Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. (stanford.edu)
  • gene-expression
  • Epigenetics is the term for regulation of gene expression, other than via changes in the DNA sequence. (qiagen.com)
  • Enzymes that chemically modify genomic DNA and histones, as well as epigenetic chromatin remodeling factors, regulate chromatin accessibility and therefore gene expression. (qiagen.com)
  • reveal
  • Our experiments on 10X Chromium linked read sequencing trio data reveal that HAPDeNovo eliminates 80 to 99% of false positives regardless of how large the candidate DNM set is.CONCLUSIONS: HAPDeNovo leverages the haplotype information from linked read sequencing to remove spurious false positive DNMs effectively, and it increases accuracy of DNM detection dramatically without sacrificing sensitivity. (stanford.edu)
  • conservation
  • We found that the C. elegans ems ortholog is able to substitute for fly ems in brain development, indicating that sequence conservation rather than conservation of biological function is important. (biologists.org)
  • synthetic
  • We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. (stanford.edu)
  • human
  • Fifty-six homeodomain families found in human and/or fruit fly are also found in Nematostella , though seventeen families shared by human and fly appear absent in Nematostella . (biomedcentral.com)
  • analysis
  • Copy number variation (CNV) analysis, using array-based comparative genomic hybridization (array CGH), excluded the possibility of microdeletion or microduplication. (sigmaaldrich.com)
  • br />Used for any analysis based on sequence alignment, structure comparison, or evaluation of sequence features such as composition. (uniprot.org)
  • coverage
  • Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20*) raw short-read-sequence coverage. (stanford.edu)
  • basis
  • As a destructive pathogen to sugar industry, the S. scitamineum genome will facilitate future research on the genomic basis and the pathogenic mechanisms of sugarcane smut. (biomedcentral.com)