COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies
Sign Up to like & getrecommendations! Published in 2022 at "Ecology and Evolution"
DOI: 10.1002/ece3.9549
Abstract: Abstract Monitoring community composition of Foraminifera (single‐celled marine protists) provides valuable insights into environmental conditions in marine ecosystems. Despite the efficiency of environmental DNA (eDNA) and bulk‐sample DNA (bulk‐DNA) metabarcoding to assess the presence of… read more here.
Keywords: dna; large benthic; bulk dna; foraminifera ... See more keywords
Abstract 4689: Subclone-specific evolution of tumor phenotypes – A framework to study subclone-specific gene expression from a combination of bulk DNA and single cell RNA sequencing data
Sign Up to like & getrecommendations! Published in 2019 at "Tumor Biology"
DOI: 10.1158/1538-7445.am2019-4689
Abstract: Several approaches are now available for subclonal reconstruction of heterogeneous tumor biopsies from somatic variant allele frequencies measured in bulk DNA sequencing datasets, including our own SubcloneSeeker program. However, to understand how chemoresistance, relapse, or… read more here.
Keywords: bulk dna; tumor; cell; subclone specific ... See more keywords
Determination of complete chromosomal haplotypes by bulk DNA sequencing
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DOI: 10.1186/s13059-021-02330-1
Abstract: Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk… read more here.
Keywords: complete chromosomal; dna sequencing; determination complete; chromosomal haplotypes ... See more keywords
Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology"
DOI: 10.1186/s13059-022-02600-6
Abstract: Clonal analysis of tumour sequencing data enables the evaluation of the relationship of histologically distinct synchronous lesions, such as co-existing benign areas, and temporally distinct tumours, such as primary-recurrence comparisons. In this review, we summarise… read more here.
Keywords: statistical approaches; evaluating statistical; bulk dna; define clonal ... See more keywords
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
Sign Up to like & getrecommendations! Published in 2024 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1012631
Abstract: Motivation DNA sequencing of multiple bulk samples from a tumor provides the opportunity to investigate tumor heterogeneity and reconstruct a phylogeny of a patient’s cancer. However, since bulk DNA sequencing of tumor tissue measures thousands… read more here.
Keywords: problem; dna sequencing; bulk dna; reconstruction ... See more keywords