Progress in forensic bone DNA analysis: Lessons learned from ancient DNA

M Hofreiter, J Sneberger, M Pospisek… - Forensic Science …, 2021 - Elsevier
Research on ancient and forensic DNA is related in many ways, and the two fields must deal
with similar obstacles. Therefore, communication between these two communities has the …

[HTML][HTML] Strategies for improving detection of circulating tumor DNA using next generation sequencing

R Tébar-Martínez, J Martín-Arana… - Cancer Treatment …, 2023 - Elsevier
Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive
tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from …

Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning

N Liang, B Li, Z Jia, C Wang, P Wu, T Zheng… - Nature biomedical …, 2021 - nature.com
The low abundance of circulating tumour DNA (ctDNA) in plasma samples makes the
analysis of ctDNA biomarkers for the detection or monitoring of early-stage cancers …

The sponge microbiome project

L Moitinho-Silva, S Nielsen, A Amir, A Gonzalez… - …, 2017 - academic.oup.com
Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in
southwest China covers several different habitats and environments. However, not much …

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

A Serin Harmanci, AO Harmanci, X Zhou - Nature communications, 2020 - nature.com
RNA sequencing experiments generate large amounts of information about expression
levels of genes. Although they are mainly used for quantifying expression levels, they …

Rapid species-level metagenome profiling and containment estimation with sylph

J Shaw, YW Yu - Nature Biotechnology, 2024 - nature.com
Profiling metagenomes against databases allows for the detection and quantification of
microorganisms, even at low abundances where assembly is not possible. We introduce …

Clonal hematopoiesis and risk of incident lung cancer

R Tian, B Wiley, J Liu, X Zong, B Truong… - Journal of Clinical …, 2023 - ascopubs.org
PURPOSE To prospectively examine the association between clonal hematopoiesis (CH)
and subsequent risk of lung cancer. METHODS Among 200,629 UK Biobank (UKBB) …

On the causes, consequences, and avoidance of PCR duplicates: towards a theory of library complexity

NC Rochette, AG Rivera‐Colón, J Walsh… - Molecular ecology …, 2023 - Wiley Online Library
Library preparation protocols for most sequencing technologies involve PCR amplification of
the template DNA, which open the possibility that a given template DNA molecule is …

Germline de novo mutations in families with Mendelian cancer syndromes caused by defects in DNA repair

K Sherwood, JC Ward, I Soriano, L Martin… - nature …, 2023 - nature.com
DNA repair defects underlie many cancer syndromes. We tested whether de novo germline
mutations (DNMs) are increased in families with germline defects in polymerase …

Hologenomic data generation and analysis in wild vertebrates

C Pietroni, N Gaun, A Leonard… - Methods in Ecology …, 2024 - Wiley Online Library
Hologenomics, the joint analysis of host genomes and microbial metagenomes, has the
potential to address fundamental biological questions from a systemic host‐microbiota …