Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Origins of DNA replication in eukaryotes

Y Hu, B Stillman - Molecular cell, 2023 - cell.com
Errors occurring during DNA replication can result in inaccurate replication, incomplete
replication, or re-replication, resulting in genome instability that can lead to diseases such as …

Current and future perspectives of liquid biopsies in genomics-driven oncology

E Heitzer, IS Haque, CES Roberts… - Nature Reviews …, 2019 - nature.com
Precision oncology seeks to leverage molecular information about cancer to improve patient
outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by …

Resolving genetic heterogeneity in cancer

S Turajlic, A Sottoriva, T Graham… - Nature Reviews Genetics, 2019 - nature.com
To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones
mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the …

Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing

C Kim, R Gao, E Sei, R Brandt, J Hartman, T Hatschek… - Cell, 2018 - cell.com
Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops
resistance to chemotherapy. An unresolved question is whether resistance is caused by the …

Breast tumours maintain a reservoir of subclonal diversity during expansion

DC Minussi, MD Nicholson, H Ye, A Davis, K Wang… - Nature, 2021 - nature.com
Our knowledge of copy number evolution during the expansion of primary breast tumours is
limited,. Here, to investigate this process, we developed a single-cell, single-molecule DNA …

[HTML][HTML] Single-cell genomic variation induced by mutational processes in cancer

T Funnell, CH O'Flanagan, MJ Williams, A McPherson… - Nature, 2022 - nature.com
How cell-to-cell copy number alterations that underpin genomic instability in human cancers
drive genomic and phenotypic variation, and consequently the evolution of cancer, remains …

Integrated omics: tools, advances and future approaches

BB Misra, C Langefeld, M Olivier… - Journal of molecular …, 2019 - jme.bioscientifica.com
With the rapid adoption of high-throughput omic approaches to analyze biological samples
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …

Aneuploidy and complex genomic rearrangements in cancer evolution

TM Baker, S Waise, M Tarabichi, P Van Loo - Nature cancer, 2024 - nature.com
Mutational processes that alter large genomic regions occur frequently in developing
tumors. They range from simple copy number gains and losses to the shattering and …

A practical guide to cancer subclonal reconstruction from DNA sequencing

M Tarabichi, A Salcedo, AG Deshwar… - Nature …, 2021 - nature.com
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer
evolution studies, providing insight into the clonality and relative ordering of mutations and …