Adi Steif
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View article: A Human Breast Cell Atlas Mapping the Homeostatic Cellular Shifts in the Adult Breast
A Human Breast Cell Atlas Mapping the Homeostatic Cellular Shifts in the Adult Breast Open
One of the barriers for breast cancer prevention and treatment is our poor understanding of the dynamic cellular shifts that naturally occur within the breast and how these changes contribute to tumour initiation. In this study we report t…
View article: Tumour evolution at single-cell resolution
Tumour evolution at single-cell resolution Open
Tumours are heterogeneous populations of cells that evolve dynamically in response to selective pressures. Bulk genome sequencing has been used successfully to characterize constituent populations in tumours. However, it is difficult to de…
View article: Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires Open
Summary Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes …
View article: clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers
clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers Open
Measuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and re…
View article: Correction to: ReMixT: clone-specific genomic structure estimation in cancer
Correction to: ReMixT: clone-specific genomic structure estimation in cancer Open
implies that at least one segment end is left disconnected (Fig. 2 d).
View article: ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data Open
Next-generation sequencing (NGS) of bulk tumour tissue can identify constituent cell populations in cancers and measure their abundance. This requires computational deconvolution of allelic counts from somatic mutations, which may be incap…
View article: Additional file 5 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Additional file 5 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data Open
List of mutually exclusive mutations (MEMs). A zip archive of five txt files that list the MEMs (see the main text) found in TNBC xenograft and ITH HGSOvCa datasets as well as the MEMs merged by PyClone and multi-sample PyClone. (ZIP 7 kb)
View article: Additional file 2 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Additional file 2 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data Open
Simulated data inputs. An excel file containing bulk allele counts and single cell genotypes generated from the Generalized Dollo model used as input to ddClone and existing methods in simulation studies. These data were used to assess the…
View article: Additional file 4 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Additional file 4 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data Open
Real data benchmarks. An excel file containing the multi-sample PyClone results for both TNBC xenograft and ITH HGSOvCa datasets used as benchmark to assess the performance of ddClone and existing methods. The performance metrics reported …
View article: Additional file 3 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Additional file 3 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data Open
Real data inputs. An excel file containing bulk data allele counts and single cell genotypes from both TNBC xenograft and ITH HGSOvCa datasets used as input to ddClone and existing methods. These data were used to assess the performance of…
View article: E-scape: Interactive visualization of single cell phylogenetics and spatio-temporal evolution in cancer
E-scape: Interactive visualization of single cell phylogenetics and spatio-temporal evolution in cancer Open
Inference of clonal dynamics and tumour evolution has fundamental importance in understanding the major clinical endpoints in cancer: development of treatment resistance, relapse and metastasis. DNA sequencing technology has made measuring…
View article: Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates Open
Significance The study of cell-to-cell genomic differences in complex multicellular systems such as cancer requires genome sequencing of large numbers of single cells. This in turn necessitates the uniform amplification of single-cell geno…