A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations

Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis

(2021) Abhishek Sarkar et al.   NATURE GENETICS

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

(2020) Akdes Serin Harmanci et al.   Nature Communications

Exploiting evolutionary steering to induce collateral drug sensitivity in cancer

(2020) Ahmet Acar et al.   Nature Communications

Pervasive chromosomal instability and karyotype order in tumour evolution

(2020) Thomas B. K. Watkins et al.   NATURE

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

(2020) Simone Zaccaria et al.   NATURE BIOTECHNOLOGY

Subclonal reconstruction of tumors by using machine learning and population genetics

(2020) Giulio Caravagna et al.   NATURE GENETICS

Measuring evolutionary cancer dynamics from genome sequencing, one patient at a time

(2020) Giulio Caravagna   Statistical Applications in Genetics and Molecular Biology

Resolving genetic heterogeneity in cancer

(2019) Samra Turajlic et al.   NATURE REVIEWS GENETICS

Somatic mutation and clonal expansions in human tissues

(2019) Inigo Martincorena   Genome Medicine

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

(2018) Georgios Vlachogiannis et al.   SCIENCE

Copy number signatures and mutational processes in ovarian carcinoma

(2018) Geoff Macintyre et al.   NATURE GENETICS

Detecting repeated cancer evolution from multi-region tumor sequencing data

(2018) Giulio Caravagna et al.   NATURE METHODS

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Algorithmic methods to infer the evolutionary trajectories in cancer progression

(2016) Giulio Caravagna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution

(2015) Nicholas McGranahan et al.   CANCER CELL

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE