LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data

Computational methods for single-cell omics across modalities

(2020) Mirjana Efremova et al.   NATURE METHODS

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

(2019) Lei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

(2019) Daniele Ramazzotti et al.   BMC BIOINFORMATICS

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

(2019) Anna S. Nam et al.   NATURE

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data

(2019) Salem Malikic et al.   Nature Communications

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

(2019) Ketevan Chkhaidze et al.   PLoS Computational Biology

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples

(2019) Matthew A. Myers et al.   Cell Systems

SNV identification from single-cell RNA sequencing data

(2019) Patricia M Schnepp et al.   HUMAN MOLECULAR GENETICS

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data

(2019) Hamim Zafar et al.   GENOME RESEARCH

OUP accepted manuscript

(2018)   BIOINFORMATICS

Radiologic and Genomic Evolution of Individual Metastases during HER2 Blockade in Colorectal Cancer

(2018) Giulia Siravegna et al.   CANCER CELL

Adoptive immunotherapy using PRAME-specific T cells in medulloblastoma

(2018) Domenico Orlando et al.   CANCER RESEARCH

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

Inferring parsimonious migration histories for metastatic cancers

(2018) Mohammed El-Kebir et al.   NATURE GENETICS

High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics

(2018) Maurizio Pellegrino et al.   GENOME RESEARCH

Intra-tumour diversification in colorectal cancer at the single-cell level

(2018) Sophie F. Roerink et al.   NATURE

Detecting repeated cancer evolution from multi-region tumor sequencing data

(2018) Giulio Caravagna et al.   NATURE METHODS

Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial

(2018) Khurum H. Khan et al.   Cancer Discovery

E-scape: interactive visualization of single-cell phylogenetics and cancer evolution

(2017) Maia A Smith et al.   NATURE METHODS

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Driving CAR T-cells forward

(2016) Hollie J. Jackson et al.   Nature Reviews Clinical Oncology

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

Identification of COL1A1 and COL1A2 as candidate prognostic factors in gastric cancer

(2016) Jun Li et al.   World Journal of Surgical Oncology

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures

(2016) Mohammed El-Kebir et al.   Cell Systems

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

(2015) Mohammed El-Kebir et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

The first five years of single-cell cancer genomics and beyond

(2015) Nicholas E. Navin   GENOME RESEARCH

Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics

(2015) A. Goodspeed et al.   MOLECULAR CANCER RESEARCH

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity

(2015) Bartlomiej Waclaw et al.   NATURE

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

(2015) Iain C Macaulay et al.   NATURE METHODS

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

(2015) Jong Kyoung Kim et al.   Nature Communications

Large-Scale Label-Free Comparative Proteomics Analysis of Polo-Like Kinase 1 Inhibition via the Small-Molecule Inhibitor BI 6727 (Volasertib) in BRAFV600E Mutant Melanoma Cells

(2014) Brian D. Cholewa et al.   JOURNAL OF PROTEOME RESEARCH

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

(2014) Peter Eirew et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Investigating the Relation between Stochastic Differentiation, Homeostasis and Clonal Expansion in Intestinal Crypts via Multiscale Modeling

(2014) Alex Graudenzi et al.   PLoS One

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

(2014) A. P. Patel et al.   SCIENCE

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics

(2013) A. Sottoriva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

(2012) Yingrui Li et al.   GigaScience

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

BCR-ABL kinase is dead; long live the CML stem cell

(2010) Alexander Perl et al.   JOURNAL OF CLINICAL INVESTIGATION

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide screen of promoter methylation identifies novel markers in melanoma

(2009) Y. Koga et al.   GENOME RESEARCH

A multi-marker assay to distinguish malignant melanomas from benign nevi

(2009) M. Kashani-Sabet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA