BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

Modeling DNA methylation dynamics with approaches from phylogenetics

(2014) J. A. Capra et al.   BIOINFORMATICS

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

Differences in DNA Methylation Signatures Reveal Multiple Pathways of Progression From Adenoma to Colorectal Cancer

(2014) Yanxin Luo et al.   GASTROENTEROLOGY

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Cancer Evolution: Mathematical Models and Computational Inference

(2014) Niko Beerenwinkel et al.   SYSTEMATIC BIOLOGY

Intratumor DNA Methylation Heterogeneity Reflects Clonal Evolution in Aggressive Prostate Cancer

(2014) David Brocks et al.   Cell Reports

Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity

(2014) Vanessa Almendro et al.   Cell Reports

Phylogenetic Quantification of Intra-tumour Heterogeneity

(2014) Roland F. Schwarz et al.   PLoS Computational Biology

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

(2013) Salim Akhter Chowdhury et al.   BIOINFORMATICS

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

(2013) Raheleh Salari et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

The Implications of Clonal Genome Evolution for Cancer Medicine

(2013) Samuel Aparicio et al.   NEW ENGLAND JOURNAL OF MEDICINE

TrAp: a tree approach for fingerprinting subclonal tumor composition

(2013) Francesco Strino et al.   NUCLEIC ACIDS RESEARCH

Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution

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

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

Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity

(2013) Subhajyoti De et al.   PLoS Genetics

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

Single-Molecule Genomic Data Delineate Patient-Specific Tumor Profiles and Cancer Stem Cell Organization

(2012) A. Sottoriva et al.   CANCER RESEARCH

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

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

(2012) Moritz Gerstung et al.   Nature Communications

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Evolutionary Distances in the Twilight Zone—A Rational Kernel Approach

(2011) Roland F. Schwarz et al.   PLoS One

Discovering Biological Progression Underlying Microarray Samples

(2011) Peng Qiu et al.   PLoS Computational Biology

Applying unmixing to gene expression data for tumor phylogeny inference

(2010) Russell Schwartz et al.   BMC BIOINFORMATICS

Mutation and epigenetic molecular clocks in cancer

(2010) D. Shibata   CARCINOGENESIS

Use of Methylation Patterns to Determine Expansion of Stem Cell Clones in Human Colon Tissue

(2010) Trevor A. Graham et al.   GASTROENTEROLOGY

Tracing the tumor lineage

(2010) Nicholas E. Navin et al.   Molecular Oncology

A Differentiation-Based Phylogeny of Cancer Subtypes

(2010) Markus Riester et al.   PLoS Computational Biology

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

Network-Based Inference of Cancer Progression from Microarray Data

(2008) Yongjin Park et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics