SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

(2014) Niccolo Bolli et al.   Nature Communications

Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing

(2014) Andrew E. O. Hughes et al.   PLoS Genetics

Cancer heterogeneity: implications for targeted therapeutics

(2013) R Fisher et al.   BRITISH JOURNAL OF CANCER

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing

(2013) Joep de Ligt et al.   HUMAN MUTATION

Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

(2013) M J Walter et al.   LEUKEMIA

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

Runx1 and p21 synergistically limit the extent of hair follicle stem cell quiescence in vivo

(2013) J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation

(2013) F. Wang et al.   SCIENCE

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides

(2012) J. B. Egan et al.   BLOOD

Clonal competition with alternating dominance in multiple myeloma

(2012) J. J. Keats et al.   BLOOD

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

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Opening Pandora's Box—the new biology of driver mutations and clonal evolution in cancer as revealed by next generation sequencing

(2012) Qianli C Ma et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Pretreatment Epidermal Growth Factor Receptor (EGFR) T790M Mutation Predicts Shorter EGFR Tyrosine Kinase Inhibitor Response Duration in Patients With Non–Small-Cell Lung Cancer

(2012) Kang-Yi Su et al.   JOURNAL OF CLINICAL ONCOLOGY

Minor clone provides a reservoir for relapse in multiple myeloma

(2012) F Magrangeas et al.   LEUKEMIA

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Variational Learning for Finite Dirichlet Mixture Models and Applications

(2012) Wentao Fan et al.   IEEE Transactions on Neural Networks and Learning Systems

Bayesian Estimation of Beta Mixture Models with Variational Inference

(2011) Zhanyu Ma et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine

(2010) M Gerlinger et al.   BRITISH JOURNAL OF CANCER

The Common Feature of Leukemia-Associated IDH1 and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting α-Ketoglutarate to 2-Hydroxyglutarate

(2010) Patrick S. Ward et al.   CANCER CELL

Preexistence and Clonal Selection of MET Amplification in EGFR Mutant NSCLC

(2010) Alexa B. Turke et al.   CANCER CELL

A Comprehensive Survey of Clonal Diversity Measures in Barrett's Esophagus as Biomarkers of Progression to Esophageal Adenocarcinoma

(2010) L. M. F. Merlo et al.   Cancer Prevention Research

IDH1 and IDH2 Mutations Are Frequent Genetic Alterations in Acute Myeloid Leukemia and Confer Adverse Prognosis in Cytogenetically Normal Acute Myeloid Leukemia With NPM1 Mutation Without FLT3 Internal Tandem Duplication

(2010) Peter Paschka et al.   JOURNAL OF CLINICAL ONCOLOGY

Genetic variegation of clonal architecture and propagating cells in leukaemia

(2010) Kristina Anderson et al.   NATURE

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Efficient uncertainty minimization for fuzzy spectral clustering

(2009) Brian S. White et al.   PHYSICAL REVIEW E

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA