Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics

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

(2013) Salim Akhter Chowdhury et al.   BIOINFORMATICS

Methods and challenges in timing chromosomal abnormalities within cancer samples

(2013) Elizabeth Purdom et al.   BIOINFORMATICS

Advances for studying clonal evolution in cancer

(2013) Li Ding et al.   CANCER LETTERS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Learning Oncogenetic Networks by Reducing to Mixed Integer Linear Programming

(2013) Hossein Shahrabi Farahani et al.   PLoS One

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

Single-Cell Genetic Analysis of Ductal Carcinoma in Situ and Invasive Breast Cancer Reveals Enormous Tumor Heterogeneity yet Conserved Genomic Imbalances and Gain of MYC during Progression

(2012) Kerstin Heselmeyer-Haddad et al.   AMERICAN JOURNAL OF PATHOLOGY

Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability

(2012) L. I. Shlush et al.   BLOOD

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

Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples

(2012) Ayshwarya Subramanian et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response

(2012) N. J. Szerlip et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Pathways in BRCA1-Associated Breast Tumors

(2012) Filipe C. Martins et al.   Cancer Discovery

Mosaic Amplification of Multiple Receptor Tyrosine Kinase Genes in Glioblastoma

(2011) Matija Snuderl et al.   CANCER CELL

Accurate Reconstruction of the Temporal Order of Mutations in Neoplastic Progression

(2011) Kathleen Sprouffske et al.   Cancer Prevention Research

MYC and Metastasis

(2011) A. Wolfer et al.   CANCER RESEARCH

Estimation of rearrangement phylogeny for cancer genomes

(2011) C. D. Greenman et al.   GENOME RESEARCH

A Metric for Phylogenetic Trees Based on Matching

(2011) Yu Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Evolution of human BCR–ABL1 lymphoblastic leukaemia-initiating cells

(2011) Faiyaz Notta et al.   NATURE

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data

(2011) Y. Tao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype

(2010) So Yeon Park et al.   JOURNAL OF CLINICAL INVESTIGATION

Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis

(2010) Eric Letouzé et al.   GENOME BIOLOGY

Fluorescence in Situ Hybridization Markers for Prediction of Cervical Lymph Node Metastases

(2009) Darawalee Wangsa et al.   AMERICAN JOURNAL OF PATHOLOGY

Evolutionary Theory of Cancer

(2009) Camille Stephan-Otto Attolini et al.   Annals of the New York Academy of Sciences

Tumor heterogeneity: Causes and consequences

(2009) Andriy Marusyk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Inferring progression models for CGH data

(2009) Jun Liu et al.   BIOINFORMATICS

Quantifying cancer progression with conjunctive Bayesian networks

(2009) M. Gerstung et al.   BIOINFORMATICS

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores

(2008) J. Bogojeska et al.   BIOINFORMATICS

Stability analysis of mixtures of mutagenetic trees

(2008) Jasmina Bogojeska et al.   BMC BIOINFORMATICS

Cell Lineage Analysis of a Mouse Tumor

(2008) D. Frumkin et al.   CANCER RESEARCH

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