Cancer Evolution: Mathematical Models and Computational Inference

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

Using single cell sequencing data to model the evolutionary history of a tumor

(2014) Kyung Kim et al.   BMC BIOINFORMATICS

Evolution of the Cancer Stem Cell Model

(2014) Antonija Kreso et al.   Cell Stem Cell

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research

(2014) M. Hidalgo et al.   Cancer Discovery

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

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

Inferring Clonal Composition from Multiple Sections of a Breast Cancer

(2014) Habil Zare et al.   PLoS Computational Biology

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

(2014) Christopher A. Miller et al.   PLoS Computational Biology

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

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data

(2013) Nicholas B. Larson et al.   BIOINFORMATICS

Methods and challenges in timing chromosomal abnormalities within cancer samples

(2013) Elizabeth Purdom et al.   BIOINFORMATICS

Clinical and biological implications of driver mutations in myelodysplastic syndromes

(2013) E. Papaemmanuil et al.   BLOOD

Chromoplexy: A New Category of Complex Rearrangements in the Cancer Genome

(2013) Michael M. Shen   CANCER CELL

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Single-cell mutational profiling and clonal phylogeny in cancer

(2013) N. E. Potter et al.   GENOME RESEARCH

A deterministic model for the occurrence and dynamics of multiple mutations in hierarchically organized tissues

(2013) B. Werner et al.   Journal of the Royal Society Interface

Selection and adaptation during metastatic cancer progression

(2013) Christoph A. Klein   NATURE

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Tumour heterogeneity and cancer cell plasticity

(2013) Corbin E. Meacham et al.   NATURE

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Influence of tumour micro-environment heterogeneity on therapeutic response

(2013) Melissa R. Junttila et al.   NATURE

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA

(2013) Muhammed Murtaza et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

Biopsies: next-generation biospecimens for tailoring therapy

(2013) Mark Basik et al.   Nature Reviews Clinical Oncology

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

(2013) Sarah-Jane Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Measurement of Cancer Cell Growth Heterogeneity through Lentiviral Barcoding Identifies Clonal Dominance as a Characteristic of In Vivo Tumor Engraftment

(2013) Olivier Nolan-Stevaux et al.   PLoS One

Learning Oncogenetic Networks by Reducing to Mixed Integer Linear Programming

(2013) Hossein Shahrabi Farahani et al.   PLoS One

Impact of deleterious passenger mutations on cancer progression

(2013) C. D. McFarland 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

Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation

(2013) C. Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

(2013) Elza C de Bruin et al.   Genome Medicine

Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution

(2013) Rui Zhao et al.   PLoS Computational Biology

Evolutionary dynamics of cancer in response to targeted combination therapy

(2013) Ivana Bozic et al.   eLife

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

Cellular Heterogeneity and Molecular Evolution in Cancer

(2012) Vanessa Almendro et al.   Annual Review of Pathology-Mechanisms of Disease

Estimating the order of mutations during tumorigenesis from tumor genome sequencing data

(2012) Ahrim Youn et al.   BIOINFORMATICS

Efficient sampling for Bayesian inference of conjunctive Bayesian networks

(2012) T. Sakoparnig et al.   BIOINFORMATICS

Impact of Tumor Progression on Cancer Incidence Curves

(2012) E. G. Luebeck et al.   CANCER RESEARCH

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

Preventive Evolutionary Medicine of Cancers

(2012) Michael E. Hochberg et al.   Evolutionary Applications

Modelling the evolution of genetic instability during tumour progression

(2012) Ruchira S. Datta et al.   Evolutionary Applications

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

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

A branching process model of ovarian cancer

(2012) Kaveh Danesh et al.   JOURNAL OF THEORETICAL BIOLOGY

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Cancer sequencing unravels clonal evolution

(2012) Carlos Caldas   NATURE BIOTECHNOLOGY

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

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA

(2012) T. Forshew et al.   Science Translational Medicine

Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling

(2012) Y. Yuan et al.   Science Translational Medicine

Evolution of the cancer genome

(2012) Ondrej Podlaha et al.   TRENDS IN GENETICS

Dynamics of targeted cancer therapy

(2012) Ivana Bozic et al.   TRENDS IN MOLECULAR MEDICINE

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

(2012) Moritz Gerstung et al.   Nature Communications

Circumventing Cancer Drug Resistance in the Era of Personalized Medicine

(2012) Levi A. Garraway et al.   Cancer Discovery

Nonheritable Cellular Variability Accelerates the Evolutionary Processes of Cancer

(2012) Steven A. Frank et al.   PLOS BIOLOGY

A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis

(2012) Yu-Kang Cheng et al.   PLoS Computational Biology

Traveling waves of selective sweeps

(2011) Rick Durrett et al.   ANNALS OF APPLIED PROBABILITY

Investigating prostate cancer tumour–stroma interactions: clinical and biological insights from an evolutionary game

(2011) D Basanta et al.   BRITISH JOURNAL OF CANCER

Accurate Reconstruction of the Temporal Order of Mutations in Neoplastic Progression

(2011) Kathleen Sprouffske et al.   Cancer Prevention Research

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Intratumor Heterogeneity in Evolutionary Models of Tumor Progression

(2011) Rick Durrett et al.   GENETICS

Assessment of palindromes as platforms for DNA amplification in breast cancer

(2011) J. Guenthoer et al.   GENOME RESEARCH

Estimation of rearrangement phylogeny for cancer genomes

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

Secondary Somatic Mutations Restoring BRCA1/2 Predict Chemotherapy Resistance in Hereditary Ovarian Carcinomas

(2011) Barbara Norquist et al.   JOURNAL OF CLINICAL ONCOLOGY

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Why don't we get more cancer? A proposed role of the microenvironment in restraining cancer progression

(2011) Mina J Bissell et al.   NATURE MEDICINE

Decoding cell lineage from acquired mutations using arbitrary deep sequencing

(2011) Cheryl A Carlson et al.   NATURE METHODS

Evolutionary Distances in the Twilight Zone—A Rational Kernel Approach

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

Multiscale Modelling of Vascular Tumour Growth in 3D: The Roles of Domain Size and Boundary Conditions

(2011) Holger Perfahl et al.   PLoS One

Overlooking Evolution: A Systematic Analysis of Cancer Relapse and Therapeutic Resistance Research

(2011) C. Athena Aktipis et al.   PLoS One

The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis

(2011) Moritz Gerstung et al.   PLoS One

Optimization of Dosing for EGFR-Mutant Non-Small Cell Lung Cancer with Evolutionary Cancer Modeling

(2011) J. Chmielecki et al.   Science Translational Medicine

Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer

(2011) Anup Dewanji et al.   PLoS Computational Biology

Evolutionary Games with Affine Fitness Functions: Applications to Cancer

(2011) Moritz Gerstung et al.   Dynamic Games and Applications

Selection in spatial stochastic models of cancer: Migration as a key modulator of fitness

(2010) Craig J Thalhauser et al.   Biology Direct

Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer

(2010) S L Cooke et al.   BRITISH JOURNAL OF CANCER

The Origins and Implications of Intratumor Heterogeneity

(2010) F. Michor et al.   Cancer Prevention Research

Cell Selection as Driving Force in Lung and Colon Carcinogenesis

(2010) H. Schollnberger et al.   CANCER RESEARCH

The Speed of Evolution in Large Asexual Populations

(2010) Su-Chan Park et al.   JOURNAL OF STATISTICAL PHYSICS

Waiting Time Models of Cancer Progression

(2010) MORITZ GERSTUNG et al.   Mathematical Population Studies

Tracing the tumor lineage

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

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE

Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation

(2010) Ramin Nazarian et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Using DNA Methylation Patterns to Infer Tumor Ancestry

(2010) You Jin Hong et al.   PLoS One

A mathematical framework to determine the temporal sequence of somatic genetic events in cancer

(2010) Camille Stephan-Otto Attolini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Accumulation of driver and passenger mutations during tumor progression

(2010) I. Bozic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary dynamics of tumor progression with random fitness values

(2010) Rick Durrett et al.   THEORETICAL POPULATION BIOLOGY

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

A waiting time problem arising from the study of multi-stage carcinogenesis

(2009) Rick Durrett et al.   ANNALS OF APPLIED PROBABILITY

Mutational Heterogeneity in Human Cancers: Origin and Consequences

(2009) Jesse J. Salk et al.   Annual Review of Pathology-Mechanisms of Disease

Quantifying cancer progression with conjunctive Bayesian networks

(2009) M. Gerstung et al.   BIOINFORMATICS

Markov models for accumulating mutations

(2009) N. Beerenwinkel et al.   BIOMETRIKA

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

(2009) C. D. Greenman et al.   BIOSTATISTICS

Cancer phenotype as the outcome of an evolutionary game between normal and malignant cells

(2009) D Dingli et al.   BRITISH JOURNAL OF CANCER

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Mechanisms of change in gene copy number

(2009) P. J. Hastings et al.   NATURE REVIEWS GENETICS

Evolution of resistance and progression to disease during clonal expansion of cancer

(2009) Richard Durrett et al.   THEORETICAL POPULATION BIOLOGY

Cell Lineage Analysis of a Mouse Tumor

(2008) D. Frumkin et al.   CANCER RESEARCH

The clonal evolution of metastases from primary serous epithelial ovarian cancers

(2008) Lalarukh Khalique et al.   INTERNATIONAL JOURNAL OF CANCER

Angiogenesis and vascular remodelling in normal and cancerous tissues

(2008) Markus R. Owen et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Evaluation of screening strategies for pre-malignant lesions using a biomathematical approach

(2008) Jihyoun Jeon et al.   MATHEMATICAL BIOSCIENCES

Age-specific incidence of cancer: Phases, transitions, and biological implications

(2008) R. Meza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA