Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

MCMC Methods for Multi-Response Generalized Linear Mixed Models: TheMCMCglmmRPackage

(2015) Jarrod D. Hadfield   Journal of Statistical Software

Novel algorithms and the benefits of comparative validation

(2013) R. Smith et al.   BIOINFORMATICS

The promise of single-cell sequencing

(2013) James Eberwine et al.   NATURE METHODS

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

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

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

Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation

(2013) L. Vermeulen et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

BIM, PUMA, and the Achilles' Heel of Oncogene Addiction

(2013) A. Roulston et al.   Science Signaling

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

Simultaneous Identification of Multiple Driver Pathways in Cancer

(2013) Mark D. M. Leiserson et al.   PLoS Computational Biology

Fast stochastic algorithm for simulating evolutionary population dynamics

(2012) William H. Mather et al.   BIOINFORMATICS

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

Cumulative disease progression models for cross-sectional data: A review and comparison

(2012) Katrin Hainke et al.   BIOMETRICAL JOURNAL

Modelling the evolution of genetic instability during tumour progression

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

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Intratumor Heterogeneity: Seeing the Wood for the Trees

(2012) T. A. Yap et al.   Science Translational Medicine

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

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

Accurate Reconstruction of the Temporal Order of Mutations in Neoplastic Progression

(2011) Kathleen Sprouffske et al.   Cancer Prevention Research

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Germline Fitness-Based Scoring of Cancer Mutations

(2011) Andrej Fischer et al.   GENETICS

Intratumor Heterogeneity in Evolutionary Models of Tumor Progression

(2011) Rick Durrett et al.   GENETICS

De novo discovery of mutated driver pathways in cancer

(2011) F. Vandin et al.   GENOME RESEARCH

Oncogenetic tree modeling of human hepatocarcinogenesis

(2011) Thomas Longerich et al.   INTERNATIONAL JOURNAL OF CANCER

The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis

(2011) Moritz Gerstung et al.   PLoS One

Reproducible Research in Computational Science

(2011) R. D. Peng   SCIENCE

Identifying cancer driver genes in tumor genome sequencing studies

(2010) Ahrim Youn et al.   BIOINFORMATICS

Publish your computer code: it is good enough

(2010) Nick Barnes   NATURE

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

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

Quantifying cancer progression with conjunctive Bayesian networks

(2009) M. Gerstung et al.   BIOINFORMATICS

Bayesian inference for generalized linear mixed models

(2009) Y. Fong et al.   BIOSTATISTICS

Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction

(2009) Ji Luo et al.   CELL

Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression

(2009) Swapnali Pathare et al.   INTERNATIONAL JOURNAL OF CANCER

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

(2009) Håvard Rue et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

Oncogene Addiction

(2008) I. B. Weinstein et al.   CANCER RESEARCH

Oncogenetic tree model of somatic mutations and DNA methylation in colon tumors

(2008) Carol Sweeney et al.   GENES CHROMOSOMES & CANCER