Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

(2014) Iman Hajirasouliha et al.   BIOINFORMATICS

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

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

(2013) Nicholas B. Larson et al.   BIOINFORMATICS

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt 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

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

(2011) Arief Gusnanto et al.   BIOINFORMATICS

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of next-generation genomic data in cancer: accomplishments and challenges

(2010) L. Ding et al.   HUMAN MOLECULAR GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia

(2008) C. G. Mullighan et al.   SCIENCE