Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing

(2020) Rujin Wang et al.   Cell Systems

High throughput error corrected Nanopore single cell transcriptome sequencing

(2020) Kevin Lebrigand et al.   Nature Communications

Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line

(2020) Enrique I. Velazquez-Villarreal et al.   Communications Biology

Pervasive chromosomal instability and karyotype order in tumour evolution

(2020) Thomas B. K. Watkins et al.   NATURE

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

(2020) Simone Zaccaria et al.   NATURE BIOTECHNOLOGY

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

(2019) Mandeep Singh et al.   Nature Communications

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

(2019) Emma Laks et al.   CELL

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Tracking the Evolution of Non–Small-Cell Lung Cancer

(2017) Mariam Jamal-Hanjani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy

(2017) John M. Bell et al.   NUCLEIC ACIDS RESEARCH

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases

(2017) Stephanie U. Greer et al.   Genome Medicine

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

REC8 functions as a tumor suppressor and is epigenetically downregulated in gastric cancer, especially in EBV-positive subtype

(2016) J Yu et al.   ONCOGENE

Alteration of WWOX in human cancer, a clinical view

(2015) Izabela Baryła et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

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

(2014) Gavin Ha et al.   GENOME RESEARCH

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Allele-specific copy number profiling by next-generation DNA sequencing

(2014) Hao Chen et al.   NUCLEIC ACIDS RESEARCH

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Cancer epigenomics: beyond genomics

(2012) Juan Sandoval et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS