Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes

MQuad enables clonal substructure discovery using single cell mitochondrial variants

(2022) Aaron Wing Cheung Kwok et al.   Nature Communications

Precise identification of cancer cells from allelic imbalances in single cell transcriptomes

(2022) Mi K. Trinh et al.   Communications Biology

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance

(2021) Anton J. M. Larsson et al.   PLoS Computational Biology

Cellsnp-lite: an efficient tool for genotyping single cells

(2021) Xianjie Huang et al.   BIOINFORMATICS

Co-evolution of tumor and immune cells during progression of multiple myeloma

(2021) Ruiyang Liu et al.   Nature Communications

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

(2021) Chi-Yun Wu et al.   NATURE BIOTECHNOLOGY

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

(2020) Akdes Serin Harmanci et al.   Nature Communications

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

(2020) Simone Zaccaria et al.   NATURE BIOTECHNOLOGY

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

(2020) Simone Zaccaria et al.   Nature Communications

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

(2019) Nikolas Barkas et al.   NATURE METHODS

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Cytokeratin-8 in Anaplastic Thyroid Carcinoma: More Than a Simple Structural Cytoskeletal Protein

(2018) Dehuang Guo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comparison of phasing strategies for whole human genomes

(2018) Yongwook Choi et al.   PLoS Genetics

Interferon-Gamma at the Crossroads of Tumor Immune Surveillance or Evasion

(2018) Flávia Castro et al.   Frontiers in Immunology

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations

(2018) Po-Ru Loh et al.   NATURE

Single-cell mutation identification via phylogenetic inference

(2018) Jochen Singer et al.   Nature Communications

scphaser: haplotype inference using single-cell RNA-seq data

(2016) Daniel Edsgärd et al.   BIOINFORMATICS

Visualizing tumor evolution with the fishplot package for R

(2016) Christopher A. Miller et al.   BMC GENOMICS

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

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

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains

(2015) Artyom A. Alekseyenko et al.   GENES & DEVELOPMENT

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation

(2015) Björn Reinius et al.   NATURE REVIEWS GENETICS

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

(2014) Gavin Ha et al.   GENOME RESEARCH

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

(2014) Jared O'Connell et al.   PLoS Genetics

OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes

(2013) Christopher Yau   BIOINFORMATICS

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Haplotype-based profiling of subtle allelic imbalance with SNP arrays

(2012) S. Vattathil et al.   GENOME RESEARCH

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

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