Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

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

(2019) Leif S. Ludwig et al.   CELL

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Comparison of computational methods for imputing single-cell RNA-sequencing data

(2018) Lihua Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Population dynamics of normal human blood inferred from somatic mutations

(2018) Henry Lee-Six et al.   NATURE

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

(2017) Alicia N Schep et al.   NATURE METHODS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

(2017) Lixin Chen et al.   SCIENCE

Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing

(2017) Jacqueline Morris et al.   Cell Reports

Protective mitochondrial transfer from bone marrow stromal cells to acute myeloid leukemic cells during chemotherapy

(2016) R. Moschoi et al.   BLOOD

A generic, cost-effective, and scalable cell lineage analysis platform

(2016) Tamir Biezuner et al.   GENOME RESEARCH

Transfer of mitochondria from astrocytes to neurons after stroke

(2016) Kazuhide Hayakawa et al.   NATURE

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Mitochondrial dynamics and inheritance during cell division, development and disease

(2014) Prashant Mishra et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Preleukemic mutations in human acute myeloid leukemia affect epigenetic regulators and persist in remission

(2014) M. R. Corces-Zimmerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

(2014) Young Seok Ju et al.   eLife

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

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

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

Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia

(2012) M. Jan et al.   Science Translational Medicine

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

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

JunB Protects against Myeloid Malignancies by Limiting Hematopoietic Stem Cell Proliferation and Differentiation without Affecting Self-Renewal

(2009) Marianne Santaguida et al.   CANCER CELL

A Methodological Approach to Tracing Cell Lineage in Human Epithelial Tissues

(2009) Tariq G. Fellous et al.   STEM CELLS