Cellular barcoding to decipher clonal dynamics in disease

Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells

(2022) Jue Feng et al.   IMMUNITY

Life histories of myeloproliferative neoplasms inferred from phylogenies

(2022) Nicholas Williams et al.   NATURE

Decade-long leukaemia remissions with persistence of CD4+ CAR T cells

(2022) J. Joseph Melenhorst et al.   NATURE

CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information

(2022) Shou-Wen Wang et al.   NATURE BIOTECHNOLOGY

Deep distributed computing to reconstruct extremely large lineage trees

(2022) Naoki Konno et al.   NATURE BIOTECHNOLOGY

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

(2022) Dian Yang et al.   CELL

Capybara: A computational tool to measure cell identity and fate transitions

(2022) Wenjun Kong et al.   Cell Stem Cell

Clonal dynamics of haematopoiesis across the human lifespan

(2022) Emily Mitchell et al.   NATURE

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations

(2022) Tyler E. Miller et al.   NATURE BIOTECHNOLOGY

Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders

(2022) Sara Bizzotto et al.   NATURE REVIEWS NEUROSCIENCE

A time-resolved, multi-symbol molecular recorder via sequential genome editing

(2022) Junhong Choi et al.   NATURE

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

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Phylodynamics for cell biologists

(2021) T. Stadler et al.   SCIENCE

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

(2021) Jeffrey J. Quinn et al.   SCIENCE

Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms

(2021) Debra Van Egeren et al.   Cell Stem Cell

Gene therapy trials for sickle cell disease halted after two patients develop cancer

(2021) Jocelyn Kaiser   SCIENCE

The bone microenvironment invigorates metastatic seeds for further dissemination

(2021) Weijie Zhang et al.   CELL

Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development

(2021) Luyi Tian et al.   IMMUNITY

Somatic mutation landscapes at single-molecule resolution

(2021) Federico Abascal et al.   NATURE

Lineage tracing of human development through somatic mutations

(2021) Michael Spencer Chapman et al.   NATURE

Lineage tracing and analog recording in mammalian cells by single-site DNA writing

(2021) Theresa B. Loveless et al.   Nature Chemical Biology

Imaging cell lineage with a synthetic digital recording system

(2021) Ke-Huan K. Chow et al.   SCIENCE

Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states

(2021) Kamen P. Simeonov et al.   CANCER CELL

A body map of somatic mutagenesis in morphologically normal human tissues

(2021) Ruoyan Li et al.   NATURE

Cycling cancer persister cells arise from lineages with distinct programs

(2021) Yaara Oren et al.   NATURE

Extensive phylogenies of human development inferred from somatic mutations

(2021) Tim H. H. Coorens et al.   NATURE

Clonal dynamics in early human embryogenesis inferred from somatic mutation

(2021) Seongyeol Park et al.   NATURE

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection

(2021) Seyedeh M. Zekavat et al.   NATURE MEDICINE

Somatic Mutations in “Benign” Disease

(2021) Satu Mustjoki et al.   NEW ENGLAND JOURNAL OF MEDICINE

Embryo-scale, single-cell spatial transcriptomics

(2021) Sanjay R. Srivatsan et al.   SCIENCE

Rates and patterns of clonal oncogenic mutations in the normal human brain

(2021) Javier Ganz et al.   Cancer Discovery

Association of clonal hematopoiesis with chronic obstructive pulmonary disease

(2021) Peter G. Miller et al.   BLOOD

Donor Clonal Hematopoiesis and Recipient Outcomes After Transplantation

(2021) Christopher J. Gibson et al.   JOURNAL OF CLINICAL ONCOLOGY

Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis

(2021) Peter Geon Kim et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A heritable, non-genetic road to cancer evolution

(2021) Tamara Prieto et al.   NATURE

Mutant clones in normal epithelium outcompete and eliminate emerging tumours

(2021) B. Colom et al.   NATURE

Non-genetic determinants of malignant clonal fitness at single-cell resolution

(2021) Katie A. Fennell et al.   NATURE

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

(2021) Ronan Chaligne et al.   NATURE GENETICS

Computational analysis of cancer genome sequencing data

(2021) Isidro Cortés-Ciriano et al.   NATURE REVIEWS GENETICS

Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis

(2021) S. Avagyan et al.   SCIENCE

Clonal hematopoiesis is associated with risk of severe Covid-19

(2021) Kelly L. Bolton et al.   Nature Communications

Cancer Causative Mutations Occurring in Early Embryogenesis

(2021) Fresia Pareja et al.   Cancer Discovery

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli

(2020) Cayetano Pleguezuelos-Manzano et al.   NATURE

Tobacco smoking and somatic mutations in human bronchial epithelium

(2020) Kenichi Yoshida et al.   NATURE

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung et al.   NATURE

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

The mutational landscape of normal human endometrial epithelium

(2020) Luiza Moore et al.   NATURE

Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma

(2020) David J. H. Shih et al.   NATURE GENETICS

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

(2020) Sydney M. Shaffer et al.   CELL

Somatic Evolution in Non-neoplastic IBD-Affected Colon

(2020) Sigurgeir Olafsson et al.   CELL

Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding

(2020) Weike Pei et al.   Cell Stem Cell

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

(2020) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters

(2020) Christian Umkehrer et al.   NATURE BIOTECHNOLOGY

Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells

(2020) Melissa A. Walker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

(2020) Hamim Zafar et al.   Nature Communications

Unraveling Hematopoiesis through the Lens of Genomics

(2020) L. Alexander Liggett et al.   CELL

Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells

(2020) Erik L. Bao et al.   NATURE

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

(2020) Alexander G. Bick et al.   NATURE

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

(2020) Anna S. Nam et al.   NATURE REVIEWS GENETICS

Emergence of Neuronal Diversity during Vertebrate Brain Development

(2020) Bushra Raj et al.   NEURON

Extensive heterogeneity in somatic mutation and selection in the human bladder

(2020) Andrew R. J. Lawson et al.   SCIENCE

Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development

(2020) Sadie VanHorn et al.   DEVELOPMENTAL CELL

Clonal-level lineage commitment pathways of hematopoietic stem cells in vivo

(2019) Rong Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Leif S. Ludwig et al.   CELL

Somatic Mutations Increase Hepatic Clonal Fitness and Regeneration in Chronic Liver Disease

(2019) Min Zhu et al.   CELL

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

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

(2019) Jin Xu et al.   eLife

Quantitative evidence for early metastatic seeding in colorectal cancer

(2019) Zheng Hu et al.   NATURE GENETICS

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

(2019) Simon F. Brunner et al.   NATURE

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

Genome Sequencing during a Patient’s Journey through Cancer

(2019) Jyoti Nangalia et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal hematopoiesis in human aging and disease

(2019) Siddhartha Jaiswal et al.   SCIENCE

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Clonal analysis of lineage fate in native haematopoiesis

(2018) Alejo E. Rodriguez-Fraticelli et al.   NATURE

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

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

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

Hierarchically related lineage-restricted fates of multipotent haematopoietic stem cells

(2018) Joana Carrelha et al.   NATURE

Population dynamics of normal human blood inferred from somatic mutations

(2018) Henry Lee-Six et al.   NATURE

DNA-based memory devices for recording cellular events

(2018) Ravi U. Sheth et al.   NATURE REVIEWS GENETICS

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Aplastic Anemia

(2018) Neal S. Young   NEW ENGLAND JOURNAL OF MEDICINE

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Regeneration of the entire human epidermis using transgenic stem cells

(2017) Tobias Hirsch et al.   NATURE

Tracing the origins of relapse in acute myeloid leukaemia to stem cells

(2017) Liran I. Shlush et al.   NATURE

The evolution of tumour phylogenetics: principles and practice

(2017) Russell Schwartz et al.   NATURE REVIEWS GENETICS

Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease

(2017) Siddhartha Jaiswal et al.   NEW ENGLAND JOURNAL OF MEDICINE

In Vivo Tracking of Human Hematopoiesis Reveals Patterns of Clonal Dynamics during Early and Steady-State Reconstitution Phases

(2016) Luca Biasco et al.   Cell Stem Cell

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Metastasis as an evolutionary process

(2016) S. Turajlic et al.   SCIENCE

Inferring the Origin of Metastases from Cancer Phylogenies

(2015) W. S. Hong et al.   CANCER RESEARCH

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

(2015) Colin S Cooper et al.   NATURE GENETICS

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

Differentiation imbalance in single oesophageal progenitor cells causes clonal immortalization and field change

(2014) Maria P. Alcolea et al.   NATURE CELL BIOLOGY

Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study

(2014) Mariam Jamal-Hanjani et al.   PLOS BIOLOGY

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

Clonally dominant cardiomyocytes direct heart morphogenesis

(2012) Vikas Gupta et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

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

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

Barrett’s Esophagus: A Review of the Literature

(2011) Erin W. Gilbert et al.   JOURNAL OF GASTROINTESTINAL SURGERY

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Survival of children with mosaic Down syndrome

(2010) Mikyong Shin et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL