Phylodynamics for cell biologists

Maps of variability in cell lineage trees

(2019) Damien G. Hicks et al.   PLoS Computational Biology

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

(2019) D. Merino et al.   Nature Communications

Resolving genetic heterogeneity in cancer

(2019) Samra Turajlic et al.   NATURE REVIEWS GENETICS

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

(2019) Julien Delile et al.   DEVELOPMENT

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

(2019) Leif S. Ludwig et al.   CELL

Decoy fitness peaks, tumor suppression, and aging

(2019) Kelly C. Higa et al.   AGING CELL

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Inferring population dynamics from single-cell RNA-sequencing time series data

(2019) David S. Fischer et al.   NATURE BIOTECHNOLOGY

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

(2019) Leticia De Mattos-Arruda et al.   Cell Reports

Multi-omic molecular comparison of primary versus metastatic pancreatic tumours

(2019) Gagandeep Brar et al.   BRITISH JOURNAL OF CANCER

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

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

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Unravelling cellular relationships during development and regeneration using genetic lineage tracing

(2019) Chloé S. Baron et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rapid evolution and biogeographic spread in a colorectal cancer

(2019) Joao M. Alves et al.   Nature Communications

Somatic evolutionary timings of driver mutations

(2018) Karen Gomez et al.   BMC CANCER

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

(2018) Anna K. Casasent et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes

(2018) Ikram Ullah et al.   JOURNAL OF CLINICAL INVESTIGATION

On the statistical analysis of single cell lineage trees

(2018) Tanja Stadler et al.   JOURNAL OF THEORETICAL BIOLOGY

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany 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

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Multi-locus data distinguishes between population growth and multiple merger coalescents

(2018) Jere Koskela   Statistical Applications in Genetics and Molecular Biology

Evolution of Barrett’s esophagus through space and time at single-crypt and whole-biopsy levels

(2018) Pierre Martinez et al.   Nature Communications

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm

(2018) Michael K. Strasser et al.   Nature Communications

DiSNE Movie Visualization and Assessment of Clonal Kinetics Reveal Multiple Trajectories of Dendritic Cell Development

(2018) Dawn S. Lin et al.   Cell Reports

Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data

(2018) Abdul Balaparya et al.   NATURE GENETICS

Minimal functional driver gene heterogeneity among untreated metastases

(2018) Johannes G. Reiter et al.   SCIENCE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

The evolutionary landscape of colorectal tumorigenesis

(2018) William Cross et al.   Nature Ecology & Evolution

Transcriptional recording by CRISPR spacer acquisition from RNA

(2018) Florian Schmidt et al.   NATURE

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

(2018) Leonardo Beccari et al.   NATURE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution

(2018) Thomas O. McDonald et al.   NATURE GENETICS

Neutral tumor evolution?

(2018) Maxime Tarabichi et al.   NATURE GENETICS

The Structured Coalescent and Its Approximations

(2017) Nicola F. Müller et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Kirsten L. Frieda et al.   NATURE

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

(2017) Young Seok Ju et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

Between-region genetic divergence reflects the mode and tempo of tumor evolution

(2017) Ruping Sun et al.   NATURE GENETICS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu 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

The evolution of tumour phylogenetics: principles and practice

(2017) Russell Schwartz et al.   NATURE REVIEWS GENETICS

Multiplex recording of cellular events over time on CRISPR biological tape

(2017) Ravi U. Sheth et al.   SCIENCE

Forward and backward evolutionary processes and allele frequency spectrum in a cancer cell population

(2017) Hisashi Ohtsuki et al.   THEORETICAL POPULATION BIOLOGY

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

(2017) Weiwei Zhai et al.   Nature Communications

Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations

(2017) David Brown et al.   Nature Communications

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

(2017) Stephanie Tzouanas Schmidt et al.   ACS Synthetic Biology

Mouse embryonic stem cells can differentiate via multiple paths to the same state

(2017) James Alexander Briggs et al.   eLife

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

Stem Cell Differentiation as a Non-Markov Stochastic Process

(2017) Patrick S. Stumpf et al.   Cell Systems

eSTGt: a programming and simulation environment for population dynamics

(2016) Adam Spiro et al.   BMC BIOINFORMATICS

Emerging Imaging and Genomic Tools for Developmental Systems Biology

(2016) Zhe Liu et al.   DEVELOPMENTAL CELL

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

(2016) Tamir Biezuner et al.   GENOME RESEARCH

Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues

(2016) Patrick Smadbeck et al.   Journal of the Royal Society Interface

The Diversity and Molecular Evolution of B-Cell Receptors during Infection

(2016) Kenneth B. Hoehn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Persistent HIV-1 replication maintains the tissue reservoir during therapy

(2016) Ramon Lorenzo-Redondo et al.   NATURE

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

(2016) Philipp S. Hoppe et al.   NATURE

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Early and multiple origins of metastatic lineages within primary tumors

(2016) Zi-Ming Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Concise Review: Stem Cell Population Biology: Insights from Hematopoiesis

(2016) Adam L. MacLean et al.   STEM CELLS

Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

(2016) Sahand Hormoz et al.   Cell Systems

Continuous single cell imaging reveals sequential steps of plasmacytoid dendritic cell development from common dendritic cell progenitors

(2016) Ezgi Dursun et al.   Scientific Reports

Inferring the Origin of Metastases from Cancer Phylogenies

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

Morphogen rules: design principles of gradient-mediated embryo patterning

(2015) J. Briscoe et al.   DEVELOPMENT

Cell dynamics and gene expression control in tissue homeostasis and development

(2015) P. Rue et al.   Molecular Systems Biology

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

Using tumour phylogenetics to identify the roots of metastasis in humans

(2015) Kamila Naxerova et al.   Nature Reviews Clinical Oncology

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

(2015) Shaoping Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Eight challenges in phylodynamic inference

(2015) Simon D.W. Frost et al.   Epidemics

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Lineage grammars: describing, simulating and analyzing population dynamics

(2014) Adam Spiro et al.   BMC BIOINFORMATICS

Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation

(2014) B. L. Cheeseman et al.   Journal of the Royal Society Interface

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

Cancer Evolution: Mathematical Models and Computational Inference

(2014) Niko Beerenwinkel et al.   SYSTEMATIC BIOLOGY

Determining Lineage Pathways from Cellular Barcoding Experiments

(2014) Leïla Perié et al.   Cell Reports

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

(2014) Veronika Boskova et al.   PLoS Computational Biology

A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics

(2013) T. G. Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unravelling stem cell dynamics by lineage tracing

(2013) Cédric Blanpain et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

(2013) T. Stadler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics

(2013) A. Sottoriva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clinical drug resistance linked to interconvertible phenotypic and functional states of tumor-propagating cells in multiple myeloma

(2012) A. Chaidos et al.   BLOOD

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Morphogenesis of the Caenorhabditis elegans vulva

(2012) Adam J. Schindler et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Universal patterns of stem cell fate in cycling adult tissues

(2011) A. M. Klein et al.   DEVELOPMENT

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology