Ageing and sources of transcriptional heterogeneity

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

OUP accepted manuscript

(2018)   Briefings in Functional Genomics

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

Mass cytometry: a powerful tool for dissecting the immune landscape

(2018) Yannick Simoni et al.   CURRENT OPINION IN IMMUNOLOGY

The Transcription Factor ThPOK Orchestrates Stochastic Interchromosomal Interactions Required for IFNB1 Virus-Inducible Gene Expression

(2018) Chrysa Nikopoulou et al.   MOLECULAR CELL

Estrogen‐dependent control and cell‐to‐cell variability of transcriptional bursting

(2018) Christoph Fritzsch et al.   Molecular Systems Biology

Modulation of transcriptional burst frequency by histone acetylation

(2018) Damien Nicolas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Feeders facilitate telomere maintenance and chromosomal stability of embryonic stem cells

(2018) Renpeng Guo et al.   Nature Communications

The Impact of Pancreatic Beta Cell Heterogeneity on Type 1 Diabetes Pathogenesis

(2018) Richard K. P. Benninger et al.   Current Diabetes Reports

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

The chromatin accessibility signature of human immune aging stems from CD8+T cells

(2017) Duygu Ucar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells

(2017) Jiho Choi et al.   NATURE

Derivation of ground-state female ES cells maintaining gamete-derived DNA methylation

(2017) Masaki Yagi et al.   NATURE

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Deciphering the mRNP Code: RNA-Bound Determinants of Post-Transcriptional Gene Regulation

(2017) Niels H. Gehring et al.   TRENDS IN BIOCHEMICAL SCIENCES

Noise reduction as an emergent property of single-cell aging

(2017) Ping Liu et al.   Nature Communications

Effect of transcription factor resource sharing on gene expression noise

(2017) Dipjyoti Das et al.   PLoS Computational Biology

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

Biophysical and biomolecular determination of cellular age in humans

(2017) Jude M. Phillip et al.   Nature Biomedical Engineering

Signaling Networks Determining Life Span

(2016) Celine E. Riera et al.   Annual Review of Biochemistry

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

The Aging Epigenome

(2016) Lauren N. Booth et al.   MOLECULAR CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

A continuum model of transcriptional bursting

(2016) Adam M Corrigan et al.   eLife

Noise Facilitates Transcriptional Control under Dynamic Inputs

(2015) Ryan A. Kellogg et al.   CELL

H3K36 methylation promotes longevity by enhancing transcriptional fidelity

(2015) Payel Sen et al.   GENES & DEVELOPMENT

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

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

(2015) Björn Reinius et al.   NATURE REVIEWS GENETICS

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

(2014) Z. Hu et al.   GENES & DEVELOPMENT

Deconstructing transcriptional heterogeneity in pluripotent stem cells

(2014) Roshan M. Kumar et al.   NATURE

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Transcription factors: specific DNA binding and specific gene regulation

(2014) Anne-Laure Todeschini et al.   TRENDS IN GENETICS

Changes in Nucleosome Occupancy Associated with Metabolic Alterations in Aged Mammalian Liver

(2014) Irina M. Bochkis et al.   Cell Reports

Noise propagation through extracellular signaling leads to fluctuations in gene expression

(2013) Omar P Tabbaa et al.   BMC Systems Biology

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

(2013) Christopher R. Brown et al.   PLOS BIOLOGY

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

Replicative and Chronological Aging in Saccharomyces cerevisiae

(2012) Valter D. Longo et al.   Cell Metabolism

Cdc42 Activity Regulates Hematopoietic Stem Cell Aging and Rejuvenation

(2012) Maria Carolina Florian et al.   Cell Stem Cell

Subpopulations of GFP-Marked Mouse Pancreatic β-Cells Differ in Size, Granularity, and Insulin Secretion

(2012) Hitoshi Katsuta et al.   ENDOCRINOLOGY

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Morphogen Gradients: From Generation to Interpretation

(2011) Katherine W. Rogers et al.   Annual Review of Cell and Developmental Biology

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

Chromatin structure as a mediator of aging

(2010) Jason Feser et al.   FEBS LETTERS

Elevated Histone Expression Promotes Life Span Extension

(2010) Jason Feser et al.   MOLECULAR CELL

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

DNA looping provides stability and robustness to the bacteriophage   switch

(2009) M. J. Morelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

(2008) Effie Apostolou et al.   CELL

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

DNA looping can enhance lysogenic CI transcription in phage lambda

(2008) L. M. Anderson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA