Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

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

(2018) Christoph Fritzsch et al.   Molecular Systems Biology

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

(2018) Monique G. P. van der Wijst et al.   NATURE GENETICS

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Single-cell transcriptional dynamics of flavivirus infection

(2018) Fabio Zanini et al.   eLife

High prevalence of clonal monoallelic expression

(2018) Sébastien Vigneau et al.   NATURE GENETICS

Reply to ‘High prevalence of clonal monoallelic expression’

(2018) Björn Reinius et al.   NATURE GENETICS

Prolylcarboxypeptidase deficiency is associated with increased blood pressure, glomerular lesions, and cardiac dysfunction independent of altered circulating and cardiac angiotensin II

(2017) Christoph Maier et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Pals1 Haploinsufficiency Results in Proteinuria and Cyst Formation

(2017) Thomas Weide et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

What shapes eukaryotic transcriptional bursting?

(2017) Damien Nicolas et al.   Molecular BioSystems

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Transgenic expression of human APOL1 risk variants in podocytes induces kidney disease in mice

(2017) Pazit Beckerman et al.   NATURE MEDICINE

Visualizing adenosine-to-inosine RNA editing in single mammalian cells

(2017) Ian A Mellis et al.   NATURE METHODS

Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain

(2017) Wei-Chao Huang et al.   NEURON

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression

(2017) Daniel Andergassen et al.   eLife

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation

(2016) Maria Vera et al.   Annual Review of Genetics

Assessing characteristics of RNA amplification methods for single cell RNA sequencing

(2016) Hannah R. Dueck et al.   BMC GENOMICS

Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells

(2016) Shin Kobayashi et al.   DEVELOPMENT

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in anH19loss-of-imprinting mutant

(2016) Paul Ginart et al.   GENES & DEVELOPMENT

What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism

(2016) Orsolya Symmons et al.   MOLECULAR CELL

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq

(2016) Björn Reinius et al.   NATURE GENETICS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Developmental regulation of X-chromosome inactivation

(2016) Bernhard Payer   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Biased Allelic Expression in Human Primary Fibroblast Single Cells

(2015) Christelle Borel et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Monoallelic Expression of Olfactory Receptors

(2015) Kevin Monahan et al.   Annual Review of Cell and Developmental Biology

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Clarifying Tissue Clearing

(2015) Douglas S. Richardson et al.   CELL

X-chromosome inactivation in female patients with Fabry disease

(2015) L. Echevarria et al.   CLINICAL GENETICS

X-chromosome inactivation: new insights into cis and trans regulation

(2015) Rafael Galupa et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The origin of the mammalian kidney: implications for recreating the kidney in vitro

(2015) M. Takasato et al.   DEVELOPMENT

Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip

(2015) Sydney M. Shaffer et al.   LAB ON A CHIP

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

(2015) Björn Reinius et al.   NATURE REVIEWS GENETICS

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

(2015) Jong Kyoung Kim et al.   Nature Communications

Noncanonical Genomic Imprinting Effects in Offspring

(2015) Paul J. Bonthuis et al.   Cell Reports

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

(2014) Elsa Abranches et al.   DEVELOPMENT

Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation

(2014) Mélanie A. Eckersley-Maslin et al.   DEVELOPMENTAL CELL

Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression

(2014) Anne-Valerie Gendrel et al.   DEVELOPMENTAL CELL

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

X chromosome regulation: diverse patterns in development, tissues and disease

(2014) Xinxian Deng et al.   NATURE REVIEWS GENETICS

Cellular Resolution Maps of X Chromosome Inactivation: Implications for Neural Development, Function, and Disease

(2014) Hao Wu et al.   NEURON

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

(2014) Q. Deng et al.   SCIENCE

Random monoallelic expression: regulating gene expression one allele at a time

(2014) Mélanie A. Eckersley-Maslin et al.   TRENDS IN GENETICS

Cubilin expression is monoallelic and epigenetically augmented via PPARs

(2013) Obaidullah Aseem et al.   BMC GENOMICS

The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains

(2013) T. Takada et al.   GENOME RESEARCH

Skewed X Chromosome Inactivation and Female Preponderance in Autoimmune Thyroid Disease: An Association Study and Meta-Analysis

(2013) Matthew J. Simmonds et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

Visualizing SNVs to quantify allele-specific expression in single cells

(2013) Marshall J Levesque et al.   NATURE METHODS

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

(2013) Marshall J Levesque et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Advances in understanding chromosome silencing by the long non-coding RNA Xist

(2012) T. Sado et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transcriptome-Wide Survey of Mouse CNS-Derived Cells Reveals Monoallelic Expression within Novel Gene Families

(2012) Sierra M. Li et al.   PLoS One

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Mammalian Kidney Development: Principles, Progress, and Projections

(2012) M. H. Little et al.   Cold Spring Harbor Perspectives in Biology

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

(2012) Brian DeVeale et al.   PLoS Genetics

Autosomal monoallelic expression in the mouse

(2012) Lillian M Zwemer et al.   GENOME BIOLOGY

Subspecific origin and haplotype diversity in the laboratory mouse

(2011) Hyuna Yang et al.   NATURE GENETICS

Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres

(2011) Fuchou Tang et al.   PLoS One

Skewed X inactivation in manifesting carriers of Duchenne muscular dystrophy

(2010) Mieko Yoshioka et al.   CLINICAL GENETICS

Antigen Receptor Allelic Exclusion: An Update and Reappraisal

(2010) B. L. Brady et al.   JOURNAL OF IMMUNOLOGY

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

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

(2008) Arjun Raj et al.   CELL

Aquaporin water channels in mammals

(2008) Kenichi Ishibashi et al.   Clinical and Experimental Nephrology

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Dynamic Proteomics of Individual Cancer Cells in Response to a Drug

(2008) A. A. Cohen et al.   SCIENCE