Discovering sparse transcription factor codes for cell states and state transitions during development

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states

(2017) Sumin Jang et al.   eLife

Beta-Poisson model for single-cell RNA-seq data analyses

(2016) Trung Nghia Vu et al.   BIOINFORMATICS

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Foxp2 Regulates Identities and Projection Patterns of Thalamic Nuclei During Development

(2016) Haruka Ebisu et al.   CEREBRAL CORTEX

Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex

(2016) Luciano C. Greig et al.   NEURON

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Transcription factor 7-like 1 is involved in hypothalamo–pituitary axis development in mice and humans

(2016) Carles Gaston-Massuet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Common genetic variation in ETV6 is associated with colorectal cancer susceptibility

(2016) Meilin Wang et al.   Nature Communications

Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos

(2016) Elo Madissoon et al.   Scientific Reports

The characterization of an intestine-like genomic signature maintained during Barrett’s-associated adenocarcinogenesis reveals an NR5A2-mediated promotion of cancer cell survival

(2016) Shane P. Duggan et al.   Scientific Reports

Ctip1 Regulates the Balance between Specification of Distinct Projection Neuron Subtypes in Deep Cortical Layers

(2016) Mollie B. Woodworth et al.   Cell Reports

Statistical Mechanics of Optimal Convex Inference in High Dimensions

(2016) Madhu Advani et al.   Physical Review X

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Ebf2 is required for development of dopamine neurons in the midbrain periaqueductal gray matter of mouse

(2015) Qiaoqiao Yang et al.   Developmental Neurobiology

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Specification of Cortical Subcerebral Projection Neurons Depends on the Direct Repression of TBR1 by CTIP1/BCL11a

(2015) J. Canovas et al.   JOURNAL OF NEUROSCIENCE

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

Bcl11a (Ctip1) Controls Migration of Cortical Projection Neurons through Regulation of Sema3c

(2015) Christoph Wiegreffe et al.   NEURON

Epigenetic control of intestinal barrier function and inflammation in zebrafish

(2015) Lindsay Marjoram et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

CD41 Marks the Initial Myelo-Erythroid Lineage Specification in Adult Mouse Hematopoiesis: Redefinition of Murine Common Myeloid Progenitor

(2015) Kohta Miyawaki et al.   STEM CELLS

Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells

(2015) Henry Garcia et al.   Oncotarget

Genetic programs controlling cortical interneuron fate

(2014) Nicoletta Kessaris et al.   CURRENT OPINION IN NEUROBIOLOGY

The Hippo pathway effectors TAZ and YAP in development, homeostasis and disease

(2014) X. Varelas   DEVELOPMENT

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

(2014) Simona Lodato et al.   NATURE NEUROSCIENCE

Brn4 and TH synergistically promote the differentiation of neural stem cells into dopaminergic neurons

(2014) Xuefeng Tan et al.   NEUROSCIENCE LETTERS

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing

(2014) Jason M. Knight et al.   Scientific Reports

Sox2 Acts in a Dose-Dependent Fashion to Regulate Proliferation of Cortical Progenitors

(2014) Daniel W. Hagey et al.   Cell Reports

Essential role of the IRF8-KLF4 transcription factor cascade in murine monocyte differentiation

(2013) D. Kurotaki et al.   BLOOD

Sp8 and COUP-TF1 Reciprocally Regulate Patterning and Fgf Signaling in Cortical Progenitors

(2013) Ugo Borello et al.   CEREBRAL CORTEX

The transcription factor Otx2 regulates choroid plexus development and function

(2013) P. A. Johansson et al.   DEVELOPMENT

Midbrain dopaminergic neurons: A review of the molecular circuitry that regulates their development

(2013) Shane V. Hegarty et al.   DEVELOPMENTAL BIOLOGY

Dmrta1 regulates proneural gene expression downstream of Pax6 in the mammalian telencephalon

(2013) Takako Kikkawa et al.   GENES TO CELLS

FOXO3 determines the accumulation of α-synuclein and controls the fate of dopaminergic neurons in the substantia nigra

(2013) Emilda Pino et al.   HUMAN MOLECULAR GENETICS

The Satb1 Protein Directs Hematopoietic Stem Cell Differentiation toward Lymphoid Lineages

(2013) Yusuke Satoh et al.   IMMUNITY

Antagonistic Regulation by the Transcription Factors C/EBPα and MITF Specifies Basophil and Mast Cell Fates

(2013) Xiaopeng Qi et al.   IMMUNITY

Trp53 Deficiency Protects against Acute Intestinal Inflammation

(2013) M. E. Spehlmann et al.   JOURNAL OF IMMUNOLOGY

CREB3L1 Is a Metastasis Suppressor That Represses Expression of Genes Regulating Metastasis, Invasion, and Angiogenesis

(2013) P. Mellor et al.   MOLECULAR AND CELLULAR BIOLOGY

Reprogramming fibroblasts to neural-precursor-like cells by structured overexpression of pallial patterning genes

(2013) Marilena Raciti et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

NFIB is a governor of epithelial–melanocyte stem cell behaviour in a shared niche

(2013) Chiung-Ying Chang et al.   NATURE

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

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Molecular logic of neocortical projection neuron specification, development and diversity

(2013) Luciano Custo Greig et al.   NATURE REVIEWS NEUROSCIENCE

A Modular Gain-of-Function Approach to Generate Cortical Interneuron Subtypes from ES Cells

(2013) Edmund Au et al.   NEURON

SOX2-LIN28/let-7 pathway regulates proliferation and neurogenesis in neural precursors

(2013) F. Cimadamore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Members of the high mobility group B protein family are dynamically expressed in embryonic neural stem cells

(2013) Ariel B Abraham et al.   Proteome Science

Assembly of the Auditory Circuitry by a Hox Genetic Network in the Mouse Brainstem

(2013) Maria Di Bonito et al.   PLoS Genetics

Transcriptome Analysis Identifies Regulators of Hematopoietic Stem and Progenitor Cells

(2013) Roi Gazit et al.   Stem Cell Reports

Genetic and physical interaction of Meis2, Pax3 and Pax7 during dorsal midbrain development

(2012) Zsuzsa Agoston et al.   BMC DEVELOPMENTAL BIOLOGY

POU-III Transcription Factors (Brn1, Brn2, and Oct6) Influence Neurogenesis, Molecular Identity, and Migratory Destination of Upper-Layer Cells of the Cerebral Cortex

(2012) Martin H. Dominguez et al.   CEREBRAL CORTEX

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

Interneuron, interrupted: molecular pathogenesis of ARX mutations and X-linked infantile spasms

(2012) Pedro R Olivetti et al.   CURRENT OPINION IN NEUROBIOLOGY

Gbx2 Directly Restricts Otx2 Expression to Forebrain and Midbrain, Competing with Class III POU Factors

(2012) F. Inoue et al.   MOLECULAR AND CELLULAR BIOLOGY

HMGA regulates the global chromatin state and neurogenic potential in neocortical precursor cells

(2012) Yusuke Kishi et al.   NATURE NEUROSCIENCE

Dynamic FoxG1 Expression Coordinates the Integration of Multipolar Pyramidal Neuron Precursors into the Cortical Plate

(2012) Goichi Miyoshi et al.   NEURON

Krüppel-like Factor 4 Regulates Intestinal Epithelial Cell Morphology and Polarity

(2012) Tianxin Yu et al.   PLoS One

Essential contribution of IRF3 to intestinal homeostasis and microbiota-mediated Tslp gene induction

(2012) H. Negishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signaling Mechanisms Controlling Cell Fate and Embryonic Patterning

(2012) N. Perrimon et al.   Cold Spring Harbor Perspectives in Biology

CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma progression

(2012) Anke H. Sillars-Hardebol et al.   CELLULAR ONCOLOGY

The EMT regulator Zeb2/Sip1 is essential for murine embryonic hematopoietic stem/progenitor cell differentiation and mobilization

(2011) S. Goossens et al.   BLOOD

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

COUP-TFII Expressing Interneurons in Human Fetal Forebrain

(2011) Gisela Reinchisi et al.   CEREBRAL CORTEX

RORβ Induces Barrel-like Neuronal Clusters in the Developing Neocortex

(2011) Denis Jabaudon et al.   CEREBRAL CORTEX

Hes1 regulates the number and anterior–posterior patterning of mesencephalic dopaminergic neurons at the mid/hindbrain boundary (isthmus)

(2011) Yoko Kameda et al.   DEVELOPMENTAL BIOLOGY

SOX2 expression levels distinguish between neural progenitor populations of the developing dorsal telencephalon

(2011) Scott R. Hutton et al.   DEVELOPMENTAL BIOLOGY

Tracing Cells for Tracking Cell Lineage and Clonal Behavior

(2011) Margaret E. Buckingham et al.   DEVELOPMENTAL CELL

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

The transcription factor Foxg1 regulates telencephalic progenitor proliferation cell autonomously, in part by controlling Pax6 expression levels

(2011) Martine N Manuel et al.   Neural Development

Serotonergic inputs to FoxP2 neurons of the pre-locus coeruleus and parabrachial nuclei that project to the ventral tegmental area

(2011) R.L. Miller et al.   NEUROSCIENCE

Kernel density estimation via diffusion

(2010) Z. I. Botev et al.   ANNALS OF STATISTICS

NF-κB in the regulation of epithelial homeostasis and inflammation

(2010) Andy Wullaert et al.   CELL RESEARCH

Mouse atonal homolog 1 directs intestinal progenitors to secretory cell rather than absorptive cell fate

(2010) Kelli L. VanDussen et al.   DEVELOPMENTAL BIOLOGY

A Framework for Feature Selection in Clustering

(2010) Daniela M. Witten et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

The serum response factor (SRF)/megakaryocytic acute leukemia (MAL) network participates in megakaryocyte development

(2010) C Ragu et al.   LEUKEMIA

Meis1 specifies positional information in the retina and tectum to organize the zebrafish visual system

(2010) Timothy Erickson et al.   Neural Development

Sox10 directs neural stem cells toward the oligodendrocyte lineage by decreasing Suppressor of Fused expression

(2010) C. D. Pozniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BMP Signaling Promotes the Growth of Primary Human Colon Carcinomas in vivo

(2010) A. Lorente-Trigos et al.   Journal of Molecular Cell Biology

Dynamic patterning at the pylorus: Formation of an epithelial intestine–stomach boundary in late fetal life

(2009) Xing Li et al.   DEVELOPMENTAL DYNAMICS

SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells

(2009) Taeko K. Noah et al.   EXPERIMENTAL CELL RESEARCH

Foxa1 and Foxa2 Control the Differentiation of Goblet and Enteroendocrine L- and D-Cells in Mice

(2009) Diana Z. Ye et al.   GASTROENTEROLOGY

Sharp Thresholds for High-Dimensional and Noisy Sparsity Recovery Using $\ell _{1}$-Constrained Quadratic Programming (Lasso)

(2009) Martin J. Wainwright   IEEE TRANSACTIONS ON INFORMATION THEORY

Ventral Mesencephalon-Enriched Genes That Regulate the Development of Dopaminergic Neurons In Vivo

(2009) M. Yin et al.   JOURNAL OF NEUROSCIENCE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

SOX6 controls dorsal progenitor identity and interneuron diversity during neocortical development

(2009) Eiman Azim et al.   NATURE NEUROSCIENCE

Observed universality of phase transitions in high-dimensional geometry, with implications for modern data analysis and signal processing

(2009) D. Donoho et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Stem Cells, Self-Renewal, and Differentiation in the Intestinal Epithelium

(2008) Laurens G. van der Flier et al.   Annual Review of Physiology

Cell Lineage Analysis of a Mouse Tumor

(2008) D. Frumkin et al.   CANCER RESEARCH

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL

Zic1 and Zic4 regulate zebrafish roof plate specification and hindbrain ventricle morphogenesis

(2008) Gina E. Elsen et al.   DEVELOPMENTAL BIOLOGY

Loss of intestinal crypt progenitor cells owing to inactivation of both Notch1 and Notch2 is accompanied by derepression of CDK inhibitors p27Kip1 and p57Kip2

(2008) Orbicia Riccio et al.   EMBO REPORTS

Absence of the transcription factorNfibdelays the formation of the basilar pontine and other mossy fiber nuclei

(2008) Asli Kumbasar et al.   JOURNAL OF COMPARATIVE NEUROLOGY

COUP-TFII Is Preferentially Expressed in the Caudal Ganglionic Eminence and Is Involved in the Caudal Migratory Stream

(2008) S. Kanatani et al.   JOURNAL OF NEUROSCIENCE

An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors

(2008) Ittai Ben-Porath et al.   NATURE GENETICS

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY

Essential functions of the Williams-Beuren syndrome-associated TFII-I genes in embryonic development

(2008) B. Enkhmandakh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analytical distributions for stochastic gene expression

(2008) V. Shahrezaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA