The origin and evolution of cell types

A maximum-likelihood approach for building cell-type trees by lifting

(2016) Nishanth Ulhas Nair et al.   BMC GENOMICS

The Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts

(2016) Koryu Kin et al.   Genome Biology and Evolution

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy

(2016) Arun Rajendra Chavan et al.   PLACENTA

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1

(2016) Mauris C. Nnamani et al.   Cell Reports

Variation is function: Are single cell differences functionally important?

(2015) Hannah Dueck et al.   BIOESSAYS

A Competition Mechanism for a Homeotic Neuron Identity Transformation in C. elegans

(2015) Patricia M. Gordon et al.   DEVELOPMENTAL CELL

Wiring for independence: Positive feedback motifs facilitate individuation of traits in development and evolution

(2015) Mihaela Pavličev et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called “species signal”

(2015) Jacob M. Musser et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Migratory neuronal progenitors arise from the neural plate borders in tunicates

(2015) Alberto Stolfi et al.   NATURE

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Single-cell epigenomics: techniques and emerging applications

(2015) Omer Schwartzman et al.   NATURE REVIEWS GENETICS

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

(2015) Nikolaos Stefanakis et al.   NEURON

Gastric pouches and the mucociliary sole: setting the stage for nervous system evolution

(2015) D. Arendt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Merkel cells and neurons keep in touch

(2015) Seung-Hyun Woo et al.   TRENDS IN CELL BIOLOGY

Homeotic Transformations of Neuronal Cell Identities

(2015) Paola Arlotta et al.   TRENDS IN NEUROSCIENCES

The alternative splicing factor Nova2 regulates vascular development and lumen formation

(2015) Costanza Giampietro et al.   Nature Communications

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

(2015) Cong Liang et al.   Nature Communications

Cell-type Phylogenetics and the Origin of Endometrial Stromal Cells

(2015) Koryu Kin et al.   Cell Reports

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

(2015) Hannah Dueck et al.   GENOME BIOLOGY

Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

(2015) Cameron Sokolik et al.   Cell Systems

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Novel Cell Types, Neurosecretory Cells, and Body Plan of the Early-Diverging Metazoan Trichoplax adhaerens

(2014) Carolyn L. Smith et al.   CURRENT BIOLOGY

Structural evolution of cell types by step-wise assembly of cellular modules

(2014) Kaia Achim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord

(2014) M. D. Borromeo et al.   DEVELOPMENT

Exclusive multipotency and preferential asymmetric divisions in post-embryonic neural stem cells of the fish retina

(2014) L. Centanin et al.   DEVELOPMENT

Single cell dissection of early kidney development: multilineage priming

(2014) E. W. Brunskill et al.   DEVELOPMENT

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

(2014) Sui Wang et al.   DEVELOPMENTAL CELL

Cyclic Decidualization of the Human Endometrium in Reproductive Health and Failure

(2014) Birgit Gellersen et al.   ENDOCRINE REVIEWS

Evolution of mammalian pregnancy and the origin of the decidual stromal cell

(2014) Günter P. Wagner et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Specification of Spatial Identities of Cerebellar Neuron Progenitors by Ptf1a and Atoh1 for Proper Production of GABAergic and Glutamatergic Neurons

(2014) M. Yamada et al.   JOURNAL OF NEUROSCIENCE

Interneuron cell types are fit to function

(2014) Adam Kepecs et al.   NATURE

Maintenance of postmitotic neuronal cell identity

(2014) Evan S Deneris et al.   NATURE NEUROSCIENCE

Intrinsically different retinal progenitor cells produce specific types of progeny

(2014) Connie Cepko   NATURE REVIEWS NEUROSCIENCE

Lessons from miR-143/145: the importance of cell-type localization of miRNAs

(2014) Oliver A. Kent et al.   NUCLEIC ACIDS RESEARCH

Development of the annelid axochord: Insights into notochord evolution

(2014) A. Lauri et al.   SCIENCE

Pre-metazoan origins and evolution of the cadherin adhesome

(2014) P. S. Murray et al.   Biology Open

Transient Receptor Potential Channels and Mechanosensation

(2013) Niels Eijkelkamp et al.   Annual Review of Neuroscience

The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications

(2013) David Lagman et al.   BMC EVOLUTIONARY BIOLOGY

The bilaterian forebrain: an evolutionary chimaera

(2013) Maria Antonietta Tosches et al.   CURRENT OPINION IN NEUROBIOLOGY

Transcriptional regulation of the peripheral nervous system in Ciona intestinalis

(2013) W. Joyce Tang et al.   DEVELOPMENTAL BIOLOGY

A novel N-terminal motif is responsible for the evolution of neural crest-specific gene-regulatory activity in vertebrate FoxD3

(2013) Hiroki Ono et al.   DEVELOPMENTAL BIOLOGY

Otx2 and Onecut1 Promote the Fates of Cone Photoreceptors and Horizontal Cells and Repress Rod Photoreceptors

(2013) Mark M. Emerson et al.   DEVELOPMENTAL CELL

Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice

(2013) Mihaela Pavlicev et al.   Genome Biology and Evolution

The evolution and development of vertebrate lateral line electroreceptors

(2013) C. V. H. Baker et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Comprehensive Expression Analyses of Neural Cell-Type-Specific miRNAs Identify New Determinants of the Specification and Maintenance of Neuronal Phenotypes

(2013) A. Jovicic et al.   JOURNAL OF NEUROSCIENCE

Combinatorial temporal patterning in progenitors expands neural diversity

(2013) Omer Ali Bayraktar et al.   NATURE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals

(2013) T. Oosterveen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of phototransduction, vertebrate photoreceptors and retina

(2013) Trevor D. Lamb   PROGRESS IN RETINAL AND EYE RESEARCH

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

(2013) Michael A. Lodato et al.   PLoS Genetics

Evolution of Synapse Complexity and Diversity

(2012) Richard D. Emes et al.   Annual Review of Neuroscience

Expansion of transducin subunit gene families in early vertebrate tetraploidizations

(2012) David Lagman et al.   GENOMICS

Low Activation and Fast Inactivation of Transducin in Carp Cones

(2012) Shuji Tachibanaki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Independent evolution of striated muscles in cnidarians and bilaterians

(2012) Patrick R. H. Steinmetz et al.   NATURE

Transcription factor Foxp3 and its protein partners form a complex regulatory network

(2012) Dipayan Rudra et al.   NATURE IMMUNOLOGY

Synaptic scaffold evolution generated components of vertebrate cognitive complexity

(2012) Jess Nithianantharajah et al.   NATURE NEUROSCIENCE

Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain

(2012) Miao He et al.   NEURON

Functionalization of a protosynaptic gene expression network

(2012) C. Conaco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: Facts and models

(2012) Juan I. Korenbrot   PROGRESS IN RETINAL AND EYE RESEARCH

Bringing balance by force: live cell extrusion controls epithelial cell numbers

(2012) George T. Eisenhoffer et al.   TRENDS IN CELL BIOLOGY

Regulation of Terminal Differentiation Programs in the Nervous System

(2011) Oliver Hobert   Annual Review of Cell and Developmental Biology

The evolution of menstruation: A new model for genetic assimilation

(2011) Deena Emera et al.   BIOESSAYS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Epithelia, an Evolutionary Novelty of Metazoans

(2011) Sally P. Leys et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The progesterone receptor regulates implantation, decidualization, and glandular development via a complex paracrine signaling network

(2011) Margeaux Wetendorf et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds

(2011) Zhe Wang et al.   NATURE

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

Regulation of POU4F3 gene expression in hair cells by 5′ DNA in mice

(2011) M. Masuda et al.   NEUROSCIENCE

Primordial neurosecretory apparatus identified in the choanoflagellate Monosiga brevicollis

(2011) P. Burkhardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

(2010) Alexandre Alié et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary novelties

(2010) Günter P. Wagner et al.   CURRENT BIOLOGY

Evolutionary emergence of synaptic nervous systems: what can we learn from the non-synaptic, nerveless Porifera?

(2010) Michael Nickel   INVERTEBRATE BIOLOGY

ARFGAP2 and ARFGAP3 Are Essential for COPI Coat Assembly on the Golgi Membrane of Living Cells

(2010) Fredrik Kartberg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

N-cadherin mediates plasticity-induced long-term spine stabilization

(2010) Pablo Mendez et al.   JOURNAL OF CELL BIOLOGY

Persistence of Coordinated Long-Term Potentiation and Dendritic Spine Enlargement at Mature Hippocampal CA1 Synapses Requires N-Cadherin

(2010) O. Bozdagi et al.   JOURNAL OF NEUROSCIENCE

Replacing the rod with the cone transducin α subunit decreases sensitivity and accelerates response decay

(2010) C.-K. Chen et al.   JOURNAL OF PHYSIOLOGY-LONDON

Differences in the SNARE evolution of fungi and metazoa: Figure 1

(2009) Nickias Kienle et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Inhibitory and excitatory subtypes of cochlear nucleus neurons are defined by distinct bHLH transcription factors, Ptf1a and Atoh1

(2009) T. Fujiyama et al.   DEVELOPMENT

Neurog2 is a direct downstream target of the Ptf1a-Rbpj transcription complex in dorsal spinal cord

(2009) R. M. Henke et al.   DEVELOPMENT

SRp38 Regulates Alternative Splicing and Is Required for Ca2+ Handling in the Embryonic Heart

(2009) Ying Feng et al.   DEVELOPMENTAL CELL

The evolution of complex biomaterial performance: The case of spider silk

(2009) B. O. Swanson et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Different Transcription Factors RegulatenestinGene Expression during P19 Cell Neural Differentiation and Central Nervous System Development

(2009) Zhigang Jin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gene regulatory logic of dopamine neuron differentiation

(2009) Nuria Flames et al.   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

The evolution of hierarchical gene regulatory networks

(2009) Douglas H. Erwin et al.   NATURE REVIEWS GENETICS

The origin and evolution of synapses

(2009) Tomás J. Ryan et al.   NATURE REVIEWS NEUROSCIENCE

LMO4 Controls the Balance between Excitatory and Inhibitory Spinal V2 Interneurons

(2009) Kaumudi Joshi et al.   NEURON

HoxA-11 and FOXO1A Cooperate to Regulate Decidual Prolactin Expression: Towards Inferring the Core Transcriptional Regulators of Decidual Genes

(2009) Vincent J. Lynch et al.   PLoS One

atonal- and achaete-scute-related genes in the annelid Platynereis dumerilii: insights into the evolution of neural basic-Helix-Loop-Helix genes

(2008) Elena Simionato et al.   BMC EVOLUTIONARY BIOLOGY

Rod and cone photoreceptors: Molecular basis of the difference in their physiology

(2008) Satoru Kawamura et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

A Regulatory Network to Segregate the Identity of Neuronal Subtypes

(2008) Seunghee Lee et al.   DEVELOPMENTAL CELL

Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking

(2008) Carolin Weimer et al.   JOURNAL OF CELL BIOLOGY

Rac regulates the interaction of fascin with protein kinase C in cell migration

(2008) M. Parsons et al.   JOURNAL OF CELL SCIENCE

Identification of molecular markers of bipolar cells in the murine retina

(2008) Douglas S. Kim et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Evolutionary expansion and anatomical specialization of synapse proteome complexity

(2008) Richard D Emes et al.   NATURE NEUROSCIENCE

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

Multigene Phylogeny of Choanozoa and the Origin of Animals

(2008) Kamran Shalchian-Tabrizi et al.   PLoS One

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals

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

Regulatory logic of neuronal diversity: Terminal selector genes and selector motifs

(2008) O. Hobert   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE