Properties of developmental gene regulatory networks.

Forcing cells to change lineages. Nature (2009) 5.99

Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell (2010) 2.84

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A (2010) 2.81

Direct lineage conversions: unnatural but useful? Nat Biotechnol (2011) 2.69

Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube. Cell (2012) 2.54

Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J Intern Med (2012) 2.13

Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet (2012) 1.68

Hierarchical evolution of the bacterial sporulation network. Curr Biol (2010) 1.50

A blueprint for engineering cell fate: current technologies to reprogram cell identity. Cell Res (2013) 1.50

Towards genome-scale signalling network reconstructions. Nat Rev Genet (2010) 1.39

Modularity and design principles in the sea urchin embryo gene regulatory network. FEBS Lett (2009) 1.39

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. Genes Dev (2010) 1.39

Maintaining differentiated cellular identity. Nat Rev Genet (2012) 1.32

The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. Dev Biol (2009) 1.21

Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Mol Cell Biol (2012) 1.15

Evolutionary crossroads in developmental biology: sea urchins. Development (2011) 1.11

Network design principles from the sea urchin embryo. Curr Opin Genet Dev (2009) 1.10

Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait Loci. Genetics (2014) 1.09

Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits. BMC Evol Biol (2011) 1.09

A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics (2009) 1.08

Zfp206, Oct4, and Sox2 are integrated components of a transcriptional regulatory network in embryonic stem cells. J Biol Chem (2009) 1.06

Building developmental gene regulatory networks. Birth Defects Res C Embryo Today (2009) 1.02

A Boolean model of the gene regulatory network underlying Mammalian cortical area development. PLoS Comput Biol (2010) 1.00

Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster. PLoS Comput Biol (2013) 0.99

Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis. Dev Biol (2012) 0.96

Transcriptional networks in epithelial-mesenchymal transition. PLoS One (2011) 0.95

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Evodevo (2013) 0.94

Dissecting high-dimensional phenotypes with bayesian sparse factor analysis of genetic covariance matrices. Genetics (2013) 0.92

Uncovering a dynamic feature of the transcriptional regulatory network for anterior-posterior patterning in the Drosophila embryo. PLoS One (2013) 0.91

Cell signalling regulates dynamics of Nanog distribution in embryonic stem cell populations. J R Soc Interface (2012) 0.91

Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet (2014) 0.91

Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res (2015) 0.90

The transcriptional programme controlled by Runx1 during early embryonic blood development. Dev Biol (2012) 0.90

Learning to get along despite struggling to get by. Genome Biol (2009) 0.89

Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. Mol Reprod Dev (2010) 0.89

Dpp-induced Egfr signaling triggers postembryonic wing development in Drosophila. Proc Natl Acad Sci U S A (2013) 0.87

Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis. Dev Biol (2012) 0.86

Simulating cortical development as a self constructing process: a novel multi-scale approach combining molecular and physical aspects. PLoS Comput Biol (2013) 0.86

C. elegans BED domain transcription factor BED-3 controls lineage-specific cell proliferation during organogenesis. Dev Biol (2009) 0.85

MED GATA factors promote robust development of the C. elegans endoderm. Dev Biol (2015) 0.85

Cardiac expression of ms1/STARS, a novel gene involved in cardiac development and disease, is regulated by GATA4. Mol Cell Biol (2012) 0.85

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer. Development (2012) 0.84

Measurement of gene regulation in individual cells reveals rapid switching between promoter states. Science (2016) 0.83

Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory network states. Wiley Interdiscip Rev Dev Biol (2011) 0.82

Competition among gene regulatory networks imposes order within the eye-antennal disc of Drosophila. Development (2013) 0.81

Integration of an abdominal Hox complex with Pax2 yields cell-specific EGF secretion from Drosophila sensory precursor cells. Development (2012) 0.81

Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. BMC Syst Biol (2012) 0.80

Perturbation analysis analyzed--athematical modeling of intact and perturbed gene regulatory circuits for animal development. Dev Biol (2010) 0.80

Multicolor labeling in developmental gene regulatory network analysis. Methods Mol Biol (2014) 0.80

Discrete levels of Twist activity are required to direct distinct cell functions during gastrulation and somatic myogenesis. PLoS One (2014) 0.79

Identification of cis-regulatory modules encoding temporal dynamics during development. BMC Genomics (2014) 0.79

A provisional gene regulatory atlas for mouse heart development. PLoS One (2014) 0.78

Developmental gene regulatory networks in sea urchins and what we can learn from them. F1000Res (2016) 0.78

The ascl1a and dlx genes have a regulatory role in the development of GABAergic interneurons in the zebrafish diencephalon. Dev Biol (2013) 0.78

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome Res (2015) 0.77

A review of integration strategies to support gene regulatory network construction. ScientificWorldJournal (2012) 0.77

Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71. Sci Rep (2015) 0.77

A Membrane-Embedded Amino Acid Couples the SpoIIQ Channel Protein to Anti-Sigma Factor Transcriptional Repression during Bacillus subtilis Sporulation. J Bacteriol (2016) 0.77

Model transcriptional networks with continuously varying expression levels. BMC Evol Biol (2011) 0.76

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes. Genome Res (2017) 0.75

Eric Davidson: Steps to a gene regulatory network for development. Dev Biol (2016) 0.75

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6. PLoS Genet (2016) 0.75

Characterization of transcription factor response kinetics in parallel. BMC Biotechnol (2016) 0.75

Genetic and environmental factors affecting cryptic variations in gene regulatory networks. BMC Evol Biol (2013) 0.75

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC Syst Biol (2014) 0.75

Developmental biologist Eric H. Davidson, 1937-2015. Proc Natl Acad Sci U S A (2015) 0.75

DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan. Biophys J (2017) 0.75

Convergent occurrence of the developmental hourglass in plant and animal embryogenesis? Ann Bot (2016) 0.75

Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos. PeerJ (2015) 0.75

An Intronic cis-Regulatory Element Is Crucial for the Alpha Tubulin Pl-Tuba1a Gene Activation in the Ciliary Band and Animal Pole Neurogenic Domains during Sea Urchin Development. PLoS One (2017) 0.75

De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus. PLoS One (2016) 0.75

Stepwise Progression of Embryonic Patterning. Trends Genet (2016) 0.75

A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation. Nat Commun (2017) 0.75

Prenatal chromosomal microarray for the Catholic physician. Linacre Q (2014) 0.75

Retinal Expression of the Drosophila eyes absent Gene Is Controlled by Several Cooperatively Acting Cis-regulatory Elements. PLoS Genet (2016) 0.75

The Role of SHI/STY/SRS Genes in Organ Growth and Carpel Development Is Conserved in the Distant Eudicot Species Arabidopsis thaliana and Nicotiana benthamiana. Front Plant Sci (2017) 0.75

The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. Cell (1991) 4.63

Gene regulatory networks for development. Proc Natl Acad Sci U S A (2005) 4.45

Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci U S A (2008) 3.27

Characterization of the Drosophila segment determination morphome. Dev Biol (2007) 2.39

Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. Proc Natl Acad Sci U S A (2003) 2.30

Regulatory logic of neuronal diversity: terminal selector genes and selector motifs. Proc Natl Acad Sci U S A (2008) 2.28

A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science (2007) 2.04

A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres. Proc Natl Acad Sci U S A (2007) 2.00

cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev Biol (2006) 1.96

How the Dorsal gradient works: insights from postgenome technologies. Proc Natl Acad Sci U S A (2008) 1.70

The Xenopus Brachyury promoter is activated by FGF and low concentrations of activin and suppressed by high concentrations of activin and by paired-type homeodomain proteins. Genes Dev (1997) 1.66

cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. Dev Biol (2005) 1.63

A gene regulatory network armature for T lymphocyte specification. Proc Natl Acad Sci U S A (2008) 1.58

Development. Built to run, not fail. Science (2007) 1.50

Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev Biol (2007) 1.48

Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo. Proc Natl Acad Sci U S A (2008) 1.46

Anterior-posterior positional information in the absence of a strong Bicoid gradient. Proc Natl Acad Sci U S A (2009) 1.46

Dissecting early regulatory relationships in the lamprey neural crest gene network. Proc Natl Acad Sci U S A (2008) 1.36

A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2. Proc Natl Acad Sci U S A (2008) 1.30

Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus. Proc Natl Acad Sci U S A (2008) 1.25

The T-box transcription factor Brachyury regulates expression of eFGF through binding to a non-palindromic response element. Development (1998) 1.20

Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway. Dev Cell (2006) 1.17

The Caenorhabditis elegans vulva: a post-embryonic gene regulatory network controlling organogenesis. Proc Natl Acad Sci U S A (2008) 0.99

A new method, using cis-regulatory control, for blocking embryonic gene expression. Dev Biol (2008) 0.89

Redundant mechanisms mediate bristle patterning on the Drosophila thorax. Proc Natl Acad Sci U S A (2008) 0.86

LvNumb works synergistically with Notch signaling to specify non-skeletal mesoderm cells in the sea urchin embryo. Development (2008) 0.85

A call for transparent reporting to optimize the predictive value of preclinical research. Nature (2012) 14.63

A genomic regulatory network for development. Science (2002) 9.67

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A (2001) 6.39

Parkin-deficient mice exhibit nigrostriatal deficits but not loss of dopaminergic neurons. J Biol Chem (2003) 4.36

Shadow enhancers as a source of evolutionary novelty. Science (2008) 3.71

Full-length human mutant huntingtin with a stable polyglutamine repeat can elicit progressive and selective neuropathogenesis in BACHD mice. J Neurosci (2008) 3.54

Heterosynaptic dopamine neurotransmission selects sets of corticostriatal terminals. Neuron (2004) 3.16

Early and progressive sensorimotor anomalies in mice overexpressing wild-type human alpha-synuclein. J Neurosci (2004) 2.64

Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell (2013) 2.42

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A (2008) 2.25

Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A (2003) 2.24

Assessment and surgical outcomes for mild type I and severe type II cortical dysplasia: a critical review and the UCLA experience. Epilepsia (2009) 1.99

The corticostriatal pathway in Huntington's disease. Prog Neurobiol (2006) 1.99

Transient and progressive electrophysiological alterations in the corticostriatal pathway in a mouse model of Huntington's disease. J Neurosci (2003) 1.88

Repeated exposure to methamphetamine causes long-lasting presynaptic corticostriatal depression that is renormalized with drug readministration. Neuron (2008) 1.81

How the Dorsal gradient works: insights from postgenome technologies. Proc Natl Acad Sci U S A (2008) 1.70

Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc Natl Acad Sci U S A (2006) 1.66

Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci U S A (2005) 1.55

Differential electrophysiological properties of dopamine D1 and D2 receptor-containing striatal medium-sized spiny neurons. Eur J Neurosci (2008) 1.49

Dopamine enhancement of NMDA currents in dissociated medium-sized striatal neurons: role of D1 receptors and DARPP-32. J Neurophysiol (2002) 1.47

Age-dependent alterations of corticostriatal activity in the YAC128 mouse model of Huntington disease. J Neurosci (2009) 1.43

Differential susceptibility to excitotoxic stress in YAC128 mouse models of Huntington disease between initiation and progression of disease. J Neurosci (2009) 1.40

Pathological cell-cell interactions are necessary for striatal pathogenesis in a conditional mouse model of Huntington's disease. Mol Neurodegener (2007) 1.39

Where do you think you are going? The NMDA-D1 receptor trap. Sci STKE (2006) 1.34

Epileptogenesis in pediatric cortical dysplasia: the dysmature cerebral developmental hypothesis. Epilepsy Behav (2006) 1.32

Striatal potassium channel dysfunction in Huntington's disease transgenic mice. J Neurophysiol (2004) 1.30

Alterations in cortical excitation and inhibition in genetic mouse models of Huntington's disease. J Neurosci (2009) 1.28

Differential electrophysiological changes in striatal output neurons in Huntington's disease. J Neurosci (2011) 1.27

Elevated tonic extracellular dopamine concentration and altered dopamine modulation of synaptic activity precede dopamine loss in the striatum of mice overexpressing human α-synuclein. J Neurosci Res (2011) 1.26

Morphological and electrophysiological characterization of abnormal cell types in pediatric cortical dysplasia. J Neurosci Res (2003) 1.24

Contralateral hemimicrencephaly and clinical-pathological correlations in children with hemimegalencephaly. Brain (2005) 1.24

Increased GABAergic function in mouse models of Huntington's disease: reversal by BDNF. J Neurosci Res (2004) 1.17

Dopamine modulation of excitatory currents in the striatum is dictated by the expression of D1 or D2 receptors and modified by endocannabinoids. Eur J Neurosci (2009) 1.16

Alterations in N-methyl-D-aspartate receptor sensitivity and magnesium blockade occur early in development in the R6/2 mouse model of Huntington's disease. J Neurosci Res (2005) 1.15

Neurofibromin regulates corticostriatal inhibitory networks during working memory performance. Proc Natl Acad Sci U S A (2010) 1.12

Dual regulation by the Hunchback gradient in the Drosophila embryo. Proc Natl Acad Sci U S A (2008) 1.12

Network design principles from the sea urchin embryo. Curr Opin Genet Dev (2009) 1.10

Alterations in striatal synaptic transmission are consistent across genetic mouse models of Huntington's disease. ASN Neuro (2010) 1.09

Altered cortical glutamate receptor function in the R6/2 model of Huntington's disease. J Neurophysiol (2005) 1.06

Multiple sources of striatal inhibition are differentially affected in Huntington's disease mouse models. J Neurosci (2013) 1.04

Conservation of enhancer location in divergent insects. Proc Natl Acad Sci U S A (2009) 1.03

Dopamine and glutamate in Huntington's disease: A balancing act. CNS Neurosci Ther (2010) 1.03

Genetic mouse models of Huntington's disease: focus on electrophysiological mechanisms. ASN Neuro (2010) 1.03

Neurofilament-M interacts with the D1 dopamine receptor to regulate cell surface expression and desensitization. J Neurosci (2002) 1.03

Functional and molecular development of striatal fast-spiking GABAergic interneurons and their cortical inputs. Eur J Neurosci (2005) 1.02

Cytomegalic interneurons: a new abnormal cell type in severe pediatric cortical dysplasia. J Neuropathol Exp Neurol (2007) 1.01

A critical window of CAG repeat-length correlates with phenotype severity in the R6/2 mouse model of Huntington's disease. J Neurophysiol (2011) 1.01

Modulation of AMPA currents by D2 dopamine receptors in striatal medium-sized spiny neurons: are dendrites necessary? Eur J Neurosci (2004) 1.00

Human cortical dysplasia and epilepsy: an ontogenetic hypothesis based on volumetric MRI and NeuN neuronal density and size measurements. Cereb Cortex (2004) 0.99

Immature neurons and GABA networks may contribute to epileptogenesis in pediatric cortical dysplasia. Epilepsia (2007) 0.99

Dopamine imbalance in Huntington's disease: a mechanism for the lack of behavioral flexibility. Front Neurosci (2013) 0.99

Are cytomegalic neurons and balloon cells generators of epileptic activity in pediatric cortical dysplasia? Epilepsia (2005) 0.99

Neuronal coupling via connexin36 contributes to spontaneous synaptic currents of striatal medium-sized spiny neurons. J Neurosci Res (2008) 0.97

Striatal neurochemical changes in transgenic models of Huntington's disease. J Neurosci Res (2002) 0.96

NMDA receptor alterations in neurons from pediatric cortical dysplasia tissue. Cereb Cortex (2004) 0.94

Altered corticostriatal neurotransmission and modulation in dopamine transporter knock-down mice. J Neurophysiol (2007) 0.93

Improvement of neuropathology and transcriptional deficits in CAG 140 knock-in mice supports a beneficial effect of dietary curcumin in Huntington's disease. Mol Neurodegener (2012) 0.93

Alpha-synuclein overexpression in mice alters synaptic communication in the corticostriatal pathway. J Neurosci Res (2010) 0.91

Altered Balance of Activity in the Striatal Direct and Indirect Pathways in Mouse Models of Huntington's Disease. Front Syst Neurosci (2011) 0.91

Temporal regulation of single-minded target genes in the ventral midline of the Drosophila central nervous system. Dev Biol (2013) 0.89

Dissecting the contribution of individual receptor subunits to the enhancement of N-methyl-d-aspartate currents by dopamine D1 receptor activation in striatum. Front Syst Neurosci (2011) 0.88

Mycobacterium abscessus empyema in a lung transplant recipient. J Heart Lung Transplant (2002) 0.87

Development and serotonergic modulation of NMDA bursting in rat trigeminal motoneurons. J Neurophysiol (2002) 0.87

Regional and cell-type-specific effects of DAMGO on striatal D1 and D2 dopamine receptor-expressing medium-sized spiny neurons. ASN Neuro (2012) 0.86

DEAF-1 regulates immunity gene expression in Drosophila. Proc Natl Acad Sci U S A (2008) 0.86

Comparative study of cellular and synaptic abnormalities in brain tissue samples from pediatric tuberous sclerosis complex and cortical dysplasia type II. Epilepsia (2010) 0.84

Development of striatal fast-spiking GABAergic interneurons. Prog Brain Res (2007) 0.84

A hypothesis regarding the pathogenesis and epileptogenesis of pediatric cortical dysplasia and hemimegalencephaly based on MRI cerebral volumes and NeuN cortical cell densities. Epilepsia (2007) 0.84

Evidence for behavioral benefits of early dietary supplementation with CoEnzymeQ10 in a slowly progressing mouse model of Huntington's disease. Mol Cell Neurosci (2011) 0.84

Pyramidal cell responses to gamma-aminobutyric acid differ in type I and type II cortical dysplasia. J Neurosci Res (2008) 0.83

Changes in expression of N-methyl-D-aspartate receptor subunits occur early in the R6/2 mouse model of Huntington's disease. Dev Neurosci (2006) 0.83

Basic mechanisms of epileptogenesis in pediatric cortical dysplasia. CNS Neurosci Ther (2014) 0.82

Forebrain striatal-specific expression of mutant huntingtin protein in vivo induces cell-autonomous age-dependent alterations in sensitivity to excitotoxicity and mitochondrial function. ASN Neuro (2011) 0.82

Dopamine reduction of GABA currents in striatal medium-sized spiny neurons is mediated principally by the D(1) receptor subtype. Neurochem Res (2006) 0.82

Drug-primed reinstatement of cocaine seeking in mice: increased excitability of medium-sized spiny neurons in the nucleus accumbens. ASN Neuro (2013) 0.81

In Rasmussen encephalitis, hemichannels associated with microglial activation are linked to cortical pyramidal neuron coupling: a possible mechanism for cellular hyperexcitability. CNS Neurosci Ther (2014) 0.81

Enhanced GABAergic network and receptor function in pediatric cortical dysplasia Type IIB compared with Tuberous Sclerosis Complex. Neurobiol Dis (2011) 0.81

Rescuing the Corticostriatal Synaptic Disconnection in the R6/2 Mouse Model of Huntington's Disease: Exercise, Adenosine Receptors and Ampakines. PLoS Curr (2010) 0.80

Frontal cortical synaptic communication is abnormal in Disc1 genetic mouse models of schizophrenia. Schizophr Res (2013) 0.80

Effects of the Pimelic Diphenylamide Histone Deacetylase Inhibitor HDACi 4b on the R6/2 and N171-82Q Mouse Models of Huntington's Disease. PLoS Curr (2013) 0.79

Age-dependent biphasic changes in ischemic sensitivity in the striatum of Huntington's disease R6/2 transgenic mice. J Neurophysiol (2004) 0.79

Electrophysiological alterations in subthalamic neurons after unilateral dopamine depletion in the rat. J Neurosci Res (2005) 0.78

Interneurons, GABAA currents, and subunit composition of the GABAA receptor in type I and type II cortical dysplasia. Epilepsia (2010) 0.77

Dysfunctional channels are making noise in CAG triplet repeat disorders. Exp Neurol (2006) 0.77

Dopamine-NMDA receptor interactions: twenty years later. Dev Neurosci (2012) 0.76

Opioid self-administration results in cell-type specific adaptations of striatal medium spiny neurons. Behav Brain Res (2013) 0.76

2B or not 2B: a tail of two NMDA receptor subunits. Neuron (2012) 0.75

Enhanced epileptogenic susceptibility in a genetic model of reactive synaptogenesis: the spastic Han-Wistar rat. Dev Neurosci (2002) 0.75