Published in Nature on December 16, 2010
Transcription factors: from enhancer binding to developmental control. Nat Rev Genet (2012) 5.00
Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell (2012) 4.22
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04
Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells. Cell Stem Cell (2012) 2.93
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol (2014) 2.70
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Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube. Cell (2012) 2.54
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Predictive computation of genomic logic processing functions in embryonic development. Proc Natl Acad Sci U S A (2012) 2.11
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
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Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science (2014) 1.80
Impulse control: temporal dynamics in gene transcription. Cell (2011) 1.79
A gene regulatory network for root epidermis cell differentiation in Arabidopsis. PLoS Genet (2012) 1.75
Coordination of progenitor specification and growth in mouse and chick spinal cord. Science (2014) 1.74
High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc (2013) 1.73
Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet (2012) 1.68
Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature (2014) 1.66
Cis-regulatory control of corticospinal system development and evolution. Nature (2012) 1.43
Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu Rev Pharmacol Toxicol (2012) 1.41
Direct induction of haematoendothelial programs in human pluripotent stem cells by transcriptional regulators. Nat Commun (2014) 1.27
Gene regulatory networks governing pancreas development. Dev Cell (2013) 1.25
MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise. Nat Commun (2013) 1.24
Bistable responses in bacterial genetic networks: designs and dynamical consequences. Math Biosci (2011) 1.08
Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown. Dev Biol (2012) 1.05
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Multiple time-scales and the developmental dynamics of social systems. Philos Trans R Soc Lond B Biol Sci (2012) 1.02
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Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo. Proc Natl Acad Sci U S A (2014) 0.97
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Pax6 interactions with chromatin and identification of its novel direct target genes in lens and forebrain. PLoS One (2013) 0.96
The developmental regulator Pax6 is essential for maintenance of islet cell function in the adult mouse pancreas. PLoS One (2013) 0.94
Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. Sci Rep (2012) 0.94
Making sense of transcription networks. Cell (2015) 0.94
The orchestration of mammalian tissue morphogenesis through a series of coherent feed-forward loops. J Biol Chem (2011) 0.92
Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. PLoS Genet (2014) 0.92
Pharyngeal mesoderm regulatory network controls cardiac and head muscle morphogenesis. Proc Natl Acad Sci U S A (2012) 0.92
Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res (2014) 0.91
Hematopoiesis. Cold Spring Harb Perspect Biol (2012) 0.91
Translational control in germline stem cell development. J Cell Biol (2014) 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
An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell (2017) 0.91
The transcriptional programme controlled by Runx1 during early embryonic blood development. Dev Biol (2012) 0.90
Genetic changes shaping the human brain. Dev Cell (2015) 0.89
Transcriptional regulation of haematopoietic transcription factors. Stem Cell Res Ther (2011) 0.89
A quantitative atlas of Even-skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos. Evodevo (2014) 0.88
The evolution of phenotypic correlations and "developmental memory". Evolution (2014) 0.88
Evolutionary bioscience as regulatory systems biology. Dev Biol (2011) 0.88
Cytokine-induced megakaryocytic differentiation is regulated by genome-wide loss of a uSTAT transcriptional program. EMBO J (2015) 0.87
Gene regulatory network of renal primordium development. Pediatr Nephrol (2013) 0.87
Ptch1 overexpression drives skin carcinogenesis and developmental defects in K14Ptch(FVB) mice. J Invest Dermatol (2012) 0.86
Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis. Dev Biol (2012) 0.86
Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and "swarm intelligence". Cancer Metastasis Rev (2013) 0.86
Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. PLoS Comput Biol (2014) 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
The biology of the germ line in echinoderms. Mol Reprod Dev (2014) 0.84
Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell (2016) 0.84
C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis. Stem Cell Reports (2015) 0.84
Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin. Development (2013) 0.84
The chromatin landscape and transcription factors in T cell programming. Trends Immunol (2014) 0.83
Distinct regulatory mechanisms act to establish and maintain Pax3 expression in the developing neural tube. PLoS Genet (2013) 0.83
Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment. Nat Immunol (2016) 0.83
Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs. Dev Cell (2016) 0.83
The pharmacology of regenerative medicine. Pharmacol Rev (2013) 0.83
Let's push things forward: disruptive technologies and the mechanics of tissue assembly. Integr Biol (Camb) (2013) 0.83
Models of human core transcriptional regulatory circuitries. Genome Res (2016) 0.83
Logics and properties of a genetic regulatory program that drives embryonic muscle development in an echinoderm. Elife (2015) 0.82
Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory network states. Wiley Interdiscip Rev Dev Biol (2011) 0.82
New developmental evidence supports a homeotic frameshift of digit identity in the evolution of the bird wing. Front Zool (2014) 0.82
Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications. Nat Rev Genet (2016) 0.81
Some considerations about a report on 'Public health in an era of genomic-based and personalized medicine' from the Public Health Foundation, Cambridge. J Community Genet (2011) 0.81
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From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis. Philos Trans R Soc Lond B Biol Sci (2014) 0.81
Design principles of stripe-forming motifs: the role of positive feedback. Sci Rep (2014) 0.80
How difficult is inference of mammalian causal gene regulatory networks? PLoS One (2014) 0.80
Cellular reprogramming in skin cancer. Semin Cancer Biol (2014) 0.80
Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses. Biol Open (2013) 0.80
VEGFA-dependent and -independent pathways synergise to drive Scl expression and initiate programming of the blood stem cell lineage in Xenopus. Development (2013) 0.80
The evolutionary dynamics of major regulators for sexual development among Hymenoptera species. Front Genet (2015) 0.79
The Relationship between Gene Network Structure and Expression Variation among Individuals and Species. PLoS Genet (2015) 0.79
Mechanistic research in aquatic toxicology: perspectives and future directions. Aquat Toxicol (2011) 0.79
Cooperative Wnt-Nodal Signals Regulate the Patterning of Anterior Neuroectoderm. PLoS Genet (2016) 0.79
Why detailed model gene studies in higher eukaryotes are still necessary. Immunology (2013) 0.79
Studying gene expression system regulation at the program level. PLoS One (2013) 0.79
Co-option and de novo gene evolution underlie molluscan shell diversity. Mol Biol Evol (2017) 0.78
Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis. Cell Rep (2015) 0.78
MIST1 and PTF1 Collaborate in Feed-forward Regulatory Loops that Maintain the Pancreatic Acinar Phenotype in Adult Mice. Mol Cell Biol (2016) 0.78
Modularity of CHIP/LDB transcription complexes regulates cell differentiation. Fly (Austin) (2011) 0.78
In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression. J Bioinform Comput Biol (2014) 0.78
A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Nat Commun (2017) 0.78
An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability. Elife (2016) 0.77
Experimental approaches for gene regulatory network construction: the chick as a model system. Genesis (2012) 0.76
A new paradigm for animal symmetry. Interface Focus (2015) 0.76
Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Direct conversion of fibroblasts to functional neurons by defined factors. Nature (2010) 18.76
In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature (2008) 16.21
Network motifs: theory and experimental approaches. Nat Rev Genet (2007) 15.04
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Gene regulatory networks and the evolution of animal body plans. Science (2006) 6.42
Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature (2006) 6.28
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Forcing cells to change lineages. Nature (2009) 5.99
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol (2003) 5.85
The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol (1985) 5.79
Defining network topologies that can achieve biochemical adaptation. Cell (2009) 5.49
Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell (2006) 5.39
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Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature (2008) 5.08
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Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment. Dev Cell (2002) 4.37
MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc Natl Acad Sci U S A (2005) 3.69
Nanog and transcriptional networks in embryonic stem cell pluripotency. Cell Res (2007) 3.56
Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Dev Biol (2007) 3.49
The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell (2009) 3.38
Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci U S A (2008) 3.27
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A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. Genes Dev (2008) 2.66
The evolution of hierarchical gene regulatory networks. Nat Rev Genet (2009) 2.62
Repression of the transcription factor Th-POK by Runx complexes in cytotoxic T cell development. Science (2008) 2.43
Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics (2004) 2.30
Regulatory logic of neuronal diversity: terminal selector genes and selector motifs. Proc Natl Acad Sci U S A (2008) 2.28
Shavenbaby couples patterning to epidermal cell shape control. PLoS Biol (2006) 2.23
Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development. Proc Natl Acad Sci U S A (2007) 2.15
Response delays and the structure of transcription networks. J Mol Biol (2003) 2.15
Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling. Mol Cell (2009) 2.11
PU.1 inhibits the erythroid program by binding to GATA-1 on DNA and creating a repressive chromatin structure. EMBO J (2005) 2.07
Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput Biol (2006) 2.06
Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification. Dev Biol (2006) 1.98
Mutually repressive interactions between the gap genes giant and Krüppel define middle body regions of the Drosophila embryo. Development (1991) 1.88
A logical analysis of the Drosophila gap-gene system. J Theor Biol (2001) 1.82
How the Dorsal gradient works: insights from postgenome technologies. Proc Natl Acad Sci U S A (2008) 1.70
Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci U S A (2007) 1.62
High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development. Gene Expr Patterns (2010) 1.61
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. Dev Biol (2009) 1.59
Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog. PLoS Biol (2010) 1.58
Genetic and epigenetic mechanisms of gene regulation during lens development. Prog Retin Eye Res (2007) 1.56
A recurrent network involving the transcription factors PU.1 and Gfi1 orchestrates innate and adaptive immune cell fates. Immunity (2009) 1.55
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Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into cooperativity, priming, and irreversibility. PLoS Comput Biol (2009) 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
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence. Dev Biol (2008) 1.45
Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution. Proc Natl Acad Sci U S A (2008) 1.43
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev Biol (2009) 1.42
Functional cross-antagonism between transcription factors FLI-1 and EKLF. Mol Cell Biol (2003) 1.42
Establishing and interpreting graded Sonic Hedgehog signaling during vertebrate neural tube patterning: the role of negative feedback. Cold Spring Harb Perspect Biol (2009) 1.41
Modularity and design principles in the sea urchin embryo gene regulatory network. FEBS Lett (2009) 1.39
Dissecting early regulatory relationships in the lamprey neural crest gene network. Proc Natl Acad Sci U S A (2008) 1.36
The transcription/migration interface in heart precursors of Ciona intestinalis. Science (2008) 1.32
Pax3:Foxc2 reciprocal repression in the somite modulates muscular versus vascular cell fate choice in multipotent progenitors. Dev Cell (2009) 1.31
A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus. BMC Dev Biol (2007) 1.30
Xenopus as a model system to study transcriptional regulatory networks. Proc Natl Acad Sci U S A (2005) 1.28
Tbx20-related genes, mid and H15, are required for tinman expression, proper patterning, and normal differentiation of cardioblasts in Drosophila. Mech Dev (2005) 1.27
A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. Proc Natl Acad Sci U S A (2009) 1.24
CD4-CD8 lineage differentiation: Thpok-ing into the nucleus. J Immunol (2009) 1.21
The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. Dev Biol (2009) 1.21
A transcriptional network coordinately determines transmitter and peptidergic fate in the dorsal spinal cord. Dev Biol (2008) 1.19
meis1 regulates cyclin D1 and c-myc expression, and controls the proliferation of the multipotent cells in the early developing zebrafish eye. Development (2008) 1.14
Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate. PLoS Comput Biol (2010) 1.12
Developmental gene regulatory networks in the zebrafish embryo. Biochim Biophys Acta (2008) 1.12
Network design principles from the sea urchin embryo. Curr Opin Genet Dev (2009) 1.10
The molecular circuitry governing retinal determination. Biochim Biophys Acta (2008) 1.10
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Role of T-box gene tbx-2 for anterior foregut muscle development in C. elegans. Dev Biol (2006) 0.99
The Caenorhabditis elegans vulva: a post-embryonic gene regulatory network controlling organogenesis. Proc Natl Acad Sci U S A (2008) 0.99
Transcriptional control of precursor proliferation in the early phases of pituitary development. Curr Opin Genet Dev (2004) 0.97
Pattern formation by dynamically interacting network motifs. Proc Natl Acad Sci U S A (2009) 0.95
An integrated view of precambrian eumetazoan evolution. Cold Spring Harb Symp Quant Biol (2010) 0.89
Evolution of gene regulatory network architectures: examples of subcircuit conservation and plasticity between classes of echinoderms. Biochim Biophys Acta (2009) 0.87
Modeling the spatio-temporal network that drives patterning in the vertebrate central nervous system. Biochim Biophys Acta (2009) 0.86
Decision by committee: new light on the CD4/CD8-lineage choice. Immunol Cell Biol (2008) 0.85
The core endodermal gene network of vertebrates: combining developmental precision with evolutionary flexibility. Bioessays (2008) 0.84