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• 4DXpress: a database for cross-species expression pattern comparisons
• A Versatile, Low-Cost, Multiway Microfluidic Sorter for Droplets, Cells, and Embryos.
• A conserved role for Snail as a potentiator of active transcription.
• A core transcriptional network for early mesoderm development in Drosophila melanogaster.
• A functional genomics approach to identify new regulators of Wnt signaling.
• A proteolytic fragment of histone deacetylase 4 protects the heart from failure by regulating the hexosamine biosynthetic pathway.
• A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development.
• A temporal map of transcription factor activity: Mef2 directly regulates at all stages of muscle target genes development
• A topographical map of spatiotemporal patterns of gene expression.
• A transcription factor collective defines cardiac cell fate and reflects lineage history.
• Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.
• Analysis of variation at transcription factor binding sites in Drosophila and humans.
• Analyzing transcription factor occupancy during embryo development using ChIP-seq.
• BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.
• Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
• ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos.
• Challenges for modeling global gene regulatory networks during development: insights from Drosophila.
• Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation.
• Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila.
• Chromatin accessibility profiling methods
• Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?
• Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation.
• Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs
• Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
• CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.
• Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity.
• Combinatorial binding predicts spatio-temporal cis-regulatory activity.
• Conservation and divergence in developmental networks: a view from Drosophila myogenesis.
• Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.
• Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis.
• Correlation Does Not Imply Causation: Histone Methyltransferases, but Not Histone Methylation, SET the Stage for Enhancer Activation.
• Developmental control of nuclear size and shape by Kugelkern and Kurzkern.
• Developmental enhancers and chromosome topology.
• Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.
• Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements
• Dynamic CRM occupancy reflects a temporal map of developmental progression.
• Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila.
• Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets.
• Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families
• Expanding the mesodermal transcriptional network by genome-wide identification of Zinc finger homeodomain 1 (Zfh1) targets.
• FourCSeq: analysis of 4C sequencing data.
• Fragmentation of DNA in a sub-microliter microfluidic sonication device.
• Gene expression during the life cycle of Drosophila melanogaster.
• Genetic variants regulating expression levels and isoform diversity during embryogenesis.
• Genomics and development: Taking developmental biology to new heights.
• Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
• Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network
• Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
• Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing.
• Integrating transcriptional and signalling networks during muscle development.
• Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis.
• Logical modelling of Drosophila signalling pathways.
• Mes2, a MADF-containing transcription factor essential for Drosophila development.
• Model-based method for transcription factor target identification with limited data.
• Molecular biology: A fly in the face of genomics.
• Myofilin, a protein in the thick filaments of insect muscle.
• Next-generation sequencing-based detection of germline L1-mediated transductions.
• Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis.
• Notch and Ras signaling pathway effector genes expressed in fusion competent and founder cells during Drosophila myogenesis.
• Opbp is a new architectural/insulator protein required for ribosomal gene expression.
• Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state.
• Predictive features of gene expression variation reveal mechanistic link with differential expression
• Promoter shape varies across populations and affects promoter evolution and expression noise.
• Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.
• Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.
• Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity.
• Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network.
• The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila
• The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
• The Role of Chromatin Accessibility in cis-Regulatory Evolution.
• The cis-regulatory dynamics of embryonic development at single-cell resolution.
• The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription
• The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
• The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
• The importance of being specified: cell fate decisions and their role in cell biology.
• The road ahead in genetics and genomics
• The role of chromatin accessibility in cis-regulatory evolution
• The role of transcription in shaping the spatial organization of the genome
• Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
• Transcription factors: from enhancer binding to developmental control.
• Ultrasensitive proteome analysis using paramagnetic bead technology.
• Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity
• cis-Regulatory networks during development: a view of Drosophila.
• easyRNASeq: a bioconductor package for processing RNA-Seq data.
• scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation