Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

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Cis-regulatory elements operating in the trophoblast

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Discovering the complete enhancer map of human herpesviruses using a natural language processing model

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The XSER1 lncRNA acts as an enhancer RNA and confers resistance to pathogens by promoting chromatin loop formation in rice

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Transcription factors as drivers of 3D enhancer-promoter interactions

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Molecular co-accessibility identifies coordinated regulation between distant cis-regulatory elements

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Enhancer Trafficking: Free Throws and Three-Pointers

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Temporal establishment of neural cell identityin vivoandin vitro

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Identification of cis-Elements for RNA Subcellular Localization Through REL-seq

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RNA Sequencing: A Potent Transcription Profiling Tool

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Enhancers have more cofactor specificity than we think: A potential new way to classify enhancers based on their functional cofactor requirements

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Characterization of Gene Regulatory Elements in Human Fetal Cortical Development: Enhancing Our Understanding of Neurodevelopmental Disorders and Evolution

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An Unbiased Approach to Identifying Cellular Reprogramming-Inducible Enhancers

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Enhancer‐dependent gene regulation in space, time, and malignancies

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Evolutionarily Conserved DHX9/MLE Helicase Is Involved in the Regulation of Its Own mRNA Expression Level in Drosophila melanogaster

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Regulatory Elements for Gene Therapy of Epilepsy

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Deregulated enhancer‐promoter communication in cancer through altered nuclear architecture

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MLE (DHX9) Helicase Regulates the Expression of Constitutive and Inducible Isoforms of the Conserved Nuclear Receptor FTZ-F1 (NR5A3)

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Analysis of biased allelic enhancer activity of schizophrenia-linked common variants

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Machine learning tools for deciphering the regulatory logic of enhancers in health and disease

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EnhancerDetector: enhancer discovery from human to fly via interpretable deep learning

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Methods to Detect and Associate Divergence in Cis-Regulatory Elements to Phenotypic Divergence

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Enhanced dissection of the regulatory genome

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The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes

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Epigenetics, Enhancers, and Cancer

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ИЗУЧЕНИЕ СВОЙСТВ НОВОГО ЭКДИЗОНЗАВИСИМОГО ЭНХАНСЕРА

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Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data

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Functional genomics of psychiatric disease risk using genome engineering

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Integration of Count Difference and Curve Similarity in Negative Regulatory Element Detection

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AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain

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Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants

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TRIP through the chromatin: A high throughput exploration of enhancer regulatory landscapes

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A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays

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Computational prediction of CRISPR-impaired non-coding regulatory regions

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Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology

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Meta-analysis of massive parallel reporter assays enables functional regulatory elements predictionPreprint

Kreimer, A., Yan, Z., Ahituv, N., & Yosef, N. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/202002 · Cited by 2

Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genomePreprint

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Discovery of directional chromatin-associated regulatory motifs affecting human gene transcriptionPreprint

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Induction of C 4 genes evolved through changes in cis allowing integration into ancestral C 3 gene regulatory networksPreprint

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Methylation-mediated retuning on the enhancer-to-silencer activity scale of networked regulatory elements guides driver-gene misregulationPreprint

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Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seqPreprint

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A spatial genome aligner for multiplexed DNA-FISHPreprint

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Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancerPreprint

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Assessment of glucocorticoid-induced enhancer activity of eSNP regions using STARR-seq reveals novel molecular mechanisms in psychiatric disordersPreprint

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SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C dataPreprint

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Next-generation plasmids for transgenesis in zebrafish and beyondPreprint

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Non-coding mutations at enhancer clusters contribute to pancreatic ductal adenocarcinomaPreprint

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BRAIN-MAGNET: A novel functional genomics atlas coupled with convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elementsPreprint

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Simultaneous Prediction of Functional States and Types of cis -regulatory Modules Reveals Their Prevalent Dual Uses as Enhancers and SilencersPreprint

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Gene regulatory activity associated with PCOS revealed DENND1A -dependent testosterone productionPreprint

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Targeted mutagenesis of specific genomic DNA sequences in animals for the in vivo generation of variant librariesPreprint

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Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contextsPreprint

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The gene regulatory effects of selective glucocorticoid receptor ligandsPreprint

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Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflowPreprint

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The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA BiologyPreprint

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Taking a STAP at Core Promoter-Transcriptional Cofactor Specificity.

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Gene regulatory networks controlling neuronal development

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Detection of gene cis-regulatory element perturbations in single-cell transcriptomes

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Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage

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An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level

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3D organization of enhancers in MuSCs

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Massively parallel reporter assays identify enhancer elements in oesophageal Adenocarcinoma

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Profiling regulatory elements in vivo by genome-wide methods

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Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms

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Functional Validation of Noncoding Variants Associated With Nonsyndromic Orofacial Cleft

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High-throughput capture of actively transcribed region-interacting sequences reveals an intricate promoter-centered regulatory network

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SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors

Wu, S., Guyot, R., Zekri, Y., Jiang, W., & Flamant, F. (2025) · Scientific Reports · doi:10.1038/s41598-025-29970-8 · Cited by 1

Cooperativity between regulatory elements acts as a modulator of enhancer function

Balasubramanian, D., Masoura, M., & Ghavi-Helm, Y. (2026) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102427 · Cited by 2

Heterogeneous NF-κB activation and enhancer features shape transcription in Drosophila immunity

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Systematic analysis of functional genetic and epigenetic variants in colorectal cancer

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Genome-wide discovery of cis-regulatory elements in a large genome

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A functional overlap between actively transcribed genes and chromatin insulator elements

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Enhancer-based gene therapy: a new path for precision medicine

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STARR-CRAAVT: A platform to identify cell type-specific regulatory elements for next-generation gene therapy

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KAS‐Seq Captures Global Transcription Dynamics and Active Single‐Stranded Enhancers in Rice

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Genome Evolution in Social Insects

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Regulatory Genomics – Decoding Drosophila Regulatory Sequences

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From the Beauty of Genomic Landscapes to the Strength of Transcriptional Mechanisms

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Cloning and expression analysis of alcohol dehydrogenase (Adh) hybrid promoter isolated from Zea mays

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Diff-ATAC-STARR-Seq: A Method for Genome-Wide Functional Screening of Enhancer Activity in Vivo

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Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation

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