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

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No Need to Stick Together to Be Connected: Multiple Types of Enhancers’ Networking

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Dinucleotide tag‐based parallel reporter gene assay method enables efficient identification of regulatory mutations

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Functional Definition of Thyroid Hormone Response Elements Based on a Synthetic STARR-seq Screen

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Considerations for the Use of Viral Vectors in Nonhuman Primates

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Characterising the genetic basis of immune response variation to identify causal mechanisms underlying disease susceptibility

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Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

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A statistical framework for predicting critical regions of p53-dependent enhancers

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Massively Parallel Analysis of Regulatory RNA Sequences

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The “computable egg”: Myth or useful concept?

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Improved Prediction of Regulatory Element Using Hybrid Abelian Complexity Features with DNA Sequences

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The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional?Preprint

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Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regionsPreprint

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BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants

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Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration

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ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks

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Dual promoter–enhancer activities reflect a unified regulatory logic

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Exonic enhancers are a widespread class of dual-function regulatory elements

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The untold story between enhancers and skeletal muscle development

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Tile by tile: capturing the evolutionary mosaic of human conditions

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The Fire Ant Social Chromosome Exerts a Major Influence on Genome Regulation

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Applications of high-throughput reporter assays to gene regulation studies

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Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes

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Bayesian estimation of genetic regulatory effects in high-throughput reporter assays

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Prevalent use and evolution of exonic regulatory sequences in the human genome

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TF-High-Evolutionary: In Vivo Mutagenesis of Gene Regulatory Networks for the Study of the Genetics and Evolution of the Drosophila Regulatory Genome

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HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo

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Dissecting cardiovascular disease-associated noncoding genetic variants using human iPSC models

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An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genome

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Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions

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Dynamic chromatin organization: Role in development and disease

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The Newly Emerging View of the Genome

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Single embryo-resolution quantitative analysis of reporters permits multiplex spatial cis -regulatory analysis

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A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve

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Molecular and Cellular Biology of the Right Heart

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Approches haut débit pour l’étude des séquences cis-régulatrices

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MicroRNA miR-1002 Enhances NMNAT-Mediated Stress Response by Modulating Alternative Splicing

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Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers That Drive Differentiation of Pancreatic Cells

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The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives

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Mining the Utricularia gibba genome for insulator-like elements for genetic engineering

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Recruitment of transcriptional effectors by Cas9 creates cis-regulatory elements and demonstrates distance-dependent transcriptional regulation

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A Random Screen Using a Novel Reporter Assay System Reveals a Set of Sequences That Are Preferred as the TATA or TATA-Like Elements in the CYC1 Promoter of Saccharomyces cerevisiae

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The Current State of the Neuroanatomy Toolkit in the Fruit Fly Drosophila melanogaster

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Shaping the nebulous enhancer in the era of high-throughput assays and genome editing

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Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

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3D Genomics

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5. Collaborative Study on the Genetics of Alcoholism: Functional genomics

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Investigating enhancer evolution with massively parallel reporter assays

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Genetics of congenital heart disease: Beyond half-measures

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Direct control of somatic stem cell proliferation by the Drosophila testis stem cell nichePreprint

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Identification of essential regulatory elements in the human genomePreprint

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Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity MappingPreprint

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

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Context transcription factors establish cooperative environments and mediate enhancer communicationPreprint

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Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for GenomicsPreprint

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Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seqPreprint

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Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomesPreprint

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Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring

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Enhancer Trajectories in Lineage Commitment: Regulatory Logic of States and Cooperation

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From Natural Discovery to AI‐Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering

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Chromatin architectures underlying plasmid-based assays for regulatory variant effects

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Characterization of caffeine response regulatory variants in vascular endothelial cells

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EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow

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Advances in computational and experimental approaches for deciphering transcriptional regulatory networks

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Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer

Davidson, B. S. A., Arcila-Galvis, J. E., Trevisán-Herraz, M., Mikulášová, A., Brackley, C. A., Russell, L. J., & Rico, D. (2024) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2024.1294510 · Cited by 4

Systematic functional characterization of non-coding regulatory SNPs associated with central obesity

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Synthetic tunable promoters for flexible control of multi-gene expression in mammalian cells

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Enhancer Elements in Plants: Genomic Context and Biological Functions

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Integrating natural and engineered genetic variations to decode regulatory influence on blood traits

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Insect Regulatory Genomics

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How to find genomic regions relevant for gene regulation

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Methods of massive parallel reporter assays for investigation of enhancers

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YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation

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Accelerated Computing A Biomedical Engineering and Medical Science Perspective

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Decoding gene regulation with CRISPR perturbations

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ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types

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Multilayered Mechanisms for Long-range Regulatory Interactions in Eukaryotic Transcription

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Genetic Variation in Long-Range Enhancers

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Enhancing the hunt for enhancers

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Fast training on large genomics data using distributed Support Vector Machines

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A Survey of the Computational Methods for Enhancers and Enhancer-target Predictions

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Genetic engineering: Lassoing genomic libraries

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Development of a high efficient promoter finding method based on transient transfection

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Leveraging technological innovations to investigate evolutionary transitions to eusociality

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Recent Advances in Genetic Engineering Tools for Metabolic Engineering

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Graph-based data integration predicts long-range regulatory interactions across the human genomePreprint

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Predicting enhancers using a small subset of high confidence examples and co-trainingPreprint

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Regulatory DNA in A . thaliana can tolerate high levels of sequence divergencePreprint

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Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolutionPreprint

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