Decoding enhancers using massively parallel reporter assays

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The accessible chromatin landscape of the human genome

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An atlas of active enhancers across human cell types and tissues

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The evolutionary significance of cis-regulatory mutations

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The long-range interaction landscape of gene promoters

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High-Resolution Mapping and Characterization of Open Chromatin across the Genome

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Interchromosomal Interactions and Olfactory Receptor Choice

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Massively parallel functional dissection of mammalian enhancers in vivo

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Enhancer RNAs and regulated transcriptional programs

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Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

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Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

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Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

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A High-Resolution Enhancer Atlas of the Developing Telencephalon

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Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

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Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

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Parallel, tag-directed assembly of locally derived short sequence reads

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Massively parallel functional annotation of 3′ untranslated regions

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FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

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Evaluation of TRAP-sequencing technology with a versatile conditional mouse model

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The Hydrodynamic Tail Vein Assay as a Tool for the Study of Liver Promoters and Enhancers

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Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional Regulation

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Gene Regulatory Sequences and Human Disease

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GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

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The Post-GWAS Era: From Association to Function

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Towards a comprehensive catalogue of validated and target-linked human enhancers

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Variant interpretation: functional assays to the rescue

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Molecular and evolutionary processes generating variation in gene expression

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Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

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Enhancer redundancy in development and disease

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Evaluating Enhancer Function and Transcription

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Limb development: a paradigm of gene regulation

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Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

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The power of multiplexed functional analysis of genetic variants

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Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

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lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

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Massively parallel characterization of transcriptional regulatory elements

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Gene Regulatory Elements, Major Drivers of Human Disease

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Functional assessment of human enhancer activities using whole-genome STARR-sequencing

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Functional regulatory variants implicate distinct transcriptional networks in dementia

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Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

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Characterization of noncoding regulatory DNA in the human genome

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Machine learning dissection of human accelerated regions in primate neurodevelopment

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Imputation of Orofacial Clefting Data Identifies Novel Risk Loci and Sheds Light on the Genetic Background of Cleft Lip ± Cleft Palate and Cleft Palate Only.

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MPRAnalyze: statistical framework for massively parallel reporter assays

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Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

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Neurobiological functions of transcriptional enhancers

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Predicting functional variants in enhancer and promoter elements using RegulomeDB

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Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism

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Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli

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MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

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Massively parallel characterization of regulatory elements in the developing human cortex

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Mutations in ACTRT1 and its enhancer RNA elements lead to aberrant activation of Hedgehog signaling in inherited and sporadic basal cell carcinomas

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Secondary structures in RNA synthesis, splicing and translation

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Global Quantitative Mapping of Enhancers in Rice by STARR-Seq

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The chromatin signatures of enhancers and their dynamic regulation

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Pregnancy, preeclampsia and maternal aging: From epidemiology to functional genomics

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Leveraging massively parallel reporter assays for evolutionary questions

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Linking genome variants to disease: scalable approaches to test the functional impact of human mutations

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Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease

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Human genome-wide measurement of drug-responsive regulatory activity

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Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays.

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Gene networks and the evolution of plant morphology

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Unravelling the complex genetics of common kidney diseases: from variants to mechanisms

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Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology

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How the avidity of polymerase binding to the –35/–10 promoter sites affects gene expression

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Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy

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Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation

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A screen of 1,049 schizophrenia and 30 Alzheimer's‐associated variants for regulatory potential

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Decoding enhancer complexity with machine learning and high-throughput discovery

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Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription

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Precision medicine in rare diseases: What is next?

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Parallel functional testing identifies enhancers active in early postnatal mouse brain

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An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries

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Progress, Challenges, and Surprises in Annotating the Human Genome

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Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

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Focus on your locus with a massively parallel reporter assay

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Implications of juvenile idiopathic arthritis genetic risk variants for disease pathogenesis and classification

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High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction

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Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries

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Genetic and Epigenetic Control of Heart DevelopmentPreprint

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Evolutionary genetics of skin pigmentation in African populations

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Dynamic enhancer landscapes in human craniofacial development

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Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

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Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

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Studying transcription factor function in the genome at molecular resolution

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Using CRISPR to understand and manipulate gene regulation

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Broad H3K4me3 domains: Maintaining cellular identity and their implication in super‐enhancer hijacking

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An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila

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Evolutionary Origins of Pax6 Control of Crystallin Genes

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Computational and experimental methods for classifying variants of unknown clinical significance.Preprint

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Analysis of long and short enhancers in melanoma cell states

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Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits

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CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

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Risks and Function of Breast Cancer Susceptibility Alleles

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Large-scale analysis of the integration of enhancer-enhancer signals by promotersPreprint

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A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences

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Epigenetics of neural differentiation: Spotlight on enhancers

Giacoman-Lozano, M., Meléndez-Ramírez, C., Martínez-Ledesma, E., Durán, R. C., & Velasco, I. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1001701 · Cited by 22 · see citing works

An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo

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Modelling and design of transcriptional enhancers

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RAEdb: a database of enhancers identified by high-throughput reporter assays

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Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids

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Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assayPreprint

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Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

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Identification of a novel strong promoter from the anhydrobiotic midge, Polypedilum vanderplanki, with conserved function in various insect cell lines

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BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression

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Neurogenesis in Caenorhabditis elegans

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Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma

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A systematic evaluation of the design and context dependencies of massively parallel reporter assays

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Using a Massively-Parallel Reporter Assay to Evaluate Synthetic Enhancer Sequences Acting with Cell Type Specificity

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In-depth functional dissection of enhancers

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Deciphering how regulatory DNA encodes regulatory function using massively parallel reporter assays

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Deciphering Gene Regulation Using Massively Parallel Reporter Assays

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