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

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Context transcription factors establish cooperative environments and mediate enhancer communication

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Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing

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

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Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells

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Characterization of sequence determinants of enhancer function using natural genetic variation

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Epigenetics of neural differentiation: Spotlight on enhancers

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Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential

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

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4See: A Flexible Browser to Explore 4C Data

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Enhancers associated with unstable RNAs are rare in plants

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Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

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Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

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Regulatory genome variants in human susceptibility to infection

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Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

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The role of single-cell genomics in human genetics

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Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice

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eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways

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Emerging insights into enhancer biology and function

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A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity

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Myeloid Leukemia Factor Acts in a Chaperone Complex to Regulate Transcription Factor Stability and Gene Expression

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Plant Promoters: Characterization and Applications in Transgenic Technology

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Anno genominis XX: 20 years of Arabidopsis genomics

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The quantitative impact of 3′UTRs on gene expression

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MAPCap allows high-resolution detection and differential expression analysis of transcription start sites

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Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes

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Epigenomic profiling of glucocorticoid responses identifies cis-regulatory disruptions impacting steroid resistance in childhood acute lymphoblastic leukemia

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Enhancer scanning to locate regulatory regions in genomic loci

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Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states

Zhou, J., & Troyanskaya, O. G. (2016) · Nature Communications · doi:10.1038/ncomms10528 · Cited by 17

Epigenomic landscape of enhancer elements during Hydra head organizer formation

Reddy, P. C., Gungi, A., Ubhe, S., & Galande, S. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-020-00364-6 · Cited by 15

The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification

Bertolino, E., Reinitz, J., & Manu (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.02.030 · Cited by 18

Cis-regulatory elements: systematic identification and horticultural applications

Li, T., Zeng, W., Zhu, F., & Lü, P. (2025) · aBIOTECH · doi:10.1007/s42994-025-00237-0 · Cited by 17

Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay

Mouri, K., Dewey, H. B., Castro, R., Berenzy, D., Kales, S., & Tewhey, R. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100234 · Cited by 18

Optimized high-throughput screening of non-coding variants identified from genome-wide association studies

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Short tandem repeats are important contributors to silencer elements in T cells

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Uncovering hidden enhancers through unbiased in vivo testing

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3D genomics imposes evolution of the domain model of eukaryotic genome organization

Razin, S. V., & Vassetzky, Y. S. (2016) · Chromosoma · doi:10.1007/s00412-016-0604-7 · Cited by 16

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data

Thibodeau, A., Khetan, S., Eroğlu, A., Tewhey, R., Stitzel, M. L., & Ucar, D. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009670 · Cited by 16

STARR-seq: genome-wide quantitative enhancer activity maps and the evolution of cis-regulatory elements

Arnold, C. D. (2013)

STARR-seq enterprise

Moorefield, B. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2539

STARR-seq — Principles and applications

Muerdter, F., Boryń, Ł. M., & Arnold, C. D. (2015) · Genomics · doi:10.1016/j.ygeno.2015.06.001 · Cited by 109

Enhancing the hunt for enhancers

Flintoft, L. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3426 · Cited by 3

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

Vanhille, L., Griffon, A., Maqbool, M. A., Zacarias-Cabeza, J., Dao, L. T. M., Fernandez, N., Ballester, B., Andrau, J. C., & Spicuglia, S. (2015) · Nature Communications · doi:10.1038/ncomms7905 · Cited by 158