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

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400

Targeted gene expression as a means of altering cell fates and generating dominant phenotypes

Brand, A. H., & Perrimon, N. (1993) · Development · doi:10.1242/dev.118.2.401 · Cited by 9,510

Tandem repeats finder: a program to analyze DNA sequences

Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374

The Genome Sequence of Drosophila melanogaster

Adams, M. D., Celniker, S., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) · Science · doi:10.1126/science.287.5461.2185 · Cited by 5,902

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302

miRBase: integrating microRNA annotation and deep-sequencing data

Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634

Deciphering the Gene Regulatory Landscape Encoded in DNA Biophysical Features

Pataskar, A., Vanderlinden, W., Emmerig, J., Singh, A. P., Lipfert, J., & Tiwari, V. K. (2019) · iScience · doi:10.1016/j.isci.2019.10.055 · Cited by 9

How to study enhancers in non-traditional insect models

Tomoyasu, Y., & Halfon, M. S. (2020) · Journal of Experimental Biology · doi:10.1242/jeb.212241 · Cited by 9

Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

Baxter, J. S., Johnson, N., Tomczyk, K., Gillespie, A., Maguire, S. L., Brough, R., Fachal, L., Michailidou, K., Bolla, M. K., Wang, Q., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.05.013 · Cited by 9

Multiplexed functional genomic assays to decipher the noncoding genome

Cooper, Y. A., Guo, Q., & Geschwind, D. H. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac194 · Cited by 10

DNA methylation-environment interactions in the human genome

Johnston, R. A., Aracena, K. A., Barreiro, L. B., Lea, A. J., & Tung, J. (2023) · eLife · doi:10.7554/elife.89371 · Cited by 8

Enhancers and their dynamics during hematopoietic differentiation and emerging strategies for therapeutic action

Cico, A., Andrieu‐Soler, C., & Soler, É. (2016) · FEBS Letters · doi:10.1002/1873-3468.12424 · Cited by 11

Direct visualization of transcriptional activation by physical enhancer–promoter proximityPreprint

Chen, H., Fujioka, M., Jaynes, J. B., & Gregor, T. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/099523 · Cited by 11

The role of transposon activity in shapingcis-regulatory element evolution after whole-genome duplicationPreprint

Monsen, Ø., Grønvold, L., Datsomor, A. K., Harvey, T. N., Kijas, J., Suh, A., Hvidsten, T. R., & Sandve, S. R. (2025) · Genome Research · doi:10.1101/gr.278931.124 · Cited by 8

Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers

Heer, M., Giudice, L., Mengoni, C., Giugno, R., & Rico, D. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad229 · Cited by 8

Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

Guzman, C., Duttke, S. H. C., Zhu, Y., Saldanha, C. D. A., Downes, N. L., Benner, C. W., & Heinz, S. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad562 · Cited by 7

Identification, Design, and Application of Noncoding Cis-Regulatory Elements

Xu, L., & Liu, Y. (2024) · Biomolecules · doi:10.3390/biom14080945 · Cited by 9

Translation of genome-wide association study: from genomic signals to biological insights

Bruner, W. S., & Grant, S. F. A. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1375481 · Cited by 10

Towards functional maps of non-coding variants in cancer

Wang, Y., & Hon, G. C. (2024) · Frontiers in Genome Editing · doi:10.3389/fgeed.2024.1481443 · Cited by 8

Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee

Jones, B. M., Webb, A. E., Geib, S. M., Sim, S. B., Schweizer, R. M., Branstetter, M. G., Evans, J. D., & Kocher, S. D. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae229 · Cited by 8

Technical and biological sources of noise confound multiplexed enhancer AAV screening

Hunker, A. C., Mich, J. K., Taskin, N., Torkelson, A., Cardenas, T., Lalanne, J., Mahoney, J. T., Bertagnolli, D., Chakka, A. B., Chakrabarty, R., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72147-8 · Cited by 8

Harnessing Unsupervised Ensemble Learning for Biomedical Applications: A Review of Methods and Advances

Ahsen, M. E. (2025) · Mathematics · doi:10.3390/math13030420 · Cited by 10

Using omics data and genome editing methods to decipher GWAS loci associated with coronary artery disease

Chignon, A., & Lettre, G. (2025) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2024.118621 · Cited by 9

Enhancer RNA Transcriptome‐Wide Association Study Reveals a Distinctive Class of Pan‐Cancer Susceptibility eRNAs

Chen, W., Wang, Z., Wang, Y., Lin, J., Chen, S., Chen, H., Ma, X., Zou, X., Li, X., Qin, Y., et al. (2025) · Advanced Science · doi:10.1002/advs.202411974 · Cited by 8

DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers

Doyle, C., Herka, K., Flynn, S. M., Melidis, L., Dhir, S., Schoenfelder, S., Tannahill, D., & Balasubramanian, S. (2025) · Genome biology · doi:10.1186/s13059-025-03627-1 · Cited by 10

Lineage-specific regulatory evolution: insights from massively parallel reporter assays

Easterlin, R., & Ahituv, N. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102372 · Cited by 6

Identification and application of bioparts for plant synthetic biology

Koo, H., Jung, M., Lee, S., Go, S., & Kim, Y. (2025) · Molecules and Cells · doi:10.1016/j.mocell.2025.100273 · Cited by 8

EAP-LSTM: A Bi-LSTM-Based Deep Learning Framework for Quantitatively Predicting Enhancer Activity in Drosophila and Human Cell Lines

Zhang, Y., Dai, L., Dou, Y., Li, X., Lu, C. F., & Wu, H. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3620986 · Cited by 8

Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites

Giorgio, E. D., Benetti, R., Kerschbamer, E., Xodo, L. E., & Brancolini, C. (2023) · International review of cytology · doi:10.1016/bs.ircmb.2023.03.013 · Cited by 9

Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis

Chen, X., Duan, Y.-Y., Jia, Y., Dong, Q.-H., Shi, W., Zhang, Y., Dong, S., Li, M., Liu, Z., Chen, F., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100501 · Cited by 8

From sequence to consequence: Deciphering the complex cis-regulatory landscape

Dsilva, G. J., & Galande, S. (2024) · Journal of Biosciences · doi:10.1007/s12038-024-00431-0 · Cited by 9

Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells

Fan, S., Ma, L., Song, C., Xu, H., Zhong, B., & Lin, Y. (2024) · Cell Systems · doi:10.1016/j.cels.2024.08.007 · Cited by 8

Transcription-controlling regulatory elements of the eukaryotic genome

Razin, S. V., Gavrilov, A. A., & Ulianov, S. V. (2015) · Molecular Biology · doi:10.1134/s0026893315020119 · Cited by 8

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Dibaeinia, P., & Sinha, S. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab765 · Cited by 8

Molecular and experimental tools to design synthetic enhancers

Vaknin, I., & Amit, R. (2022) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102728 · Cited by 8

STARR-seq for high-throughput identification of plant enhancers

Zhang, L., Yung, W., & Huang, M. (2022) · Trends in Plant Science · doi:10.1016/j.tplants.2022.08.008 · Cited by 8

Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity

Schofield, J. A., & Hahn, S. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112387 · Cited by 9

Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles

Yang, X. H., Wang, B., & Cunningham, J. M. (2015) · BMC Medical Genomics · doi:10.1186/1755-8794-8-s2-s6 · Cited by 8

Housekeeping and tissue-specific cis-regulatory elements: Recipes for specificity and recipes for activity

Russo, M., Natoli, G., & Ghisletti, S. (2017) · Transcription · doi:10.1080/21541264.2017.1378158 · Cited by 8

Anaemia, macrocytosis, vitamin B12 and folate levels in elderly Zimbabweans.

Allain, T. J., Gomo, Z. A. R., Wilson, A. O., Ndemera, B., Adamchak, D. J., & Matenga, J. A. (1997) · PubMed · Cited by 8

Simple Expression Domains Are Regulated by Discrete CRMs During Drosophila Oogenesis

Revaitis, N. T., Marmion, R. A., Farhat, M., Ekiz, V., Wang, W., & Yakoby, N. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.043810 · Cited by 8

Sequence-based correction of barcode bias in massively parallel reporter assaysPreprint

Lee, D., Kapoor, A., Lee, C., Mudgett, M., Beer, M., & Chakravarti, A. (2021) · Genome Research · doi:10.1101/gr.268599.120 · Cited by 8

Massively parallel approaches for characterizing noncoding functional variation in human evolution

Rong, S., Root, E., & Reilly, S. K. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102256 · Cited by 9

Integrating Arabidopsis and crop species gene discovery for crop improvement

Bevan, M. W., Messerer, M., Gundlach, H., Kamal, N. M., Hall, A. J. W., Spannagl, M., & Mayer, K. (2025) · The Plant Cell · doi:10.1093/plcell/koaf087 · Cited by 6

Human Synthetic Biology and Programmable Gene Regulation Control

Thurm, A. R., Carattini, G. L. J., & Bintu, L. (2025) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120423-013542 · Cited by 7

Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors

Psatha, N., Sova, P., Georgolopoulos, G., Paschoudi, K., Iwata, M., Bloom, J. E., Ulyanova, T., Wang, H., Kirtsou, A., Vasiloudis, N.-I., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59235-x · Cited by 9

Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Zhou, Z., Cheng, Y., Lieberth, J., Zhang, J., Jin, Y., Li, A., Yu, H., Ozer, A., & Lis, J. T. (2026) · Cell · doi:10.1016/j.cell.2026.06.033 · Cited by 11

Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus

Dong, D., Zi-Sheng, W. A. N. G., Liu, M., Zhang, Q., Xu, W., Yu, W., Zhu, J., Yang, X., Zhang, Q., Zhu, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64005-w · Cited by 7

3D‐Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma

Feng, Y., Wang, P., Cai, L., Zhan, M., He, F., Wang, J., Li, Y., Gega, E., Zhang, W., Zhao, W., et al. (2022) · Advanced Genetics · doi:10.1002/ggn2.202100010 · Cited by 7

Translating non-coding genetic associations into a better understanding of immune-mediated disease

Stankey, C. T., & Lee, J. C. (2023) · Disease Models & Mechanisms · doi:10.1242/dmm.049790 · Cited by 9

MAE-seq refines regulatory elements across the genome

Zhu, X., Huang, Q., Huang, L., Luo, J., Li, Q., Kong, D., Deng, B., Gu, Y., Wang, X., Li, C., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1129 · Cited by 8

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs

Wang, C., Chen, C., Lei, B., Qin, S., Zhang, Y., Li, K., Zhang, S., & Liu, Y. (2024) · Genetics Selection Evolution · doi:10.1186/s12711-024-00897-4 · Cited by 8

Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo

Murray, J. I. (2018) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.314 · Cited by 8

Heart Enhancers: Development and Disease Control at a Distance

Yuan, X., Scott, I. C., & Wilson, M. D. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.642975 · Cited by 7

Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation

Gui, Y., Grzyb, K., Thomas, M. H., Ohnmacht, J., Garcia, P., Buttini, M., Skupin, A., Sauter, T., & Sinkkonen, L. (2021) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00418-3 · Cited by 7

Underlying causes for prevalent false positives and false negatives in STARR-seq data

Ni, P., Wu, S., & Su, Z. (2023) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqad085 · Cited by 8

SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks

Pan, J.-H., & Du, P.-F. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad494 · Cited by 7

Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome

Uvarova, A. N., Ткаченко, Е. А., Stasevich, E. M., Zheremyan, E. A., Korneev, K. V., & Kuprash, D. V. (2024) · Biochemistry (Moscow) · doi:10.1134/s0006297924060026 · Cited by 7

Chromatin Properties of Regulatory DNA Probed by Manipulation of Transcription Factors

Sharov, A. A., Nishiyama, A., Qian, Y., Dudekula, D. B., Longo, D. L., Schlessinger, D., & Ko, M. S. H. (2014) · Journal of Computational Biology · doi:10.1089/cmb.2013.0126 · Cited by 7

On the cause and mechanism of phenoptosis

Walker, R. F. (2017) · Biochemistry (Moscow) · doi:10.1134/s0006297917120069 · Cited by 7

CAMIO: a transgenic CRISPR pipeline to create diverse targeted genome deletions in Drosophila

Chen, H.-M., García‐Marqués, J., Sugino, K., Wei, D., Miyares, R. L., & Lee, T. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa177 · Cited by 8

High-throughput identification of RNA localization elements reveals a regulatory role for A/G rich sequencesPreprint

Arora, A., Gutierrez, R. C., Eletto, D., Becker, R., Brown, M. R., Moor, A. E., Russ, H. A., & Taliaferro, J. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.20.465152 · Cited by 7

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communicationPreprint

Kribelbauer, J. F., Gardeux, V., Llimos, G., Faltejsková, K., Russeil, J., Grenningloh, N., Levassor, L., Steiner, C., Vondrášek, J., & Deplancke, B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.08.627402 · Cited by 6

Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity

Baniulyte, G., McCann, A. A., Woodstock, D. L., & Sammons, M. A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1143 · Cited by 6

Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

Wan, J., van Ouwerkerk, A. F., Mouren, J.-C., Heredia, C., Pradel, L. C., Ballester, B., Andrau, J., & Spicuglia, S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1270 · Cited by 7

High‐throughput quantitative assessment of ABA‐responsive elements at single‐nucleotide resolution

Sun, F., Deng, Y., Zhao, W., Xiong, Y., Zhao, L., & Zhang, L. (2025) · Quantitative Biology · doi:10.1002/qub2.87 · Cited by 6

A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction

Cuomo, M., Costabile, D., Monica, R. D., Buonaiuto, M., Trio, F., Riso, G. D., Visconti, R., & Chiariotti, L. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf274 · Cited by 7

Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide

Zhang, J., Leung, A. K.-Y., Zhu, Y., Yao, L., Willis, A., Pan, X., Ozer, A., Zhou, Z., Siklenka, K., Barrera, A., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03828-8 · Cited by 7

Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

Lyu, R., Gao, Y., Wu, T., Ye, C., Wang, P., & He, C. (2024) · Nature Communications · doi:10.1038/s41467-024-50680-8 · Cited by 7

How our brains are built: emerging approaches to understand human-specific features

Moss, N. D., Lollis, D., & Silver, D. L. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102278 · Cited by 7

Machine learning and deep learning for the advancement of epigenomics

Machnicka, M. A., & Wilczyński, B. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817964-2.00009-5 · Cited by 6

Functional genomics and epigenomics of atrial fibrillation

Victorino, J., Álvarez, A., & Manzanares, M. (2021) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2021.04.003 · Cited by 6

Cis-regulatory atlas of primary human CD4+ T cells

Stefan, K., & Barski, A. (2023) · BMC Genomics · doi:10.1186/s12864-023-09288-3 · Cited by 6

Toward Identification of Functional Sequences and Variants in Noncoding DNA

Monti, R., & Ohler, U. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-122120-110102 · Cited by 6

Cis-regulatory variation: significance in biomedicine and evolution

Friedensohn, S., & Sawarkar, R. (2014) · Cell and Tissue Research · doi:10.1007/s00441-014-1855-3 · Cited by 6

Genome-wide identification of hypoxia-induced enhancer regions

Kamps‐Hughes, N., Preston, J. L., Randel, M. A., & Johnson, E. A. (2015) · PeerJ · doi:10.7717/peerj.1527 · Cited by 6

Studying a novel ecdysone-dependent enhancer

Nikolenko, J. V., Краснов, А. Н., Mazina, M. Y., Georgieva, S. G., & Vorobyeva, N. E. (2017) · Doklady Biochemistry and Biophysics · doi:10.1134/s160767291703022x · Cited by 6

Novel mRNAs 3′ end-associated cis-regulatory elements with epigenomic signatures of mammalian enhancers in the Arabidopsis genome

Wang, H. V., & Chekanova, J. A. (2019) · RNA · doi:10.1261/rna.071209.119 · Cited by 6

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

Penzar, D., Zinkevich, A. O., Vorontsov, I. E., Sitnik, V. V., Favorov, A. V., Makeev, V. J., & Kulakovskiy, I. V. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.01078 · Cited by 6

Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers

Takeuchi, C., Yokoshi, M., Kondo, S., Shibuya, A., Saito, K., Fukaya, T., Siomi, H., & Iwasaki, Y. W. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1034 · Cited by 6

Functional organization of an Mbp enhancer exposes striking transcriptional regulatory diversity within myelinating glia

Dionne, N., Dib, S., Finsen, B. R., Denarier, É., Kuhlmann, T., Drouin, R., Kokoeva, M. V., Hudson, T. J., Siminovitch, K. A., Friedman, H. C., et al. (2015) · Glia · doi:10.1002/glia.22923 · Cited by 5

Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterizationPreprint

Muerdter, F., Boryń, Ł. M., Woodfin, A. R., Neumayr, C., Rath, M., Zabidi, M. M. A., Pagani, M., Haberle, V., Kazmar, T., Catarino, R. R., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/164590 · Cited by 6

Atrial Fibrillation Is a Complex Trait

Shoemaker, M. B., & Roden, D. M. (2020) · Circulation Research · doi:10.1161/circresaha.120.317112 · Cited by 5

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strandsPreprint

Roberts, B. S., Partridge, E. C., Moyers, B. A., Agarwal, V., Newberry, K. M., Martin, B., Shendure, J., Myers, R., & Cooper, G. M. (2021) · Genome Research · doi:10.1101/gr.270751.120 · Cited by 6

Eight principal chromatin states functionally segregate the fly genome into developmental and housekeeping rolesPreprint

Delandre, C., McMullen, J. P. D., Paulsen, J., Collas, P., & Marshall, O. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.30.514435 · Cited by 6

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regenerationPreprint

Kawaguchi, A., Wang, J., Knapp, D., Murawala, P., Nowoshilow, S., Masselink, W., Taniguchi‐Sugiura, Y., Fei, J., & Tanaka, E. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.14.516253 · Cited by 6

CRISPRi with barcoded expression reporters dissects regulatory networks in human cellsPreprint

Kim, J., Muller, R. Y., Bondra, E. R., & Ingolia, N. T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.06.611573 · Cited by 6

Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domainPreprint

Huang, Y., Verstegen, M. J. A. M., Tjalsma, S. J. D., Krijger, P. H. L., Gupta, K., Park, M., Boettiger, A. N., & de Laat, W. L. (2025) · Genes & Development · doi:10.1101/gad.352235.124 · Cited by 7

Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR

FitzPatrick, V., Leemans, C., van Arensbergen, J., van Steensel, B., & Bussemaker, H. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad232 · Cited by 4

Systematic screening of enhancer-blocking insulators in Drosophila identifies their DNA sequence determinants

Tonelli, A., Cousin, P., Jankowski, A., Wang, B., Dorier, J., Barraud, J. F., Zunjarrao, S. S., & Gambetta, M. C. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.10.017 · Cited by 6

Decoding tissue-specific enhancers in plants using massively parallel assays and deep learning

(邓雅欣), Y. D., Zhao, W., (熊逸雪), Y. X., Naeem, M. S., Lu, S., Zhou, X., Zhao, L., & Zhang, L. (2025) · The Plant Cell · doi:10.1093/plcell/koaf236 · Cited by 5

Bridging the variant-to-function gap in type 2 diabetes: advances and challenges

Maynard, A. G., Bhardwaj, R., Jones, T. R., & Claussnitzer, M. (2025) · Diabetologia · doi:10.1007/s00125-025-06600-6 · Cited by 7

The IGVF catalog—from genetic variation to function

Li, D., Liu, S., Assis, P., Li, M., Dong, S., Whaling, I., Jolanki, O., Kagda, M. S., Zhang, W., Macias-Velasco, J. F., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1341 · Cited by 5

Generative AI for synthetic biology: Designing biological parts, circuits, and genomes

Kim, N., Carluccio, G. D., Zhang, K., & Collins, J. J. (2026) · Cell Systems · doi:10.1016/j.cels.2026.101533 · Cited by 5

Epigenetic regulation of cis-regulatory elements and transcription factors during development

Khan, S., Mishra, R. K., & Srivastava, S. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-821785-6.00004-9 · Cited by 5

Viral influencers: deciphering the role of endogenous retroviral LTR12 repeats in cellular gene expression

Krchlíková, V., Lu, Y., & Sauter, D. (2025) · Journal of Virology · doi:10.1128/jvi.01351-24 · Cited by 6

Deconstructing the GWAS library: next-generation GWAS

Zhang, W., Koslowski, S., Benzaki, M., Lee, C. J. M., Zhu, Y., Mak, M. C. E., Zhu, Y., Loong, S. S. E., Lettre, G., Anene-Nzelu, C. G., et al. (2025) · Physiological Reviews · doi:10.1152/physrev.00025.2024 · Cited by 5

Deciphering cis -regulatory elements using REgulamentary

Riva, S. G., Sanders, E., Georgiades, E., Venkatesh, S. S., Sergeant, M. J., Gür, E. R., Herrmann, J. C., Baxter, M. D., & Hughes, J. R. (2026) · Bioinformatics Advances · doi:10.1093/bioadv/vbag079 · Cited by 5

A Set of Structural Features Defines the Cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster

López, Y., Vandenbon, A., & Nakai, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0104342 · Cited by 5

Epigenetic analysis of human postmortem brain tissue

Islam, S. A., Lussier, A. A., & Kobor, M. S. (2018) · Handbook of clinical neurology · doi:10.1016/b978-0-444-63639-3.00017-7 · Cited by 6

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner

Lou, S., Cotter, K. A., Li, T., Liang, J. H., Mohsen, H., Liu, J. J., Zhang, J., Cohen, S. M., Xu, J., Yu, H., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1007860 · Cited by 4

Emergence of enhancers at late DNA replicating regions

Cornejo‐Páramo, P., Petrova, V., Zhang, X., Young, R. S., & Wong, E. S. W. (2024) · Nature Communications · doi:10.1038/s41467-024-47391-5 · Cited by 6

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems

Lobel, J. H., & Ingolia, N. T. (2025) · Genome biology · doi:10.1186/s13059-025-03610-w · Cited by 4

Transcriptional Dynamics at Brain Enhancers: from Functional Specialization to Neurodegeneration

Vermunt, M. W., & Creyghton, M. P. (2016) · Current Neurology and Neuroscience Reports · doi:10.1007/s11910-016-0689-7 · Cited by 5

United colours of chromatin? Developmental genome organisation in flies

Delandre, C., & Marshall, O. J. (2019) · Biochemical Society Transactions · doi:10.1042/bst20180605 · Cited by 10

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Mann, A., & Bhatia, S. (2019) · Biomedicines · doi:10.3390/biomedicines7030071 · Cited by 5

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