Decoding enhancers using massively parallel reporter assays

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422

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

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 1×

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707

The accessible chromatin landscape of the human genome

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233

Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression

Richard, D. J., Capellini, T. D., & Diekman, B. O. (2023) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00574.2022 · Cited by 18

The quantitative impact of 3′UTRs on gene expression

West, J. D., Smith, H. J., Vu, L. T., Fogarty, E. A., Matreyek, K. A., Fowler, D. M., & Grimson, A. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf568 · Cited by 20

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity

Kosicki, M., Cintrón, D. L., Keukeleire, P., Schubach, M., Page, N. F., Georgakopoulos‐Soares, I., Akiyama, J. A., Plajzer-Frick, I., Novak, C. S., Kato, M., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60064-1 · Cited by 27

Topology regulatory elements: From shaping genome architecture to gene regulation

Chen, L., & Long, H. K. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102723 · Cited by 15

Multiplexed long-read plasmid validation and analysis using OnRampPreprint

Mumm, C., Drexel, M. L., McDonald, T. L., Diehl, A. G., Switzenberg, J. A., & Boyle, A. P. (2023) · Genome Research · doi:10.1101/gr.277369.122 · Cited by 15

Decoding polygenic diseases: advances in noncoding variant prioritization and validation

Chin, I. M., Gardell, Z. A., & Corces, M. R. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.03.005 · Cited by 18

Craniofacial developmental biology in the single-cell era

Tseng, K.-C., & Crump, J. G. (2023) · Development · doi:10.1242/dev.202077 · Cited by 18

Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

Farley, E. J., Eggleston, H., & Riehle, M. M. (2021) · Insects · doi:10.3390/insects12020186 · Cited by 11

Harnessing pluripotent stem cells as models to decipher human evolution

Dannemann, M., & Romero, I. G. (2021) · FEBS Journal · doi:10.1111/febs.15885 · Cited by 14

Archaic hominin genomics provides a window into gene expression evolution

Yan, S. M., & McCoy, R. C. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.014 · Cited by 13

Genome editing to define the function of risk loci and variants in rheumatic disease

Baglaenko, Y., Macfarlane, D., Marson, A., Nigrovic, P. A., & Raychaudhuri, S. (2021) · Nature Reviews Rheumatology · doi:10.1038/s41584-021-00637-8 · Cited by 12

MPRAbase a Massively Parallel Reporter Assay databasePreprint

Zhao, J., Baltoumas, F. A., Konnaris, M. A., Mouratidis, I., Liu, Z., Sims, J., Agarwal, V., Pavlopoulos, G. A., Georgakopoulos‐Soares, I., & Ahituv, N. (2025) · Genome Research · doi:10.1101/gr.280387.124 · Cited by 12

Identification of 27 allele-specific regulatory variants in Parkinson’s disease using a massively parallel reporter assay

Farrow, S. L., Gokuladhas, S., Schierding, W. S., Pudjihartono, M., Perry, J. K., Cooper, A. A., & O'Sullivan, J. M. (2024) · npj Parkinson s Disease · doi:10.1038/s41531-024-00659-5 · Cited by 14

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Frochaux, M., Sleiman, M. S. B., Gardeux, V., Dainese, R., Hollis, B., Litovchenko, M., Braman, V. S., Andreani, T., Osman, D., & Deplancke, B. (2020) · Genome biology · doi:10.1186/s13059-019-1912-z · Cited by 13

Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences

Georgakopoulos‐Soares, I., Mouratidis, I., Parada, G. E., Matharu, N. K., Hemberg, M., & Ahituv, N. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1052 · Cited by 13

Super-enhancer interactomes from single cells link clustering and transcriptionPreprint

Le, D. J., Hafner, A., Gaddam, S., Wang, K., & Boettiger, A. N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.08.593251 · Cited by 13

Screening for functional regulatory variants in open chromatin using GenIE-ATAC

Cooper, S., Schwartzentruber, J., Coomber, E. L., Wu, Q., & Bassett, A. R. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad332 · Cited by 12

Mapping MAVE data for use in human genomics applications

Arbesfeld, J. A., Da, E. Y., Stevenson, J., Kuzma, K., Paul, A., Farris, T. R., Capodanno, B. J., Grindstaff, S. B., Riehle, K. P., Saraiva-Agostinho, N., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03647-x · Cited by 17

Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction

van Weerd, J. H., Mohan, R. A., van Duijvenboden, K., Hooijkaas, I. B., Wakker, V., Boukens, B. J., Barnett, P., & Christoffels, V. M. (2020) · eLife · doi:10.7554/elife.56697 · Cited by 12

Decoding transcriptional states in cancer

Wouters, J., Atak, Z. K., & Aerts, S. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.01.003 · Cited by 13

The non-coding genome in genetic brain disorders: new targets for therapy?

Salsench, E. M., Karkala, F., Lanko, K., & Barakat, T. S. (2021) · Essays in Biochemistry · doi:10.1042/ebc20200121 · Cited by 11

A Multilayered Post– Genome‐Wide Association Study Analysis Pipeline Defines Functional Variants and Target Genes for Systemic Lupus Erythematosus

Fazel‐Najafabadi, M., Looger, L. L., Rallabandi, H. R., & Nath, S. K. (2024) · Arthritis & Rheumatology · doi:10.1002/art.42829 · Cited by 11

Rapid and quantitative functional interrogation of human enhancer variant activity in live mice

Hollingsworth, E. W., Liu, T. A., Alcantara, J. A., Chen, C. X., Jacinto, S. H., & Kvon, E. Z. (2025) · Nature Communications · doi:10.1038/s41467-024-55500-7 · Cited by 15

Making Biological Sense of Genetic Studies of Age-Related Macular Degeneration

Singh, N., Swaroop, A., & Ratnapriya, R. (2021) · Advances in Experimental Medicine and Biology · doi:10.1007/978-3-030-66014-7_8 · Cited by 11

The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia

Wan, M., Liu, Y., Li, D., Snyder, R. J., Elkin, L. B., Day, C. R., Rodriguez, J., Grunseich, C., Mahley, R. W., Watts, J. A., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae696 · Cited by 10

Genomic annotation of disease-associated variants reveals shared functional contexts

Kyono, Y., Kitzman, J. O., & Parker, S. C. J. (2019) · Diabetologia · doi:10.1007/s00125-019-4823-3 · Cited by 9

Functional annotation of breast cancer risk loci: current progress and future directions

Cardoso, S. R., Gillespie, A., Haider, S. A., & Fletcher, O. (2021) · British Journal of Cancer · doi:10.1038/s41416-021-01612-6 · Cited by 10

Breaking enhancers to gain insights into developmental defects

Armendariz, D. A., Sundarrajan, A., & Hon, G. C. (2023) · eLife · doi:10.7554/elife.88187 · Cited by 9

From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering

Delker, R. K., & Mann, R. S. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-63904-8_3 · Cited by 10

A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome

Phan, L. T., Oh, C., He, T., & Manavalan, B. (2023) · PROTEOMICS · doi:10.1002/pmic.202200409 · Cited by 11

Mammalian genome writing: Unlocking new length scales for genome engineering

Pinglay, S., Atwater, J. T., Brosh, R., Shendure, J., Maurano, M. T., & Boeke, J. D. (2026) · Cell · doi:10.1016/j.cell.2025.12.034 · Cited by 11

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

Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals

Kliesmete, Z., Wange, L. E., Vieth, B., Esgleas, M., Radmer, J., Hülsmann, M., Geuder, J., Richter, D., Ohnuki, M., Götz, M., et al. (2023) · eLife · doi:10.7554/elife.83593 · Cited by 9

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

Georgakopoulos-Soares, I., Jain, N., Gray, J. M., & Hemberg, M. (2015) · bioRxiv · doi:10.1093/bioinformatics/btw584 · Cited by 11

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

Comoglio, F., Park, H. J., Schoenfelder, S., Barozzi, I., Bode, D., Fraser, P., & Green, A. R. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/163113 · 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

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

U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assays

Dao, K., Jungers, C. F., Djuranović, S., & Mustoe, A. M. (2025) · Nature Communications · doi:10.1038/s41467-025-62000-9 · Cited by 11

GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations

Chen, H., Petty, L. E., Bush, W. S., Naj, A. C., & Below, J. E. (2019) · Current Genetic Medicine Reports · doi:10.1007/s40142-019-0159-z · Cited by 8

Differentially Active and Conserved Neural Enhancers Define Two Forms of Adaptive Noncoding Evolution in Humans

Pizzollo, J., Zintel, T. M., & Babbitt, C. C. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac108 · Cited by 7

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

Functional assays for transcription mechanisms in high-throughput

Qiu, C., & Kaplan, C. D. (2019) · Methods · doi:10.1016/j.ymeth.2019.02.017 · Cited by 9

Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activityPreprint

Kosicki, M., Cintrón, D. L., Page, N. F., Georgakopoulos‐Soares, I., Akiyama, J. A., Plajzer-Frick, I., Novak, C. S., Kato, M., Hunter, R. D., von Maydell, K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.22.590634 · Cited by 8

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

In vivo mapping of mutagenesis sensitivity of human enhancers

Kosicki, M., Zhang, B., Hecht, V., Pampari, A., Cook, L. E., Slaven, N., Akiyama, J., Plajzer-frick, I., Novak, C. S., Kato, M., et al. (2025) · Nature · doi:10.1038/s41586-025-09182-w · Cited by 6

Culture Wars: Empirically Determining the Best Approach for Plasmid Library Amplification

Mateyko, N., & de Boer, C. G. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00377 · Cited by 7

Analysis of the landscape of human enhancer sequences in biological databases

Mulero-Hernández, J., & Fernández‐Breis, J. T. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.045 · Cited by 9

Development of a Tet-On Inducible Expression System for the Anhydrobiotic Cell Line, Pv11

Tokumoto, S., Miyata, Y., Usui, K., Deviatiiarov, R. M., Takahiro, O., Kondratieva, S., Shagimardanova, E. I., Gusev, O., Cornette, R., Itoh, M., et al. (2020) · Insects · doi:10.3390/insects11110781 · Cited by 8

Identifying the lungs as a susceptible site for allele-specific regulatory changes associated with type 1 diabetes risk

Ho, D., Nyaga, D. M., Schierding, W. S., Saffery, R., Perry, J. K., Taylor, J. A., Vickers, M. H., Kempa-Liehr, A. W., & O'Sullivan, J. M. (2021) · Communications Biology · doi:10.1038/s42003-021-02594-0 · Cited by 6

MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assaysPreprint

Ireland, W. T., & Kinney, J. B. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/054676 · Cited by 8

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 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

Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome

Hata, T., Satoh, S., Takada, N., Matsuo, M., & Obokata, J. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab069 · Cited by 6

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

OnRamp: rapid nanopore plasmid validationPreprint

Mumm, C., Drexel, M. L., McDonald, T. L., Diehl, A. G., Switzenberg, J. A., & Boyle, A. P. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.15.484480 · Cited by 6

Mapping MAVE data for use in human genomics applicationsPreprint

Arbesfeld, J. A., Da, E. Y., Stevenson, J., Kuzma, K., Paul, A., Farris, T. R., Capodanno, B. J., Grindstaff, S. B., Riehle, K. P., Saraiva-Agostinho, N., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.20.545702 · 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

Identification of potential functional variants and genes at 18q21.1 associated with the carcinogenesis of colorectal cancer

Cheng, X., Zhang, F., Gong, J., Li, Y., Zhou, D., Wang, J., Vong, E. G., Yuan, Y., Lai, M., & Zhang, D. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010050 · Cited by 5

Optimizing Nucleic Acid Delivery Systems through Barcode Technology

Park, S., Kim, M., & Lee, J. W. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.3c00602 · Cited by 6

Genomic resources for dissecting the role of non-protein coding variation in gene-environment interactions

Levings, D. C., Shaw, K. E., & Lacher, S. E. (2020) · Toxicology · doi:10.1016/j.tox.2020.152505 · Cited by 6

Learning Useful Representations of DNA Sequences From ChIP-Seq Datasets for Exploring Transcription Factor Binding Specificities

Quan, L., Sun, X., Wu, J., Mei, J., Huang, L., He, R., Nie, L., Chen, Y., & Lyu, Q. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.3026787 · Cited by 5

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

Przytycki, P. F., & Pollard, K. S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/847657 · Cited by 5

A Human Accelerated Region is a Leydig cell GLI2 Enhancer that Affects Male-Typical BehaviorPreprint

Norman, A. R., Ryu, A. H., Jamieson, K., Thomas, S., Shen, Y., Ahituv, N., Pollard, K. S., & Reiter, J. F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.27.428524 · Cited by 5

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

Deng, R., Perenthaler, E., Nikoncuk, A., Yousefi, S., Lanko, K., Schot, R., Maresca, M., Salsench, E. M., Sanderson, L. E., Parker, M. J., et al. (2025) · Cell · doi:10.1016/j.cell.2025.10.029 · Cited by 6

Controlling gene expression using AI designed Cis-regulatory elements

Xia, Y., & Huo, Y. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.108802 · Cited by 4

Functional characterization of OXTR -associated enhancers

Cintrón, D. L., Sheng, R. R., & Ahituv, N. (2025) · Human Molecular Genetics · doi:10.1093/hmg/ddaf022 · Cited by 4

Cis -regulatory landscapes in the evolution and development of the mammalian skull

Kaucká, M. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0079 · Cited by 4

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

Martinez-Ara, M., Comoglio, F., & van Steensel, B. (2024) · eLife · doi:10.7554/elife.91994.3 · Cited by 5

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

España, A. P., Santiago‐Algarra, D., Pradel, L. C., & Spicuglia, S. (2017) · Biologie Aujourd hui · doi:10.1051/jbio/2018015 · Cited by 4

Computational Assessment of the Expression-Modulating Potential for Non-Coding Variants

Shi, F., Wang, Y., Huang, D., Liang, Y., Liang, N., Chen, X., & Gao, G. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.10.003 · Cited by 3

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

Ho, E. Y.-K., Cao, Q., Gu, M., Chan, R. W.-L., Wu, Q., Gerstein, M., & Yip, K. Y.-L. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz030 · Cited by 4

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

Niu, L., Wan, J., Sun, J., Huang, Y., He, N., Li, L., & Hou, C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.20.346908 · Cited by 3

CADD-SV – a framework to score the effects of structural variants in health and diseasePreprint

Kleinert, P., & Kircher, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.10.451798 · Cited by 6

Enhancers in T Cell development and malignant lesions

Zhang, T., & Zou, L. (2024) · Cell Death Discovery · doi:10.1038/s41420-024-02160-7 · Cited by 3

Enhancer regulation in cancer: from epigenetics to m6A RNA modification

Vasukutty, A., Bhattarai, P. Y., & Choi, H. S. (2025) · Archives of Pharmacal Research · doi:10.1007/s12272-025-01561-1 · Cited by 5

Chromatin architectures underlying plasmid-based assays for regulatory variant effects

Mallory, B. J., Tullius, T. W., Biar, C. G., Herlihy, C. P., Gustafson, J. A., Bohaczuk, S. C., Dubocanin, D., Beliveau, B. J., Schweppe, D. K., Starita, L. M., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.04.027 · Cited by 6

Advances in computational and experimental approaches for deciphering transcriptional regulatory networks

Moeckel, C. M., Mouratidis, I., Chantzi, N., Uzun, Y., & Georgakopoulos‐Soares, I. (2024) · BioEssays · doi:10.1002/bies.202300210 · Cited by 4

Non-coding variation in dementias: mechanisms, insights, and challenges

Rogers, B. B., & Cochran, J. N. (2025) · npj Dementia · doi:10.1038/s44400-025-00012-4 · Cited by 3

Statistical considerations for the analysis of massively parallel reporter assays data

Qiao, D., Zigler, C. M., Cho, M. H., Silverman, E. K., Zhou, X., Castaldi, P. J., & Laird, N. M. (2020) · Genetic Epidemiology · doi:10.1002/gepi.22337 · Cited by 3

Multinomial Convolutions for Joint Modeling of Regulatory Motifs and Sequence Activity Readouts

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Reducing uncertainty in genetic testing with Saturation Genome Editing

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