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

Semi-supervised segmentation and genome annotationPreprint

Chan, R. C. W., McNeil, M., Roberts, E. G., Mendez, M., Libbrecht, M. W., & Hoffman, M. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.30.926923 · Cited by 1

Large-scale analysis of Drosophila core promoter function using synthetic promotersPreprint

Qi, Z., Jung, C., Bandilla, P., Ludwig, C., Heron, M., Kiesel, A., Philippou-Massier, J., Nikolov, M., Renna, A., Schnepf, M., et al. (2020) · bioRxiv · doi:10.1101/2020.10.15.339325 · Cited by 10

A transcription start site map in human pancreatic islets reveals functional regulatory signaturesPreprint

Varshney, A., Kyono, Y., Elangovan, V. R., Wang, C., Erdos, M. R., Narisu, N., Albanus, R. D., Orchard, P., Stitzel, M. L., Collins, F. S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/812552 · Cited by 1

Genome-wide rules of nucleosome phasingPreprint

Baldi, S., Jain, D. S., Harpprecht, L., Zabel, A., Scheibe, M., Butter, F., Straub, T., & Becker, P. B. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/093666 · Cited by 1

Tissue-specific versus pleiotropic enhancers within the bric-a-brac tandem gene duplicates display differential regulatory activity and evolutionary conservationPreprint

Bourbon, H.-M. G., Benetah, M. H., Guillou, E., Mojica-Vázquez, L. H., Baanannou, A., Bernat-Fabre, S., Loubière, V., Bantignies, F., Cavalli, G., & Boube, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.25.436949 · Cited by 1

Genome-wide oscillations in G + C density and sequence conservationPreprint

Moqtaderi, Z., Brown, S. J., & Bender, W. W. (2021) · Genome Research · doi:10.1101/gr.274332.120 · Cited by 1

Learning the histone codes of gene regulation with large genomic windows and three-dimensional chromatin interactions using transformerPreprint

Lee, D., Yang, J., & Kim, S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.30.472333 · Cited by 1

DNA methylation-environment interactions in the human genomePreprint

Johnston, R. A., Aracena, K. A., Barreiro, L. B., Lea, A. J., & Tung, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.19.541437 · Cited by 1

Genome-wide identification of silencers in human cellsPreprint

Zhu, X., Wang, C., Kong, D., Luo, J., Deng, B., Gu, Y., Kong, S., Huang, L., Liu, Y., & Zhang, Y. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.20.545673 · Cited by 1

The discovery of an evolutionarily conserved enhancer within the MYEOV locus suggests an unexpected role for this non-coding region in cancerPreprint

Davidson, B. S. A., Arcila-Galvis, J. E., Trevisán-Herraz, M., Mikulášová, A., Brackley, C. A., Russell, L. J., & Rico, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.18.558245 · Cited by 1

Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectorsPreprint

Psatha, N., Sova, P., Georgolopoulos, G., Paschoudi, K., Iwata, M., Bloom, J. E., Ulyanova, T., Wang, H., Kirtsou, A., Vasiloudis, N.-I., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.04.559165 · Cited by 1

EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networksPreprint

Garza, A. B., García, R., Solis, L. M., Halfon, M. S., & Girgis, H. Z. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.23.573198 · Cited by 1

Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancerPreprint

Pan, Y., Chiu, T.-P., Zhou, L., Chan, P., Kuo, T. T., Battaglin, F., Soni, S., Jayachandran, P., Li, J. J., Lenz, H., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.26.590360 · Cited by 2

Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assaysPreprint

Butts, J. C., Rong, S., Gosai, S. J., Castro, R. I., Noon, M., Adeniran, K., Ghosh, R., Sabeti, P. C., Tewhey, R., & Reilly, S. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.16.648420 · Cited by 3

Principles and functional consequences of plasmid chromatinization in mammalian cellsPreprint

Mallory, B. J., Tullius, T. W., Biar, C. G., Gustafson, J. A., Bohaczuk, S. C., Dubocanin, D., Starita, L. M., & Stergachis, A. B. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.27.656122 · Cited by 1

A systematic delineation of 3′UTR regulatory elements and their contextual associations

Liang, N., Li, J., Ding, Y., Wang, Y., Champer, J., Ren, L., & Gao, G. (2026) · Cell Systems · doi:10.1101/2025.06.09.658412 · Cited by 1

Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolutionPreprint

Tulloch, A. J., Delgado, R. N., Catta-Preta, R., & Cepko, C. L. (2025) · eLife · doi:10.7554/elife.107565 · Cited by 1

Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sitesPreprint

Bose, M. L., Tovar, A., Kyono, Y., Varshney, A., Kitzman, J., & Parker, S. C. J. (2025) · bioRxiv · doi:10.1101/2025.10.13.659964 · Cited by 2

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryoPreprint

Chen, S., Loubière, V., Hollingsworth, E. W., Jacinto, S. H., Dizehchi, A., Schreiber, J. M., Kvon, E. Z., & Stark, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.22.695948 · Cited by 1

Classical enhancers couple cis -regulatory logic with transcriptional condensates and 3D genome architecturePreprint

Tiusanen, V., Patel, D., Xia, J., Xu, C., Datta, S., Yun, J. W., Cancellieri, S., Fei, L., Yilmaz, M., Pitkänen, E., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.23.701252 · Cited by 1

Functional Identification and Characterization of cis-Regulatory Elements

Fiore, C. (2015) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k70863h7

Assessing modularity of developmental enhancers in Drosophila melanogaster

Martin, T. L. (2014) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Patient Individual Parameterization of Cardiac Ventricular Tachycardia Termination Algorithm

Schinner, M. (2013) · Biomedizinische Technik/Biomedical Engineering · doi:10.1515/bmt-2013-4299

MINING DNA ELEMENTS INVOLVED IN TARGETING OF CHROMATIN MODIFIERS

Philip, P. (2014) · DiVA at Umeå University (Umeå University)

METHOD Open Access

Maretty, L., Sibbesen, J. A., & Krogh, A. (2014)

Comparative Genomics of Transcription Factor Binding in Drosophila

Carl, S. H., & Russell, S. R. H. (2015) · Entomology in focus · doi:10.1007/978-3-319-24235-4_7

Computational modeling of gene expression from regulatory sequences

Samee, M. A. H. (2015) · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)

Mapping regulatory DNA that governs Drosophila eggshell patterning

Pope, N. (2013) · Rutgers University Community Repository (Rutgers University) · doi:10.7282/t35q4tqr

OVERLAPPING SEQUENCE FEATURES OF MAMMALIAN ENHANCERS COORDINATELY CONTROL ENGAGEMENT OF TRANSCRIPTION FACTOR CONSENSUS SITES AND NUCLEOSOMAL OCCUPANCY

Barozzi, I. (2014) · Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) · doi:10.13130/barozzi-iros-giacomo_phd2014-03-25

Massively Parallel Sequencing-Based Analyses of Genome and Protein Function

Kamps-Hughes, N. (2015) · Scholars' Bank (University of Oregon)

Lymphocyte Identity and Genomic Switches

Kanno, Y., Witte, S. J., & O’Shea, J. J. (2016) · Epigenetics and human health · doi:10.1007/978-3-319-27186-6_3

SURVEY AND SUMMARY Chromatin and epigenetic features of long-range gene regulation

Harmston, N., & Lenhard, B. (2013)

Transcriptional and epigenetic control of gene expression in embryo development

Boija, A. (2016) · DiVA (Stockholm University)

Transcriptional Regulation: When 1+1≠2

Thormann, V., Borschiwer, M., & Meijsing, S. H. (2016) · Springer eBooks · doi:10.1007/978-3-319-45723-9_1

Quantifying Eukaryotic Gene Regulation in Hormone Response and Disease.

Vockley, C. M. (2016) · DukeSpace (Duke University)

Analysis of whole-genome binding patterns of GAGA and CNC transcription factors during Drosophila melanogaster development

Brusentsov, I. I., Karagodin, D. A., Baricheva, E. M., & Merkulova, T. I. (2016) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj16.193

Epigenetics and Chromatin Remodeling

Kinyamu, H. K., Mackey, L. C., Crusselle‐Davis, V. J., & Archer, T. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.65388-6

Exploring the Human Genome for Functional Non-Coding Sequences and Variation: Implications for Understanding Peripheral Nerve Biology.

Law, W. (2016) · Deep Blue (University of Michigan)

New Technology Development for Next-Generation Sequencing

Randel, M. A. (2017) · Scholars' Bank (University of Oregon)

Determinants of Transcription Initiation Directionality in MetazoansPreprint

Ibrahim, M. M., Calviello, A. K., Glahs, A., Kolundžić, E., Hirsekorn, A., Carda, A., Tursun, B., Zinzen, R. P., Lacadie, S. A., & Ohler, U. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/224642

CRISPRing the Human Genome for Functional Regulatory Elements

Lopes, R. (2018) · RePub (Erasmus University Rotterdam)

Unbiased genome-scale identification of cis -regulatory modules in the human genome by GRAMcPreprint

Guay, C. L., & Nam, J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/468405

Organizational Properties of a Functional Mammalian Cis-RegulomePreprint

Chaudhri, V. K., Dienger-Stambaugh, K., Wu, Z., Shreshtha, M., & Singh, H. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3275279

Multiplex cis-regulatory analysis

Nam, J. (2019) · Methods in cell biology · doi:10.1016/bs.mcb.2019.01.009

Discovering functional sequences with RELICS, an analysis method for tiling CRISPR screensPreprint

Fiaux, P. C., Chen, H. V., Chen, A. R., Chen, P. B., & McVicker, G. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/687293

Gene regulation during development by chromatin and the Super Elongation Complex

Dahlberg, O. (2014) · KTH Publication Database DiVA (KTH Royal Institute of Technology)

The Control of Gene Expression in Macrophages

Ostuni, R., & Natoli, G. (2014) · Springer eBooks · doi:10.1007/978-1-4939-1311-4_26

Gene regulatory networks STARR-ing B cells

de Paz, A. M., & Josefowicz, S. Z. (2019) · Nature Immunology · doi:10.1038/s41590-019-0566-z

Adaptation of STARR-seq method to be used with 3 rd generation integrase-deficient promoterless lentiviral vectorsPreprint

Matjusaitis, M., Tedesco, D., & Ciukas, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.24.169714

Detecting regulatory elements in high-throughput reporter assaysPreprint

Kim, Y., Johnson, G. D., Seo, J., Barrera, A., Majoros, W. H., Ochoa, A., Allen, A. S., & Reddy, T. E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.07.241901

Massively parallel identification of causal variants underlying gene expression differences in a yeast crossPreprint

Renganaath, K., Cheung, R., Day, L., Kosuri, S., Kruglyak, L., & Albert, F. (2020) · bioRxiv · doi:10.1101/2020.08.31.276337

Genome-wide discovery of gene regulatory networks in the midgestation mouse placenta

Starks, R. R. (2020) · Iowa State University Digital Repository (Iowa State University) · doi:10.31274/etd-20210114-144

Eukaryotic Genome in Three Dimensions

Razin, S. V., Gavrilov, A. A., & Ulianov, S. V. (2020) · Springer eBooks · doi:10.1007/978-3-030-62532-0_2

At least two to tango: Choreographing chromatin through cooperative footprints

Abdulhay, N. J., & Ramani, V. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.022

Epigenetics of muscle disorders

Oltra, E. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823928-5.00023-2

Author response: Analysis of long and short enhancers in melanoma cell states

Mauduit, D., Taskiran, I. I., Minnoye, L., Waegeneer, M. D., Christiaens, V., Hulselmans, G. J., Demeulemeester, J., Wouters, J., & Aerts, S. (2021) · eLife · doi:10.7554/elife.71735.sa2

Correction to: Epigenetic and Transcriptional Networks Underlying Atrial Fibrillation

(2020) · Circulation Research · doi:10.1161/res.0000000000000429

Faculty Opinions recommendation of Systematic identification of silencers in human cells.

Cavalli, G., & Stefano, M. D. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737421758.793585100

Faculty Opinions recommendation of Dynamic interplay between enhancer-promoter topology and gene activity.

Spivakov, M. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733676902.793549158

Recent Advances in Cardiovascular Development

Editors, T. (2013) · Circulation Research · doi:10.1161/circresaha.113.302820

Peer Review #3 of "Genome-wide identification of hypoxia-induced enhancer regions (v0.1)"

(2015) · PeerJ · doi:10.7287/peerj.1527v0.1/reviews/3

Peer Review #2 of "Genome-wide identification of hypoxia-induced enhancer regions (v0.2)"

(2015) · PeerJ · doi:10.7287/peerj.1527v0.2/reviews/2

Faculty Opinions recommendation of Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.

Lightman, S. L., & Stubbs, F. E. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733793022.793553249

Transcription and Epigenetic Regulation

Merchant, J. L. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809954-4.00001-3

Faculty Opinions recommendation of Dynamic interplay between enhancer-promoter topology and gene activity.

Martı́-Renom, M. A. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733676902.793550307

Faculty Opinions recommendation of Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development.

Mefford, H. C. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736437709.793571951

Faculty Opinions recommendation of Transcription imparts architecture, function and logic to enhancer units.

Sharrocks, A. D. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738702238.793579142

Peer Review #1 of "Genome-wide identification of hypoxia-induced enhancer regions (v0.1)"

(2015) · PeerJ · doi:10.7287/peerj.1527v0.1/reviews/1

Genomic Studies of BEAF-32 in Drosophila

McKowen, J. K. (2021) · doi:10.31390/gradschool_dissertations.5515

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

Matoba, N., Quiroga, I. Y., Phanstiel, D. H., & Won, H. (2020) · Journal of Visualized Experiments · doi:10.3791/60428-v

Emergence of new enhancers at late DNA replicating regionsPreprint

Cornejo‐Páramo, P., Petrova, V., Zhang, X., Young, R. S., & Wong, E. S. W. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.22.521323

Identification of Barley Enhancers across Genome via STARR-seqPreprint

Zhou, W., Shi, H., Wang, Z., Huang, Y., Ni, L., Chen, X., Liu, Y., Li, H., Li, C., & Liu, Y. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.10.519735

Crosstalk between chromatin and the transcription factor Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineagePreprint

Mancheno-Ferris, A., Immarigeon, C., Rivero, A., Depierre, D., Chanard, N., Fosseprez, O., Aughey, G., Lhoumaud, P., Anglade, J., Southall, T. D., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.03.522588

Practical application of massively parallel reporter assay in biotechnology and medicine

Romanov, S. E., & Laktionov, P. P. (2023) · Journal of clinical practice · doi:10.17816/clinpract115063

Explain-seq: an end-to-end pipeline from training to interpretation of sequence-based deep learning modelsPreprint

Zhao, N., Wang, S., Huang, Q., Dong, S., & Boyle, A. P. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.23.525250

A possible expansion of the VISTA enhancer databasePreprint

Ni, P., Wu, S., & Su, Z. (2023) · Research Square · doi:10.21203/rs.3.rs-3044929/v1

DNA methylation-environment interactions in the human genomePreprint

Johnston, R. A., Aracena, K. A., Barreiro, L. B., Lea, A. J., & Tung, J. (2023) · eLife · doi:10.7554/elife.89371.1

Non-coding mutations at enhancer clusters contribute to pancreatic ductal adenocarcinomaPreprint

Wang, J., Patel, M. B., Maniati, E., Atanur, S. S., Pal, D., Rio‐Machín, A., Heward, J. A., Kocher, H. M., Fitzgibbon, J., & Pradeepa, M. M. (2023) · Research Square · doi:10.21203/rs.3.rs-3120592/v1

Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique

Nowling, R. J., Njoya, K., Peters, J. G., & Riehle, M. M. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1182567 · Cited by 1

Towards a comprehensive regulatory map of Mammalian GenomesPreprint

Gonçalves, T. M., Stewart, C. L., Baxley, S. D., Xu, J., Li, D., Gabel, H. W., Wang, T., Avraham, O., & Zhao, G. (2023) · Research Square · doi:10.21203/rs.3.rs-3294408/v1 · Cited by 1

Enhancer target prediction: state-of-the-art approaches and future prospects

Umarov, R. K., & Hon, C.-C. (2023) · Biochemical Society Transactions · doi:10.1042/bst20230917

Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling outputPreprint

Joosten, S. E. P., Gregoricchio, S., Stelloo, S., Yapıcı, E., Huang, C.-C. F., Collier, M. D., Morova, T., Altıntaş, U. B., Kim, Y., Canisius, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.30.564691

Reviewer #2 (Public Review): DNA methylation-environment interactions in the human genome

(2024) · eLife · doi:10.7554/elife.89371.2.sa0

DNA methylation-environment interactions in the human genomePreprint

Johnston, R. A., Aracena, K. A., Barreiro, L. B., Lea, A. J., & Tung, J. (2024) · eLife · doi:10.7554/elife.89371.2

Prediction of transcription factor binding using epigenomics and genome variation data

Baumgarten, N. (2023) · Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) · doi:10.21248/gups.82138

Enhancer RNA transcriptome-wide association study reveals an atlas of pan-cancer susceptibility eRNAsPreprint

Chen, W., Wang, Z., Lin, J., Chen, S., Chen, H., Ma, X., Zou, X., Li, X., Wang, Y., Qin, Y., et al. (2024) · medRxiv · doi:10.1101/2024.02.29.24303580

Additional file 4 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352114

Additional file 8 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352129

Additional file 5 of Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Y., Zhang, Y., Liu, H., Gao, Y., Liu, Y., Chen, L., Liu, L., Irwin, D. M., Hou, C., Zhou, Z., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20222687

Additional file 2 of Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Y., Zhang, Y., Liu, H., Gao, Y., Liu, Y., Chen, L., Liu, L., Irwin, D. M., Hou, C., Zhou, Z., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20222675

Additional file 7 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352126

Additional file 3 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352111

Additional file 5 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352120

Additional file 6 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352123

Additional file 1 of Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Y., Zhang, Y., Liu, H., Gao, Y., Liu, Y., Chen, L., Liu, L., Irwin, D. M., Hou, C., Zhou, Z., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20222672

Additional file 6 of Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Y., Zhang, Y., Liu, H., Gao, Y., Liu, Y., Chen, L., Liu, L., Irwin, D. M., Hou, C., Zhou, Z., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20222690

Additional file 9 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Lee, D., Shi, M., Moran, J. R., Wall, M., Zhang, J., Liu, J. J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352132

Additional file 7 of Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Y., Zhang, Y., Liu, H., Gao, Y., Liu, Y., Chen, L., Liu, L., Irwin, D. M., Hou, C., Zhou, Z., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20222693

Additional file 8 of Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Y., Zhang, Y., Liu, H., Gao, Y., Liu, Y., Chen, L., Liu, L., Irwin, D. M., Hou, C., Zhou, Z., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20222696

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