Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

An integrated encyclopedia of DNA elements in the human genome

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

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 · see citing works

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,933 · see citing works

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 · see citing works

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works

Mapping and analysis of chromatin state dynamics in nine human cell types

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works

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 · see citing works

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 · see citing works

ChromHMM: automating chromatin-state discovery and characterization

Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works

Predicting effects of noncoding variants with deep learning–based sequence model

Zhou, J., & Troyanskaya, O. G. (2015) · Nature Methods · doi:10.1038/nmeth.3547 · Cited by 2,338 · see citing works

Quantifying similarity between motifs

Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L., & Noble, W. S. (2007) · Genome Biology · doi:10.1186/gb-2007-8-2-r24 · Cited by 2,058 · see citing works

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872 · see citing works

Architecture of the human regulatory network derived from ENCODE data

Gerstein, M., Kundaje, A. B., Hariharan, M., Landt, S. G., Yan, K., Cheng, C., Mu, X. J., Khurana, E., Rozowsky, J. S., Alexander, R. P., et al. (2012) · Nature · doi:10.1038/nature11245 · Cited by 1,418 · see citing works

<i>FTO</i> Obesity Variant Circuitry and Adipocyte Browning in Humans

Claussnitzer, M., Dankel, S. N., Kim, K.-H., Quon, G., Meuleman, W., Haugen, C., Glunk, V., Sousa, I. S., Beaudry, J. L., Puviindran, V., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1502214 · Cited by 1,332 · see citing works

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

Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125 · see citing works

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108 · see citing works

The Neuron-Restrictive Silencer Factor (NRSF): A Coordinate Repressor of Multiple Neuron-Specific Genes

Schoenherr, C. J., & Anderson, D. J. (1995) · Science · doi:10.1126/science.7871435 · Cited by 1,088 · see citing works

Discovery and characterization of chromatin states for systematic annotation of the human genome

Ernst, J., & Kellis, M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1662 · Cited by 1,033 · see citing works

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

Canver, M. C., Smith, E. C., Sher, F., Pinello, L., Sanjana, N. E., Shalem, O., Chen, D. D., Schupp, P. G., Vinjamur, D. S., Garcia, S. P., et al. (2015) · Nature · doi:10.1038/nature15521 · Cited by 886 · see citing works

Transposable elements have rewired the core regulatory network of human embryonic stem cells

Kunarso, G., Chia, N., Jeyakani, J., Hwang, C., Lu, X., Chan, Y.-S., Ng, H., & Bourque, G. (2010) · Nature Genetics · doi:10.1038/ng.600 · Cited by 777 · see citing works

An expansive human regulatory lexicon encoded in transcription factor footprints

Neph, S. J., Vierstra, J. D., Stergachis, A. B., Reynolds, A. P., Haugen, E., Vernot, B., Thurman, R. E., John, S., Sandstrom, R. S., Johnson, A., et al. (2012) · Nature · doi:10.1038/nature11212 · Cited by 746 · see citing works

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2137 · Cited by 711 · see citing works

Epigenetic reprogramming in cancer

Suvà, M. L., Riggi, N., & Bernstein, B. E. (2013) · Science · doi:10.1126/science.1230184 · Cited by 706 · see citing works

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

Gröschel, S., Sanders, M. A., Hoogenboezem, R., de Wit, E., Bouwman, B. A. M., Erpelinck, C., van der Velden, V. H. J., Havermans, M., Avellino, R., van Lom, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.019 · Cited by 687 · see citing works

Evolution of the mammalian transcription factor binding repertoire via transposable elementsPreprint

Bourque, G., Leong, B., Vega, V. B., Chen, X., Lee, Y. L., Srinivasan, K. G., Chew, J.-L., Ruan, Y., Wei, C., Ng, H., et al. (2008) · Genome Research · doi:10.1101/gr.080663.108 · Cited by 579 · see citing works

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Hoffman, M. M., Buske, O. J., Wang, J., Weng, Z., Bilmes, J., & Noble, W. S. (2012) · Nature Methods · doi:10.1038/nmeth.1937 · Cited by 566 · see citing works

Genome-wide chromatin state transitions associated with developmental and environmental cues

Zhu, J., Adli, M., Zou, J., Verstappen, G., Coyne, M. J., Zhang, X.-L., Durham, T. J., Miri, M., Deshpande, V., Jager, P. D., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.033 · Cited by 553 · see citing works

Massively parallel functional dissection of mammalian enhancers in vivo

Patwardhan, R. P., Hiatt, J. B., Witten, D. M., Kim, M. J., Smith, R. P., May, D., Lee, C., Andrie, J. M., Lee, S.-I., Cooper, G. M., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2136 · Cited by 536 · see citing works

Integrative annotation of chromatin elements from ENCODE data

Hoffman, M. M., Ernst, J., Wilder, S. P., Kundaje, A. B., Harris, R. S., Libbrecht, M., Giardine, B. M., Ellenbogen, P. M., Bilmes, J. A., Birney, E., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1284 · Cited by 521 · see citing works

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Pique-Regi, R., Degner, J. F., Pai, A. A., Gaffney, D. J., Gilad, Y., & Pritchard, J. K. (2011) · Genome Research · doi:10.1101/gr.112623.110 · Cited by 521 · see citing works

Retroelements and the human genome: New perspectives on an old relation

Bannert, N., & Kurth, R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404838101 · Cited by 517 · see citing works

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identityPreprint

Song, L., Zhang, Z., Grasfeder, L. L., Boyle, A. P., Giresi, P. G., Lee, B.-K., Sheffield, N. C., Gräf, S., Huss, M., Keefe, D., et al. (2011) · Genome Research · doi:10.1101/gr.121541.111 · Cited by 500 · see citing works

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

Tewhey, R., Kotliar, D., Park, D. S., Liu, B., Winnicki, S., Reilly, S. K., Andersen, K. G., Mikkelsen, T. S., Lander, E. S., Schaffner, S. F., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.027 · Cited by 480 · see citing works

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

Kheradpour, P., & Kellis, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1249 · Cited by 443 · see citing works

A method to predict the impact of regulatory variants from DNA sequence

Lee, D., Gorkin, D. U., Baker, M., Strober, B. J., Asoni, A. L., McCallion, A. S., & Beer, M. (2015) · Nature Genetics · doi:10.1038/ng.3331 · Cited by 417 · see citing works

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

Sherwood, R. I., Hashimoto, T., O'Donnell, C. W., Lewis, S., Barkal, A. A., van Hoff, J. P., Karun, V., Jaakkola, T., & Gifford, D. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2798 · Cited by 416 · see citing works

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Hoffman, M. M., Buske, O. J., Wang, J., Weng, Z., Bilmes, J., & Noble, W. S. (2012) · eScholarship@UMassChan · Cited by 397 · see citing works

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

Korkmaz, G., Lopes, R., Ugalde, A. P., Nevedomskaya, E., Han, R., Myacheva, K., Zwart, W. T., Elkon, R., & Agami, R. (2016) · Nature Biotechnology · doi:10.1038/nbt.3450 · Cited by 391 · see citing works

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53

Wang, T., Zeng, J., Lowe, C. B., Sellers, R. G., Salama, S. R., Yang, M., Burgess, S. M., Brachmann, R. K., & Haussler, D. H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703637104 · Cited by 389 · see citing works

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

Patwardhan, R. P., Lee, C., Litvin, O., Young, D. L., Pe'er, D., & Shendure, J. (2009) · Nature Biotechnology · doi:10.1038/nbt.1589 · Cited by 377 · see citing works

Identifying novel constrained elements by exploiting biased substitution patterns

Garber, M., Guttman, M., Clamp, M., Zody, M. C., Friedman, N., & Xie, X. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp190 · Cited by 370 · see citing works

Saturation editing of genomic regions by multiplex homology-directed repair

Findlay, G. M., Boyle, E. A., Hause, R. J., Klein, J. C., & Shendure, J. (2014) · Nature · doi:10.1038/nature13695 · Cited by 362 · see citing works

Locus-specific editing of histone modifications at endogenous enhancers

Mendenhall, E. M., Williamson, K. E., Reyon, D., Zou, J., Ram, O., Joung, J. K., & Bernstein, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2701 · Cited by 362 · see citing works

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

Ulirsch, J. C., Nandakumar, S. K., Wang, L., Giani, F. C., Zhang, X., Rogov, P., Melnikov, A., McDonel, P., Do, R., Mikkelsen, T. S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.048 · Cited by 328 · see citing works

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

LeProust, E. M., Peck, B. J., Spirin, K., McCuen, H. B., Moore, B., Namsaraev, E., & Caruthers, M. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq163 · Cited by 326 · see citing works

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

Kheradpour, P., Ernst, J., Melnikov, A., Rogov, P., Wang, L., Zhang, X., Alston, J., Mikkelsen, T. S., & Kellis, M. (2013) · Genome Research · doi:10.1101/gr.144899.112 · Cited by 315 · see citing works

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cellsPreprint

Boyle, A. P., Song, L., Lee, B., London, D., Keefe, D., Birney, E., Iyer, V. R., Crawford, G. E., & Furey, T. S. (2010) · Genome Research · doi:10.1101/gr.112656.110 · Cited by 305 · see citing works

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Hoffman, M. M., Buske, O. J., Wang, J., Weng, Z., Bilmes, J. A., & Noble, W. S. (2013) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/2506583.2506701 · Cited by 288 · see citing works

High-throughput mapping of regulatory DNA

Rajagopal, N., Srinivasan, S., Kooshesh, K., Guo, Y., Edwards, M. D., Banerjee, B., Syed, T., Emons, B. J. M., Gifford, D. K., & Sherwood, R. I. (2016) · Nature Biotechnology · doi:10.1038/nbt.3468 · Cited by 238 · see citing works

Complex effects of nucleotide variants in a mammalian cis -regulatory element

Kwasnieski, J. C., Mogno, I., Myers, C. A., Corbo, J. C., & Cohen, B. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210678109 · Cited by 233 · see citing works

High-throughput functional testing of ENCODE segmentation predictions

Kwasnieski, J. C., Fiore, C., Chaudhari, H. G., & Cohen, B. A. (2014) · Genome Research · doi:10.1101/gr.173518.114 · Cited by 224 · see citing works

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

Li, Y., Rivera, C. M., Ishii, H., Jin, F., Selvaraj, S., Lee, A. Y., Dixon, J. R., & Ren, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114485 · Cited by 212 · see citing works

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis -regulatory function of ChIP-seq peaks

White, M. A., Myers, C. A., Corbo, J. C., & Cohen, B. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307449110 · Cited by 195 · see citing works

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

Piper, J., Elze, M. C., Cauchy, P., Cockerill, P. N., Bonifer, C., & Ott, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt850 · Cited by 194 · see citing works

Expression profiling of the developing and mature Nrl −/− mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl

Yoshida, S., Mears, A. J., Friedman, J. S., Carter, T., He, S., Oh, E. C. T., Jing, Y., Farjo, R. A., Fleury, G. A., Barlow, C., et al. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh160 · Cited by 182 · see citing works

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 · see citing works

High-throughput functional comparison of promoter and enhancer activities

Nguyen, T. A., Jones, R. D., Snavely, A. R., Pfenning, A. R., Kirchner, R., Hemberg, M., & Gray, J. M. (2016) · Genome Research · doi:10.1101/gr.204834.116 · Cited by 146 · see citing works

Functional footprinting of regulatory DNA

Vierstra, J., Reik, A., Chang, K.-H., Stehling-Sun, S., Zhou, Y., Hinkley, S. J., Paschon, D. E., Zhang, L., Psatha, N., Bendana, Y. R., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3554 · Cited by 133 · see citing works

Chromatin-wide Profiling of DYRK1A Reveals a Role as a Gene-Specific RNA Polymerase II CTD Kinase

Vona, C. D., Bezdan, D., Islam, A. B. M. M. K., Salichs, E., López-Bigas, N., Ossowski, S., & de la Luna, S. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.026 · Cited by 129 · see citing works

Massively parallel cis-regulatory analysis in the mammalian central nervous systemPreprint

Shen, S. Q., Myers, C. A., Hughes, A. E. O., Byrne, L. C., Flannery, J. G., & Corbo, J. C. (2015) · Genome Research · doi:10.1101/gr.193789.115 · Cited by 123 · see citing works

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

Diao, Y., Li, B., Meng, Z., Jung, I., Lee, A. Y., Dixon, J., Maliskova, L., Guan, K.-L., Shen, Y., & Ren, B. (2016) · Genome Research · doi:10.1101/gr.197152.115 · Cited by 122 · see citing works

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activityPreprint

Sammons, M. A., Zhu, J., Drake, A. M., & Berger, S. L. (2014) · Genome Research · doi:10.1101/gr.181883.114 · Cited by 114 · see citing works

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell typesPreprint

Ernst, J., & Kellis, M. (2013) · Genome Research · doi:10.1101/gr.144840.112 · Cited by 95 · see citing works

Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO

Raghav, S. K., Waszak, S. M., Krier, I., Gubelmann, C., Isakova, A., Mikkelsen, T. S., & Deplancke, B. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.03.017 · Cited by 92 · see citing works

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

Murtha, M. J., Keskin, Z. T., Tang, Z., Strino, F., Chen, X. X., Wang, Y., Xi, X., Basilico, C., Brown, S. M., Bonneau, R., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2885 · Cited by 90 · see citing works

Large Maf Transcription Factors: Cousins of AP-1 Proteins and Important Regulators of Cellular Differentiation

Yang, Y., & Cvekl, A. (2016) · Einstein Journal of Biology and Medicine · doi:10.23861/ejbm20072347 · Cited by 90 · see citing works

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

Blattler, A., Yao, L., Wang, Y., Ye, Z., Jin, V. X., & Farnham, P. J. (2013) · Epigenetics &amp; Chromatin · doi:10.1186/1756-8935-6-13 · Cited by 82 · see citing works

Function-based identification of mammalian enhancers using site-specific integration

Dickel, D. E., Zhu, Y., Nord, A. S., Wylie, J. N., Akiyama, J. A., Afzal, V., Plajzer-Frick, I., Kirkpatrick, A. M., Göttgens, B., Bruneau, B. G., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2886 · Cited by 81 · see citing works

Mathematical Statistics

Bickel, P. J., & Doksum, K. A. (2015) · Chapman & Hall/CRC eBooks · doi:10.1201/b18312 · Cited by 74 · see citing works

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Gisselbrecht, S. S., Barrera, L. A., Porsch, M., Aboukhalil, A., Estep, P. W., Vedenko, A., Palagi, A., Kim, Y., Zhu, X., Busser, B. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2558 · Cited by 62 · see citing works

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

Watts, J. A., Zhang, C., Klein–Szanto, A. J., Kormish, J. D., Fu, J., Zhang, M. Q., & Zaret, K. S. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002277 · Cited by 61 · see citing works

Massively Parallel Reporter Assays in Cultured Mammalian Cells

Melnikov, A., Zhang, X., Rogov, P., Wang, L., & Mikkelsen, T. S. (2014) · Journal of Visualized Experiments · doi:10.3791/51719 · Cited by 53 · see citing works

Design optimization methods for genomic DNA tiling arraysPreprint

Bertone, P., Trifonov, V., Rozowsky, J. S., Schubert, F., Emanuelsson, O., Karro, J. E., Kao, M., Snyder, M. P., & Gerstein, M. (2005) · Genome Research · doi:10.1101/gr.4452906 · Cited by 53 · see citing works

Comprehensive Analysis of the Palindromic Motif TCTCGCGAGA: A Regulatory Element of the HNRNPK Promoter

Mikuła, M., Gaj, P., Dzwonek, K., Rubel, T., Karczmarski, J., Paziewska, A., Dzwonek, A., Brągoszewski, P., Dadlez, M., & Ostrowski, J. (2010) · DNA Research · doi:10.1093/dnares/dsq016 · Cited by 37 · see citing works

Systematic RNAi Studies on the Role of Sp/KLF Factors in Globin Gene Expression and Erythroid Differentiation

Hu, J., Navas, P. A., Cao, H., Stamatoyannopoulos, G., & Song, C.-Z. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.12.047 · Cited by 34 · see citing works

Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays

Eichner, J., Zeller, G., Laubinger, S., & Rätsch, G. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-55 · Cited by 24 · see citing works

Computational Identification of Active Enhancers in Model Organisms

Wang, C.-Q., Zhang, M. Q., & Zhang, Z.-H. (2013) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2013.04.002 · Cited by 23 · see citing works

RNA global alignment in the joint sequence–structure space using elastic shape analysis

Laborde, J., Robinson, D., Srivastava, A., Klassen, E. P., & Zhang, J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt187 · Cited by 17 · see citing works

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399 · see citing works

Chromatin-state discovery and genome annotation with ChromHMM

Ernst, J., & Kellis, M. (2017) · Nature Protocols · doi:10.1038/nprot.2017.124 · Cited by 918 · see citing works

Linear models enable powerful differential activity analysis in massively parallel reporter assays

Myint, L., Avramopoulos, D., Goff, L., & Hansen, K. (2017) · BMC Genomics · doi:10.1186/s12864-019-5556-x · Cited by 140 · see citing works

Extreme Polygenicity of Complex Traits Is Explained by Negative Selection

O'Connor, L. J., Schoech, A. P., Hormozdiari, F., Gazal, S., Patterson, N., & Price, A. L. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.07.003 · Cited by 268 · see citing works

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Esposito, D., Weile, J., Shendure, J., Starita, L. M., Papenfuss, A. T., Roth, F. P., Fowler, D. M., & Rubin, A. F. (2019) · Genome biology · doi:10.1186/s13059-019-1845-6 · Cited by 248 · see citing works

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

Hess, G. T., Tycko, J., Yao, D., & Bassik, M. C. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.029 · Cited by 234 · see citing works

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

Barakat, T. S., Halbritter, F., Zhang, M., Rendeiro, A. F., Perenthaler, E., Bock, C., & Chambers, I. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.06.014 · Cited by 214 · see citing works

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

Wang, X., He, L., Goggin, S. M., Saadat, A., Wang, L., Sinnott-Armstrong, N., Claussnitzer, M., & Kellis, M. (2018) · Nature Communications · doi:10.1038/s41467-018-07746-1 · Cited by 159 · see citing works

Multiple causal variants underlie genetic associations in humans

Abell, N. S., DeGorter, M. K., Gloudemans, M. J., Greenwald, E., Smith, K. S., He, Z., & Montgomery, S. B. (2022) · Science · doi:10.1126/science.abj5117 · Cited by 186 · see citing works

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Viñuela, A., Varshney, A., van de Bunt, M., Prasad, R. B., Asplund, O., Bennett, A., Boehnke, M., Brown, A. A., Erdos, M. R., Fadista, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18581-8 · Cited by 152 · see citing works

Massively parallel characterization of transcriptional regulatory elements

Agarwal, V., Inoue, F., Schubach, M., Penzar, D., Martin, B. K., Dash, P. M., Keukeleire, P., Zhang, Z., Sohota, A., Zhao, J., et al. (2025) · Nature · doi:10.1038/s41586-024-08430-9 · Cited by 146 · see citing works

3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

Uyehara, C. M., & Apostolou, E. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112068 · Cited by 143 · see citing works

Machine-guided design of cell-type-targeting cis-regulatory elements

Gosai, S. J., Castro, R. I., Fuentes, N., Butts, J. C., Mouri, K., Alasoadura, M., Kales, S., Nguyen, T. T. L., Noche, R. R., Rao, A. S., et al. (2024) · Nature · doi:10.1038/s41586-024-08070-z · Cited by 142 · see citing works

Functional regulatory variants implicate distinct transcriptional networks in dementia

Cooper, Y. A., Teyssier, N., Dräger, N. M., Guo, Q., Davis, J. E., Sattler, S. M., Yang, Z., Patel, A. M., Wu, S. J., Kosuri, S., et al. (2022) · Science · doi:10.1126/science.abi8654 · Cited by 120 · see citing works

High‐throughput identification of RNA nuclear enrichment sequences

Shukla, C. J., McCorkindale, A. L., Gerhardinger, C., Korthauer, K. D., Cabili, M. N., Shechner, D. M., Irizarry, R. A., Maass, P. G., & Rinn, J. L. (2018) · The EMBO Journal · doi:10.15252/embj.201798452 · Cited by 122 · see citing works

Systematic interrogation of human promoters

Weingarten-Gabbay, S., Nir, R., Lubliner, S., Sharon, E., Kalma, Y., Weinberger, A., & Segal, E. (2019) · Genome Research · doi:10.1101/gr.236075.118 · Cited by 110 · see citing works

A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences

Linder, J., Bogard, N., Rosenberg, A. B., & Seelig, G. (2020) · Cell Systems · doi:10.1016/j.cels.2020.05.007 · Cited by 107 · see citing works

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

Levchenko, А., Kanapin, A. A., Samsonova, A. A., & Gainetdinov, R. R. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx240 · Cited by 103 · see citing works

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

Movva, R., Greenside, P., Marinov, G. K., Nair, S., Shrikumar, A., & Kundaje, A. B. (2019) · PLoS ONE · doi:10.1371/journal.pone.0218073 · Cited by 87 · see citing works

BANP opens chromatin and activates CpG-island-regulated genes

Grand, R. S., Burger, L., Gräwe, C., Michael, A. K., Isbel, L., Heß, D., Hoerner, L., Iešmantavičius, V., Durdu, S., Pregnolato, M., et al. (2021) · Nature · doi:10.1038/s41586-021-03689-8 · Cited by 91 · see citing works

Deep flanking sequence engineering for efficient promoter design using DeepSEED

Zhang, P., Wang, H., Xu, H., Wei, L., Liu, L., Hu, Z., & Wang, X. (2023) · Nature Communications · doi:10.1038/s41467-023-41899-y · Cited by 91 · see citing works

A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers

Li, Y., Liang, J. H., Ozer, A., Leung, A. K.-Y., Lis, J. T., & Yu, H. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01211-7 · Cited by 84 · see citing works

Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer functionPreprint

Zhang, X.-O., Gingeras, T., & Weng, Z. (2019) · Genome Research · doi:10.1101/gr.249789.119 · Cited by 89 · see citing works

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expressionPreprint

Huang, D., Petrykowska, H. M., Miller, B., Elnitski, L. L., & Ovcharenko, I. (2019) · Genome Research · doi:10.1101/gr.247007.118 · Cited by 84 · see citing works

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

Bravo González-Blas, C., Matetovici, I., Hillen, H., Taskiran, I. I., Vandepoel, R., Christiaens, V., Sansores-García, L., Verboven, E., Hulselmans, G., Poovathingal, S., et al. (2024) · Nature Cell Biology · doi:10.1038/s41556-023-01316-4 · Cited by 85 · see citing works

Scalable Functional Assays for the Interpretation of Human Genetic Variation

Tabet, D. R., Parikh, V. N., Mali, P., Roth, F. P., & Claussnitzer, M. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-072920-032107 · Cited by 83 · see citing works

Widespread Enhancer Activity from Core Promoters

Medina-Rivera, A., Santiago-Algarra, D., Puthier, D., & Spicuglia, S. (2018) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.03.004 · Cited by 78 · see citing works

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

Perenthaler, E., Yousefi, S., Niggl, E., & Barakat, T. S. (2019) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2019.00352 · Cited by 71 · see citing works

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function

Benton, M. L., Talipineni, S. C., Kostka, D., & Capra, J. A. (2019) · BMC Genomics · doi:10.1186/s12864-019-5779-x · Cited by 68 · see citing works

Transcriptional regulation by promoters with enhancer function

Dao, L. T. M., & Spicuglia, S. (2018) · Transcription · doi:10.1080/21541264.2018.1486150 · Cited by 69 · see citing works

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk

Reshef, Y. A., Finucane, H. K., Kelley, D. R., Gusev, A., Kotliar, D., Ulirsch, J. C., Hormozdiari, F., Nasser, J., O’Connor, L., van de Geijn, B., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0196-7 · Cited by 68 · see citing works

Fast activation maximization for molecular sequence design

Linder, J., & Seelig, G. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04437-5 · Cited by 72 · see citing works

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification

Hoffman, G. E., Bendl, J. M., Girdhar, K., Schadt, E. E., & Roussos, P. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz808 · Cited by 62 · see citing works

Cis and trans effects differentially contribute to the evolution of promoters and enhancers

Mattioli, K., Oliveros, W., Gerhardinger, C., Andergassen, D., Maass, P., Rinn, J., & Melé, M. (2020) · Genome Biology · doi:10.1186/s13059-020-02110-3 · Cited by 41 · see citing works

Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers

Young, R. S., Kumar, Y., Bickmore, W. A., & Taylor, M. S. (2017) · Genome biology · doi:10.1186/s13059-017-1379-8 · Cited by 60 · see citing works

ENdb: a manually curated database of experimentally supported enhancers for human and mouse

Bai, X., Shi, S., Ai, B., Jiang, Y., Liu, Y., Han, X., Xu, M., Pan, Q., Wang, F., Wang, Q., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz973 · Cited by 62 · see citing works

Leveraging massively parallel reporter assays for evolutionary questions

Romero, I. G., & Lea, A. J. (2023) · Genome biology · doi:10.1186/s13059-023-02856-6 · Cited by 62 · see citing works

Enhancer–silencer transitions in the human genomePreprint

Huang, D., & Ovcharenko, I. (2022) · Genome Research · doi:10.1101/gr.275992.121 · Cited by 57 · see citing works

Recent advances in high-throughput approaches to dissect enhancer function

Santiago‐Algarra, D., Dao, L. T. M., Pradel, L. C., España, A. P., & Spicuglia, S. (2017) · F1000Research · doi:10.12688/f1000research.11581.1 · Cited by 56 · see citing works

Massively parallel techniques for cataloguing the regulome of the human brain

Townsley, K. G., Brennand, K., & Huckins, L. M. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-00740-1 · Cited by 52 · see citing works

Identification of Functional Variants in the FAM13A Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Locus by Massively Parallel Reporter Assays

Castaldi, P. J., Guo, F., Qiao, D., Du, F., Naing, Z. Z. C., Li, Y., Pham, B., Mikkelsen, T. S., Cho, M. H., Silverman, E. K., et al. (2018) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201802-0337oc · Cited by 51 · see citing works

Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters

Lalanne, J., Regalado, S. G., Domcke, S., Calderon, D., Martin, B., Li, X., Li, T., Suiter, C. C., Lee, C., Trapnell, C., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02260-3 · Cited by 53 · see citing works

The evolution of Great Apes has shaped the functional enhancers' landscape in human embryonic stem cells

Glinsky, G. V., & Barakat, T. S. (2019) · Stem Cell Research · doi:10.1016/j.scr.2019.101456 · Cited by 49 · see citing works

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

Pena, R. N., Ros‐Freixedes, R., Tör, M., & Estany, J. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17122100 · Cited by 48 · see citing works

Resolving mechanisms of immune‐mediated disease in primary CD4 T cells

Bourges, C., Groff, A. F., Burren, O. S., Gerhardinger, C., Mattioli, K., Hutchinson, A., Hu, T. X., Anand, T., Epping, M. W., Wallace, C., et al. (2020) · EMBO Molecular Medicine · doi:10.15252/emmm.202012112 · Cited by 45 · see citing works

Enhancers in the Peril lincRNA locus regulate distant but not local genes

Groff, A., Barutcu, A. R., Lewandowski, J. P., & Rinn, J. L. (2018) · Genome Biology · doi:10.1186/s13059-018-1589-8 · Cited by 26 · see citing works

Cis-regulatory landscapes of four cell types of the retina

Hartl, D., Krebs, A. R., Jüttner, J., Roska, B., & Schübeler, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx923 · Cited by 37 · see citing works

Algorithm for cellular reprogramming

Ronquist, S., Patterson, G., Muir, L. A., Lindsly, S., Chen, H., Brown, M. A., Wicha, M. S., Bloch, A. M., Brockett, R. W., & Rajapakse, I. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1712350114 · Cited by 40 · see citing works

Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts

Mulvey, B., Lagunas, T., & Dougherty, J. D. (2020) · Biological Psychiatry · doi:10.1016/j.biopsych.2020.06.011 · Cited by 40 · see citing works

Cell cycle–dependent localization of the proteasome to chromatin

Kito, Y., Matsumoto, M., Hatano, A., Takami, T., Oshikawa, K., Matsumoto, A., & Nakayama, K. I. (2020) · Scientific Reports · doi:10.1038/s41598-020-62697-2 · Cited by 39 · see citing works

Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation

Chen, P.-S. B., Fiaux, P. C., Zhang, K., Li, B., Kubo, N., Jiang, S., Hu, R., Rooholfada, E., Wu, S.-H., Wang, M.-C., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111630 · Cited by 31 · see citing works

Functional mapping of androgen receptor enhancer activity

Huang, C.-C. F., Lingadahalli, S., Morova, T., Özturan, D., Hu, E., Yu, I. P. L., Linder, S., Hoogstraat, M., Stelloo, S., Sar, F., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02339-6 · Cited by 35 · see citing works

Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays

Davis, J. E., Insigne, K. D., Jones, E. M., Hastings, Q. B., Boldridge, W. C., & Kosuri, S. (2020) · Cell Systems · doi:10.1016/j.cels.2020.05.011 · Cited by 34 · see citing works

Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity

Yin, C., Castillo-Hair, S. M., Byeon, G. W., Bromley, P., Meuleman, W. R. A., & Seelig, G. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101302 · Cited by 29 · see citing works

Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer

Ropri, A. S., DeVaux, R. S., Eng, J., Chittur, S. V., & Herschkowitz, J. I. (2021) · Breast Cancer Research · doi:10.1186/s13058-021-01479-8 · Cited by 30 · see citing works

Identifying Novel Enhancer Elements with CRISPR-Based Screens

Klein, J. C., Chen, W., Gasperini, M. J., & Shendure, J. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00778 · Cited by 29 · see citing works

Analysis of long and short enhancers in melanoma cell states

Mauduit, D., Minnoye, L., Taskiran, I. I., Waegeneer, M. D., Christiaens, V., Hulselmans, G., Demeulemeester, J., Wouters, J., & Aerts, S. (2021) · eLife · doi:10.7554/elife.71735 · Cited by 26 · see citing works

Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

Jagoda, E., Marnetto, D., Senevirathne, G., Gonzalez, V., Baid, K., Montinaro, F., Richard, D. J., Falzarano, D., LeBlanc, E. V., Colpitts, C. C., et al. (2023) · eLife · doi:10.7554/elife.71235 · Cited by 27 · see citing works

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

Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 20 · see citing works

Next steps in the identification of gene targets for type 1 diabetes

Grant, S. F. A., Wells, A. D., & Rich, S. S. (2020) · Diabetologia · doi:10.1007/s00125-020-05248-8 · Cited by 20 · see citing works

Machine-guided design of synthetic cell type-specific cis -regulatory elementsPreprint

Gosai, S. J., Castro, R. I., Fuentes, N., Butts, J. C., Kales, S., Noche, R. R., Mouri, K., Sabeti, P. C., Reilly, S. K., & Tewhey, R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.08.552077 · Cited by 18 · see citing works

An in vivo systemic massively parallel platform for deciphering animal tissue-specific regulatory function

Brown, A. R., Fox, G. A., Kaplow, I. M., Lawler, A. J., Phan, B. N., Gadey, L., Wirthlin, M. E., Ramamurthy, E., May, G. E., Chen, Z., et al. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1533900 · Cited by 16 · see citing works

Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity

Colbran, L. L., Chen, L., & Capra, J. A. (2019) · Genetics · doi:10.1534/genetics.118.301895 · Cited by 16 · see citing works

RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mousePreprint

Farrell, C. M., Goldfarb, T., Rangwala, S. H., Astashyn, A., Ermolaeva, O. D., Hem, V., Katz, K., Kodali, V. K., Ludwig, F., Wallin, C., et al. (2021) · Genome Research · doi:10.1101/gr.275819.121 · Cited by 17 · see citing works

Using Human Genetics to Drive Drug Discovery: A Perspective

Fox, C. S. (2019) · American Journal of Kidney Diseases · doi:10.1053/j.ajkd.2018.12.045 · Cited by 16 · see citing works

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 16 · see citing works

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

Morova, T., Ding, Y., Huang, C.-C. F., Sar, F., Schwarz, T., Giambartolomei, C., Baca, S. C., Grishin, D., Hach, F., Gusev, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1198 · Cited by 17 · see citing works

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

Hussain, S., Sadouni, N., van Essen, D., Dao, L. T. M., Ferré, Q., Charbonnier, G., Torres, M., Gallardo, F., Lecellier, C., Sexton, T., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad187 · Cited by 16 · see citing works

Modeling and designing enhancers by introducing and harnessing transcription factor binding units

Li, J., Zhang, P., Xi, X., Liu, L., Wei, L., & Wang, X. (2025) · Nature Communications · doi:10.1038/s41467-025-56749-2 · Cited by 16 · see citing works

Epromoters are new players in the regulatory landscape with potential pleiotropic roles

Malfait, J., Wan, J., & Spicuglia, S. (2023) · BioEssays · doi:10.1002/bies.202300012 · Cited by 14 · see citing works

Functional characterization of enhancer activity during a long terminal repeat's evolutionPreprint

Du, A. Y., Zhuo, X., Sundaram, V., Jensen, N. O., Chaudhari, H. G., Saccone, N. L., Cohen, B. A., & Wang, T. (2022) · Genome Research · doi:10.1101/gr.276863.122 · Cited by 14 · see citing works

Dynamic neuro-immune regulation of psychiatric risk loci in human neurons

Townsley, K. G., Lee, S. H., Williams, S., Cartwright, S., Cohen, S., Sen, A., Jia, M., Young, H. E., Dobbyn, L., Deans, M., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-77114-x · Cited by 13 · see citing works

Dissecting intercellular and intracellular signaling networks with barcoded genetic tools

Herholt, A., Sahoo, V. K., Popović, L., Wehr, M. C., & Rossner, M. J. (2021) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2021.09.002 · Cited by 13 · see citing works

Trans MPRA: A framework for assaying the role of many trans -acting factors at many enhancersPreprint

Calderon, D., Ellis, A., Daza, R. M., Martin, B., Tome, J. M., Chen, W., Chardon, F. M., Leith, A., Lee, C., Trapnell, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.30.321323 · Cited by 13 · see citing works

Strategies for effectively modelling promoter-driven gene expression using transfer learningPreprint

Reddy, A. J., Herschl, M. H., Geng, X., Kolli, S., Lu, A. X., Kumar, A., Hsu, P. D., Levine, S., & Ioannidis, N. M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.24.529941 · Cited by 13 · see citing works

Functional interrogation of autoimmune disease genetics using CRISPR/Cas9 technologies and massively parallel reporter assays

Ding, J., Frantzeskos, A., & Orozco, G. (2021) · Seminars in Immunopathology · doi:10.1007/s00281-021-00887-4 · Cited by 12 · see citing works

Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders

Pratt, B. M., & Won, H. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.08.013 · Cited by 12 · see citing works

Polygenicity of complex traits is explained by negative selectionPreprint

O’Connor, L. J., Schoech, A. P., Hormozdiari, F., Gazal, S., Patterson, N. J., & Price, A. L. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/420497 · Cited by 13 · see citing works

Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation

Li, S., Kvon, E. Z., Visel, A., Pennacchio, L. A., & Ovcharenko, I. (2019) · Genome biology · doi:10.1186/s13059-019-1750-z · Cited by 11 · see citing works

Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease

Wamsley, B., & Geschwind, D. H. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.032 · Cited by 11 · see citing works

A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

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. (2021) · Diabetes · doi:10.2337/db20-1087 · Cited by 11 · see citing works

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 10 · see citing works

Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases

Ren, N., Dai, S., Ma, S., & Yang, F. (2022) · Clinical Genetics · doi:10.1111/cge.14282 · Cited by 11 · see citing works

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 · see citing works

SERPINA1 modulates expression of amyloidogenic transthyretin

Niemietz, C., Bezerra, F., Almeida, M. R., Guo, S., Monia, B. P., Saraiva, M. J., Schütz, P., Schmidt, H., & Zibert, A. (2020) · Experimental Cell Research · doi:10.1016/j.yexcr.2020.112217 · Cited by 9 · see citing works

Quantifying Intensities of Transcription Factor-DNA Binding by Learning From an Ensemble of Protein Binding Microarrays

Quan, L., Mei, J., He, R., Sun, X., Nie, L., Li, K., & Lyu, Q. (2021) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2021.3058518 · Cited by 9 · see citing works

Predicting Transcriptional Regulatory Activities with Deep Convolutional NetworksPreprint

Paggi, J., Lamb, A., Tian, K., Hsu, I., Cedoz, P.-L., & Kawthekar, P. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/099879 · Cited by 9 · see citing works

Extensive binding of nebulous human transcription factors to genomic dark matterPreprint

Razavi, R., Fathi, A., Yellan, I., Brechalov, A. V., Laverty, K. U., Jolma, A., Hernández-Corchado, A., Zheng, H., Yang, A. W. H., Albu, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.11.622123 · Cited by 9 · see citing works

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 8 · see citing works

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 8 · see citing works

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 · see citing works

Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins

Fong, S., & Capra, J. A. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac159 · Cited by 7 · see citing works

ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase

Chinnam, N. B., Thapar, R., Arvai, A., Sarker, A. H., Soll, J. M., Paul, T., Syed, A., Rosenberg, D. J., Hammel, M., Bacolla, A., et al. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107368 · Cited by 6 · see citing works

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 · see citing works

funMotifs: Tissue-specific transcription factor motifsPreprint

Umer, H. M., Garbulowska, K. S., Marzouka, N., Khaliq, Z., Wadelius, C., & Komorowski, J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/683722 · Cited by 7 · see citing works

Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation

Párraga, A. A., Nylund, P., Diamanti, K., Garrido-Zabala, B., Tziola, S. I., Vasquez, L. J., Pyl, P. T., Raykova, D., Skaftason, A., Ma, A., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-17093-z · Cited by 7 · see citing works

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 · see citing works

The contribution of silencer variants to human diseases

Huang, D., & Ovcharenko, I. (2024) · Genome biology · doi:10.1186/s13059-024-03328-1 · Cited by 6 · see citing works

Functional annotation of noncoding mutations in cancer

Umer, H. M., Smolińska, K., Komorowski, J., & Wadelius, C. (2021) · Life Science Alliance · doi:10.26508/lsa.201900523 · Cited by 6 · see citing works

Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms

Patel, Z. M., & Hughes, T. (2021) · Genome Biology · doi:10.1186/s13059-021-02503-y · Cited by 6 · see citing works

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

Wang, X., He, L., Goggin, S. M., Saadat, A., Wang, L., Sinnott-Armstrong, N., Claussnitzer, M., & Kellis, M. (2018) · Nature Communications · doi:10.1038/s41467-018-07746-1 · Cited by 159 · see citing works

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

Kheradpour, P., Ernst, J., Melnikov, A., Rogov, P., Wang, L., Zhang, X., Alston, J., Mikkelsen, T. S., & Kellis, M. (2013) · Genome Research · doi:10.1101/gr.144899.112 · Cited by 315 · see citing works

ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genomePreprint

Hansen, T. J., & Hodges, E. C. (2022) · Genome Research · doi:10.1101/gr.276766.122 · Cited by 69 · see citing works

Meta-analysis of massive parallel reporter assays enables functional regulatory elements predictionPreprint

Kreimer, A., Yan, Z., Ahituv, N., & Yosef, N. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/202002 · Cited by 2 · see citing works

A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells

Maricque, B., Dougherty, J., & Cohen, B. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw942 · Cited by 56 · see citing works