Systematic dissection of genomic features determining transcription factor binding and enhancer function

Multilineage potential of adult human mesenchymal stem cells

Pittenger, M. F., Mackay, A. M., Beck, S. C., Jaiswal, R. K., Douglas, R., Mosca, J. D., Moorman, M. A., Simonetti, D. W., Craig, S., & Marshak, D. R. (1999) · Science · doi:10.1126/science.284.5411.143 · Cited by 21,052 · see citing works

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

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · 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

FIMO: scanning for occurrences of a given motif

Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247 · see citing works

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · 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

Transcription factors: from enhancer binding to developmental control

Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works

A CBP Integrator Complex Mediates Transcriptional Activation and AP-1 Inhibition by Nuclear Receptors

Kamei, Y., Xu, L., Heinzel, T., Torchia, J., Kurokawa, R., Gloss, B., Lin, S.-C., Heyman, R. A., Rose, D. W., Glass, C. K., et al. (1996) · Cell · doi:10.1016/s0092-8674(00)81118-6 · Cited by 2,150 · see citing works

TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes

Matys, V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj143 · Cited by 2,142 · see citing works

Genome-Wide Location and Function of DNA Binding Proteins

Ren, B., Robert, F., Wyrick, J. J., Aparicio, O. M., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N. M., Kanin, E. I., et al. (2000) · Science · doi:10.1126/science.290.5500.2306 · Cited by 1,768 · see citing works

C/EBPα induces adipogenesis through PPARγ: a unified pathwayPreprint

Rosen, E. D., Hsu, C.-H., Wang, X., Sakai, S., Freeman, M. W., Gonzalez, F. J., & Spiegelman, B. M. (2002) · Genes & Development · doi:10.1101/gad.948702 · Cited by 1,497 · see citing works

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454 · 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

DNA-Binding Specificities of Human Transcription Factors

Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P. M. A., Morgunova, E. Y., Enge, M., Taipale, M., Wei, G., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.009 · Cited by 1,228 · see citing works

Transcriptional activation by recruitment

Ptashne, M., & Gann, A. (1997) · Nature · doi:10.1038/386569a0 · Cited by 1,158 · see citing works

A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

Wei, C.-L., Wu, Q., Vega, V. B., Chiu, K. P., Ng, P., Zhang, T., Shahab, A., Yong, H. C., Fu, Y., Weng, Z., et al. (2006) · Cell · doi:10.1016/j.cell.2005.10.043 · Cited by 1,141 · 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

Diversity and Complexity in DNA Recognition by Transcription Factors

Badis, G., Berger, M., Philippakis, A. A., Talukder, S., Gehrke, A. R., Jaeger, S., Chan, E. T., Metzler, G., Vedenko, A., Chen, X., et al. (2009) · Science · doi:10.1126/science.1162327 · Cited by 1,031 · see citing works

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Mathelier, A., Zhao, X., Zhang, A. W., Parcy, F., Worsley-Hunt, R., Arenillas, D. J., Buchman, S., Chen, C., Chou, A., Ienasescu, H., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt997 · Cited by 983 · see citing works

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

Lupien, M., Eeckhoute, J., Meyer, C. A., Wang, Q., Zhang, Y., Li, W., Carroll, J. S., Liu, X. S., & Brown, M. (2008) · Cell · doi:10.1016/j.cell.2008.01.018 · Cited by 983 · see citing works

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

John, S., Sabo, P. J., Thurman, R. E., Sung, M.-H., Biddie, S. C., Johnson, T. A., Hager, G. L., & Stamatoyannopoulos, J. A. (2011) · Nature Genetics · doi:10.1038/ng.759 · Cited by 954 · see citing works

PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scalePreprint

Lefterova, M. I., Zhang, Y., Steger, D. J., Schupp, M., Schug, J., Cristancho, A. G., Feng, D., Zhuo, D. X., Stoeckert, C. J., Liu, X. S., et al. (2008) · Genes & Development · doi:10.1101/gad.1709008 · Cited by 826 · see citing works

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factorsPreprint

Wang, J., Zhuang, J., Iyer, S., Lin, X.-Y., Whitfield, T. W., Greven, M. C., Pierce, B. G., Dong, X., Kundaje, A. B., Cheng, Y., et al. (2012) · Genome Research · doi:10.1101/gr.139105.112 · Cited by 820 · see citing works

Close encounters of many kinds: Fos-Jun interactions that mediate transcription regulatory specificity

Chinenov, Y. V., & Kerppola, T. K. (2001) · Oncogene · doi:10.1038/sj.onc.1204385 · Cited by 715 · 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

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

Berman, B. P., Nibu, Y., Pfeiffer, B. D., Tomančák, P., Celniker, S., Levine, M., Rubin, G. M., & Eisen, M. B. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.231608898 · Cited by 605 · see citing works

A systems approach to measuring the binding energy landscapes of transcription factors.

Maerkl, S. J., & Quake, S. R. (2007) · Science · doi:10.1126/science.1131007 · Cited by 584 · see citing works

Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesisPreprint

Nielsen, R., Pedersen, T. Å., Hagenbeek, D., Moulos, P., Siersbæk, R., Megens, E., Denissov, S., Børgesen, M., Françoijs, K., Mandrup, S., et al. (2008) · Genes & Development · doi:10.1101/gad.501108 · Cited by 520 · see citing works

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

Mikkelsen, T. S., Zhao, X. D., Zhang, X., Wang, L., Gimble, J. M., Lander, E. S., & Rosen, E. D. (2010) · Cell · doi:10.1016/j.cell.2010.09.006 · Cited by 519 · see citing works

Nucleoprotein complexes that regulate gene expression in adipocyte differentiation: direct participation of c-fos

Distel, R. J., Ro, J., Rosen, B. S., Groves, D. L., & Spiegelman, B. M. (1987) · Cell · doi:10.1016/0092-8674(87)90621-0 · Cited by 506 · see citing works

The myb gene family in cell growth, differentiation and apoptosis

Oh, I.-H., & Reddy, E. P. (1999) · Oncogene · doi:10.1038/sj.onc.1202839 · Cited by 498 · see citing works

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

Slattery, M. G., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B. H., Bussemaker, H. J., et al. (2011) · Cell · doi:10.1016/j.cell.2011.10.053 · Cited by 497 · 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

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

Badis, G., Chan, E. T., van Bakel, H., Peña‐Castillo, L., Tillo, D., Tsui, K., Carlson, C. D., Gossett, A. J., Hasinoff, M. J., Warren, C. L., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.11.020 · Cited by 472 · 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

Regulation of Neuronal Traits by a Novel Transcriptional Complex

Ballas, N., Battaglioli, E., Atouf, F., Andrés, M. E., Chenoweth, J. G., Anderson, M. E., Bürger, C., Moniwa, M., Davie, J., Bowers, W. J., et al. (2001) · Neuron · doi:10.1016/s0896-6273(01)00371-3 · Cited by 416 · 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

High-resolution DNA-binding specificity analysis of yeast transcription factorsPreprint

Zhu, C., Byers, K. J. R. P., McCord, R. P., Shi, Z., Berger, M. F., Newburger, D. E., Saulrieta, K., Smith, Z. D., Shah, M. V., Radhakrishnan, M., et al. (2009) · Genome Research · doi:10.1101/gr.090233.108 · Cited by 399 · see citing works

The histone acetylase PCAF is a nuclear receptor coactivatorPreprint

Blanco, J. C. G., Minucci, S., Lü, J., Yang, X., Walker, K. K., Chen, H., Evans, R. M., Nakatani, Y., & Ozato, K. (1998) · Genes & Development · doi:10.1101/gad.12.11.1638 · Cited by 388 · see citing works

Regulation of Organogenesis by the Caenorhabditis elegans FoxA Protein PHA-4

Gaudet, J., & Mango, S. E. (2002) · Science · doi:10.1126/science.1065175 · Cited by 363 · see citing works

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

Gordân, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R., & Bulyk, M. L. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.03.014 · Cited by 356 · see citing works

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

Siersbæk, R., Nielsen, R., John, S., Sung, M., Baek, S., Loft, A., Hager, G. L., & Mandrup, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.65 · Cited by 350 · see citing works

Nucleosome-mediated cooperativity between transcription factors

Mirny, L. A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913805107 · Cited by 349 · see citing works

Synergistic activation and repression of transcription by Drosophila homeobox proteins

Han, K., Levine, M., & Manley, J. L. (1989) · Cell · doi:10.1016/0092-8674(89)90580-1 · Cited by 338 · see citing works

Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design.

Vinson, C. R., Hai, T., & Boyd, S. M. (1993) · Genes & Development · doi:10.1101/gad.7.6.1047 · Cited by 336 · see citing works

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Inoue, F., Kircher, M., Martin, B., Cooper, G. M., Witten, D. M., McManus, M. T., Ahituv, N., & Shendure, J. (2017) · Genome Research · doi:10.1101/gr.212092.116 · Cited by 331 · see citing works

Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen

Jiang, J. (1993) · Cell · doi:10.1016/0092-8674(93)90402-c · Cited by 327 · 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

Animal Transcription Networks as Highly Connected, Quantitative Continua

Biggin, M. D. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.09.008 · Cited by 308 · see citing works

Three Functional Classes of Transcriptional Activation Domains

Blau, J., Xiao, H., McCracken, S. A., O’Hare, P., Greenblatt, J., & Bentley, D. L. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.5.2044 · Cited by 268 · see citing works

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

Grove, C. A., Masi, F. D., Barrasa, M. I., Newburger, D. E., Alkema, M. J., Bulyk, M. L., & Walhout, A. J. M. (2009) · Cell · doi:10.1016/j.cell.2009.04.058 · Cited by 267 · see citing works

C/ATF, a member of the activating transcription factor family of DNA-binding proteins, dimerizes with CAAT/enhancer-binding proteins and directs their binding to cAMP response elements.

Vallejo, M., Ron, D., Miller, C. P., & Habener, J. F. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.10.4679 · Cited by 266 · see citing works

A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites

Polach, K. J., & Widom, J. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0288 · Cited by 249 · see citing works

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

Gotea, V., Visel, A., Westlund, J. M., Nobrega, M. A., Pennacchio, L. A., & Ovcharenko, I. (2010) · Genome Research · doi:10.1101/gr.104471.109 · Cited by 248 · see citing works

Atf4 Regulates Obesity, Glucose Homeostasis, and Energy Expenditure

Seo, J. H., Fortuno, E. S., Suh, J. M., Stenesen, D., Tang, W., Parks, E. J., Adams, C. M., Townes, T. M., & Graff, J. M. (2009) · Diabetes · doi:10.2337/db09-0335 · Cited by 243 · see citing works

Cross-talk between glucocorticoid receptor and AP-1

Herrlich, P. A. (2001) · Oncogene · doi:10.1038/sj.onc.1204388 · Cited by 229 · see citing works

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

Guertin, M. J., & Lis, J. T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001114 · Cited by 228 · see citing works

Program-Specific Distribution of a Transcription Factor Dependent on Partner Transcription Factor and MAPK Signaling

Zeitlinger, J., Simon, I., Harbison, C. T., Hannett, N. M., Volkert, T. L., Fink, G. R., & Young, R. A. (2003) · Cell · doi:10.1016/s0092-8674(03)00301-5 · Cited by 224 · 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

p300 Interacts with the N- and C-terminal Part of PPARγ2 in a Ligand-independent and -dependent Manner, Respectively

Gelman, L., Zhou, G., Lluis Fajas, A., Raspé, E., Fruchart, J., & Auwerx, J. H. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.12.7681 · Cited by 223 · see citing works

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

Raveh-Sadka, T., Levo, M., Shabi, U., Shany, B., Keren, L., Lotan‐Pompan, M., Zeevi, D., Sharon, E., Weinberger, A., & Segal, E. (2012) · Nature Genetics · doi:10.1038/ng.2305 · Cited by 221 · see citing works

Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA

Sekiya, T., Muthurajan, U. M., Luger, K., Tulin, A. V., & Zaret, K. S. (2009) · Genes & Development · doi:10.1101/gad.1775509 · Cited by 221 · see citing works

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Li, X.-Y., Thomas, S., Sabo, P. J., Eisen, M. B., Stamatoyannopoulos, J. A., & Biggin, M. D. (2011) · Genome Biology · doi:10.1186/gb-2011-12-4-r34 · Cited by 217 · see citing works

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

Barozzi, I., Simonatto, M., Bonifacio, S., Yang, L., Rohs, R., Ghisletti, S., & Natoli, G. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.006 · Cited by 209 · see citing works

FOXO-binding partners: it takes two to tango

van der Vos, K. E., & Coffer, P. J. (2008) · Oncogene · doi:10.1038/onc.2008.22 · Cited by 208 · 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

Mitotic Clonal Expansion during Preadipocyte Differentiation: Calpain-mediated Turnover of p27

Patel, Y. M., & Lane, M. D. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m910445199 · Cited by 192 · see citing works

Cell‐specific inhibitory and stimulatory effects of Fos and Jun on transcription activation by nuclear receptors.

Shemshedini, L., Knauthe, R., Sassone‐Corsi, P., Pornon, A., & Gronemeyer, H. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb04953.x · Cited by 188 · see citing works

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182 · see citing works

Functional analysis of transcription factor binding sites in human promoters

Whitfield, T. W., Wang, J., Collins, P. J., Partridge, E. C., Aldred, S. F., Trinklein, N. D., Myers, R., & Weng, Z. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-r50 · Cited by 178 · see citing works

Homotypic Regulatory Clusters in DrosophilaPreprint

Lifanov, A. P., Makeev, V. J., Nazina, A. G., & Papatsenko, D. (2003) · Genome Research · doi:10.1101/gr.668403 · Cited by 163 · see citing works

Pioneer Factors, Genetic Competence, and Inductive Signaling: Programming Liver and Pancreas Progenitors from the EndodermPreprint

Zaret, K. S., Watts, J. A., Xu, J., Wandzioch, E., Smale, S. T., & Sekiya, T. (2008) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2008.73.040 · Cited by 159 · see citing works

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

Erwin, G. D., Oksenberg, N., Truty, R., Kostka, D., Murphy, K. K., Ahituv, N., Pollard, K. S., & Capra, J. A. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003677 · Cited by 154 · see citing works

Selective DNA bending by a variety of bZIP proteins.

Kerppola, T. K., & Curran, T. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.9.5479 · Cited by 146 · see citing works

Unraveling determinants of transcription factor binding outside the core binding sitePreprint

Levo, M., Zalckvar, E., Sharon, E., Machado, A. C. D., Kalma, Y., Lotan‐Pompan, M., Weinberger, A., Zohar Yakhini, B., Rohs, R., & Segal, E. (2015) · Genome Research · doi:10.1101/gr.185033.114 · Cited by 144 · see citing works

A widespread role of the motif environment in transcription factor binding across diverse protein familiesPreprint

Dror, I., Golan, T., Levy, C., Rohs, R., & Mandel‐Gutfreund, Y. (2015) · Genome Research · doi:10.1101/gr.184671.114 · Cited by 144 · see citing works

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

Fisher, W. W., Li, J. J., Hammonds, A. S., Brown, J. B., Pfeiffer, B. D., Weiszmann, R., MacArthur, S., Thomas, S., Stamatoyannopoulos, J. A., Eisen, M. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1209589110 · Cited by 140 · see citing works

Interferon Regulatory Factors Are Transcriptional Regulators of Adipogenesis

Eguchi, J., Yan, Q.-W., Schones, D. E., Kamal, M., Hsu, C.-H., Zhang, M. Q., Crawford, G. E., & Rosen, E. D. (2008) · Cell Metabolism · doi:10.1016/j.cmet.2007.11.002 · Cited by 132 · see citing works

A proline-rich TGF-beta-responsive transcriptional activator interacts with histone H3.Preprint

Alevizopoulos, A., Dusserre, Y., Tsai-Pflugfelder, M., von der Weid, T., Wahli, W., & Mermod, N. (1995) · Genes & Development · doi:10.1101/gad.9.24.3051 · Cited by 129 · see citing works

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

Waki, H., Nakamura, M., Yamauchi, T., Wakabayashi, K.-I., Yu, J., Hirose, L., Take, K., Sun, W., Iwabu, M., Okada‐Iwabu, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002311 · Cited by 124 · see citing works

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinityPreprint

Rowan, S., Siggers, T., Lachke, S. A., Yue, Y., Bulyk, M. L., & Maas, R. L. (2010) · Genes & Development · doi:10.1101/gad.1890410 · Cited by 109 · see citing works

Non‐DNA‐binding cofactors enhance DNA‐binding specificity of a transcriptional regulatory complex

Siggers, T., Duyzend, M., Reddy, J., Khan, S., & Bulyk, M. L. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.89 · Cited by 107 · see citing works

Sequence features that drive human promoter function and tissue specificityPreprint

Landolin, J. M., Johnson, D. S., Trinklein, N. D., Aldred, S. F., Medina, C., Shulha, H. P., Weng, Z., & Myers, R. (2010) · Genome Research · doi:10.1101/gr.100370.109 · Cited by 106 · see citing works

Cell cycle regulation by the B-Myb transcription factor

Joaquin, M., & Watson, R. J. (2003) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-003-3037-4 · Cited by 102 · see citing works

A chromatin-mediated mechanism for specification of conditional transcription factor targets

Buck, M. J., & Lieb, J. D. (2006) · Nature Genetics · doi:10.1038/ng1917 · Cited by 96 · see citing works

Mechanisms by which transcription factors gain access to target sequence elements in chromatin

Guertin, M. J., & Lis, J. (2012) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2012.11.008 · Cited by 84 · see citing works

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics

Simicevic, J., Schmid, A. W., Gilardoni, P. A., Zoller, B., Raghav, S. K., Krier, I., Gubelmann, C., Lisacek, F., Naef, F., Moniatte, M., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2441 · Cited by 83 · see citing works

Global comparative transcriptome analysis of cartilage formation in vivo

Cameron, T. L., Belluoccio, D., Farlie, P. G., Brachvogel, B., & Bateman, J. F. (2009) · BMC Developmental Biology · doi:10.1186/1471-213x-9-20 · Cited by 81 · see citing works

The Forkhead Factor FoxE1 Binds to the Thyroperoxidase Promoter during Thyroid Cell Differentiation and Modifies Compacted Chromatin Structure

Cuesta, I., Zaret, K. S., & Santisteban, P. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00758-07 · Cited by 79 · see citing works

Nuclear Factor 1 Is Required for Both Hormone-Dependent Chromatin Remodeling and Transcriptional Activation of the Mouse Mammary Tumor Virus Promoter

Hebbar, P. B., & Archer, T. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.3.887-898.2003 · Cited by 57 · see citing works

Activating transcription factor 4 regulates adipocyte differentiation via altering the coordinate expression of CCATT /enhancer binding protein β and peroxisome proliferator‐activated receptor γ

Yu, K., Mo, D., Wu, M., Chen, H., Chen, L., Li, M., & Chen, Y. (2014) · FEBS Journal · doi:10.1111/febs.12792 · Cited by 52 · see citing works

Negative Regulation of Chondrocyte Differentiation by Transcription Factor AP-2α

Huang, Z., Xu, H., & Sandell, L. J. (2004) · Journal of Bone and Mineral Research · doi:10.1359/jbmr.2004.19.2.245 · Cited by 51 · see citing works

Transcription factor Snail is a novel regulator of adipocyte differentiation via inhibiting the expression of peroxisome proliferator-activated receptor γ

Lee, Y., Kim, S. H., Lee, Y. J., Kang, E. S., Lee, B., Soo, B., Kim, J. W., Song, D. H., & Lee, H. C. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1363-8 · Cited by 50 · see citing works

Mechanisms of FOXC2- and FOXD1-mediated Regulation of the RIα Subunit of cAMP-dependent Protein Kinase Include Release of Transcriptional Repression and Activation by Protein Kinase Bα and cAMP

Dahle, M. K., Grønning, L. M., Cederberg, A., Blomhoff, H. K., Miura, N., Enerbäck, S., Taskén, K. A., & Taskén, K. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200131200 · Cited by 47 · see citing works

Purified Cofactors and Histone H1 Mediate Transcriptional Regulation by CTF/NF-I

Dusserre, Y., & Mermod, N. (1992) · Molecular and Cellular Biology · doi:10.1128/mcb.12.11.5228 · Cited by 46 · see citing works

Purified cofactors and histone H1 mediate transcriptional regulation by CTF/NF-I

Dusserre, Y., & Mermod, N. (1992) · Molecular and Cellular Biology · doi:10.1128/mcb.12.11.5228-5237.1992 · Cited by 43

Chromatin Domain Boundaries Delimited by a Histone-binding Protein in Yeast

Ferrari, S., Simmen, K. C., Dusserre, Y., Müller, K., Fourel, G., Gilson, É., & Mermod, N. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m410346200 · Cited by 32 · see citing works

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Isakova, A., Berset, Y., Vassily Hatzimanikatis, A., & Deplancke, B. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.691154 · Cited by 20 · see citing works

Integrating regulatory information via combinatorial control of the transcription cyclePreprint

Scholes, C., DePace, A. H., & Sánchez, Á. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/039339 · Cited by 3 · see citing works

Determinants of enhancer and promoter activities of regulatory elements

Andersson, R., & Sandelin, A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0173-8 · Cited by 713 · 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

Towards a comprehensive catalogue of validated and target-linked human enhancers

Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works

Transcription factors: Bridge between cell signaling and gene regulation

Weidemüller, P., Kholmatov, M. M., Petsalaki, E., & Zaugg, J. B. (2021) · PROTEOMICS · doi:10.1002/pmic.202000034 · Cited by 282 · see citing works

DeepSTARR predicts enhancer activity from DNA sequence and enables the <i>de novo</i> design of enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2021) · doi:10.1101/2021.10.05.463203 · Cited by 284

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2022) · Nature Genetics · doi:10.1038/s41588-022-01048-5 · Cited by 283 · 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

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activationPreprint

Catarino, R. R., & Stark, A. (2018) · Genes & Development · doi:10.1101/gad.310367.117 · Cited by 205 · see citing works

Sequence determinants of human gene regulatory elements

Sahu, B., Hartonen, T., Pihlajamaa, P., Wei, B., Dave, K., Zhu, F., Kaasinen, E., Lidschreiber, K., Lidschreiber, M., Daub, C. O., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-01009-4 · Cited by 198 · see citing works

Generating specificity in genome regulation through transcription factor sensitivity to chromatin

Isbel, L., Grand, R. S., & Schübeler, D. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00512-6 · Cited by 149 · see citing works

Enhancer grammar in development, evolution, and disease: dependencies and interplay

Jindal, G. A., & Farley, E. K. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.02.016 · Cited by 147 · see citing works

Chromatin accessibility: methods, mechanisms, and biological insights

Mansisidor, A., & Risca, V. I. (2022) · Nucleus · doi:10.1080/19491034.2022.2143106 · Cited by 150 · 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

A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation

Rabani, M., Pieper, L. M., Chew, G.-L., & Schier, A. F. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.014 · Cited by 125 · see citing works

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

Inoue, F., Kreimer, A., Ashuach, T., Ahituv, N., & Yosef, N. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.09.010 · Cited by 107 · see citing works

NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program

Hiraike, Y., Waki, H., Yu, J., Nakamura, M., Miyake, K., Nagano, G., Nakaki, R., Ken, S., Kobayashi, H., Yamamoto, S., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3590 · Cited by 102 · see citing works

Transcription factor binding site orientation and order are major drivers of gene regulatory activity

Georgakopoulos-Soares, I., Deng, C., Agarwal, V., Chan, C. S. Y., Zhao, J., Inoue, F., & Ahituv, N. (2023) · Nature Communications · doi:10.1038/s41467-023-37960-5 · Cited by 82 · see citing works

The Cancer Epigenome: Exploiting Its Vulnerabilities for Immunotherapy

Yau, H. L., Ettayebi, I., & Carvalho, D. D. D. (2018) · Trends in Cell Biology · doi:10.1016/j.tcb.2018.07.006 · Cited by 98 · see citing works

Molecular and Cellular Insights into the Development of Uterine Fibroids

Machado-Lopez, A., Simón, C., & Mas, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22168483 · Cited by 100 · 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

Positional specificity of different transcription factor classes within enhancers

Grossman, S. R., Engreitz, J., Ray, J. P., Nguyen, T. H., Hacohen, N., & Lander, E. S. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1804663115 · Cited by 88 · see citing works

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

de Almeida, B. P., Schaub, C., Pagani, M., Secchia, S., Furlong, E. E. M., & Stark, A. (2024) · Nature · doi:10.1038/s41586-023-06905-9 · Cited by 87 · see citing works

A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity

Maricque, B. B., Chaudhari, H. G., & Cohen, B. A. (2019) · Nature Biotechnology · doi:10.1038/nbt.4285 · Cited by 83 · see citing works

The Role of Peroxisome Proliferator-Activated Receptor Gamma (PPARG) in Adipogenesis: Applying Knowledge from the Fish Aquaculture Industry to Biomedical Research

Wafer, R., Tandon, P., & Minchin, J. (2017) · Frontiers in Endocrinology · doi:10.3389/fendo.2017.00102 · Cited by 72 · see citing works

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells

King, D., Hong, C. K., Shepherdson, J. L., Granas, D. M., Maricque, B. B., & Cohen, B. A. (2020) · eLife · doi:10.7554/elife.41279 · Cited by 76 · see citing works

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications

Backenroth, D., He, Z., Kiryluk, K., Boeva, V., Petukhova, L., Khurana, E., Christiano, A. M., Buxbaum, J. D., & Ionita‐Laza, I. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.03.026 · Cited by 73 · see citing works

A transcription factor collective defines the HSN serotonergic neuron regulatory landscape

Lloret-Fernández, C., Maicas, M., Mora-Martínez, C., Artacho, A., Jimeno-Martín, Á., Chirivella, L., Weinberg, P., & Flames, N. (2018) · eLife · doi:10.7554/elife.32785 · Cited by 67 · see citing works

Challenges of Translating Gene Regulatory Information into Agronomic Improvements

Springer, N. M., de León, N., & Erich Grotewold, A. (2019) · Trends in Plant Science · doi:10.1016/j.tplants.2019.07.004 · Cited by 67 · see citing works

Mechanisms governing target search and binding dynamics of hypoxia-inducible factors

Chen, Y., Cattoglio, C., Dailey, G. M., Zhu, Q., Tjian, R., & Darzacq, X. (2022) · eLife · doi:10.7554/elife.75064 · Cited by 60 · see citing works

Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems

Yu, T. C., Liu, W. L., Brinck, M. S., Davis, J. E., Shek, J., Bower, G., Einav, T., Insigne, K. D., Phillips, R., Kosuri, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20094-3 · Cited by 59 · see citing works

Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs

Qiu, Y., & Köhler, C. (2020) · Biochemical Society Transactions · doi:10.1042/bst20190937 · Cited by 55 · see citing works

A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cellsPreprint

Singh, G., Mullany, S., Moorthy, S. D., Zhang, R., Mehdi, T., Tian, R., Duncan, A. G., Moses, A. M., & Mitchell, J. A. (2021) · Genome Research · doi:10.1101/gr.272468.120 · Cited by 51 · see citing works

Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas

Moyo, M., Parker, J. B., & Chakravarti, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14701-6 · Cited by 51 · see citing works

Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4

Hoeksema, M. A., Shen, Z., Holtman, I. R., Zheng, A., Spann, N. J., Cobo, I., Gymrek, M., & Glass, C. K. (2021) · Science Advances · doi:10.1126/sciadv.abf9808 · Cited by 50 · 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

Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance

Caratti, G., Stifel, U., Caratti, B., Jamil, A. J. M., Chung, K., Kiehntopf, M., Gräler, M. H., Blüher, M., Rauch, A., & Tuckermann, J. P. (2023) · Nature Communications · doi:10.1038/s41467-023-37831-z · Cited by 51 · see citing works

Rewriting regulatory DNA to dissect and reprogram gene expression

Martyn, G. E., Montgomery, M. T., Jones, H., Guo, K., Doughty, B. R., Linder, J., Bisht, D., Xia, F., Cai, X. S., Chen, Z., et al. (2023) · Cell · doi:10.1016/j.cell.2025.03.034 · Cited by 52 · see citing works

Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation

Kreimer, A., Ashuach, T., Inoue, F., Khodaverdian, A., Deng, C., Yosef, N., & Ahituv, N. (2022) · Nature Communications · doi:10.1038/s41467-022-28659-0 · Cited by 43 · see citing works

Designing Eukaryotic Gene Expression Regulation Using Machine Learning

de Jongh, R. P. H., van Dijk, A. D. J., Julsing, M. K., Schaap, P. J., & de Ridder, D. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.07.007 · Cited by 46 · 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

A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivoPreprint

Hughes, A. E. O., Myers, C. A., & Corbo, J. C. (2018) · Genome Research · doi:10.1101/gr.231886.117 · Cited by 45 · see citing works

A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons

Mikl, M., Eletto, D., Nijim, M., Lee, M., Lafzi, A., Mhamedi, F., David, O., Sain, S. B., Handler, K., & Moor, A. E. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac806 · Cited by 44 · see citing works

Learning the Regulatory Code of Gene Expression

Zrimec, J., Buric, F., Kokina, M., García, V., & Zelezniak, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.673363 · Cited by 43 · see citing works

Functional dissection of complex trait variants at single-nucleotide resolution

Siraj, L., Castro, R. I., Dewey, H. B., Kales, S., Butts, J. C., Nguyen, T. T. L., Kanai, M., Berenzy, D., Mouri, K., Wang, Q. S., et al. (2026) · Nature · doi:10.1038/s41586-026-10121-6 · Cited by 51 · 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

Adaptive Landscapes in the Age of Synthetic Biology

Yi, X., & Dean, A. M. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz004 · Cited by 38 · see citing works

Local sequence features that influence AP-1 cis-regulatory activityPreprint

Chaudhari, H. G., & Cohen, B. A. (2018) · Genome Research · doi:10.1101/gr.226530.117 · Cited by 36 · see citing works

Structure and function of an ectopic Polycomb chromatin domain

De, S., Cheng, Y., Sun, M.-A., Gehred, N., & Kassis, J. A. (2019) · Science Advances · doi:10.1126/sciadv.aau9739 · Cited by 34 · 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

Silencing an insulin-induced lncRNA, LncASIR, impairs the transcriptional response to insulin signalling in adipocytes

Degirmenci, U., Li, J., Lim, Y. C., Siang, D. T. C., Lin, S., Liang, H., & Sun, L. (2019) · Scientific Reports · doi:10.1038/s41598-019-42162-5 · Cited by 32 · see citing works

PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids

Jourdon, A., Scuderi, S., Capauto, D., Abyzov, A. S., & Vaccarino, F. M. (2020) · Neuropsychopharmacology · doi:10.1038/s41386-020-0763-3 · Cited by 29 · see citing works

A structural mechanism of nuclear receptor biased agonism

Nemetchek, M. D., Chrisman, I. M., Rayl, M. L., Voss, A. H., & Hughes, T. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215333119 · Cited by 36 · see citing works

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

Schöne, S., Bothe, M., Einfeldt, E., Borschiwer, M., Benner, P., Vingron, M., Thomas‐Chollier, M., & Meijsing, S. H. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007793 · Cited by 27 · see citing works

CRUP: a comprehensive framework to predict condition-specific regulatory units

Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., Schöpflin, R., Li, N., Kinkley, S., Römer-Hillmann, A., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1860-7 · Cited by 27 · see citing works

High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection

Vangala, P., Murphy, R., Quinodoz, S. A., Gellatly, K. J., McDonel, P. E., Guttman, M., & Garber, M. G. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.09.005 · Cited by 29 · see citing works

Information content differentiates enhancers from silencers in mouse photoreceptors

Friedman, R. Z., Granas, D. M., Myers, C. A., Corbo, J. C., Cohen, B. A., & White, M. A. (2021) · eLife · doi:10.7554/elife.67403 · Cited by 28 · see citing works

An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency

Guo, W.-L., & Huang, D.-S. (2017) · Molecular BioSystems · doi:10.1039/c7mb00155j · Cited by 27 · see citing works

Manganese alters expression of proteins involved in the oxidative stress of Meyerozyma guilliermondii

Ruas, F. A. D., Barboza, N. R., Castro‐Borges, W., & Guerra‐Sá, R. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.11.001 · Cited by 27 · see citing works

Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements

Zheng, Y., & VanDusen, N. J. (2023) · Journal of Cardiovascular Development and Disease · doi:10.3390/jcdd10040144 · Cited by 25 · see citing works

Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs

Cardiello, J. F., Sanchez, G. J., Allen, M. A., & Dowell, R. D. (2019) · Transcription · doi:10.1080/21541264.2019.1704128 · Cited by 24 · see citing works

Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs

Shen, Z., Li, R. Z., Prohaska, T. A., Hoeksema, M. A., Spann, N. J., Tao, J., Fonseca, G. J., Le, T., Stolze, L. K., Sakai, M., et al. (2022) · eLife · doi:10.7554/elife.70878 · Cited by 25 · see citing works

Using synthetic biology to study gene regulatory evolution

Crocker, J., & Ilsley, G. R. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.09.001 · Cited by 23 · see citing works

Chromatin reprogramming in breast cancer

Swinstead, E. E., Paakinaho, V., & Hager, G. L. (2018) · Endocrine Related Cancer · doi:10.1530/erc-18-0033 · Cited by 23 · see citing works

Meta‐analysis of massively parallel reporter assays enables prediction of regulatory function across cell types

Kreimer, A., Yan, Z., Ahituv, N., & Yosef, N. (2019) · Human Mutation · doi:10.1002/humu.23820 · Cited by 23 · see citing works

Clock-controlled rhythmic transcription: is the clock enough and how does it work?

Beytebiere, J. R., Greenwell, B. J., Sahasrabudhe, A., & Menet, J. S. (2019) · Transcription · doi:10.1080/21541264.2019.1673636 · Cited by 23 · see citing works

Multi-omics approaches in plant biology: decoding agronomic traits for sustainable agriculture

Younas, M. U., Zuo, S., Qasim, M., Ahmad, I., Feng, Z., Korai, S. K., Zulfiqar, U., Tukhtaboeva, F., Ibrokhim, I., & Malik, T. (2025) · Plant Stress · doi:10.1016/j.stress.2025.101118 · Cited by 25 · see citing works

Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals

Alizada, A., Khyzha, N., Wang, L., Antounians, L., Chen, X., Khor, M., Liang, M., Rathnakumar, K., Weirauch, M. T., Medina-Rivera, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20765-1 · Cited by 24 · see citing works

Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid

Lewis, E. M. A., Kaushik, K., Sandoval, L. A., Antony, I., Dietmann, S., & Kroll, K. L. (2021) · Neurochemistry International · doi:10.1016/j.neuint.2021.105039 · Cited by 22 · see citing works

Transcriptional regulation of neuronal identity

Sousa, E., & Flames, N. (2021) · European Journal of Neuroscience · doi:10.1111/ejn.15551 · Cited by 19 · see citing works

Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

Bakoulis, S., Krautz, R., Alcaraz, N., Salvatore, M., & Andersson, R. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac088 · Cited by 21 · see citing works

Characterization of sequence determinants of enhancer function using natural genetic variation

Yang, M. G., Ling, E., Cowley, C. J., Greenberg, M. E., & Vierbuchen, T. (2022) · eLife · doi:10.7554/elife.76500 · Cited by 21 · see citing works

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assayPreprint

Hammelman, J., Krismer, K., Banerjee, B., Gifford, D. K., & Sherwood, R. I. (2020) · Genome Research · doi:10.1101/gr.263228.120 · Cited by 21 · see citing works

Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis

Catta-Preta, R., Lindtner, S., Ypsilanti, A. R., Seban, N., Price, J. D., Abnousi, A., Su-Feher, L., Wang, Y.-R., Cichewicz, K., Boerma, S. A., et al. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.10.004 · Cited by 12 · see citing works

PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants

(2024) · doi:10.1093/bib/bbae324 · Cited by 19 · see citing works

Active learning of enhancers and silencers in the developing neural retina

Friedman, R. Z., Ramu, A., Lichtarge, S., Wu, Y., Tripp, L., Lyon, D., Myers, C. A., Granas, D. M., Gause, M., Corbo, J. C., et al. (2025) · Cell Systems · doi:10.1016/j.cels.2024.12.004 · Cited by 17 · see citing works

Creating New β-Globin-Expressing Lentiviral Vectors by High-Resolution Mapping of Locus Control Region Enhancer Sequences

Morgan, R., Ma, F.-Y., Unti, M. J., Brown, D., Ayoub, P., Tam, C., Lathrop, L. E., Aleshe, B., Kurita, R., Nakamura, Y., et al. (2020) · Molecular Therapy: Methods & Clinical Development · doi:10.1016/j.omtm.2020.04.006 · Cited by 14 · see citing works

MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function

Shen, Z., Hoeksema, M. A., Ouyang, Z., Benner, C. W., & Glass, C. K. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa476 · Cited by 16 · see citing works

Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiationPreprint

He, A. Y., & Danko, C. G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.13.583868 · Cited by 20 · see citing works

Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data

Cain, B., Webb, J. A., Yuan, Z., Cheung, D., Lim, H., Kovall, R. A., Weirauch, M. T., & Gebelein, B. A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad318 · Cited by 15 · see citing works

Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning

Li, Y., Schwalie, P. C., Bast‐Habersbrunner, A., Mocek, S., Russeil, J., Fromme, T., Deplancke, B., & Klingenspor, M. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.053 · 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

Organizing combinatorial transcription factor recruitment atcis-regulatory modules

Dubois‐Chevalier, J., Mazrooei, P., Lupien, M., Staels, B., Lefèbvre, P., & Eeckhoute, J. (2017) · Transcription · doi:10.1080/21541264.2017.1394424 · Cited by 16 · see citing works

Widespread Epigenetic Changes to the Enhancer Landscape of Mouse Liver Induced by a Specific Xenobiotic Agonist Ligand of the Nuclear Receptor CAR

Rampersaud, A., Lodato, N. J., Shin, A., & Waxman, D. J. (2019) · Toxicological Sciences · doi:10.1093/toxsci/kfz148 · Cited by 15 · see citing works

Transcription factor interactions explain the context-dependent activity of CRX binding sites

Loell, K., Friedman, R. Z., Myers, C. A., Corbo, J. C., Cohen, B. A., & White, M. A. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011802 · Cited by 14 · see citing works

A long-range flexible billboard model of gene activation

Vockley, C. M., McDowell, I. C., D'Ippolito, A. M., & Reddy, T. E. (2017) · Transcription · doi:10.1080/21541264.2017.1317694 · Cited by 14 · see citing works

Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15

Zhang, X., Ehrlich, K. C., Yu, F., Hu, X., Meng, X., Deng, H., Shen, H., & Ehrlich, M. (2020) · Epigenetics · doi:10.1080/15592294.2020.1716491 · 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

Unusual Ways to Lose a Y Chromosome and Survive with Changed Autosomes: a Story of Mole Voles Ellobius (Mammalia, Rodentia)

Bakloushinskaya, I., & Matveevsky, S. N. (2018) · OBM Genetics · doi:10.21926/obm.genet.1803023 · Cited by 12 · see citing works

Smart Sustainable Agriculture Using Machine Learning and AI: A Review

Menaga, A., & Vasantha, S. (2022) · Lecture notes in networks and systems · doi:10.1007/978-981-16-7952-0_42 · Cited by 12 · see citing works

Genetic architecture of natural variation of cardiac performance from flies to humans

Saha, S., Spinelli, L., Mondragón, J. A. C., Kervadec, A., Lynott, M. R., Kremmer, L., Röder, L., Krifa, S., Torres, M., Brun, C., et al. (2022) · eLife · doi:10.7554/elife.82459 · Cited by 12 · see citing works

Deregulation of Transcriptional Enhancers in Cancer

Azad, F. M., & Atlasi, Y. (2021) · Cancers · doi:10.3390/cancers13143532 · Cited by 11 · see citing works

Permutational analysis of Saccharomyces cerevisiae regulatory elements

Dhillon, N., Shelansky, R. I., Townshend, B., Jain, M., Boeger, H., Endy, D., & Kamakaka, R. T. (2020) · Synthetic Biology · doi:10.1093/synbio/ysaa007 · Cited by 11 · see citing works

Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences

Kwak, I., Kim, B.-C., Lee, J., Kang, T., Garry, D. J., Zhang, J. J., & Gong, W. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05645-5 · Cited by 10 · see citing works

Mutagenesis Analysis of ABCG2 Gene Promoter of Zebrafish (Danio Rerio)

YUSNI, N. Z. B. M., Lim, L. W. K., & Chung, H. H. (2020) · Trends in Undergraduate Research · doi:10.33736/tur.2501.2020 · Cited by 10 · 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

Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivityPreprint

Jimeno-Martín, Á., Sousa, E., Brocal-Ruiz, R., Daroqui, N., Maicas, M., & Flames, N. (2022) · Genome Research · doi:10.1101/gr.275623.121 · Cited by 10 · see citing works

Biased signaling in drug discovery and precision medicine

Ji, R., & Tao, Y. (2025) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2025.108804 · Cited by 9 · see citing works

Motif-based models accurately predict cell type-specific distal regulatory elements

Cornejo‐Páramo, P., Zhang, X., Louis, L., Li, Z., Yang, Y., Wong, E. S. W., & Wong, E. S. W. (2025) · Nature Communications · doi:10.1038/s41467-025-65362-2 · Cited by 9 · see citing works

Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays

Liu, J., Shively, C. A., & Mitra, R. D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa141 · Cited by 9 · see citing works

Molecular competition can shape enhancer activity in the Drosophila embryo

Waymack, R., Gad, M., & Wunderlich, Z. (2021) · iScience · doi:10.1016/j.isci.2021.103034 · Cited by 6 · see citing works

Sequence determinants of human gene regulatory elements

Sahu, B., Hartonen, T., Pihlajamaa, P., Wei, B., Dave, K., Zhu, F., Kaasinen, E., Lidschreiber, K., Lidschreiber, M., Daub, C. O., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-01009-4 · Cited by 198 · see citing works

Transcription factor–DNA binding: beyond binding site motifs

Inukai, S., Kock, K. H., & Bulyk, M. L. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.02.007 · Cited by 387 · 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

The Functional Consequences of Variation in Transcription Factor Binding

Cusanovich, D. A., Pavlovic, B. J., Pritchard, J. K., & Gilad, Y. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004226 · Cited by 205 · see citing works

Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux

Palstra, R.-J. T. S., & Grosveld, F. G. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00195 · Cited by 50 · see citing works