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

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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

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

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

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

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

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Comparative Epigenomic Analysis of Murine and Human Adipogenesis

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

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

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

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

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

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Regulation of Neuronal Traits by a Novel Transcriptional Complex

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

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The histone acetylase PCAF is a nuclear receptor coactivatorPreprint

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

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

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Nucleosome-mediated cooperativity between transcription factors

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Synergistic activation and repression of transcription by Drosophila homeobox proteins

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Animal Transcription Networks as Highly Connected, Quantitative Continua

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

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

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Atf4 Regulates Obesity, Glucose Homeostasis, and Energy Expenditure

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Cross-talk between glucocorticoid receptor and AP-1

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

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

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

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

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

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

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

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Homotypic regulatory clusters in Drosophila.Preprint

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

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Integrating Diverse Datasets Improves Developmental Enhancer Prediction

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

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Selective DNA bending by a variety of bZIP proteins.

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Unraveling determinants of transcription factor binding outside the core binding sitePreprint

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Interferon Regulatory Factors Are Transcriptional Regulators of Adipogenesis

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

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

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

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Cell cycle regulation by the B-Myb transcription factor

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

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

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

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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

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

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

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 49

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

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

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 23

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

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

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

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

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 295

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

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

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

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

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 201

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 209

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 55