Probing DNA shape and methylation state on a genomic scale with DNase I

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DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

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Non-CG Methylation in the Human Genome

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Quantitative modeling of transcription factor binding specificities using DNA shape

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Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

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Conservation of trans-acting circuitry during mammalian regulatory evolution

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Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

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Chromatin accessibility profiling methods

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Deconvolving the Recognition of DNA Shape from Sequence

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DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

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Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci

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Epigenetic analysis of cell-free DNA by fragmentomic profiling

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Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling

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Non-random DNA fragmentation in next-generation sequencing

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Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

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DNA methylation: Precise modulation of chromatin structure and dynamics

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Evolving insights on how cytosine methylation affects protein-DNA binding

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TFBSshape: a motif database for DNA shape features of transcription factor binding sites

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Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants

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Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

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The physics of epigenetics

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Genomic methods in profiling DNA accessibility and factor localization

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Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

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Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors

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Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

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Genomic footprinting

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MPE-seq, a new method for the genome-wide analysis of chromatin structure

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High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

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Links between DNA methylation and nucleosome occupancy in the human genome

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Structural features of DNA that determine RNA polymerase II core promoter

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Genome-wide footprinting: ready for prime time?

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Sequencing Overview of Ewing Sarcoma: A Journey across Genomic, Epigenomic and Transcriptomic Landscapes

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DNA Modification Readers and Writers and Their Interplay

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Anchor: trans-cell type prediction of transcription factor binding sitesPreprint

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Following the tracks: How transcription factor binding dynamics control transcription

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Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

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

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GBshape: a genome browser database for DNA shape annotations

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Zinc Finger Readers of Methylated DNA

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Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters

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DNA methylation cues in nucleosome geometry, stability and unwrapping

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Unimolecular Chemically Modified DNA Fluorescent Probe for One-Step Quantitative Measurement of the Activity of Human Apurinic/Apyrimidinic Endonuclease 1 in Biological Samples

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Covariation between homeodomain transcription factors and the shape of their DNA binding sites

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Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

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Cytosine base modifications regulate DNA duplex stability and metabolism

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Engineering altered protein–DNA recognition specificity

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Sequencing artifacts derived from a library preparation method using enzymatic fragmentation

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CG hypomethylation in Lsh −/− mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity

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Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

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TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites

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Identification of breast cancer associated variants that modulate transcription factor binding

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Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains

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msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding

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Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

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Sensitive surface plasmon resonance detection of methyltransferase activity and screening of its inhibitors amplified by p53 protein bound to methylation-specific ds-DNA consensus sites

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Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming

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High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue

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DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes

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Structural basis of DNA methylation-dependent site selectivity of the Epstein–Barr virus lytic switch protein ZEBRA/Zta/BZLF1

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Enhancer Dysfunction in 3D Genome and Disease

Xia, J., & Wei, G. (2019) · Cells · doi:10.3390/cells8101281 · Cited by 26

Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context

Rudnizky, S., Khamis, H., Malik, O., Squires, A. H., Meller, A., Melamed, P., & Kaplan, A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1252 · Cited by 25

Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes

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A sequence environment modulates the impact of methylation on the torsional rigidity of DNA

Hörberg, J., & Reymer, A. (2018) · Chemical Communications · doi:10.1039/c8cc06550k · Cited by 24

Cys2His2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA

Hodges, A. J., Hudson, N. O., & Buck‐Koehntop, B. A. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.09.012 · Cited by 25

Dynamic enhancer function in the chromatin context

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A practical guide for DNase-seq data analysis: from data management to common applications

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A perspective on the molecular simulation of DNA from structural and functional aspects

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Novel implications of a strictly monomorphic (GCC) repeat in the human PRKACB gene

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Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolutionPreprint

Li, H., & Guan, Y. (2021) · Genome Research · doi:10.1101/gr.269613.120 · Cited by 22

On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions

Madrigal, P. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00144 · Cited by 22

Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification

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22 Evolving insights on how cytosine methylation affects protein-DNA binding

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DNA Structural Correlation in Short and Long Ranges

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Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells

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Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models

Grau, J., Schmidt, F., & Schulz, M. H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad693 · Cited by 21

Information Thermodynamics of Cytosine DNA Methylation

Sánchez, R., & Mackenzie, S. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0150427 · Cited by 19

Network-guided regression for detecting associations between DNA methylation and gene expression

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Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis

Brown, K., Takawira, L. T., Mostert‐O'Neill, M. M., Mizrachi, E., Myburg, A. A., & Hussey, S. G. (2019) · New Phytologist · doi:10.1111/nph.15897 · Cited by 17

Competitive Repression of the artPIQM Operon for Arginine and Ornithine Transport by Arginine Repressor and Leucine-Responsive Regulatory Protein in Escherichia coli

Montaguth, O. E. T., Bervoets, I., Peeters, E., & Charlier, D. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01563 · Cited by 17

“Hit‐and‐run”: Transcription factors get caught in the act

Charoensawan, V., Martinho, C., & Wigge, P. A. (2015) · BioEssays · doi:10.1002/bies.201400186 · Cited by 17

Cis-regulatory elements: systematic identification and horticultural applications

Li, T., Zeng, W., Zhu, F., & Lü, P. (2025) · aBIOTECH · doi:10.1007/s42994-025-00237-0 · Cited by 17

Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity

Werther, R. A., Hallinan, J. P., Lambert, A. R., Havens, K. A., Pogson, M., Jarjour, J., Galizi, R., Windbichler, N., Crisanti, A., Nolan, T., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx544 · Cited by 16

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences

Andrabi, M., Hutchins, A. P., Miranda‐Saavedra, D., Kono, H., Nussinov, R., Mizuguchi, K., & Ahmad, S. (2017) · Scientific Reports · doi:10.1038/s41598-017-03199-6 · Cited by 16

Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts

Nakamura, R., Uno, A., Kumagai, M., Morishita, S., & Takeda, H. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0152-2 · Cited by 14

ZNF382: A transcription inhibitor down-regulated in multiple tumors due to promoter methylation

Chen, S., Xiao, Z. Y., Zhou, J., Yang, M., Feng, S., Huang, Q., Zou, J., Zeng, T., Li, Y., Peng, L., et al. (2019) · Clinica Chimica Acta · doi:10.1016/j.cca.2019.10.021 · Cited by 15

A synergistic DNA logic predicts genome-wide chromatin accessibilityPreprint

Hashimoto, T., Sherwood, R. I., Kang, D. D., Rajagopal, N., Barkal, A. A., Zeng, H., Emons, B. J. M., Srinivasan, S., Jaakkola, T., & Gifford, D. K. (2016) · Genome Research · doi:10.1101/gr.199778.115 · Cited by 15

XL-DNase-seq: improved footprinting of dynamic transcription factors

Oh, K.-S., Ha, J., Baek, S., & Sung, M.-H. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0277-6 · Cited by 11

A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences

Nikolova, E. N., Stanfield, R. L., Dyson, H. J., & Wright, P. E. (2020) · Biochemistry · doi:10.1021/acs.biochem.0c00253 · Cited by 16

Tissue context determines the penetrance of regulatory DNA variation

Halow, J. M., Byron, R., Hogan, M. S., Ordóñez, R., Groudine, M. T., Bender, M. A., Stamatoyannopoulos, J. A., & Maurano, M. T. (2021) · Nature Communications · doi:10.1038/s41467-021-23139-3 · Cited by 15

Survey of protein–DNA interactions in Aspergillus oryzae on a genomic scale

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Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes

Baek, S., & Sung, M. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3578-9_12 · Cited by 20

Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling

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103 Probing DNA shape and methylation state on a genomic scale with DNase I

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Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

Rao, S., Chiu, T.-P., Kribelbauer, J. F., Mann, R. S., Bussemaker, H. J., & Rohs, R. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0174-4 · Cited by 97

MOESM9 of Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on proteinâ DNA binding

Rao, S., Chiu, T.-P., Kribelbauer, J., Mann, R., Bussemaker, H. J., & Rohs, R. (2018) · Figshare · doi:10.6084/m9.figshare.5862939

MOESM10 of Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on proteinâ DNA binding

Rao, S., Chiu, T.-P., Kribelbauer, J., Mann, R., Bussemaker, H. J., & Rohs, R. (2018) · Figshare · doi:10.6084/m9.figshare.5862819

MOESM1 of Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on proteinâ DNA binding

Rao, S., Chiu, T.-P., Kribelbauer, J., Mann, R., Bussemaker, H. J., & Rohs, R. (2018) · Figshare · doi:10.6084/m9.figshare.5862843