Absence of a simple code: how transcription factors read the genome

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

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

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422

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

Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982

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

Super-enhancers in the control of cell identity and disease

Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662

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

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

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

Galas, D. J., & Schmitz, A. (1978) · Nucleic Acids Research · doi:10.1093/nar/5.9.3157 · Cited by 2,109

A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system

Garner, M. M., & Revzin, A. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.13.3047 · Cited by 2,021

Integrative analysis of super enhancer SNPs for type 2 diabetes

Sun, W., Yao, S., Tang, J.-L., Liu, S., Chen, J., Deng, D., & Zeng, C. (2018) · PLoS ONE · doi:10.1371/journal.pone.0192105 · Cited by 24

Enhancement of LacI binding in vivo

Du, M., Kodner, S., & Bai, L. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz698 · Cited by 22

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data

Cao, Y., Kitanovski, S., & Hoffmann, D. E. (2020) · BMC Genomics · doi:10.1186/s12864-020-07205-6 · Cited by 23

Towards a better understanding of TF-DNA binding prediction from genomic features

Wang, Z., Gong, M., Liu, Y., Xiong, S., Wang, M., Zhou, J., & Zhang, Y. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105993 · Cited by 24

Coactivator condensation drives cardiovascular cell lineage specification

Gan, P., Eppert, M., Cruz, N. D. L., Lyons, H., Shah, A. M., Veettil, R. T., Chen, K., Pradhan, P., Bezprozvannaya, S., Xu, L., et al. (2024) · Science Advances · doi:10.1126/sciadv.adk7160 · Cited by 25

Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED

Hadžić, T., Park, D., Abruzzi, K. C., Yang, L., Trigg, J. S., Rohs, R., Rosbash, M., & Taghert, P. H. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1377 · Cited by 24

Integrative functional analysis of super enhancer SNPs for coronary artery disease

Gong, J., Qiu, C., Huang, D., Zhang, Y., Yu, S., & Zeng, C. (2018) · Journal of Human Genetics · doi:10.1038/s10038-018-0422-2 · Cited by 24

Characterization of Human Dosage-Sensitive Transcription Factor Genes

Ni, Z., Zhou, X., Aslam, S., & Niu, D. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.01208 · Cited by 23

Learning and interpreting the gene regulatory grammar in a deep learning framework

Chen, L., & Capra, J. A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008334 · Cited by 25

Coming to terms with chromatin structure

Even‐Faitelson, L., Hassan‐Zadeh, V., Baghestani, Z., & Bazett‐Jones, D. P. (2015) · Chromosoma · doi:10.1007/s00412-015-0534-9 · Cited by 24

Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout

Machado, A. C. D., Cooper, B. H., Lei, X., Felice, R. D., Chen, L., & Rohs, R. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa642 · Cited by 24

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework

Maeso, I., & Tena, J. J. (2015) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2015.12.003 · Cited by 25

Symmetry in Nucleic-Acid Double Helices

Heinemann, U., & Roske, Y. (2020) · Symmetry · doi:10.3390/sym12050737 · Cited by 22

Genes Bound by ΔFosB in Different Conditions With Recurrent Seizures Regulate Similar Neuronal Functions

Stephens, G. S., Fu, C.-H., Romain, C. P. S., Zheng, Y., Botterill, J. J., Scharfman, H. E., Liu, Y., & Chin, J. (2020) · Frontiers in Neuroscience · doi:10.3389/fnins.2020.00472 · Cited by 22

Prediction of mammalian tissue-specific CLOCK–BMAL1 binding to E-box DNA motifs

Marri, D., Filipovic, D., Kana, O. Z., Tischkau, S. A., & Bhattacharya, S. (2023) · Scientific Reports · doi:10.1038/s41598-023-34115-w · Cited by 24

Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities

Glick, Y., Orenstein, Y., Chen, D., Avrahami, D., Zor, T., Ron Shamir, A., & Gerber, D. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1327 · Cited by 20

Inherent limitations of probabilistic models for protein-DNA binding specificity

Ruan, S., & Stormo, G. D. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005638 · Cited by 22

Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors

Asada, R., Umeda, M., Adachi, A., Senmatsu, S., Abe, T., Iwasaki, H., Ohta, K., Hoffman, C. S., & Hirota, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx555 · Cited by 22

Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase

Dey, P., & Bhattacherjee, A. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b07342 · Cited by 22

OutPredict: multiple datasets can improve prediction of expression and inference of causality

Cirrone, J., Brooks, M. D., Bonneau, R., Coruzzi, G. M., & Shasha, D. E. (2020) · Scientific Reports · doi:10.1038/s41598-020-63347-3 · Cited by 22

Structures and nucleic acid-binding preferences of the eukaryotic ARID domain

Korn, S. M., & Schlundt, A. (2022) · Biological Chemistry · doi:10.1515/hsz-2021-0404 · Cited by 21

Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1

Xu, C., Kleinschmidt, H., Yang, J., Leith, E. M., Johnson, J. K., Tan, S., Mahony, S., & Bai, L. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.06.022 · Cited by 21

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

Rao, S., Machado, A. C. D., Zhou, T., Rastogi, C., Bussemaker, H. J., & Rohs, R. (2015) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1032562 · Cited by 21

Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins

Kemme, C. A., Marquez, R., Luu, R. H., & Iwahara, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx387 · Cited by 21

SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences

Estrada, J., Ruiz-Herrero, T., Scholes, C., Wunderlich, Z., & DePace, A. H. (2016) · PLoS ONE · doi:10.1371/journal.pone.0151740 · Cited by 21

Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors

Rohac, R., Crack, J. C., de Rosny, E., Gigarel, O., Brun, N. E. L., Fontecilla-Camps, J. C., & Volbeda, A. (2022) · Communications Biology · doi:10.1038/s42003-022-03745-7 · Cited by 20

PDIviz: analysis and visualization of protein–DNA binding interfaces

Ribeiro, J., Melo, F., & Schüller, A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv203 · Cited by 20

DNA Sequence Constraints Define Functionally Active Steroid Nuclear Receptor Binding Sites in Chromatin

Coons, L. A., Hewitt, S. C., Burkholder, A., McDonnell, D. P., & Korach, K. S. (2017) · Endocrinology · doi:10.1210/en.2017-00468 · Cited by 20

Tox4 modulates cell fate reprogramming

Vanheer, L., Song, J., Geest, N. D., Janiszewski, A., Talón, I., Provenzano, C., Oh, T., Chappell, J., & Pasque, V. (2019) · Journal of Cell Science · doi:10.1242/jcs.232223 · Cited by 20

Chromatin-dependent motif syntax defines differentiation trajectories

Durdu, S., Iskar, M., Isbel, L., Hoerner, L., Wirbelauer, C., Burger, L., Heß, D., Iešmantavičius, V., & Schübeler, D. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.07.005 · Cited by 19

DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences

Yao, Z., Zhang, W., Song, P., Hu, Y., & Liu, J. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad095 · Cited by 19

Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics

Burgess, D. G., Xu, J., & Freeling, M. (2015) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2015.07.001 · Cited by 19

Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding

Kurafeiski, J. D., Pinto, P., & Bornberg‐Bauer, E. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy269 · Cited by 21

Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals

Berger, M. J., Wenger, A. M., Guturu, H., & Bejerano, G. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky741 · Cited by 16

Short tandem repeats bind transcription factors to tune eukaryotic gene expressionPreprint

Horton, C. A., Alexandari, A. M., Hayes, M. G. B., Marklund, E., Schaepe, J. M., Aditham, A. K., Shah, N., Shrikumar, A., Afek, A., Greenleaf, W. J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.24.493321 · Cited by 20

The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout

Chen, X., Tsai, M., & Wolynes, P. G. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.1c11911 · Cited by 18

Regulatory insight for a Zn2Cys6 transcription factor controlling effector-mediated virulence in a fungal pathogen of wheat

John, E., Verdonk, C. J., Singh, K. B., Oliver, R. P., Lenzo, L., Morikawa, S., Soyer, J. L., Muria‐Gonzalez, M. J., Soo, D., Mousley, C. J., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012536 · Cited by 16

Modeling protein–DNA binding via high-throughput in vitro technologies

Orenstein, Y., & Ron Shamir, A. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw030 · Cited by 19

An efficient algorithm for improving structure-based prediction of transcription factor binding sites

Farrel, A., & Guo, J. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1755-0 · Cited by 19

Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection

Wang, X., Zhou, T., Wunderlich, Z., Maurano, M. T., DePace, A. H., Nuzhdin, S. V., & Rohs, R. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy099 · Cited by 18

Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components

Padroni, G., Withers, J. M., Taladriz‐Sender, A., Reichenbach, L. F., Parkinson, J. A., & Burley, G. A. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b12444 · Cited by 18

Porphyromonas gingivalis PgFur Is a Member of a Novel Fur Subfamily With Non-canonical Function

Śmiga, M., Bielecki, M., Olczak, M., & Olczak, T. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00233 · Cited by 18

SIX1 cooperates with RUNX1 and SMAD4 in cell fate commitment of Müllerian duct epithelium

Terakawa, J., Serna, V. A., Nair, D. M., Sato, S., Kawakami, K., Radovick, S., Maire, P., & Kurita, T. (2020) · Cell Death and Differentiation · doi:10.1038/s41418-020-0579-z · Cited by 19

The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element

Lara‐González, S., Machado, A. C. D., Rao, S., Napoli, A., Birktoft, J. J., Felice, R. D., Rohs, R., & Lawson, C. L. (2020) · Biochemistry · doi:10.1021/acs.biochem.0c00571 · Cited by 18

Kinetic origin of nucleosome invasion by pioneer transcription factors

Mondal, A. K., Mishra, S. K., & Bhattacherjee, A. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.10.039 · Cited by 16

Unstructured transcription factor interactions enable emergent specificity

Abidi, A. A., Cattoglio, C., Tang, N. N., Fan, V. B., Dailey, G. M., Hay, A. D., Kunamaneni, P., Milkie, D. E., Darzacq, X., Betzig, E., et al. (2026) · Science · doi:10.1126/science.aeb6487 · Cited by 21

Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation

Tsai, M., Zheng, W., Chen, M., & Wolynes, P. G. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b08287 · Cited by 17

Transcriptional reprogramming by oxidative stress occurs within a predefined chromatin accessibility landscape

Levings, D. C., Lacher, S. E., Palacios‐Moreno, J. M., & Slattery, M. G. (2021) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2021.05.016 · Cited by 20

Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state

Leviyang, S. (2021) · Cytokine X · doi:10.1016/j.cytox.2021.100056 · Cited by 17

Quantitative modeling of gene expression using DNA shape features of binding sites

Peng, P.-C., & Sinha, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw446 · Cited by 17

Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

Ehsani, R., Bahrami, S., & Drabløs, F. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1349-2 · Cited by 18

The Role of Chromatin Accessibility in cis-Regulatory Evolution

Peng, P.-C., Khoueiry, P., Girardot, C., Reddington, J. P., Garfield, D. A., Furlong, E. E. M., & Sinha, S. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz103 · Cited by 19

Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways

Hastings, R., Aditham, A. K., DelRosso, N. V., Suzuki, P., & Fordyce, P. M. (2025) · Nature Communications · doi:10.1038/s41467-024-55672-2 · Cited by 17

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

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

A combination of transcription factors mediates inducible interchromosomal contacts

Kim, S., Dunham, M. J., & Shendure, J. (2019) · eLife · doi:10.7554/elife.42499 · Cited by 15

Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems

Partridge, E. C., Watkins, T. A., & Mendenhall, E. M. (2016) · BioEssays · doi:10.1002/bies.201600028 · Cited by 15

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

Transcriptional Regulation as a Dose‐dependent Process: Insights From Transcription Factor Tuning

Noviello, G. (2025) · Open Biology · doi:10.1098/rsob.240328 · Cited by 13

Noncanonical binding of transcription factors: time to revisit specificity?

Samee, M. A. H. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-08-0325 · Cited by 15

DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

Bonnell, V. A., Zhang, Y., Brown, A. S., Horton, J., Josling, G. A., Chiu, T.-P., Rohs, R., Mahony, S., Gordân, R., & Llinás, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae585 · Cited by 19

Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1

Desjardins, G., Okon, M., Graves, B. J., & McIntosh, L. P. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00460 · Cited by 15

Proximity of Radiation Desiccation Response Motif to the core promoter is essential for basal repression as well as gamma radiation-induced gyrB gene expression in Deinococcus radiodurans

Anaganti, N., Basu, B., Mukhopadhyaya, R., & Apte, S. K. (2017) · Gene · doi:10.1016/j.gene.2017.03.002 · Cited by 15

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

Chen, Y.-T., Yang, H., & Chu, J. (2020) · Chemical Science · doi:10.1039/d0sc00480d · Cited by 15

Site-Specific Acetylation of the Transcription Factor Protein Max Modulates Its DNA Binding Activity

Nithun, R. V., Yao, Y. M., Harel, O., Habiballah, S., Afek, A., & Jbara, M. (2024) · ACS Central Science · doi:10.1021/acscentsci.4c00686 · Cited by 14

cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers

Nocente, M. C., Karamitsos, A. M., Drouineau, E., Soleil, M., Albawardi, W., Dulary, C., Ribiérre, F., Picaud, H., Alibert, O., Acker, J., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01344-0 · Cited by 18

Perspective on recent developments and challenges in regulatory and systems genomics

Zeitlinger, J., Roy, S., Ay, F., Mathelier, A., Medina-Rivera, A., Mahony, S., Sinha, S. K., & Ernst, J. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf106 · Cited by 18

DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq

Käppel, S., Eggeling, R., Rümpler, F., Groth, M., Melzer, R., & Theißen, G. (2021) · Plant Molecular Biology · doi:10.1007/s11103-020-01108-6 · Cited by 14

Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades

Ochab-Marcinek, A., Jȩdrak, J., & Tabaka, M. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp00743d · Cited by 14

Genomic and molecular control of cell type and cell type conversions

Fu, X., He, F., Li, Y., Shahveranov, A., & Hutchins, A. P. (2017) · Cell Regeneration · doi:10.1016/j.cr.2017.09.001 · Cited by 14

Thermodynamic and first-principles biomolecular simulations applied to synthetic biology: promoter and aptamer designs

Presnell, K. V., & Alper, H. S. (2017) · Molecular Systems Design & Engineering · doi:10.1039/c7me00083a · Cited by 15

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Gabitto, M. I., Rasmussen, A. W., Wapinski, O. L., Allaway, K. C., Carriero, N. J., Fishell, G., & Bonneau, R. (2020) · Nature Communications · doi:10.1038/s41467-020-14497-5 · Cited by 13

Structural insights into G-quadruplex binding by metal complexes: implications for drug design

Otoya, T. D. P., McQuaid, K. T., & Cardin, C. J. (2024) · Medicinal Chemistry Research · doi:10.1007/s00044-024-03309-w · Cited by 16

New insights in the clockwork mechanism regulating lineage specification: Lessons from the Drosophila nervous system

Cattenoz, P. B., & Giangrande, A. (2014) · Developmental Dynamics · doi:10.1002/dvdy.24228 · Cited by 13

Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites

Völkel, S., Stielow, B., Finkernagel, F., Berger, D., Stiewe, T., Nist, A., & Suske, G. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005341 · Cited by 13

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

Faltejsková, K., Jakubec, D., & Vondrášek, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21113986 · Cited by 13

Genome-wide analysis reveals widespread roles for RcREM genes in floral organ development in Rosa chinensis

Liu, J., Wu, S., Sun, J., Sun, J., Wang, H., Cao, X., Lu, J. J., Jalal, A., & Wang, C. (2021) · Genomics · doi:10.1016/j.ygeno.2021.09.017 · Cited by 13

Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

Achari, S. R., Edwards, J., Mann, R. C., Kaur, J. K., Sawbridge, T., & Summerell, B. A. (2021) · BMC Genomics · doi:10.1186/s12864-021-08033-y · Cited by 14

Evolution of a cis -Acting SNP That Controls Type VI Secretion in Vibrio cholerae

Ng, S. L., Kammann, S., Steinbach, G., Hoffmann, T., Yunker, P. J., & Hammer, B. K. (2022) · mBio · doi:10.1128/mbio.00422-22 · Cited by 11

Using GRO-Seq to Measure Circadian Transcription and Discover Circadian Enhancers

Fang, B., Guan, D., & Lazar, M. A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0381-9_10 · Cited by 12

What Cyto- and Histochemistry Can Do to Crack the Sugar Code

Habermann, F. A., Kaltner, H., Higuero, A. M., Caballero, G. G., Ludwig, A., Manning, J. C., Abad‐Rodríguez, J., & Gabius, H. (2021) · ACTA HISTOCHEMICA ET CYTOCHEMICA · doi:10.1267/ahc.21-00017 · Cited by 12

Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX

Huber, E. M., Hortschansky, P., Scheven, M. T., Misslinger, M., Haas, H., Brakhage, A. A., & Groll, M. (2022) · Structure · doi:10.1016/j.str.2022.04.001 · Cited by 11

Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila

González, A., Jafari, S., Zenere, A., Alenius, M., & Altafini, C. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006709 · Cited by 12

The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development

Zraly, C. B., Zakkar, A., Perez, J. H., Ng, J. K., White, K. P., Slattery, M. G., & Dingwall, A. K. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa082 · Cited by 12

Transcription factors—Intricate players of the bone morphogenetic protein signaling pathway

Ampuja, M., & Kallioniemi, A. H. (2017) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22502 · Cited by 11

Biochemical characterization of ferric uptake regulator (Fur) from Aliivibrio salmonicida. Mapping the DNA sequence specificity through binding studies and structural modelling

Berg, K., Pedersen, H. L., & Leiros, I. (2020) · BioMetals · doi:10.1007/s10534-020-00240-6 · Cited by 11

Structural basis of direct and inverted DNA sequence repeat recognition by helix–turn–helix transcription factors

Fernández-López, R., Ruiz, R., del Campo, I., González-Montes, L., Boer, R., de la Cruz, F., & Moncalián, G. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1024 · Cited by 11

Mass Spectrometry for Assessing Protein–Nucleic Acid Interactions

He, X., Chen, X., & Wang, Y. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c04353 · Cited by 12

Transcription factor motif quality assessment requires systematic comparative analysis

Kibet, C. K., & Machanick, P. (2016) · F1000Research · doi:10.12688/f1000research.7408.2 · Cited by 11

Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry

Goldshtein, M., Mellul, M., Deutch, G., Imashimizu, M., Takeuchi, K., Meshorer, E., Ram, O., & Lukatsky, D. B. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.02.009 · Cited by 11

Molecular analysis of mating type loci from the mycophenolic acid producer Penicillium brevicompactum: Phylogeny and MAT protein characterization suggest a cryptic sexual life cycle

Mahmoudjanlou, Y., Dahlmann, T. A., & Kück, U. (2020) · Fungal Biology · doi:10.1016/j.funbio.2020.07.006 · Cited by 11

Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation

Chen, N., Yu, J., Liu, Z., Meng, L., Li, X., & Wong, K. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae210 · Cited by 10

Skipping events impose repeated binding attempts: profound kinetic implications of protein–DNA conformational changes

Rogoulenko, E., & Levy, Y. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae333 · Cited by 10

Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding

Huynh, D., Hoffmeister, P., Friedrich, T., Zhang, K., Bartkuhn, M., Ferrante, F., Giaimo, B. D., Kovall, R. A., Borggrefe, T., Oswald, F., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56515-4 · Cited by 9

Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis

Tsukanov, A. V., Mironova, V., & Levitsky, V. G. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.938545 · Cited by 10

LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior

Stefanakis, N., Jiang, J., Liang, Y., & Shaham, S. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00049-w · Cited by 11

Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway

Gurdziel, K., Vogt, K. R., Schneider, G. K., Richards, N. W., & Gumucio, D. L. (2016) · BMC Developmental Biology · doi:10.1186/s12861-016-0106-0 · Cited by 10

The Evolution of Gene Regulatory Mechanisms in Bacteria

Dorman, C. J., Bhriain, N. N., & Dorman, M. J. (2018) · Grand challenges in biology and biotechnology · doi:10.1007/978-3-319-69078-0_6 · Cited by 11

Transcription factor motif quality assessment requires systematic comparative analysis

Kibet, C. K., & Machanick, P. (2015) · F1000Research · doi:10.12688/f1000research.7408.1 · Cited by 10

FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation

Fischer, P., Chen, H., Pacho, F., Rieder, D., Kimmel, R. A., & Meyer, D. (2019) · BMC Biology · doi:10.1186/s12915-019-0683-z · Cited by 10

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

14 Quantitative modeling of transcription factor binding specificities using DNA shape

Zhou, T., Shen, N., Yang, L., Abe, N., Horton, J., Mann, R. S., Bussemaker, H. J., Gordân, R., & Rohs, R. (2015) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1032554 · Cited by 6

Genetic Variation in Transcription Factor Binding Sites

Santpere, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24055038 · Cited by 5

Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors

Yesudhas, D., Batool, M., Anwar, M. A., Panneerselvam, S., & Choi, S. (2017) · Genes · doi:10.3390/genes8080192 · Cited by 57

Mechanisms of transcription factor selectivity

Pan, Y., Tsai, C., Ma, B., & Nussinov, R. (2010) · Trends in Genetics · doi:10.1016/j.tig.2009.12.003 · Cited by 160