Rohs, Remo

The role of DNA shape in protein–DNA recognition

Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B. (2009) · Nature

DNA and Nucleic Acid ChemistryDiffusion and Search Dynamics

Cited by 1,096

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

Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences

Genomics and Chromatin DynamicsDiffusion and Search Dynamics

Cited by 537

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

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 209

Quantum annealing versus classical machine learning applied to a simplified computational biology problem

Li, R. Y., Di Felice, R., Rohs, R., & Lidar, D. A. (2018) · npj Quantum Information

Quantum Computing Algorithms and ArchitectureDNA and Biological Computing

Cited by 202

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

Lazarovici, A., Zhou, T., Shafer, A., Dantas Machado, A. C., Riley, T. R., Sandstrom, R., Sabo, P. J., Lu, Y., Rohs, R., Stamatoyannopoulos, J. A., et al. (2013) · Proceedings of the National Academy of Sciences

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 162

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models

Yang, L., Orenstein, Y., Jolma, A., Yin, Y., Taipale, J., Shamir, R., & Rohs, R. (2017) · Molecular Systems Biology

Genomics and Chromatin DynamicsDNA and Nucleic Acid Chemistry

Cited by 126

Evolving insights on how cytosine methylation affects protein-DNA binding

Dantas Machado, A. C., Zhou, T., Rao, S., Goel, P., Rastogi, C., Lazarovici, A., Bussemaker, H. J., & Rohs, R. (2015) · Briefings in Functional Genomics

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 124

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

Deng, Z., Wang, Q., Liu, Z., Zhang, M., Machado, A. C. D., Chiu, T.-P., Feng, C., Zhang, Q., Yu, L., Qi, L., et al. (2015) · Nature Communications

Bacterial Genetics and BiotechnologyProtein Structure and Dynamics

Cited by 117

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

Hancock, S. P., Ghane, T., Cascio, D., Rohs, R., Di Felice, R., & Johnson, R. C. (2013) · Nucleic Acids Research

DNA and Nucleic Acid ChemistryDiffusion and Search Dynamics

Cited by 83

Geometric deep learning of protein–DNA binding specificity

Mitra, R., Li, J., Sagendorf, J. M., Jiang, Y., Cohen, A. S., Chiu, T.-P., Glasscock, C. J., & Rohs, R. (2024) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 75

Structure-Based Drug Design with a Deep Hierarchical Generative Model

Weller, J. A., & Rohs, R. (2024) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 47