| The role of DNA shape in protein–DNA recognition R Rohs, SM West, A Sosinsky, P Liu, RS Mann, B Honig Nature 461 (7268), 1248-1253, 2009 | 1208 | 2009 |
| Origins of specificity in protein-DNA recognition R Rohs, X Jin, SM West, R Joshi, B Honig, RS Mann Annual Review of Biochemistry 79, 233-269, 2010 | 1076 | 2010 |
| Absence of a simple code: how transcription factors read the genome M Slattery, T Zhou, L Yang, AC Dantas Machado, R Gordân, R Rohs Trends in Biochemical Sciences 39 (9), 381-399, 2014 | 604 | 2014 |
| Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins M Slattery, T Riley, P Liu, N Abe, P Gomez-Alcala, I Dror, T Zhou, R Rohs, ... Cell 147 (6), 1270-1282, 2011 | 562 | 2011 |
| Functional specificity of a Hox protein mediated by the recognition of minor groove structure R Joshi, JM Passner, R Rohs, R Jain, A Sosinsky, MA Crickmore, V Jacob, ... Cell 131 (3), 530-543, 2007 | 393 | 2007 |
| Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape R Gordân, N Shen, I Dror, T Zhou, J Horton, R Rohs, ML Bulyk Cell Reports 3 (4), 1093-1104, 2013 | 378 | 2013 |
| DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale T Zhou, L Yang, Y Lu, I Dror, AC Dantas Machado, T Ghane, R Di Felice, ... Nucleic Acids Research 41 (W1), W56-W62, 2013 | 341 | 2013 |
| Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations R Rohs, I Bloch, H Sklenar, Z Shakked Nucleic Acids Research 33 (22), 7048-7057, 2005 | 311 | 2005 |
| Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs M Kitayner, H Rozenberg, R Rohs, O Suad, D Rabinovich, B Honig, ... Nature Structural & Molecular Biology 17 (4), 423-429, 2010 | 278 | 2010 |
| Quantitative modeling of transcription factor binding specificities using DNA shape T Zhou, N Shen, L Yang, N Abe, J Horton, RS Mann, HJ Bussemaker, ... Proceedings of the National Academy of Sciences USA 112 (15), 4654-4659, 2015 | 264 | 2015 |
| Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers I Barozzi, M Simonatto, S Bonifacio, L Yang, R Rohs, S Ghisletti, G Natoli Molecular Cell 54 (5), 844-857, 2014 | 249 | 2014 |
| Methylene blue binding to DNA with alternating GC base sequence: a modeling study R Rohs, H Sklenar, R Lavery, B Röder Journal of the American Chemical Society 122 (12), 2860-2866, 2000 | 215 | 2000 |
| Probing DNA shape and methylation state on a genomic scale with DNase I A Lazarovici, T Zhou, A Shafer, AC Dantas Machado, TR Riley, ... Proceedings of the National Academy of Sciences USA 110 (16), 6376-6381, 2013 | 210 | 2013 |
| Deconvolving the recognition of DNA shape from sequence N Abe, I Dror, L Yang, M Slattery, T Zhou, HJ Bussemaker, R Rohs, ... Cell 161 (2), 307-318, 2015 | 206 | 2015 |
| Quantum annealing versus classical machine learning applied to a simplified computational biology problem RY Li, R Di Felice, R Rohs, DA Lidar npj Quantum Information 4 (1), 14, 2018 | 189 | 2018 |
| ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo GE Zentner, S Kasinathan, B Xin, R Rohs, S Henikoff Nature Communications 6, 8733, 2015 | 182 | 2015 |
| A widespread role of the motif environment in transcription factor binding across diverse protein families I Dror, T Golan, C Levy, R Rohs, Y Mandel-Gutfreund Genome Research 25 (9), 1268-1280, 2015 | 171 | 2015 |
| Unraveling determinants of transcription factor binding outside the core binding site M Levo, E Zalckvar, E Sharon, AC Dantas Machado, Y Kalma, ... Genome Research 25 (7), 1018-1029, 2015 | 169 | 2015 |
| DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding TP Chiu, F Comoglio, T Zhou, L Yang, R Paro, R Rohs Bioinformatics 32 (8), 1211-1213, 2016 | 166 | 2016 |
| DNA shape features improve transcription factor binding site predictions in vivo A Mathelier, B Xin, TP Chiu, L Yang, R Rohs, WW Wasserman Cell Systems 3 (3), 278-286, 2016 | 165 | 2016 |
Ana Carolina Dantas MachadoUniversity of California, San DiegoVerified email at alumni.usc.edu
