| Absence of a simple code: how transcription factors read the genome M Slattery, T Zhou, L Yang, ACD Machado, R Gordân, R Rohs Trends in biochemical sciences 39 (9), 381-399, 2014 | 565 | 2014 |
| 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 | 322 | 2013 |
| 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 110 (16), 6376-6381, 2013 | 200 | 2013 |
| Unraveling determinants of transcription factor binding outside the core binding site M Levo, E Zalckvar, E Sharon, ACD Machado, Y Kalma, ... Genome research 25 (7), 1018-1029, 2015 | 161 | 2015 |
| Evolving insights on how cytosine methylation affects protein–DNA binding AC Dantas Machado, T Zhou, S Rao, P Goel, C Rastogi, A Lazarovici, ... Briefings in functional genomics 14 (1), 61-73, 2015 | 137 | 2015 |
| DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation Y Chen, DL Bates, R Dey, PH Chen, ACD Machado, IA Laird-Offringa, ... Cell reports 2 (5), 1197-1206, 2012 | 119 | 2012 |
| Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator Z Deng, Q Wang, Z Liu, M Zhang, ACD Machado, TP Chiu, C Feng, ... Nature communications 6 (1), 7642, 2015 | 114 | 2015 |
| Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion Y Chen, X Zhang, AC Dantas Machado, Y Ding, Z Chen, PZ Qin, R Rohs, ... Nucleic acids research 41 (17), 8368-8376, 2013 | 83 | 2013 |
| Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen YP Chang, M Xu, ACD Machado, XJ Yu, R Rohs, XS Chen Cell reports 3 (4), 1117-1127, 2013 | 62 | 2013 |
| Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes BJ Russell, SD Brown, N Siguenza, I Mai, AR Saran, A Lingaraju, ... Cell 185 (17), 3263-3277. e15, 2022 | 59 | 2022 |
| Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site J Li, AC Dantas Machado, M Guo, JM Sagendorf, Z Zhou, L Jiang, X Chen, ... Biochemistry 56 (29), 3745-3753, 2017 | 51 | 2017 |
| Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome ACD Machado, SD Brown, A Lingaraju, V Sivaganesh, C Martino, A Chaix, ... Cell reports 40 (1), 2022 | 40 | 2022 |
| Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling X Zhang, A Carolina, D Machado, R Rohs, P Qin Biophysical Journal 106 (2), 694a, 2014 | 31 | 2014 |
| Intermittent hypoxia and hypercapnia alter diurnal rhythms of luminal gut microbiome and metabolome C Allaband, A Lingaraju, C Martino, B Russell, A Tripathi, O Poulsen, ... Msystems 6 (3), 10.1128/msystems. 00116-21, 2021 | 27 | 2021 |
| Opposites attract: shape and electrostatic complementarity in protein-DNA complexes RC Harris, T Mackoy, AC Dantas Machado, D Xu, R Rohs, MO Fenley | 22 | 2012 |
| Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout AC Dantas Machado, BH Cooper, X Lei, R Di Felice, L Chen, R Rohs Nucleic Acids Research 48 (15), 8529-8544, 2020 | 18 | 2020 |
| Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Nat Commun 6: 7642 Z Deng, Q Wang, Z Liu, M Zhang, AC Machado, TP Chiu, C Feng, ... | 15 | 2015 |
| The RNA polymerase α subunit recognizes the DNA shape of the upstream promoter element S Lara-Gonzalez, AC Dantas Machado, S Rao, AA Napoli, J Birktoft, ... Biochemistry 59 (48), 4523-4532, 2020 | 13 | 2020 |
| Proteopedia: 3D visualization and annotation of transcription factor–DNA readout modes ACD Machado, SB Saleebyan, BT Holmes, M Karelina, J Tam, SY Kim, ... Biochemistry and Molecular Biology Education 40 (6), 400-401, 2012 | 11 | 2012 |
| Innovations in biomolecular modeling and simulation R Harris, T Mackoy, A Dantas Machado, D Xu, R Rohs, M Fenley Biomolecular Sciences Series. London, UK: Royal Society of Chemistry …, 2012 | 10 | 2012 |
Remo RohsProfessor and Chair of Quantitative and Computational Biology, University of Southern CaliforniaVerified email at usc.edu
