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Ana Carolina Dantas Machado
Ana Carolina Dantas Machado
University of California, San Diego
Verified email at alumni.usc.edu - Homepage
Title
Cited by
Cited by
Year
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
6022014
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
3372013
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
2072013
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
1692015
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
1502015
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
1232012
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
1222015
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
902013
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
882022
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
672013
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
612022
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
512017
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
352021
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
312014
Gordâ n, R., and Rohs, R.(2014). Absence of a simple code: how transcription factors read the genome
M Slattery, T Zhou, L Yang, AC Dantas Machado
Trends Biochem. Sci 39, 381-399, 0
25
Opposites attract: shape and electrostatic complementarity in protein-DNA complexes
RC Harris, T Mackoy, AC Dantas Machado, D Xu, R Rohs, MO Fenley
222012
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
202020
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, ...
172015
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
162020
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
112012
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