Search Results - "Dantas, Ana Carolina"

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale by Zhou, Tianyin, Yang, Lin, Lu, Yan, Dror, Iris, Dantas Machado, Ana Carolina, Ghane, Tahereh, Di Felice, Rosa, Rohs, Remo

“…We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides…”
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Unraveling determinants of transcription factor binding outside the core binding site by Levo, Michal, Zalckvar, Einat, Sharon, Eilon, Dantas Machado, Ana Carolina, Kalma, Yael, Lotam-Pompan, Maya, Weinberger, Adina, Yakhini, Zohar, Rohs, Remo, Segal, Eran

“…Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the…”
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DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation by Chen, Yongheng, Bates, Darren L., Dey, Raja, Chen, Po-Han, Machado, Ana Carolina Dantas, Laird-Offringa, Ite A., Rohs, Remo, Chen, Lin

“…GATA transcription factors regulate transcription during development and differentiation by recognizing distinct GATA sites with a tandem of two conserved zinc…”
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Probing DNA shape and methylation state on a genomic scale with DNase I by Lazarovici, Allan, Zhou, Tianyin, Shafer, Anthony, Machado, Ana Carolina Dantas, Riley, Todd R., Sandstrom, Richard, Sabo, Peter J., Lu, Yan, Rohs, Remo, Stamatoyannopoulos, John A., Bussemaker, Harmen J.

“…DNA binding proteins find their cognate sequences within genomic DNA through recognition of specific chemical and structural features. Here we demonstrate that…”
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Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site by Li, Jun, Dantas Machado, Ana Carolina, Guo, Ming, Sagendorf, Jared M, Zhou, Zhan, Jiang, Longying, Chen, Xiaojuan, Wu, Daichao, Qu, Lingzhi, Chen, Zhuchu, Chen, Lin, Rohs, Remo, Chen, Yongheng

“…FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report…”
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DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors by Cooper, Brendon H, Dantas Machado, Ana Carolina, Gan, Yan, Aparicio, Oscar M, Rohs, Remo

“…Abstract Quantifying the nucleotide preferences of DNA binding proteins is essential to understanding how transcription factors (TFs) interact with their…”
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Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion by Chen, Yongheng, Zhang, Xiaojun, Dantas Machado, Ana Carolina, Ding, Yuan, Chen, Zhuchu, Qin, Peter Z, Rohs, Remo, Chen, Lin

“…The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs…”
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Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout by Dantas Machado, Ana Carolina, Cooper, Brendon H, Lei, Xiao, Di Felice, Rosa, Chen, Lin, Rohs, Remo

“…Abstract Myocyte enhancer factor-2B (MEF2B) has the unique capability of binding to its DNA target sites with a degenerate motif, while still functioning as a…”
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Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen by Chang, Y. Paul, Xu, Meng, Machado, Ana Carolina Dantas, Yu, Xian Jessica, Rohs, Remo, Chen, Xiaojiang S.

“…The DNA tumor virus Simian virus 40 (SV40) is a model system for studying eukaryotic replication. SV40 large tumor antigen (LTag) is the initiator/helicase…”
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Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome by Allaband, Celeste, Lingaraju, Amulya, Martino, Cameron, Russell, Baylee, Tripathi, Anupriya, Poulsen, Orit, Dantas Machado, Ana Carolina, Zhou, Dan, Xue, Jin, Elijah, Emmanuel, Malhotra, Atul, Dorrestein, Pieter C, Knight, Rob, Haddad, Gabriel G, Zarrinpar, Amir

“…Obstructive sleep apnea (OSA), characterized by intermittent hypoxia and hypercapnia (IHC), affects the composition of the gut microbiome and metabolome. The…”
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Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome by Dantas Machado, Ana Carolina, Brown, Steven D, Lingaraju, Amulya, Sivaganesh, Vignesh, Martino, Cameron, Chaix, Amandine, Zhao, Peng, Pinto, Antonio F M, Chang, Max W, Richter, R Alexander, Saghatelian, Alan, Saltiel, Alan R, Knight, Rob, Panda, Satchidananda, Zarrinpar, Amir

“…Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms, both of which are disrupted in diet-induced obesity…”
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Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling by Zhang, Xiaojun, Dantas Machado, Ana Carolina, Ding, Yuan, Chen, Yongheng, Lu, Yan, Duan, Yankun, Tham, Kenneth W, Chen, Lin, Rohs, Remo, Qin, Peter Z

“…The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the…”
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Absence of a simple code: how transcription factors read the genome by Slattery, Matthew, Zhou, Tianyin, Yang, Lin, Dantas Machado, Ana Carolina, Gordân, Raluca, Rohs, Remo

“…•TFs recognize their genomic target sites by using mechanisms at multiple levels.•Models of DNA sequence and shape can capture the in vitro TF binding…”
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Genetic control of quality melon traits by Dantas, Ana Carolina de Assis, Ricarte, Anânkia de Oliveira, Costa, José Maria da, Antônio, Rafaela Priscila, Tomaz, Francisco Linco de Souza, Nunes, Glauber Henrique de Sousa

“…This research studied the genetic control of the traits related to melon fruit quality. The F1, F2, BC1, BC2 generations from the OL x A-16 and OL x PV…”
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Integrative literature review: sleep patterns in infants attending nurseries by Cerqueira, Ana Carolina Dantas Rocha, Cardoso, Maria Vera Lúcia Moreira Leitão, Viana, Tamires Rebeca Forte, Lopes, Márcia Maria Coelho Oliveira

“…To identify evidence available in the literature about sleep patterns of infants attending nurseries. An integrative review of studies published in Portuguese,…”
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The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element by Lara-Gonzalez, Samuel, Dantas Machado, Ana Carolina, Rao, Satyanarayan, Napoli, Andrew A, Birktoft, Jens, Di Felice, Rosa, Rohs, Remo, Lawson, Catherine L

“…We demonstrate here that the α subunit C-terminal domain of Escherichia coli RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA element via its…”
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Narrative Review of the Evolution of COVID-19 Vaccination Recommendations in Countries in Latin America, Africa and the Middle East, and Asia by Spinardi, Júlia, Dantas, Ana Carolina, Carballo, Carolina, Thakkar, Karan, Akoury, Nadine Al, Kyaw, Moe Hein, del Carmen Morales Castillo, Graciela, Srivastava, Amit, Sáfadi, Marco Aurélio P.

“…The rapid rollout of vaccines to combat the coronavirus disease 2019 (COVID-19) pandemic over the past 2 years has resulted in the use of various vaccine…”
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Portosystemic shunt placement reveals blood signatures for the development of hepatic encephalopathy through mass spectrometry by Dantas Machado, Ana Carolina, Ramos, Stephany Flores, Gauglitz, Julia M., Fassler, Anne-Marie, Petras, Daniel, Aksenov, Alexander A., Kim, Un Bi, Lazarowicz, Michael, Barnard Giustini, Abbey, Aryafar, Hamed, Vodkin, Irine, Warren, Curtis, Dorrestein, Pieter C., Zarrinpar, Ali, Zarrinpar, Amir

“…Elective transjugular intrahepatic portosystemic shunt (TIPS) placement can worsen cognitive dysfunction in hepatic encephalopathy (HE) patients due to toxins,…”
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Crystal Structures of Ternary Complexes of MEF2 and NKX2–5 Bound to DNA Reveal a Disease Related Protein–Protein Interaction Interface by Lei, Xiao, Zhao, Jun, Sagendorf, Jared M., Rajashekar, Niroop, Xu, Jiang, Dantas Machado, Ana Carolina, Sen, Chandani, Rohs, Remo, Feng, Pinghui, Chen, Lin

“…MEF2 and NKX2–5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that…”
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Evolving insights on how cytosine methylation affects protein-DNA binding by Dantas Machado, Ana Carolina, Zhou, Tianyin, Rao, Satyanarayan, Goel, Pragya, Rastogi, Chaitanya, Lazarovici, Allan, Bussemaker, Harmen J, Rohs, Remo

“…Many anecdotal observations exist of a regulatory effect of DNA methylation on gene expression. However, in general, the underlying mechanisms of this effect…”
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