Search Results - "Trieu, Tuan"

MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data by Trieu, Tuan, Cheng, Jianlin

“…The three-dimensional (3D) conformation of chromosomes and genomes play an important role in cellular processes such as gene regulation, DNA replication and…”
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Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data by Trieu, Tuan, Cheng, Jianlin

“…Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene-gene…”
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Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing by Adhikari, Badri, Trieu, Tuan, Cheng, Jianlin

“…Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we…”
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GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure by Trieu, Tuan, Oluwadare, Oluwatosin, Wopata, Julia, Cheng, Jianlin

“…Abstract Motivation Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome…”
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DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure by Trieu, Tuan, Martinez-Fundichely, Alexander, Khurana, Ekta

“…Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the…”
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Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes by Trieu, Tuan, Oluwadare, Oluwatosin, Cheng, Jianlin

“…Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains…”
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Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells by Chen, Changya, Yu, Wenbao, Tober, Joanna, Gao, Peng, He, Bing, Lee, Kiwon, Trieu, Tuan, Blobel, Gerd A., Speck, Nancy A., Tan, Kai

“…Fetal hematopoietic stem cells (HSCs) undergo a developmental switch to become adult HSCs with distinct functional properties. To better understand the…”
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Effect of drying temperature and storage time on Ocimum gratissimum Linn. leaf essential oil from Central Highlands, Vietnam by Tuan Anh, Trieu, Thi Duyen, Le, My Hang, Le, Duc Lam, Tri, Giang Bach, Long, Chinh Nguyen, Duy, Quoc Toan, Tran

“…Essential oil of Ocimum gratissimum Linn. leaf is widely used in folk medicine. Extraction yeild, compositions and antioxidant activity of clove basil…”
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3D genome structure modeling by Lorentzian objective function by Trieu, Tuan, Cheng, Jianlin

“…The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation…”
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cDNA cloning, characterization and expression of cytochrome P450 family 1 (CYP1A) from Javanese medaka, Oryzias javanicus by environmental conditions by Trieu, Tuan, Yoshino, Kaminishi, Aki, Funahashi, El-Kady, A.H. Mohamed, Abeer, A. I. Hassanin, Takao, Itakura

“…Cytochrome P450 family 1 (CYP1A) subfamily genes are the most well studied CYP genes in vertebrates; however, information on CYP1A genes in Javanese medaka is…”
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Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena , Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies by Thai, Binh Thanh, Lee, Yin Peng, Gan, Han Ming, Austin, Christopher M, Croft, Laurence J, Trieu, Tuan Anh, Tan, Mun Hua

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Cloning and tissue expression of cytochrome P450 1B1 and 1C1 genes from Javanese Medaka, Oryzias Javanicus, under environmental stress conditions by Trieu, Tuan, Yoshino, Kaminishi, Aki, Funahashi, Abeer, A. I. Hassanin, Takao, Itakura

“…Cytochrome P450 1 (CYP1) is widely used as an indicator of exposure to environmental contaminants. In the study, two full-length complementary DNAs encode for…”
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Abstract 2443: Predicting the impact of somatic mutations on chromatin conformation using deep learning by Trieu, Tuan, Khurana, Ekta

“…Abstract DNA in eukaryotes is packed into hierarchical layers of loops resulting in the 3D structure of the genome. 3D genome organization plays vital roles in…”
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Preparation of La/Co/Ni-based anode catalyst for biogas-fueled solid oxide fuel cells by Nguyen, Ngoc Thi Quynh, Trieu, Tuan Anh, Yoon, Hyon Hee

“…A new type of bilayered-anode for application in biogas-fueled solid oxide fuel cells (SOFCs) was investigated. The bilayered-anode consisted of lanthanum- and…”
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Developmental chromatin programs determine oncogenic competence in melanoma by Baggiolini, Arianna, Callahan, Scott J, Montal, Emily, Weiss, Joshua M, Trieu, Tuan, Tagore, Mohita M, Tischfield, Sam E, Walsh, Ryan M, Suresh, Shruthy, Fan, Yujie, Campbell, Nathaniel R, Perlee, Sarah C, Saurat, Nathalie, Hunter, Miranda V, Simon-Vermot, Theresa, Huang, Ting-Hsiang, Ma, Yilun, Hollmann, Travis, Tickoo, Satish K, Taylor, Barry S, Khurana, Ekta, Koche, Richard P, Studer, Lorenz, White, Richard M

“…Oncogenes only transform cells under certain cellular contexts, a phenomenon called oncogenic competence. Using a combination of a human pluripotent stem…”
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Experimental Evaluation of the Effectiveness of Virtualized Mobile Core Networks in the Real Commercial Network Environment by Quang, Diep Pham, Tai, Hung Nguyen, Dac, Hoan Nguyen, The, Anh Do, Van, Hien Le, Tuan, Anh Trieu

“…In the mobile communication, over the long term, traffic growth is driven by both the rising number of smartphone subscriptions and an increasing average data…”
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GMOL: An Interactive Tool for 3D Genome Structure Visualization by Nowotny, Jackson, Wells, Avery, Oluwadare, Oluwatosin, Xu, Lingfei, Cao, Renzhi, Trieu, Tuan, He, Chenfeng, Cheng, Jianlin

“…It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting…”
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Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data by Nowotny, Jackson, Ahmed, Sharif, Xu, Lingfei, Oluwadare, Oluwatosin, Chen, Hannah, Hensley, Noelan, Trieu, Tuan, Cao, Renzhi, Cheng, Jianlin

“…The entire collection of genetic information resides within the chromosomes, which themselves reside within almost every cell nucleus of eukaryotic organisms…”
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Investigating the antibacterial mechanism of Ampelopsis cantoniensis extracts against methicillin-resistant Staphylococcus aureus via in vitro and in silico analysis by Bich, Van Ngo Thai, Nguyen, Tan Khanh, Thu, Thao Dao Thi, Tran, Linh Thuy Thi, Nguyen, Sa Vo Duong, Han, Ho Le, Pham, Long-Hung Dinh, Thanh, Trung Hoang, Duong, Van Hoa, Trieu, Tuan Anh, Tran, Manh Hung, Pham, Phu Tran Vinh

“…Methicillin-resistant Staphylococcus aureus (MRSA) is a critical pathogen responsible for a wide variety of serious infectious diseases in humans. The…”
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Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway by Carrot-Zhang, Jian, Yao, Xiaotong, Devarakonda, Siddhartha, Deshpande, Aditya, Damrauer, Jeffrey S., Silva, Tiago Chedraoui, Wong, Christopher K., Choi, Hyo Young, Felau, Ina, Robertson, A. Gordon, Castro, Mauro A.A., Bao, Lisui, Rheinbay, Esther, Liu, Eric Minwei, Trieu, Tuan, Haan, David, Yau, Christina, Hinoue, Toshinori, Liu, Yuexin, Shapira, Ofer, Kumar, Kiran, Mungall, Karen L., Zhang, Hailei, June-Koo Lee, Jake, Berger, Ashton, Gao, Galen F., Zhitomirsky, Binyamin, Liang, Wen-Wei, Zhou, Meng, Moorthi, Sitapriya, Berger, Alice H., Collisson, Eric A., Zody, Michael C., Ding, Li, Cherniack, Andrew D., Getz, Gad, Elemento, Olivier, Benz, Christopher C., Stuart, Josh, Zenklusen, J.C., Beroukhim, Rameen, Chang, Jason C., Campbell, Joshua D., Hayes, D. Neil, Yang, Lixing, Laird, Peter W., Weinstein, John N., Kwiatkowski, David J., Tsao, Ming S., Travis, William D., Khurana, Ekta, Berman, Benjamin P., Hoadley, Katherine A., Robine, Nicolas, Meyerson, Matthew, Govindan, Ramaswamy, Imielinski, Marcin

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