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308 results on '"Choi, Jeong Hyeon"'

2. Metabolic Reprogramming by MYCN Confers Dependence on the Serine-Glycine-One-Carbon Biosynthetic Pathway

Author

Xia, Yingfeng, Ye, Bingwei, Ding, Jane, Yu, Yajie, Alptekin, Ahmet, Thangaraju, Muthusamy, Prasad, Puttur D, Ding, Zhi-Chun, Park, Eun Jeong, Choi, Jeong-Hyeon, Gao, Bei, Fiehn, Oliver, Yan, Chunhong, Dong, Zheng, Zha, Yunhong, and Ding, Han-Fei

Subjects
Neurosciences, Genetics, Neuroblastoma, Cancer, Rare Diseases, Clinical Research, Pediatric, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Biosynthetic Pathways, Carbon, Cell Line, Tumor, Child, Glycine, Humans, N-Myc Proto-Oncogene Protein, Serine, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

MYCN amplification drives the development of neuronal cancers in children and adults. Given the challenge in therapeutically targeting MYCN directly, we searched for MYCN-activated metabolic pathways as potential drug targets. Here we report that neuroblastoma cells with MYCN amplification show increased transcriptional activation of the serine-glycine-one-carbon (SGOC) biosynthetic pathway and an increased dependence on this pathway for supplying glucose-derived carbon for serine and glycine synthesis. Small molecule inhibitors that block this metabolic pathway exhibit selective cytotoxicity to MYCN-amplified cell lines and xenografts by inducing metabolic stress and autophagy. Transcriptional activation of the SGOC pathway in MYCN-amplified cells requires both MYCN and ATF4, which form a positive feedback loop, with MYCN activation of ATF4 mRNA expression and ATF4 stabilization of MYCN protein by antagonizing FBXW7-mediated MYCN ubiquitination. Collectively, these findings suggest a coupled relationship between metabolic reprogramming and increased sensitivity to metabolic stress, which could be exploited as a strategy for selective cancer therapy. SIGNIFICANCE: This study identifies a MYCN-dependent metabolic vulnerability and suggests a coupled relationship between metabolic reprogramming and increased sensitivity to metabolic stress, which could be exploited for cancer therapy.See related commentary by Rodriguez Garcia and Arsenian-Henriksson, p. 3818.

Published
2019

4. P‐53: Analysis of dead pixel origins and potential defect prediction using machine learning with tabular data.

Author

Han, Jun Hee, Jeong, Yoonseob, Chun, Minkyu, Yoon, Sang Won, Choi, Jeong-Hyeon, Choi, Young Jun, Kim, Young Mi, Jung, Sang Hoon, Yang, Joon-Young, and Yoon, Sooyoung

Subjects
MACHINE learning, PROBLEM solving, FORECASTING
Abstract

Producing defect‐free products is one of the essential tasks of a manufacturing company. In this paper, the causes of dead pixels are analyzed and the coordinates of dead pixels are predicted using machine learning to solve problems of dead pixels. Unlike the existing method of analyzing defects using images, tabular data where each element contains significance were used, and detailed description of suggested models are depicted. Experiments ensured the consistency of the proposed method. [ABSTRACT FROM AUTHOR]

Published
2024
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5. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

Author

Schwartz, Tonia S, Tae, Hongseok, Yang, Youngik, Mockaitis, Keithanne, Van Hemert, John L, Proulx, Stephen R, Choi, Jeong-Hyeon, and Bronikowski, Anne M

Abstract

Abstract Background The reptiles, characterized by both diversity and unique evolutionary adaptations, provide a comprehensive system for comparative studies of metabolism, physiology, and development. However, molecular resources for ectothermic reptiles are severely limited, hampering our ability to study the genetic basis for many evolutionarily important traits such as metabolic plasticity, extreme longevity, limblessness, venom, and freeze tolerance. Here we use massively parallel sequencing (454 GS-FLX Titanium) to generate a transcriptome of the western terrestrial garter snake (Thamnophis elegans) with two goals in mind. First, we develop a molecular resource for an ectothermic reptile; and second, we use these sex-specific transcriptomes to identify differences in the presence of expressed transcripts and potential genes of evolutionary interest. Results Using sex-specific pools of RNA (one pool for females, one pool for males) representing 7 tissue types and 35 diverse individuals, we produced 1.24 million sequence reads, which averaged 366 bp in length after cleaning. Assembly of the cleaned reads from both sexes with NEWBLER and MIRA resulted in 96,379 contigs containing 87% of the cleaned reads. Over 34% of these contigs and 13% of the singletons were annotated based on homology to previously identified proteins. From these homology assignments, additional clustering, and ORF predictions, we estimate that this transcriptome contains ~13,000 unique genes that were previously identified in other species and over 66,000 transcripts from unidentified protein-coding genes. Furthermore, we use a graph-clustering method to identify contigs linked by NEWBLER-split reads that represent divergent alleles, gene duplications, and alternatively spliced transcripts. Beyond gene identification, we identified 95,295 SNPs and 31,651 INDELs. From these sex-specific transcriptomes, we identified 190 genes that were only present in the mRNA sequenced from one of the sexes (84 female-specific, 106 male-specific), and many highly variable genes of evolutionary interest. Conclusions This is the first large-scale, multi-organ transcriptome for an ectothermic reptile. This resource provides the most comprehensive set of EST sequences available for an individual ectothermic reptile species, increasing the number of snake ESTs 50-fold. We have identified genes that appear to be under evolutionary selection and those that are sex-specific. This resource will assist studies on gene expression and comparative genomics, and will facilitate the study of evolutionarily important traits at the molecular level.

Published
2010

7. Supplementary Figure S3 from Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers

Author

Noonepalle, Satish K., primary, Gu, Franklin, primary, Lee, Eun-Joon, primary, Choi, Jeong-Hyeon, primary, Han, Qimei, primary, Kim, Jaejik, primary, Ouzounova, Maria, primary, Shull, Austin Y., primary, Pei, Lirong, primary, Hsu, Pei-Yin, primary, Kolhe, Ravindra, primary, Shi, Fang, primary, Choi, Jiseok, primary, Chiou, Katie, primary, Huang, Tim H.M., primary, Korkaya, Hasan, primary, Deng, Libin, primary, Xin, Hong-Bo, primary, Huang, Shuang, primary, Thangaraju, Muthusamy, primary, Sreekumar, Arun, primary, Ambs, Stefan, primary, Tang, Shou-Ching, primary, Munn, David H., primary, and Shi, Huidong, primary

Published
2023
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8. Supplementary Figure Legends from Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers

Author

Noonepalle, Satish K., primary, Gu, Franklin, primary, Lee, Eun-Joon, primary, Choi, Jeong-Hyeon, primary, Han, Qimei, primary, Kim, Jaejik, primary, Ouzounova, Maria, primary, Shull, Austin Y., primary, Pei, Lirong, primary, Hsu, Pei-Yin, primary, Kolhe, Ravindra, primary, Shi, Fang, primary, Choi, Jiseok, primary, Chiou, Katie, primary, Huang, Tim H.M., primary, Korkaya, Hasan, primary, Deng, Libin, primary, Xin, Hong-Bo, primary, Huang, Shuang, primary, Thangaraju, Muthusamy, primary, Sreekumar, Arun, primary, Ambs, Stefan, primary, Tang, Shou-Ching, primary, Munn, David H., primary, and Shi, Huidong, primary

Published
2023
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9. Data from Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers

Author

Noonepalle, Satish K., primary, Gu, Franklin, primary, Lee, Eun-Joon, primary, Choi, Jeong-Hyeon, primary, Han, Qimei, primary, Kim, Jaejik, primary, Ouzounova, Maria, primary, Shull, Austin Y., primary, Pei, Lirong, primary, Hsu, Pei-Yin, primary, Kolhe, Ravindra, primary, Shi, Fang, primary, Choi, Jiseok, primary, Chiou, Katie, primary, Huang, Tim H.M., primary, Korkaya, Hasan, primary, Deng, Libin, primary, Xin, Hong-Bo, primary, Huang, Shuang, primary, Thangaraju, Muthusamy, primary, Sreekumar, Arun, primary, Ambs, Stefan, primary, Tang, Shou-Ching, primary, Munn, David H., primary, and Shi, Huidong, primary

Published
2023
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10. Supplementary Tables 1 through 5 from Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers

Author

Noonepalle, Satish K., primary, Gu, Franklin, primary, Lee, Eun-Joon, primary, Choi, Jeong-Hyeon, primary, Han, Qimei, primary, Kim, Jaejik, primary, Ouzounova, Maria, primary, Shull, Austin Y., primary, Pei, Lirong, primary, Hsu, Pei-Yin, primary, Kolhe, Ravindra, primary, Shi, Fang, primary, Choi, Jiseok, primary, Chiou, Katie, primary, Huang, Tim H.M., primary, Korkaya, Hasan, primary, Deng, Libin, primary, Xin, Hong-Bo, primary, Huang, Shuang, primary, Thangaraju, Muthusamy, primary, Sreekumar, Arun, primary, Ambs, Stefan, primary, Tang, Shou-Ching, primary, Munn, David H., primary, and Shi, Huidong, primary

Published
2023
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15. Table S2 from Metabolic Reprogramming by MYCN Confers Dependence on the Serine-Glycine-One-Carbon Biosynthetic Pathway

Author

Xia, Yingfeng, primary, Ye, Bingwei, primary, Ding, Jane, primary, Yu, Yajie, primary, Alptekin, Ahmet, primary, Thangaraju, Muthusamy, primary, Prasad, Puttur D., primary, Ding, Zhi-Chun, primary, Park, Eun Jeong, primary, Choi, Jeong-Hyeon, primary, Gao, Bei, primary, Fiehn, Oliver, primary, Yan, Chunhong, primary, Dong, Zheng, primary, Zha, Yunhong, primary, and Ding, Han-Fei, primary

Published
2023
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16. Data from Metabolic Reprogramming by MYCN Confers Dependence on the Serine-Glycine-One-Carbon Biosynthetic Pathway

Author

Xia, Yingfeng, primary, Ye, Bingwei, primary, Ding, Jane, primary, Yu, Yajie, primary, Alptekin, Ahmet, primary, Thangaraju, Muthusamy, primary, Prasad, Puttur D., primary, Ding, Zhi-Chun, primary, Park, Eun Jeong, primary, Choi, Jeong-Hyeon, primary, Gao, Bei, primary, Fiehn, Oliver, primary, Yan, Chunhong, primary, Dong, Zheng, primary, Zha, Yunhong, primary, and Ding, Han-Fei, primary

Published
2023
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17. Supplementary Data from Metabolic Reprogramming by MYCN Confers Dependence on the Serine-Glycine-One-Carbon Biosynthetic Pathway

Author

Xia, Yingfeng, primary, Ye, Bingwei, primary, Ding, Jane, primary, Yu, Yajie, primary, Alptekin, Ahmet, primary, Thangaraju, Muthusamy, primary, Prasad, Puttur D., primary, Ding, Zhi-Chun, primary, Park, Eun Jeong, primary, Choi, Jeong-Hyeon, primary, Gao, Bei, primary, Fiehn, Oliver, primary, Yan, Chunhong, primary, Dong, Zheng, primary, Zha, Yunhong, primary, and Ding, Han-Fei, primary

Published
2023
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18. Data from Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

Author

Pathania, Rajneesh, primary, Ramachandran, Sabarish, primary, Mariappan, Gurusamy, primary, Thakur, Priyanka, primary, Shi, Huidong, primary, Choi, Jeong-Hyeon, primary, Manicassamy, Santhakumar, primary, Kolhe, Ravindra, primary, Prasad, Puttur D., primary, Sharma, Suash, primary, Lokeshwar, Bal L., primary, Ganapathy, Vadivel, primary, and Thangaraju, Muthusamy, primary

Published
2023
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19. Supplementary Table 1 from Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

Author

Pathania, Rajneesh, primary, Ramachandran, Sabarish, primary, Mariappan, Gurusamy, primary, Thakur, Priyanka, primary, Shi, Huidong, primary, Choi, Jeong-Hyeon, primary, Manicassamy, Santhakumar, primary, Kolhe, Ravindra, primary, Prasad, Puttur D., primary, Sharma, Suash, primary, Lokeshwar, Bal L., primary, Ganapathy, Vadivel, primary, and Thangaraju, Muthusamy, primary

Published
2023
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20. Supplemental Materials and Methods from Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

Author

Pathania, Rajneesh, primary, Ramachandran, Sabarish, primary, Mariappan, Gurusamy, primary, Thakur, Priyanka, primary, Shi, Huidong, primary, Choi, Jeong-Hyeon, primary, Manicassamy, Santhakumar, primary, Kolhe, Ravindra, primary, Prasad, Puttur D., primary, Sharma, Suash, primary, Lokeshwar, Bal L., primary, Ganapathy, Vadivel, primary, and Thangaraju, Muthusamy, primary

Published
2023
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21. Supplementary Figure legends from Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

Author

Pathania, Rajneesh, primary, Ramachandran, Sabarish, primary, Mariappan, Gurusamy, primary, Thakur, Priyanka, primary, Shi, Huidong, primary, Choi, Jeong-Hyeon, primary, Manicassamy, Santhakumar, primary, Kolhe, Ravindra, primary, Prasad, Puttur D., primary, Sharma, Suash, primary, Lokeshwar, Bal L., primary, Ganapathy, Vadivel, primary, and Thangaraju, Muthusamy, primary

Published
2023
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22. Supplemental Figures from Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

Author

Pathania, Rajneesh, primary, Ramachandran, Sabarish, primary, Mariappan, Gurusamy, primary, Thakur, Priyanka, primary, Shi, Huidong, primary, Choi, Jeong-Hyeon, primary, Manicassamy, Santhakumar, primary, Kolhe, Ravindra, primary, Prasad, Puttur D., primary, Sharma, Suash, primary, Lokeshwar, Bal L., primary, Ganapathy, Vadivel, primary, and Thangaraju, Muthusamy, primary

Published
2023
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23. Supplementary Table 2 from Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth

Author

Pathania, Rajneesh, primary, Ramachandran, Sabarish, primary, Mariappan, Gurusamy, primary, Thakur, Priyanka, primary, Shi, Huidong, primary, Choi, Jeong-Hyeon, primary, Manicassamy, Santhakumar, primary, Kolhe, Ravindra, primary, Prasad, Puttur D., primary, Sharma, Suash, primary, Lokeshwar, Bal L., primary, Ganapathy, Vadivel, primary, and Thangaraju, Muthusamy, primary

Published
2023
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29. Multiple Genome Alignment by Clustering Pairwise Matches

Author

Choi, Jeong-Hyeon, Choi, Kwangmin, Cho, Hwan-Gue, Kim, Sun, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, and Lagergren, Jens, editor

Published
2005
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30. PLATCOM: Current Status and Plan for the Next Stages

Author

Choi, Kwangmin, Choi, Jeong-Hyeon, Saple, Amit, Wang, Zhiping, Lee, Jason, Kim, Sun, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Ludäscher, Bertram, editor, and Raschid, Louiqa, editor

Published
2005
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34. The Ecoresponsive Genome of "Daphnia pulex"

Author

Colbourne, John K., Pfrender, Michael E., Gilbert, Donald, Thomas, W. Kelley, Tucker, Abraham, Oakley, Todd H., Tokishita, Shinichi, Aerts, Andrea, Arnold, Georg J., Basu, Malay Kumar, Bauer, Darren J., Cáceres, Carla E., Carmel, Liran, Casola, Claudio, Choi, Jeong-Hyeon, Detter, John C., Dong, Qunfeng, Dusheyko, Serge, Eads, Brian D., Fröhlich, Thomas, Geiler-Samerotte, Kerry A., Gerlach, Daniel, Hatcher, Phil, Jogdeo, Sanjuro, Krijgsveld, Jeroen, Kriventseva, Evgenia V., Kültz, Dietmar, Laforsch, Christian, Lindquist, Erika, Lopez, Jacqueline, Manak, J. Robert, Muller, Jean, Pangilinan, Jasmyn, Patwardhan, Rupali P., Pitluck, Samuel, Pritham, Ellen J., Rechtsteiner, Andreas, Rho, Mina, Rogozin, Igor B., Sakarya, Onur, Salamov, Asaf, Schaack, Sarah, Shapiro, Harris, Shiga, Yasuhiro, Skalitzky, Courtney, Smith, Zachary, Souvorov, Alexander, Sung, Way, Tang, Zuojian, Tsuchiya, Dai, Tu, Hank, Vos, Harmjan, Wang, Mei, Wolf, Yuri I., Yamagata, Hideo, Yamada, Takuji, Ye, Yuzhen, Shaw, Joseph R., Andrews, Justen, Crease, Teresa J., Tang, Haixu, Lucas, Susan M., Robertson, Hugh M., Bork, Peer, Koonin, Eugene V., Zdobnov, Evgeny M., Grigoriev, Igor V., Lynch, Michael, and Boore, Jeffrey L.

Published
2011
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