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7. Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories

Author

Wang, Binzhong, Wu, Bin, Liu, Xueqing, Hu, Yacheng, Ming, Yao, Bai, Mingzhou, Liu, Juanjuan, Xiao, Kan, Zeng, Qingkai, Yang, Jing, Wang, Hongqi, Guo, Baifu, Tan, Chun, Hu, Zixuan, Zhao, Xun, Li, Yanhong, Yue, Zhen, Mei, Junpu, Jiang, Wei, Yang, Yuanjin, Li, Zhiyuan, Gao, Yong, Chen, Lei, Jian, Jianbo, Du, Hejun, Wang, Binzhong, Wu, Bin, Liu, Xueqing, Hu, Yacheng, Ming, Yao, Bai, Mingzhou, Liu, Juanjuan, Xiao, Kan, Zeng, Qingkai, Yang, Jing, Wang, Hongqi, Guo, Baifu, Tan, Chun, Hu, Zixuan, Zhao, Xun, Li, Yanhong, Yue, Zhen, Mei, Junpu, Jiang, Wei, Yang, Yuanjin, Li, Zhiyuan, Gao, Yong, Chen, Lei, Jian, Jianbo, and Du, Hejun

Abstract

The order Acipenseriformes, which includes sturgeons and paddlefishes, represents "living fossils" with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8n), a hexavalent (6n), two tetravalents (4n), and a divalent (2n). An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs, and further provides insights into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.

Published
2024

8. Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories

Author

Wang, Binzhong, primary, Wu, Bin, additional, Liu, Xueqing, additional, Hu, Yacheng, additional, Ming, Yao, additional, Bai, Mingzhou, additional, Liu, Juanjuan, additional, Xiao, Kan, additional, Zeng, Qingkai, additional, Yang, Jing, additional, Wang, Hongqi, additional, Guo, Baifu, additional, Tan, Chun, additional, Hu, Zixuan, additional, Zhao, Xun, additional, Li, Yanhong, additional, Yue, Zhen, additional, Mei, Junpu, additional, Jiang, Wei, additional, Yang, Yuanjin, additional, Li, Zhiyuan, additional, Gao, Yong, additional, Chen, Lei, additional, Jian, Jianbo, additional, and Du, Hejun, additional

Published
2023
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10. Whole Genome Sequencing Reveals Autooctoploidy in the Chinese Sturgeon and its Evolutionary Trajectories

Author

Wang, Binzhong, primary, Wu, Bin, additional, Liu, Xueqing, additional, Hu, Yacheng, additional, Ming, Yao, additional, Bai, Mingzhou, additional, Liu, Juanjuan, additional, Xiao, Kan, additional, Zeng, Qingkai, additional, Yang, Jing, additional, Wang, Hongqi, additional, Guo, Baifu, additional, Tan, Chun, additional, Hu, Zixuan, additional, Zhao, Xun, additional, Li, Yanhong, additional, Yue, Zhen, additional, Mei, Junpu, additional, Jiang, Wei, additional, Yang, Yuanjin, additional, Li, Zhiyuan, additional, Gao, Yong, additional, Chen, Lei, additional, Jian, Jianbo, additional, and Du, Hejun, additional

Published
2023
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11. Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Author

Jiang, Yong-hui, Yuen, Ryan K.C., Jin, Xin, Wang, Mingbang, Chen, Nong, Wu, Xueli, Ju, Jia, Mei, Junpu, Shi, Yujian, He, Mingze, Wang, Guangbiao, Liang, Jieqin, Wang, Zhe, Cao, Dandan, Carter, Melissa T., Chrysler, Christina, Drmic, Irene E., Howe, Jennifer L., Lau, Lynette, Marshall, Christian R., Merico, Daniele, Nalpathamkalam, Thomas, Thiruvahindrapuram, Bhooma, Thompson, Ann, Uddin, Mohammed, Walker, Susan, Luo, Jun, Anagnostou, Evdokia, Zwaigenbaum, Lonnie, Ring, Robert H., Wang, Jian, Lajonchere, Clara, Wang, Jun, Shih, Andy, Szatmari, Peter, Yang, Huanming, Dawson, Geraldine, Li, Yingrui, and Scherer, Stephen W.

Published
2013
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15. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

Author

Zhou, Fusheng, Cao, Hongzhi, Zuo, Xianbo, Zhang, Tao, Zhang, Xiaoguang, Liu, Xiaomin, Xu, Ricong, Chen, Gang, Zhang, Yuanwei, Zheng, Xiaodong, Jin, Xin, Gao, Jinping, Mei, Junpu, Sheng, Yujun, Li, Qibin, Liang, Bo, Shen, Juan, Shen, Changbing, Jiang, Hui, Zhu, Caihong, Fan, Xing, Xu, Fengping, Yue, Min, Yin, Xianyong, Ye, Chen, Zhang, Cuicui, Liu, Xiao, Yu, Liang, Wu, Jinghua, Chen, Mengyun, Zhuang, Xuehan, Tang, Lili, Shao, Haojing, Wu, Longmao, Li, Jian, Xu, Yu, Zhang, Yijie, Zhao, Suli, Wang, Yu, Li, Ge, Xu, Hanshi, Zeng, Lei, Wang, Jianan, Bai, Mingzhou, Chen, Yanling, Chen, Wei, Kang, Tian, Wu, Yanyan, Xu, Xun, Zhu, Zhengwei, Cui, Yong, Wang, Zaixing, Yang, Chunjun, Wang, Peiguang, Xiang, Leihong, Chen, Xiang, Zhang, Anping, Gao, Xinghua, Zhang, Furen, Xu, Jinhua, Zheng, Min, Zheng, Jie, Zhang, Jianzhong, Yu, Xueqing, Li, Yingrui, Yang, Sen, Yang, Huanming, Wang, Jian, Liu, Jianjun, Hammarstrom, Lennart, Sun, Liangdan, Wang, Jun, Zhang, Xuejun, Zhou, Fusheng, Cao, Hongzhi, Zuo, Xianbo, Zhang, Tao, Zhang, Xiaoguang, Liu, Xiaomin, Xu, Ricong, Chen, Gang, Zhang, Yuanwei, Zheng, Xiaodong, Jin, Xin, Gao, Jinping, Mei, Junpu, Sheng, Yujun, Li, Qibin, Liang, Bo, Shen, Juan, Shen, Changbing, Jiang, Hui, Zhu, Caihong, Fan, Xing, Xu, Fengping, Yue, Min, Yin, Xianyong, Ye, Chen, Zhang, Cuicui, Liu, Xiao, Yu, Liang, Wu, Jinghua, Chen, Mengyun, Zhuang, Xuehan, Tang, Lili, Shao, Haojing, Wu, Longmao, Li, Jian, Xu, Yu, Zhang, Yijie, Zhao, Suli, Wang, Yu, Li, Ge, Xu, Hanshi, Zeng, Lei, Wang, Jianan, Bai, Mingzhou, Chen, Yanling, Chen, Wei, Kang, Tian, Wu, Yanyan, Xu, Xun, Zhu, Zhengwei, Cui, Yong, Wang, Zaixing, Yang, Chunjun, Wang, Peiguang, Xiang, Leihong, Chen, Xiang, Zhang, Anping, Gao, Xinghua, Zhang, Furen, Xu, Jinhua, Zheng, Min, Zheng, Jie, Zhang, Jianzhong, Yu, Xueqing, Li, Yingrui, Yang, Sen, Yang, Huanming, Wang, Jian, Liu, Jianjun, Hammarstrom, Lennart, Sun, Liangdan, Wang, Jun, and Zhang, Xuejun

Published
2016

17. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

Author

Zhou, Fusheng, primary, Cao, Hongzhi, additional, Zuo, Xianbo, additional, Zhang, Tao, additional, Zhang, Xiaoguang, additional, Liu, Xiaomin, additional, Xu, Ricong, additional, Chen, Gang, additional, Zhang, Yuanwei, additional, Zheng, Xiaodong, additional, Jin, Xin, additional, Gao, Jinping, additional, Mei, Junpu, additional, Sheng, Yujun, additional, Li, Qibin, additional, Liang, Bo, additional, Shen, Juan, additional, Shen, Changbing, additional, Jiang, Hui, additional, Zhu, Caihong, additional, Fan, Xing, additional, Xu, Fengping, additional, Yue, Min, additional, Yin, Xianyong, additional, Ye, Chen, additional, Zhang, Cuicui, additional, Liu, Xiao, additional, Yu, Liang, additional, Wu, Jinghua, additional, Chen, Mengyun, additional, Zhuang, Xuehan, additional, Tang, Lili, additional, Shao, Haojing, additional, Wu, Longmao, additional, Li, Jian, additional, Xu, Yu, additional, Zhang, Yijie, additional, Zhao, Suli, additional, Wang, Yu, additional, Li, Ge, additional, Xu, Hanshi, additional, Zeng, Lei, additional, Wang, Jianan, additional, Bai, Mingzhou, additional, Chen, Yanling, additional, Chen, Wei, additional, Kang, Tian, additional, Wu, Yanyan, additional, Xu, Xun, additional, Zhu, Zhengwei, additional, Cui, Yong, additional, Wang, Zaixing, additional, Yang, Chunjun, additional, Wang, Peiguang, additional, Xiang, Leihong, additional, Chen, Xiang, additional, Zhang, Anping, additional, Gao, Xinghua, additional, Zhang, Furen, additional, Xu, Jinhua, additional, Zheng, Min, additional, Zheng, Jie, additional, Zhang, Jianzhong, additional, Yu, Xueqing, additional, Li, Yingrui, additional, Yang, Sen, additional, Yang, Huanming, additional, Wang, Jian, additional, Liu, Jianjun, additional, Hammarström, Lennart, additional, Sun, Liangdan, additional, Wang, Jun, additional, and Zhang, Xuejun, additional

Published
2016
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18. Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Author

Anagnostou, Evdokia, Cao, Dandan, Drmic, Irene E., Jiang, Yong-hui, Marshall, Christian R., Luo, Jun, Chrysler, Christina, Wang, Mingbang, Yuen, Ryan K.C., Lau, Lynette, Howe, Jennifer L., Carter, Melissa T., Lajonchere, Clara, Walker, Susan, Ring, Robert H., Wang, Guangbiao, He, Mingze, Nalpathamkalam, Thomas, Shi, Yujian, Ju, Jia, Mei, Junpu, Uddin, Mohammed, Thiruvahindrapuram, Bhooma, Chen, Nong, Wang, Jian, Thompson, Ann, Liang, Jieqin, Jin, Xin, Wu, Xueli, Zwaigenbaum, Lonnie, Merico, Daniele, and Wang, Zhe

Subjects
mental disorders
Abstract

Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such putative mutations was larger than has been previously reported; this yield was in part due to the comprehensive and uniform coverage afforded by WGS. Deleterious variants were found in four unrecognized, nine known, and eight candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to FMR1, which is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.

Published
2013
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19. New loci and coding variants confer risk for age-related macular degeneration in East Asians

Author

90812793, 80724278, 40402846, 50212220, Cheng, Ching Yu, Yamashiro, Kenji, Jia Chen, Li, Ahn, Jeeyun, Huang, Lulin, Huang, Lvzhen, Cheung, Chui Ming G, Miyake, Masahiro, Cackett, Peter D., Yeo, Ian Y., Laude, Augustinus, Gopal, Lingam, Naing, Thet, Liao, Jiemin, Guan Ong, Peng, Mitchell, Paul, Zhou, Peng, Xie, Xuefeng, Liang, Jinlong, Mei, Junpu, Jin, Xin, Saw, Seang Mei, Ozaki, Mineo, Mizoguchi, Takanori, Kurimoto, Yasuo, Woo, Se Joon, Chung, Hum, Yu, Hyeong Gon, Shin, Joo Young, Park, Dong Ho, Kim, In Taek, Chang, Woohyok, Sagong, Min, Lee, Sang Joon, Kim, Hyun Woong, Lee, Ji Eun, Li, Yi, Liu, Jianjun, Teo, Yik Ying, Heng, Chew Kiat, Lim, Tock Han, Yang, Suk Kyun, Song, Kyuyoung, Vithana, Eranga N., Aung, Tin, Bei, Jin Xin, Zeng, Yi Xin, Tai, E. Shyong, Li, Xiao Xin, Yang, Zhenglin, Park, Kyu Hyung, Pang, Chi Pui, Yoshimura, Nagahisa, Yin Wong, Tien, Khor, Chiea Chuen, Mathur, Ranjana, Pang, Junxiong, Sim, Kar Seng, Koh, Adrian H., Chen, Peng, Lee, Shu Yen, Wong, Doric, Chan, Choi Mun, Loh, Boon Kwang, Sun, Yaoyao, Davila, Sonia, Nakata, Isao, Nakanishi, Hideo, Akagi-Kurashige, Yumiko, Gotoh, Norimoto, Tsujikawa, Akitaka, Matsuda, Fumihiko, Mori, Keisuke, Yoneya, Shin, Sakurada, Yoichi, Iijima, Hiroyuki, Iida, Tomohiro, Honda, Shigeru, Lai, Timothy Yuk Yau, Tam, Pancy Oi Sin, Chen, Haoyu, Tang, Shibo, Ding, Xiaoyan, Wen, Feng, Lu, Fang, Zhang, Xiongze, Shi, Yi, Zhao, Peiquan, Zhao, Bowen, Sang, Jinghong, Gong, Bo, Dorajoo, Rajkumar, Yuan, Jian Min, Koh, Woon Puay, Van Dam, Rob M., Friedlander, Yechiel, Lin, Ying, Hibberd, Martin L., Foo, Jia Nee, Wang, Ningli, Wong, Chang Hua, Tan, Gavin S., Park, Sang Jun, Bhargava, Mayuri, 90812793, 80724278, 40402846, 50212220, Cheng, Ching Yu, Yamashiro, Kenji, Jia Chen, Li, Ahn, Jeeyun, Huang, Lulin, Huang, Lvzhen, Cheung, Chui Ming G, Miyake, Masahiro, Cackett, Peter D., Yeo, Ian Y., Laude, Augustinus, Gopal, Lingam, Naing, Thet, Liao, Jiemin, Guan Ong, Peng, Mitchell, Paul, Zhou, Peng, Xie, Xuefeng, Liang, Jinlong, Mei, Junpu, Jin, Xin, Saw, Seang Mei, Ozaki, Mineo, Mizoguchi, Takanori, Kurimoto, Yasuo, Woo, Se Joon, Chung, Hum, Yu, Hyeong Gon, Shin, Joo Young, Park, Dong Ho, Kim, In Taek, Chang, Woohyok, Sagong, Min, Lee, Sang Joon, Kim, Hyun Woong, Lee, Ji Eun, Li, Yi, Liu, Jianjun, Teo, Yik Ying, Heng, Chew Kiat, Lim, Tock Han, Yang, Suk Kyun, Song, Kyuyoung, Vithana, Eranga N., Aung, Tin, Bei, Jin Xin, Zeng, Yi Xin, Tai, E. Shyong, Li, Xiao Xin, Yang, Zhenglin, Park, Kyu Hyung, Pang, Chi Pui, Yoshimura, Nagahisa, Yin Wong, Tien, Khor, Chiea Chuen, Mathur, Ranjana, Pang, Junxiong, Sim, Kar Seng, Koh, Adrian H., Chen, Peng, Lee, Shu Yen, Wong, Doric, Chan, Choi Mun, Loh, Boon Kwang, Sun, Yaoyao, Davila, Sonia, Nakata, Isao, Nakanishi, Hideo, Akagi-Kurashige, Yumiko, Gotoh, Norimoto, Tsujikawa, Akitaka, Matsuda, Fumihiko, Mori, Keisuke, Yoneya, Shin, Sakurada, Yoichi, Iijima, Hiroyuki, Iida, Tomohiro, Honda, Shigeru, Lai, Timothy Yuk Yau, Tam, Pancy Oi Sin, Chen, Haoyu, Tang, Shibo, Ding, Xiaoyan, Wen, Feng, Lu, Fang, Zhang, Xiongze, Shi, Yi, Zhao, Peiquan, Zhao, Bowen, Sang, Jinghong, Gong, Bo, Dorajoo, Rajkumar, Yuan, Jian Min, Koh, Woon Puay, Van Dam, Rob M., Friedlander, Yechiel, Lin, Ying, Hibberd, Martin L., Foo, Jia Nee, Wang, Ningli, Wong, Chang Hua, Tan, Gavin S., Park, Sang Jun, and Bhargava, Mayuri

Abstract

Age-related macular degeneration (AMD) is a major cause of blindness, but presents differently in Europeans and Asians. Here, we perform a genome-wide and exome-wide association study on 2, 119 patients with exudative AMD and 5, 691 controls, with independent replication in 4, 226 patients and 10, 289 controls, all of East Asian descent, as part of The Genetics of AMD in Asians (GAMA) Consortium. We find a strong association between CETP Asp442Gly (rs2303790), an East Asian-specific mutation, and increased risk of AMD (odds ratio (OR)=1.70, P=5.60 × 10[-22]). The AMD risk allele (442Gly), known to protect from coronary heart disease, increases HDL cholesterol levels by 0.17mmoll-1 (P=5.82 × 10[-21]) in East Asians (n=7, 102). We also identify three novel AMD loci: C6orf223 Ala231Ala (OR=0.78, P=6.19 × 10[-18]), SLC44A4 Asp47Val (OR=1.27, P=1.08 × 10[-11]) and FGD6 Gln257Arg (OR=0.87, P=2.85 × 10[-8]). Our findings suggest that some of the genetic loci conferring AMD susceptibility in East Asians are shared with Europeans, yet AMD in East Asians may also have a distinct genetic signature.

Published
2015

20. Correction: Corrigendum: New loci and coding variants confer risk for age-related macular degeneration in East Asians

Author

Cheng, Ching-Yu, primary, Yamashiro, Kenji, additional, Jia Chen, Li, additional, Ahn, Jeeyun, additional, Huang, Lulin, additional, Huang, Lvzhen, additional, Cheung, Chui Ming G., additional, Miyake, Masahiro, additional, Cackett, Peter D., additional, Yeo, Ian Y., additional, Laude, Augustinus, additional, Mathur, Ranjana, additional, Pang, Junxiong, additional, Sim, Kar Seng, additional, Koh, Adrian H., additional, Chen, Peng, additional, Lee, Shu Yen, additional, Wong, Doric, additional, Chan, Choi Mun, additional, Loh, Boon Kwang, additional, Sun, Yaoyao, additional, Davila, Sonia, additional, Nakata, Isao, additional, Nakanishi, Hideo, additional, Akagi-Kurashige, Yumiko, additional, Gotoh, Norimoto, additional, Tsujikawa, Akitaka, additional, Matsuda, Fumihiko, additional, Mori, Keisuke, additional, Yoneya, Shin, additional, Sakurada, Yoichi, additional, Iijima, Hiroyuki, additional, Iida, Tomohiro, additional, Honda, Shigeru, additional, Lai, Timothy Yuk Yau, additional, Tam, Pancy Oi Sin, additional, Chen, Haoyu, additional, Tang, Shibo, additional, Ding, Xiaoyan, additional, Wen, Feng, additional, Lu, Fang, additional, Zhang, Xiongze, additional, Shi, Yi, additional, Zhao, Peiquan, additional, Zhao, Bowen, additional, Sang, Jinghong, additional, Gong, Bo, additional, Dorajoo, Rajkumar, additional, Yuan, Jian-Min, additional, Koh, Woon-Puay, additional, van Dam, Rob M., additional, Friedlander, Yechiel, additional, Lin, Yin, additional, Hibberd, Martin L., additional, Foo, Jia Nee, additional, Wang, Ningli, additional, Wong, Chang Hua, additional, Tan, Gavin S., additional, Park, Sang Jun, additional, Bhargava, Mayuri, additional, Gopal, Lingam, additional, Naing, Thet, additional, Liao, Jiemin, additional, Ong, Peng Guan, additional, Mitchell, Paul, additional, Zhou, Peng, additional, Xie, Xuefeng, additional, Liang, Jinlong, additional, Mei, Junpu, additional, Jin, Xin, additional, Saw, Seang-Mei, additional, Ozaki, Mineo, additional, Mizoguchi, Takinori, additional, Kurimoto, Yasuo, additional, Woo, Se Joon, additional, Chung, Hum, additional, Yu, Hyeong-Gon, additional, Shin, Joo Young, additional, Park, Dong Ho, additional, Kim, In Taek, additional, Chang, Woohyok, additional, Sagong, Min, additional, Lee, Sang-Joon, additional, Kim, Hyun Woong, additional, Lee, Ji Eun, additional, Li, Yi, additional, Liu, Jianjun, additional, Teo, Yik Ying, additional, Heng, Chew Kiat, additional, Lim, Tock Han, additional, Yang, Suk-Kyun, additional, Song, Kyuyoung, additional, Vithana, Eranga N., additional, Aung, Tin, additional, Bei, Jin Xin, additional, Zeng, Yi Xin, additional, Tai, E. Shyong, additional, Li, Xiao Xin, additional, Yang, Zhenglin, additional, Park, Kyu-Hyung, additional, Pang, Chi Pui, additional, Yoshimura, Nagahisa, additional, Wong, Tien Yin, additional, and Khor, Chiea Chuen, additional

Published
2015
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21. New loci and coding variants confer risk for age-related macular degeneration in East Asians

Author

Cheng, Ching-Yu, primary, Yamashiro, Kenji, additional, Jia Chen, Li, additional, Ahn, Jeeyun, additional, Huang, Lulin, additional, Huang, Lvzhen, additional, Cheung, Chui Ming G., additional, Miyake, Masahiro, additional, Cackett, Peter D., additional, Yeo, Ian Y., additional, Laude, Augustinus, additional, Mathur, Ranjana, additional, Pang, Junxiong, additional, Sim, Kar Seng, additional, Koh, Adrian H., additional, Chen, Peng, additional, Lee, Shu Yen, additional, Wong, Doric, additional, Chan, Choi Mun, additional, Loh, Boon Kwang, additional, Sun, Yaoyao, additional, Davila, Sonia, additional, Nakata, Isao, additional, Nakanishi, Hideo, additional, Akagi-Kurashige, Yumiko, additional, Gotoh, Norimoto, additional, Tsujikawa, Akitaka, additional, Matsuda, Fumihiko, additional, Mori, Keisuke, additional, Yoneya, Shin, additional, Sakurada, Yoichi, additional, Iijima, Hiroyuki, additional, Iida, Tomohiro, additional, Honda, Shigeru, additional, Lai, Timothy Yuk Yau, additional, Tam, Pancy Oi Sin, additional, Chen, Haoyu, additional, Tang, Shibo, additional, Ding, Xiaoyan, additional, Wen, Feng, additional, Lu, Fang, additional, Zhang, Xiongze, additional, Shi, Yi, additional, Zhao, Peiquan, additional, Zhao, Bowen, additional, Sang, Jinghong, additional, Gong, Bo, additional, Dorajoo, Rajkumar, additional, Yuan, Jian-Min, additional, Koh, Woon-Puay, additional, van Dam, Rob M., additional, Friedlander, Yechiel, additional, Lin, Ying, additional, Hibberd, Martin L., additional, Foo, Jia Nee, additional, Wang, Ningli, additional, Wong, Chang Hua, additional, Tan, Gavin S., additional, Park, Sang Jun, additional, Bhargava, Mayuri, additional, Gopal, Lingam, additional, Naing, Thet, additional, Liao, Jiemin, additional, Guan Ong, Peng, additional, Mitchell, Paul, additional, Zhou, Peng, additional, Xie, Xuefeng, additional, Liang, Jinlong, additional, Mei, Junpu, additional, Jin, Xin, additional, Saw, Seang-Mei, additional, Ozaki, Mineo, additional, Mizoguchi, Takanori, additional, Kurimoto, Yasuo, additional, Woo, Se Joon, additional, Chung, Hum, additional, Yu, Hyeong-Gon, additional, Shin, Joo Young, additional, Park, Dong Ho, additional, Kim, In Taek, additional, Chang, Woohyok, additional, Sagong, Min, additional, Lee, Sang-Joon, additional, Kim, Hyun Woong, additional, Lee, Ji Eun, additional, Li, Yi, additional, Liu, Jianjun, additional, Teo, Yik Ying, additional, Heng, Chew Kiat, additional, Lim, Tock Han, additional, Yang, Suk-Kyun, additional, Song, Kyuyoung, additional, Vithana, Eranga N., additional, Aung, Tin, additional, Bei, Jin Xin, additional, Zeng, Yi Xin, additional, Tai, E. Shyong, additional, Li, Xiao Xin, additional, Yang, Zhenglin, additional, Park, Kyu-Hyung, additional, Pang, Chi Pui, additional, Yoshimura, Nagahisa, additional, Yin Wong, Tien, additional, and Khor, Chiea Chuen, additional

Published
2015
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22. Sequencing-based approach identified three new susceptibility loci for psoriasis

Author

Sheng, Yujun, Jin, Xin, Xu, Jinhua, Gao, Jinping, Du, Xiaoqing, Duan, Dawei, Li, Bing, Zhao, Jinhua, Zhan, Wenying, Tang, Huayang, Tang, Xianfa, Li, Yang, Cheng, Hui, Zuo, Xianbo, Mei, Junpu, Zhou, Fusheng, Liang, Bo, Chen, Gang, Shen, Changbing, Cui, Hongzhou, Zhang, Xiaoguang, Zhang, Change, Wang, Wenjun, Zheng, Xiaodong, Fan, Xing, Wang, Zaixing, Xiao, Fengli, Cui, Yong, Li, Yingrui, Wang, Jun, Yang, Sen, Xu, Lei, Sun, Liangdan, Zhang, Xuejun, Sheng, Yujun, Jin, Xin, Xu, Jinhua, Gao, Jinping, Du, Xiaoqing, Duan, Dawei, Li, Bing, Zhao, Jinhua, Zhan, Wenying, Tang, Huayang, Tang, Xianfa, Li, Yang, Cheng, Hui, Zuo, Xianbo, Mei, Junpu, Zhou, Fusheng, Liang, Bo, Chen, Gang, Shen, Changbing, Cui, Hongzhou, Zhang, Xiaoguang, Zhang, Change, Wang, Wenjun, Zheng, Xiaodong, Fan, Xing, Wang, Zaixing, Xiao, Fengli, Cui, Yong, Li, Yingrui, Wang, Jun, Yang, Sen, Xu, Lei, Sun, Liangdan, and Zhang, Xuejun

Published
2014

23. A large-scale screen for coding variants predisposing to psoriasis

Author

Tang, Huayang, Jin, Xin, Li, Yang, Jiang, Hui, Tang, Xianfa, Yang, Xu, Cheng, Hui, Qiu, Ying, Chen, Gang, Mei, Junpu, Zhou, Fusheng, Wu, Renhua, Zuo, Xianbo, Zhang, Yong, Zheng, Xiaodong, Cai, Qi, Yin, Xianyong, Quan, Cheng, Shao, Haojing, Cui, Yong, Tian, Fangzhen, Zhao, Xia, Liu, Hong, Xiao, Fengli, Xu, Fengping, Han, Jianwen, Shi, Dongmei, Zhang, Anping, Zhou, Cheng, Li, Qibin, Fan, Xing, Lin, Liya, Tian, Hongqing, Wang, Zaixing, Fu, Huiling, Wang, Fang, Yang, Baoqi, Huang, Shaowei, Liang, Bo, Xie, Xuefeng, Ren, Yunqing, Gu, Qingquan, Wen, Guangdong, Sun, Yulin, Wu, Xueli, Dang, Lin, Xia, Min, Shan, Junjun, Li, Tianhang, Yang, Lin, Zhang, Xiuyun, Li, Yuzhen, He, Chundi, Xu, Aie, Wei, Liping, Zhao, Xiaohang, Gao, Xinghua, Xu, Jinhua, Zhang, Furen, Zhang, Jianzhong, Li, Yingrui, Sun, Liangdan, Liu, Jianjun, Chen, Runsheng, Yang, Sen, Wang, Jun, Zhang, Xuejun, Tang, Huayang, Jin, Xin, Li, Yang, Jiang, Hui, Tang, Xianfa, Yang, Xu, Cheng, Hui, Qiu, Ying, Chen, Gang, Mei, Junpu, Zhou, Fusheng, Wu, Renhua, Zuo, Xianbo, Zhang, Yong, Zheng, Xiaodong, Cai, Qi, Yin, Xianyong, Quan, Cheng, Shao, Haojing, Cui, Yong, Tian, Fangzhen, Zhao, Xia, Liu, Hong, Xiao, Fengli, Xu, Fengping, Han, Jianwen, Shi, Dongmei, Zhang, Anping, Zhou, Cheng, Li, Qibin, Fan, Xing, Lin, Liya, Tian, Hongqing, Wang, Zaixing, Fu, Huiling, Wang, Fang, Yang, Baoqi, Huang, Shaowei, Liang, Bo, Xie, Xuefeng, Ren, Yunqing, Gu, Qingquan, Wen, Guangdong, Sun, Yulin, Wu, Xueli, Dang, Lin, Xia, Min, Shan, Junjun, Li, Tianhang, Yang, Lin, Zhang, Xiuyun, Li, Yuzhen, He, Chundi, Xu, Aie, Wei, Liping, Zhao, Xiaohang, Gao, Xinghua, Xu, Jinhua, Zhang, Furen, Zhang, Jianzhong, Li, Yingrui, Sun, Liangdan, Liu, Jianjun, Chen, Runsheng, Yang, Sen, Wang, Jun, and Zhang, Xuejun

Published
2014

24. Sequencing-based approach identified three new susceptibility loci for psoriasis

Author

Sheng, Yujun, primary, Jin, Xin, additional, Xu, Jinhua, additional, Gao, Jinping, additional, Du, Xiaoqing, additional, Duan, Dawei, additional, Li, Bing, additional, Zhao, Jinhua, additional, Zhan, Wenying, additional, Tang, Huayang, additional, Tang, Xianfa, additional, Li, Yang, additional, Cheng, Hui, additional, Zuo, Xianbo, additional, Mei, Junpu, additional, Zhou, Fusheng, additional, Liang, Bo, additional, Chen, Gang, additional, Shen, Changbing, additional, Cui, Hongzhou, additional, Zhang, Xiaoguang, additional, Zhang, Change, additional, Wang, Wenjun, additional, Zheng, Xiaodong, additional, Fan, Xing, additional, Wang, Zaixing, additional, Xiao, Fengli, additional, Cui, Yong, additional, Li, Yingrui, additional, Wang, Jun, additional, Yang, Sen, additional, Xu, Lei, additional, Sun, Liangdan, additional, and Zhang, Xuejun, additional

Published
2014
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25. A large-scale screen for coding variants predisposing to psoriasis

Author

Tang, Huayang, primary, Jin, Xin, additional, Li, Yang, additional, Jiang, Hui, additional, Tang, Xianfa, additional, Yang, Xu, additional, Cheng, Hui, additional, Qiu, Ying, additional, Chen, Gang, additional, Mei, Junpu, additional, Zhou, Fusheng, additional, Wu, Renhua, additional, Zuo, Xianbo, additional, Zhang, Yong, additional, Zheng, Xiaodong, additional, Cai, Qi, additional, Yin, Xianyong, additional, Quan, Cheng, additional, Shao, Haojing, additional, Cui, Yong, additional, Tian, Fangzhen, additional, Zhao, Xia, additional, Liu, Hong, additional, Xiao, Fengli, additional, Xu, Fengping, additional, Han, Jianwen, additional, Shi, Dongmei, additional, Zhang, Anping, additional, Zhou, Cheng, additional, Li, Qibin, additional, Fan, Xing, additional, Lin, Liya, additional, Tian, Hongqing, additional, Wang, Zaixing, additional, Fu, Huiling, additional, Wang, Fang, additional, Yang, Baoqi, additional, Huang, Shaowei, additional, Liang, Bo, additional, Xie, Xuefeng, additional, Ren, Yunqing, additional, Gu, Qingquan, additional, Wen, Guangdong, additional, Sun, Yulin, additional, Wu, Xueli, additional, Dang, Lin, additional, Xia, Min, additional, Shan, Junjun, additional, Li, Tianhang, additional, Yang, Lin, additional, Zhang, Xiuyun, additional, Li, Yuzhen, additional, He, Chundi, additional, Xu, Aie, additional, Wei, Liping, additional, Zhao, Xiaohang, additional, Gao, Xinghua, additional, Xu, Jinhua, additional, Zhang, Furen, additional, Zhang, Jianzhong, additional, Li, Yingrui, additional, Sun, Liangdan, additional, Liu, Jianjun, additional, Chen, Runsheng, additional, Yang, Sen, additional, Wang, Jun, additional, and Zhang, Xuejun, additional

Published
2013
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28. Multitranscriptome analysis revealed that stromal cells in the papillary dermis promote angiogenesis in psoriasis vulgaris.

Author

Zhang B, Mei J, Liao Q, Zhou S, Huang H, Liu H, Xu X, Yu Y, Wu C, Wang W, Hu W, Zhu T, Zhang Y, Chen M, Zhu C, Yu M, Gao J, Tang X, Liu X, Guo Z, Zheng X, Zhuang W, Chen G, Tang L, Ding X, Cheng H, Li Y, Wang H, Li H, Zhang Y, Fan X, Chen R, Rong Z, Liu P, Liu S, Yue Z, Wang P, Cai Z, Gao M, Wang Z, Fang X, Zhou F, and Tang H

Abstract

Background: The pathogenesis of psoriasis, an inflammatory skin disease, is incompletely understood. Growing evidence substantiates the involvement of stromal cells in the inflammatory process., Objectives: To investigate the roles of stromal cells, including fibroblasts, vascular endothelial cells (VECs) and smooth muscle cells (VSMCs), in the psoriatic inflammatory microenvironment and the possible underlying mechanisms involved., Methods: This study employed combination of single-cell, spatial transcriptome and bulk RNA sequencing using lesional and nonlesional skin samples from patients with psoriasis vulgaris (PV) and healthy skin samples from unaffected individuals., Results: Through the analysis of transcriptome from 364,098 single cells, we uncovered WNT5A+ fibroblasts, ITIH5+ VECs and VCAN+ VSMCs with the significantly increased cell proportions in the papillary dermis of lesional skin. We defined eight unique subclusters of fibroblasts in the skin and observed a shift of WIF1+ fibroblasts towards WNT5A+ fibroblasts, with abnormal activation of the non-canonical Wnt signaling pathway and increased capabilities of angiogenesis and pro-inflammatory. For the microvascular cells, VSMCs could undergo phenotypic transformation from a contractile phenotype to a synthetic phenotype in the development of psoriatic inflammation. ITIH5+ VECs and VCAN+ VSMCs were identified with an essential role in regulating angiogenesis and vascular remodeling involved in the mechanism of psoriatic pathological changes. Ligand receptor analyses demonstrated WNT5A+ fibroblasts were extensively implicated in interactions with various cell types in skin, especially with ITIH5+ VECs and VCAN+ VSMCs within the papillary dermis., Conclusions: Interactions of stromal cells in the papillary dermis were identified as possible pathogenic elements in psoriasis vulgaris. Improving the inflammatory microenvironment by targeting stromal cells might be a potential treatment strategy for psoriasis., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Association of Dermatologists.)

Published
2024
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29. Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories.

Author

Wang B, Wu B, Liu X, Hu Y, Ming Y, Bai M, Liu J, Xiao K, Zeng Q, Yang J, Wang H, Guo B, Tan C, Hu Z, Zhao X, Li Y, Yue Z, Mei J, Jiang W, Yang Y, Li Z, Gao Y, Chen L, Jian J, and Du H

Subjects
Animals, Phylogeny, Fishes genetics, Evolution, Molecular, Whole Genome Sequencing methods, Genome genetics, Polyploidy
Abstract

The order Acipenseriformes, which includes sturgeons and paddlefishes, represents "living fossils" with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8n), a hexavalent (6n), two tetravalents (4n), and a divalent (2n). An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs, and further provides insights into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes., (© The Author(s) 2024. Published by Oxford University Press and Science Press on behalf of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.)

Published
2024
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30. Corrigendum: New loci and coding variants confer risk for age-related macular degeneration in East Asians.

Author

Cheng CY, Yamashiro K, Jia Chen L, Ahn J, Huang L, Huang L, Cheung CMG, Miyake M, Cackett PD, Yeo IY, Laude A, Mathur R, Pang J, Sim KS, Koh AH, Chen P, Lee SY, Wong D, Chan CM, Loh BK, Sun Y, Davila S, Nakata I, Nakanishi H, Akagi-Kurashige Y, Gotoh N, Tsujikawa A, Matsuda F, Mori K, Yoneya S, Sakurada Y, Iijima H, Iida T, Honda S, Lai TYY, Tam POS, Chen H, Tang S, Ding X, Wen F, Lu F, Zhang X, Shi Y, Zhao P, Zhao B, Sang J, Gong B, Dorajoo R, Yuan JM, Koh WP, van Dam RM, Friedlander Y, Lin Y, Hibberd ML, Foo JN, Wang N, Wong CH, Tan GS, Park SJ, Bhargava M, Gopal L, Naing T, Liao J, Ong PG, Mitchell P, Zhou P, Xie X, Liang J, Mei J, Jin X, Saw SM, Ozaki M, Mizoguchi T, Kurimoto Y, Woo SJ, Chung H, Yu HG, Shin JY, Park DH, Kim IT, Chang W, Sagong M, Lee SJ, Kim HW, Lee JE, Li Y, Liu J, Teo YY, Heng CK, Lim TH, Yang SK, Song K, Vithana EN, Aung T, Bei JX, Zeng YX, Tai ES, Li XX, Yang Z, Park KH, Pang CP, Yoshimura N, Wong TY, and Khor CC

Published
2015
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