Search Results - "Lam, Tommy Tsan‐Yuk"

ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data by Yu, Guangchuang, Smith, David K., Zhu, Huachen, Guan, Yi, Lam, Tommy Tsan‐Yuk, McInerny, Greg

“…Summary We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats…”
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Phylogeny-Based Evolutionary, Demographical, and Geographical Dissection of North American Type 2 Porcine Reproductive and Respiratory Syndrome Viruses by Shi, Mang, Lam, Tommy Tsan-Yuk, Hon, Chung-Chau, Murtaugh, Michael P, Davies, Peter R, Hui, Raymond Kin-Hei, Li, Jun, Wong, Lina Tik-Wim, Yip, Chi-Wai, Jiang, Jin-Wai, Leung, Frederick Chi-Ching

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Evolutionary Genetics of Human Enterovirus 71: Origin, Population Dynamics, Natural Selection, and Seasonal Periodicity of the VP1 Gene by KOK KENG TEE, LAM, Tommy Tsan-Yuk, YOKE FUN CHAN, BIBLE, Jon M, KAMARULZAMAN, Adeeba, TONG, C. Y. William, TAKEBE, Yutaka, PYBUS, Oliver G

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Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree by Yu, Guangchuang, Lam, Tommy Tsan-Yuk, Zhu, Huachen, Guan, Yi

“…Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external…”
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Genomic characterization of a new CRF01_AE/CRF07_BC case from a MSM patient in Guangdong, China by Huang, Xu‐He, Yu, Guolong, Zheng, Chenli, Zhou, Ping‐Ping, Anderson, Claire, Zhao, Jin, Lam, Tommy Tsan‐Yuk, Li, Yan, Chen, Lin, Lin, Peng, Zhang, Ming, Yan, Jin, He, Xiang

“…The CRF01_AE and CRF07_BC clades dominate the human immunodeficiency virus (HIV) epidemics in China. Both clades have been identified in the men who have sex…”
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Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic by Boni, Maciej F., Lemey, Philippe, Jiang, Xiaowei, Lam, Tommy Tsan-Yuk, Perry, Blair W., Castoe, Todd A., Rambaut, Andrew, Robertson, David L.

“…There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of…”
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Reassortment Events among Swine Influenza A Viruses in China: Implications for the Origin of the 2009 Influenza Pandemic by TSAN-YUK LAM, Tommy, HUACHEN ZHU, JIA WANG, SMITH, David K, HOLMES, Edward C, WEBSTER, Robert G, WEBBY, Richard, PEIRIS, Joseph M, YI GUAN

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Tracking the Genomic Footprints of SARS-CoV-2 Transmission by Lam, Tommy Tsan-Yuk

“…There is considerable public and scientific interest in the origin, spread, and evolution of SARS-CoV-2. Lu et al. recently conducted genomic sequencing and…”
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The rapidly expanding CRF01_AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s by Feng, Yi, He, Xiang, Hsi, Jenny H, Li, Fan, Li, Xingguang, Wang, Quan, Ruan, Yuhua, Xing, Hui, Lam, Tommy Tsan-Yuk, Pybus, Oliver G, Takebe, Yutaka, Shao, Yiming

“…OBJECTIVES:We sought to comprehensively analyze the origin, transmission patterns and sub-epidemic clusters of the HIV-1 CRF01_AE strains in China…”
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The genesis and source of the H7N9 influenza viruses causing human infections in China by Lam, Tommy Tsan-Yuk, Wang, Jia, Shen, Yongyi, Zhou, Boping, Duan, Lian, Cheung, Chung-Lam, Ma, Chi, Lycett, Samantha J., Leung, Connie Yin-Hung, Chen, Xinchun, Li, Lifeng, Hong, Wenshan, Chai, Yujuan, Zhou, Linlin, Liang, Huyi, Ou, Zhihua, Liu, Yongmei, Farooqui, Amber, Kelvin, David J., Poon, Leo L. M., Smith, David K., Pybus, Oliver G., Leung, Gabriel M., Shu, Yuelong, Webster, Robert G., Webby, Richard J., Peiris, Joseph S. M., Rambaut, Andrew, Zhu, Huachen, Guan, Yi

“…Evolutionary analyses show that H7 influenza viruses probably transferred from ducks to chickens in China on at least two independent occasions, and that…”
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Molecular characterization of the fecal microbiota in patients with nonalcoholic steatohepatitis--a longitudinal study by Wong, Vincent Wai-Sun, Tse, Chi-Hang, Lam, Tommy Tsan-Yuk, Wong, Grace Lai-Hung, Chim, Angel Mei-Ling, Chu, Winnie Chiu-Wing, Yeung, David Ka-Wai, Law, Patrick Tik-Wan, Kwan, Hoi-Shan, Yu, Jun, Sung, Joseph Jao-Yiu, Chan, Henry Lik-Yuen

“…The human gut microbiota has profound influence on host metabolism and immunity. This study characterized the fecal microbiota in patients with nonalcoholic…”
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Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013 by Watson, Simon J, Langat, Pinky, Reid, Scott M, Lam, Tommy Tsan-Yuk, Cotten, Matthew, Kelly, Michael, Van Reeth, Kristien, Qiu, Yu, Simon, Gaëlle, Bonin, Emilie, Foni, Emanuela, Chiapponi, Chiara, Larsen, Lars, Hjulsager, Charlotte, Markowska-Daniel, Iwona, Urbaniak, Kinga, Dürrwald, Ralf, Schlegel, Michael, Huovilainen, Anita, Davidson, Irit, Dán, Ádám, Loeffen, Willie, Edwards, Stephanie, Bublot, Michel, Vila, Thais, Maldonado, Jaime, Valls, Laura, Brown, Ian H, Pybus, Oliver G, Kellam, Paul

“…The emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza…”
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Genetic characterization and evolutionary analysis of 4 Newcastle disease virus isolate full genomes from waterbirds in South China during 2003–2007 by Cai, Shaoxin, Li, Jun, Wong, Mabel Ting, Jiao, Peirong, Fan, Huiying, Liu, Dawei, Liao, Ming, Jiang, Jingwei, Shi, Mang, Lam, Tommy Tsan-Yuk, Ren, Tao, Leung, Frederick Chi-Ching

“…Complete genomes of four Newcastle disease virus (NDV) strains, isolated from ducks and wild birds in Guangdong province of China from 2003 to 2007, were…”
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Geographically weighted temporally correlated logistic regression model by Liu, Yang, Lam, Kwok-Fai, Wu, Joseph T., Lam, Tommy Tsan-Yuk

“…Detecting the temporally and spatially varying correlations is important to understand the biological and disease systems. Here we proposed a geographically…”
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Robust expansion of phylogeny for fast-growing genome sequence data by Ye, Yongtao, Shum, Marcus H, Tsui, Joseph L, Yu, Guangchuang, Smith, David K, Zhu, Huachen, Wu, Joseph T, Guan, Yi, Lam, Tommy Tsan-Yuk

“…Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference…”
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Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins by Lam, Tommy Tsan-Yuk, Jia, Na, Zhang, Ya-Wei, Shum, Marcus Ho-Hin, Jiang, Jia-Fu, Zhu, Hua-Chen, Tong, Yi-Gang, Shi, Yong-Xia, Ni, Xue-Bing, Liao, Yun-Shi, Li, Wen-Juan, Jiang, Bao-Gui, Wei, Wei, Yuan, Ting-Ting, Zheng, Kui, Cui, Xiao-Ming, Li, Jie, Pei, Guang-Qian, Qiang, Xin, Cheung, William Yiu-Man, Li, Lian-Feng, Sun, Fang-Fang, Qin, Si, Huang, Ji-Cheng, Leung, Gabriel M., Holmes, Edward C., Hu, Yan-Ling, Guan, Yi, Cao, Wu-Chun

“…The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-2 1 . This outbreak has been tentatively…”
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Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States by Tan, Yi, Hassan, Ferdaus, Schuster, Jennifer E, Simenauer, Ari, Selvarangan, Rangaraj, Halpin, Rebecca A, Lin, Xudong, Fedorova, Nadia, Stockwell, Timothy B, Lam, Tommy Tsan-Yuk, Chappell, James D, Hartert, Tina V, Holmes, Edward C, Das, Suman R

“…In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete…”
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Association between inflammatory cytokines and anti-SARS-CoV-2 antibodies in hospitalized patients with COVID-19 by Jing, Xixi, Xu, Min, Song, Deye, Yue, Tingting, Wang, Yali, Zhang, Pan, Zhong, Yanjun, Zhang, Min, Lam, Tommy Tsan-Yuk, Faria, Nuno Rodrigues, De Clercq, Erik, Li, Guangdi

“…COVID-19 patients may experience "cytokine storm" when human immune system produces excessive cytokines/chemokines. However, it remains unclear whether early…”
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Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling by Su, Junhao, Lui, Wui Wang, Lee, YanLam, Zheng, Zhenxian, Siu, Gilman Kit-Hang, Ng, Timothy Ting-Leung, Zhang, Tong, Lam, Tommy Tsan-Yuk, Lao, Hiu-Yin, Yam, Wing-Cheong, Tam, Kingsley King-Gee, Leung, Kenneth Siu-Sing, Lam, Tak-Wah, Leung, Amy Wing-Sze, Luo, Ruibang

“…Sensitive detection of Mycobacterium tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug…”
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Infectivity and Transmissibility of Avian H9N2 Influenza Viruses in Pigs by Wang, Jia, Wu, Maocai, Hong, Wenshan, Fan, Xiaohui, Chen, Rirong, Zheng, Zuoyi, Zeng, Yu, Huang, Ren, Zhang, Yu, Lam, Tommy Tsan-Yuk, Smith, David K, Zhu, Huachen, Guan, Yi

“…The H9N2 influenza viruses that are enzootic in terrestrial poultry in China pose a persistent pandemic threat to humans. To investigate whether the continuous…”
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