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Association between Gut Microbiota Composition and Long-Term Vaccine Immunogenicity following Three Doses of CoronaVac

Vaccines

Li-Na Zhang, Jing-Tong Tan, Ho-Yu Ng, Yun-Shi Liao, Rui-Qi Zhang, Kwok-Hung Chan, Ivan Fan-Ngai Hung, Tommy Tsan-Yuk Lam, Ka-Shing Cheung

2024/ 3

microbiome, coronavirus, vaccine immunogenicity

The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac

International Journal of Molecular Sciences

Ho-Yu Ng, Yunshi Liao, Ruiqi Zhang, Kwok-Hung Chan, Wai-Pan To, Chun-Him Hui, Wai-Kay Seto, Wai K Leung, Ivan FN Hung, Tommy TY Lam, Ka-Shing Cheung

2024/ 2

microbiome, coronavirus, vaccine immunogenicity

Robust expansion of phylogeny for fast-growing genome sequence data

Public Library of Science

Yongtao Ye, Marcus H Shum, Joseph L Tsui, Guangchuang Yu, David K Smith, Huachen Zhu, Joseph T Wu, Yi Guan, Tommy Tsan-Yuk Lam

2024/ 2

bioinformatics tools

Binding affinity between coronavirus spike protein and human ACE2 receptor

Computational and Structural Biotechnology Journal

Marcus Ho-Hin Shum, Yang Lee, Leighton Tam, Hui Xia, Oscar Lung-Wa Chung, Zhihong Guo, Tommy Tsan-Yuk Lam

2024/ 1

vaccine immunogenicity

Immuno-persistence after the 4th and 5th dose of inactivated polio vaccines in school-aged children

NA

Kathy Leung, Chrissy Wing Kwan Pang, Tiffany Hoi Ki Lo, Juan Vargas-Zambrano, Céline Petit, Tommy Tsan-Yuk Lam, Eric Lau, Joseph Wu

2024/ 1

coronavirus

Probable airborne transmission of Burkholderia pseudomallei causing an urban outbreak of melioidosis during typhoon season in Hong Kong, China

Emerging Microbes & Infections

Wing-Gi Wu, Marcus Ho-Hin Shum, Ivan Tak-Fai Wong, Kelvin Keru Lu, Lam-Kwong Lee, Jake Siu-Lun Leung, Hiu-Yin Lao, Annie Wing-Tung Lee, Pak-Ting Hau, Chloe Toi-Mei Chan, Harmen Fung-Tin Wong, Sharon Ka-Yee Fung, Sally Choi-Ying Wong, Iain Chi-Fung Ng, Timothy Ting-Leung Ng, Ning Chow, Alex Yat-Man Ho, Mei Fan Hung, Franklin Wang-Ngai Chow, Maureen Mo-Lin Wong, Wing-Kin To, Tommy Tsan-Yuk Lam, Kristine Shik Luk, Gilman Kit-Hang Siu

2023/12

melioidosis

Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes

Nature Microbiology

Xue-Bing Ni, Xiao-Ming Cui, Jin-Yue Liu, Run-Ze Ye, Yu-Qian Wu, Jia-Fu Jiang, Yi Sun, Qian Wang, Marcus Ho-Hin Shum, Qiao-Cheng Chang, Lin Zhao, Xiao-Hu Han, Ke Ma, Shi-Jing Shen, Ming-Zhu Zhang, Wen-Bin Guo, Jin-Guo Zhu, Lin Zhan, Liang-Jing Li, Shu-Jun Ding, Dai-Yun Zhu, Jie Zhang, Luo-Yuan Xia, Xiang-Yong Oong, Xiang-Dong Ruan, Hong-Ze Shao, Teng-Cheng Que, Guang-Yuan Liu, Chun-Hong Du, En-Jiong Huang, Xin Wang, Li-Feng Du, Chong-Cai Wang, Wen-Qiang Shi, Yu-Sheng Pan, Yu-Hao Zhou, Jiang-Li Qu, Jiang Ma, Cai-Wei Gong, Qi-Qing Chen, Qian Qin, Tick Genome and Microbiome Consortium (TIGMIC), Tommy Tsan-Yuk Lam, Na Jia, Wu-Chun Cao

2023/1

ticks, virome

High Diversity of Tick-associated Microbiota from Five Tick Species in Yunnan, China

Zoonoses

Jie Zhang, Xue-Bing Ni, Zi-Yun Chen, Yun Zhang, Ran Wei, Zheng-Da Gong, Dai-Yun Zhu, Xiao-Ming Cui, Zong-Ti Shao, Hong-Bo Liu, Yu-Qiong Li, Jian Wang, Zi-Hou Gao, Xing-De Duan, Hang Jiang, Jia-Fu Jiang, Tommy Tsan-Yuk Lam, En-Jiong Huang, Na Jia, Chun-Hong Du

2023/ 8

ticks


Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Environmental Science & Technology

Xiaole Yin, Xi Chen, Xiao-Tao Jiang, Ying Yang, Bing Li, Marcus Ho-Hin Shum, Tommy TY Lam, Gabriel M Leung, Joan Rose, Concepcion Sanchez-Cid, Timothy M Vogel, Fiona Walsh, Thomas U Berendonk, Janet Midega, Chibuzor Uchea, Dominic Frigon, Gerard D Wright, Carlos Bezuidenhout, Renata C Picão, Shaikh Z Ahammad, Per Halkjær Nielsen, Philip Hugenholtz, Nicholas J Ashbolt, Gianluca Corno, Despo Fatta-Kassinos, Helmut Bürgmann, Heike Schmitt, Chang-Jun Cha, Amy Pruden, Kornelia Smalla, Eddie Cytryn, Yu Zhang, Min Yang, Yong-Guan Zhu, Arnaud Dechesne, Barth F Smets, David W Graham, Michael R Gillings, William H Gaze, Célia M Manaia, Mark CM van Loosdrecht, Pedro JJ Alvarez, Martin J Blaser, James M Tiedje, Edward Topp, Tong Zhang

2023/ 6

AMR

Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health

Journal of Virology

Peiwen Chen, Ziying Jin, Liuxia Peng, Zuoyi Zheng, Yiu-Man Cheung, Jing Guan, Liming Chen, Yiteng Huang, Xiaohui Fan, Zengfeng Zhang, Dongmei Shi, Jin Xie, Rirong Chen, Boheng Xiao, Chun Hung Yip, David K Smith, Wenshan Hong, Yongmei Liu, Lifeng Li, Jia Wang, Edward C Holmes, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan

2023/ 6

influenza

Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses

Water Research

Xiaole Yin, Liguan Li, Xi Chen, Yang-Yu Liu, Tommy Tsan-Yuk Lam, Edward Topp, Tong Zhang

2023/ 5

AMR

Probable airborne transmission of Burkholderia pseudomallei causing an urban outbreak of melioidosis during typhoon season in Hong Kong, China

Emerging Microbes & Infections

Wing-Gi Wu, Marcus Ho-Hin Shum, Ivan Tak-Fai Wong, Kelvin Keru Lu, Lam-Kwong Lee, Jake Siu-Lun Leung, Hiu-Yin Lao, Annie Wing-Tung Lee, Pak-Ting Hau, Chloe Toi-Mei Chan, Harmen Fung-Tin Wong, Sharon Ka-Yee Fung, Sally Choi-Ying Wong, Iain Chi-Fung Ng, Timothy Ting-Leung Ng, Ning Chow, Alex Yat-Man Ho, Mei Fan Hung, Franklin Wang-Ngai Chow, Maureen Mo-Lin Wong, Wing-Kin To, Tommy Tsan-Yuk Lam, Kristine Shik Luk, Gilman Kit-Hang Siu

2023/ 5

melioidosis

Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals

Nature Communications

Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Daisy YM Ng, Lydia DJ Chang, Gigi YZ Liu, Samuel MS Cheng, Tommy TY Lam, Malik Peiris, Matthew R McKay, Leo LM Poon

2023/ 3

coronavirus

Controlling avian influenza

bmj

Kathy Leung, Tommy TY Lam, Joseph T Wu

2023/ 3

influenza, wildlife genetics

Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling

Scientific Reports

Junhao Su, Wui Wang Lui, YanLam Lee, Zhenxian Zheng, Gilman Kit-Hang Siu, Timothy Ting-Leung Ng, Tong Zhang, Tommy Tsan-Yuk Lam, Hiu-Yin Lao, Wing-Cheong Yam, Kingsley King-Gee Tam, Kenneth Siu-Sing Leung, Tak-Wah Lam, Amy Wing-Sze Leung, Ruibang Luo

2023/ 3

microbiome, bioinformatics tools

New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen
Authors

Microbiome

Li-Feng Du, Ming-Zhu Zhang, Ting-Ting Yuan, Xue-Bing Ni, Wei Wei, Xiao-Ming Cui, Ning Wang, Tao Xiong, Jie Zhang, Yu-Sheng Pan, Dai-Yun Zhu, Liang-Jing Li, Luo-Yuan Xia, Tian-Hong Wang, Ran Wei, Hong-Bo Liu, Yi Sun, Lin Zhao, Tommy Tsan-Yuk Lam, Wu-Chun Cao, Na Jia

2023/ 3

ticks, microbiome

Skin infectome of patients with a tick bite history

Frontiers in Cellular and Infection Microbiology

Jie Zhang, Yuan-Chun Zheng, Yan-Li Chu, Xiao-Ming Cui, Ran Wei, Cai Bian, Hong-Bo Liu, Nan-Nan Yao, Rui-Ruo Jiang, Qiu-Bo Huo, Ting-Ting Yuan, Jie Li, Lin Zhao, Lian-Feng Li, Qian Wang, Wei Wei, Jin-Guo Zhu, Mei-Chao Chen, Yan Gao, Fei Wang, Jin-Ling Ye, Ju-Liang Song, Jia-Fu Jiang, Tommy Tsan-Yuk Lam, Xue-Bing Ni, Na Jia

2023/ 2

ticks

One Health Surveillance of Antimicrobial Use and Resistance: Challenges and Successes of Implementing Surveillance Programs in Sri Lanka

Antibiotics

Sujeewa Ariyawansa, Kuruwitage N Gunawardana, Muditha M Hapudeniya, Nimal J Manelgamage, Chinthana R Karunarathne, Roshan P Madalagama, Kamalika H Ubeyratne, Darshana Wickramasinghe, Hein M Tun, Peng Wu, Tommy TY Lam, Olivia SK Chan

2023/ 2

AMR

Surveillance of environmental contamination by antibiotics and antibiotic-resistant pathogens: abridged secondary publication

Hong Kong Med J

K Fukuda, T Lam, H Tun, JSM Peiris, BJ Cowling, T Zhang

2023/ 2

AMR

Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history

Virus Evolution

Muhammad I Qureshi, Brian M Worthington, Yongmei Liu, William Y-M Cheung, Shuo Su, Zuoyi Zheng, Lifeng Li, Tommy T-Y Lam, Yi Guan, Huachen Zhu

2023/ 1

wildlife genetics

Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data

IMeta

Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T Lam, Yi Guan, Guangchuang Yu

2022/12

bioinformatics tools

Highly pathogenic avian influenza A (H5N1) virus clade 2.3. 4.4 b in wild birds and live bird markets, Egypt

Pathogens

Rabeh El-Shesheny, Yassmin Moatasim, Sara H Mahmoud, Yi Song, Ahmed El Taweel, Mokhtar Gomaa, Mina Nabil Kamel, Mohamed El Sayes, Ahmed Kandeil, Tommy TY Lam, Pamela P McKenzie, Richard J Webby, Ghazi Kayali, Mohamed Ahmed Ali

2022/12

influenza

Nematode and Acanthocephalan Parasites of Confiscated Sunda pangolins, Manis javanica Desmarest, 1822 (Mammalia: Pholidota: Manidae), with an Updated List of the Parasites of Pangolins

Diversity

Diane P Barton, Paolo Martelli, Brian M Worthington, Tommy T-Y Lam, Xiaocheng Zhu, Shokoofeh Shamsi

2022/11

pangolins

Genotype and organ effect on the occupancy of phyllosphere prokaryotes in different rice landraces

Archives of Microbiology

Freddy Kuok San Yeo, Yin Hui Cheok, Wan Nurainie Wan Ismail, Felicia Fui Kueh-Tai, Tommy Tsan-Yuk Lam, Yee Ling Chong

2022/10

microbiome

Leo Poon, Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Lydia Chang, Gigi Liu, Daisy Ng, Samuel Cheng, Tommy Tsan-Yuk Lam, Malik Peiris, Matthew McKay

Research Square

Leo Poon, Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Lydia Chang, Gigi Liu, Daisy Ng, Samuel Cheng, Tommy Tsan-Yuk Lam, Malik Peiris, Matthew McKay

2022/ 8

coronavirus

ggmsa: A visual exploration tool for multiple sequence alignment and associated data

Briefings in Bioinformatics

Lang Zhou, Tingze Feng, Shuangbin Xu, Fangluan Gao, Tommy T Lam, Qianwen Wang, Tianzhi Wu, Huina Huang, Li Zhan, Lin Li, Yi Guan, Zehan Dai, Guangchuang Yu

2022/ 7

bioinformatics tools

Recombinant BA. 1/BA. 2 SARS-CoV-2 virus in arriving travelers, Hong Kong, february 2022

Emerging Infectious Diseases

Haogao Gu, Daisy YM Ng, Gigi YZ Liu, Samuel SM Cheng, Pavithra Krishnan, Lydia DJ Chang, Sammi SY Cheuk, Mani MY Hui, Tommy TY Lam, Malik Peiris, Leo LM Poon

2022/ 6

coronavirus

Australia as a global sink for the genetic diversity of avian influenza A virus

PLoS Pathogens

Michelle Wille, Victoria Grillo, Silvia Ban de Gouvea Pedroso, Graham W Burgess, Allison Crawley, Celia Dickason, Philip M Hansbro, Md Ahasanul Hoque, Paul F Horwood, Peter D Kirkland, Nina Yu-Hsin Kung, Stacey E Lynch, Sue Martin, Michaela McArthur, Kim O’Riley, Andrew J Read, Simone Warner, Bethany J Hoye, Simeon Lisovski, Trent Leen, Aeron C Hurt, Jeff Butler, Ivano Broz, Kelly R Davies, Patrick Mileto, Matthew J Neave, Vicky Stevens, Andrew C Breed, Tommy TY Lam, Edward C Holmes, Marcel Klaassen, Frank YK Wong

2022/ 5

influenza

Biomedical Data Visualization: Methods and Applications

Frontiers in Genetics

Tianzhi Wu, Chuan-Le Xiao, Tommy Tsan-Yuk Lam, Guangchuang Yu

2022/ 4

bioinformatics tools

Detection of a BA. 1/BA. 2 recombinant in travelers arriving in Hong Kong, February 2022

medRxiv

Haogao Gu, Daisy YM Ng, Gigi YZ Liu, Samuel SM Cheng, Pavithra Krishnan, Lydia DJ Chang, Sammi SY Cheuk, Mani MY Hui, Tommy TY Lam, Malik Peiris, Leo Poon

2022/ 4

coronavirus

Unlocking capacities of genomics for the COVID-19 response and future pandemics

Nature Methods

Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri Porozov, Tetyana I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul

2022/ 4

coronavirus, genomics, bio/epi-informatics

Association between inflammatory cytokines and anti-SARS-CoV-2 antibodies in hospitalized patients with COVID-19

Immunity & Ageing

Xixi Jing, Min Xu, Deye Song, Tingting Yue, Yali Wang, Pan Zhang, Yanjun Zhong, Min Zhang, Tommy Tsan-Yuk Lam, Nuno Rodrigues Faria, Erik De Clercq, Guangdi Li

2022/ 3

coronavirus

Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong

Nature communications

Haogao Gu, Ruopeng Xie, Dillon C Adam, Joseph L-H Tsui, Daniel K Chu, Lydia DJ Chang, Sammi SY Cheuk, Shreya Gurung, Pavithra Krishnan, Daisy YM Ng, Gigi YZ Liu, Carrie KC Wan, Samuel SM Cheng, Kimberly M Edwards, Kathy SM Leung, Joseph T Wu, Dominic NC Tsang, Gabriel M Leung, Benjamin J Cowling, Malik Peiris, Tommy TY Lam, Vijaykrishna Dhanasekaran, Leo LM Poon

2022/ 2

coronavirus

Surveillance of Rodent Pests for SARS-CoV-2 and Other Coronaviruses, Hong Kong

Emerging infectious diseases

Elliott F Miot, Brian M Worthington, Kar Hon Ng, Lucy de Guilhem de Lataillade, Mac P Pierce, Yunshi Liao, Ronald Ko, Marcus H Shum, William Y Cheung, Edward C Holmes, Kathy S Leung, Huachen Zhu, Leo L Poon, Malik J Peiris, Yi Guan, Gabriel M Leung, Joseph T Wu, Tommy T Lam

2022/ 2

coronavirus

Robust expansion of phylogeny for fast-growing genome sequence data

bioRxiv

Yongtao Ye, Marcus Shum, Joseph Tsui, Guangchuang Yu, David Smith, Huachen Zhu, Joseph Wu, Yi Guan, Tommy Tsan-Yuk Lam

2022/ 1

bio/epi-informatics

Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020

Eurosurveillance

Kathy Leung, Yao Pei, Gabriel M Leung, Tommy TY Lam, Joseph T Wu

2021/12

coronavirus, bio/epi-informatics

Genomic characterization of a new CRF01_AE/CRF07_BC case from a MSM patient in Guangdong, China

Journal of Medical Virology

Xu‐He Huang, Guolong Yu, Chenli Zheng, Ping‐Ping Zhou, Claire Anderson, Jin Zhao, Tommy Tsan‐Yuk Lam, Yan Li, Lin Chen, Peng Lin, Ming Zhang, Jin Yan, Xiang He

2021/11

other viruses

Highly Pathogenic Avian Influenza A (H5N6) Virus Clade 2.3. 4.4 h in Wild Birds and Live Poultry Markets, Bangladesh

Emerging Infectious Diseases

Jasmine CM Turner, Subrata Barman, Mohammed M Feeroz, M Kamrul Hasan, Sharmin Akhtar, Trushar Jeevan, David Walker, John Franks, Patrick Seiler, Nabanita Mukherjee, Lisa Kercher, Pamela McKenzie, Tommy Lam, Rabeh El-Shesheny, Richard J Webby

2021/ 9

influenza

Unlocking capacities of viral genomics for the COVID-19 pandemic response

ArXiv

Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Zoia Comarova, Angela Lu, Yuri Porozov, Aiping Wu, Malak S Abedalthagafi, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Jason Ladner, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul

2021/ 4

coronavirus, bio/epi-informatics

Transmission dynamics of the COVID-19 epidemic in England

International Journal of Infectious Diseases

Yang Liu, Julian W Tang, Tommy TY Lam

2021/ 3

coronavirus, bio/epi-informatics

Nowcasting epidemics of novel pathogens: lessons from COVID-19

Nature medicine

Joseph T Wu, Kathy Leung, Tommy TY Lam, Michael Y Ni, Carlos KH Wong, JS Peiris, Gabriel M Leung

2021/ 3

coronavirus, bio/epi-informatics

Genetic variation of multiple serotypes of enteroviruses associated with hand, foot and mouth disease in Southern China

Virologica Sinica

Yonghong Zhou, Le Van Tan, Kaiwei Luo, Qiaohong Liao, Lili Wang, Qi Qiu, Gang Zou, Ping Liu, Nguyen To Anh, Nguyen Thi Thu Hong, Min He, Xiaoman Wei, Shuanbao Yu, Tommy Tsan-Yuk Lam, Jie Cui, H Rogier van Doorn, Hongjie Yu

2021/ 2

other viruses

Australia as a global sink for the genetic diversity of avian influenza A virus

bioRxiv

Michelle Wille, Victoria Tiggy Grillo, Silvia Ban de Gouvea Pedroso, Graham W Burgess, Allison Crawley, Celia Dickason, Philip M Hansbro, Md Ahasanul Hoque, Paul F Horwood, Peter D Kirkland, Nina Yu-Hsin Kung, Stacey E Lynch, Sue Martin, Michaela McArthur, Kim O’Riley, Andrew J Read, Simone Warner, Bethany J Hoye, Simeon Lisovski, Trent Leen, Aeron C Hurt, Jeff Butler, Ivano Broz, Kelly R Davies, Patrick Mileto, Matthew Neave, Vicky Stevens, Andrew Breed, Tommy TY Lam, Edward C Holmes, Marcel Klaassen, Frank YK Wong

2021/ 1

influenza

Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

Eurosurveillance

Kathy Leung, Marcus HH Shum, Gabriel M Leung, Tommy TY Lam, Joseph T Wu

2021/ 1

coronavirus, bio/epi-informatics

Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance

Journal of genetics

Hung Hui Chung, Cynthia Keranti Anak Kamar, Leonard Whye Kit Lim, Jill Sela Roja, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong

2020/12

genomics

Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration

Computational Biology and Chemistry

Leonard Whye Kit Lim, Cynthia Keranti Anak Kamar, Jill Sela Roja, Hung Hui Chung, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong

2020/12

genomics

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Nature microbiology

Maciej F Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W Perry, Todd A Castoe, Andrew Rambaut, David L Robertson

2020/11

coronavirus

Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities

Cell

Na Jia, Jinfeng Wang, Wenqiang Shi, Lifeng Du, Yi Sun, Wei Zhan, Jia-Fu Jiang, Qian Wang, Bing Zhang, Peifeng Ji, Lesley Bell-Sakyi, Xiao-Ming Cui, Ting-Ting Yuan, Bao-Gui Jiang, Wei-Fei Yang, Tommy Tsan-Yuk Lam, Qiao-Cheng Chang, Shu-Jun Ding, Xian-Jun Wang, Jin-Guo Zhu, Xiang-Dong Ruan, Lin Zhao, Jia-Te Wei, Run-Ze Ye, Teng Cheng Que, Chun-Hong Du, Yu-Hao Zhou, Jing Xia Cheng, Pei-Fang Dai, Wen-Bin Guo, Xiao-Hu Han, En-Jiong Huang, Lian-Feng Li, Wei Wei, Yu-Chi Gao, Jing-Ze Liu, Hong-Ze Shao, Xin Wang, Chong-Cai Wang, Tian-Ci Yang, Qiu-Bo Huo, Wei Li, Hai-Ying Chen, Shen-En Chen, Ling-Guo Zhou, Xue-Bing Ni, Jun-Hua Tian, Yue Sheng, Tao Liu, Yu-Sheng Pan, Luo-Yuan Xia, Jie Li, Fangqing Zhao, Wu-Chun Cao, Microbiome Consortium

2020/ 9

ticks, genomics

Comparative seasonalities of influenza A, B and ‘common cold’coronaviruses–setting the scene for SARS-CoV-2 infections and possible unexpected host immune interactions

The Journal of infection

Yang Liu, Tommy TY Lam, Florence YL Lai, Mel Krajden, Steven J Drews, Todd F Hatchette, Pieter LA Fraaij, Jeroen JA van Kampen, Darmaa Badarch, Pagbajabyn Nymadawa, Kok Keng Tee, Hong Kai Lee, Evelyn SC Koay, Lance Jennings, Marion Koopmans, Julian W Tang

2020/ 8

influenza, coronavirus

Tracking the genomic footprints of SARS-CoV-2 transmission

Trends in Genetics

Tommy Tsan-Yuk Lam

2020/ 8

coronavirus

Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins

Nature

Tommy Tsan-Yuk Lam, Na Jia, Ya-Wei Zhang, Marcus Ho-Hin Shum, Jia-Fu Jiang, Hua-Chen Zhu, Yi-Gang Tong, Yong-Xia Shi, Xue-Bing Ni, Yun-Shi Liao, Wen-Juan Li, Bao-Gui Jiang, Wei Wei, Ting-Ting Yuan, Kui Zheng, Xiao-Ming Cui, Jie Li, Guang-Qian Pei, Xin Qiang, William Yiu-Man Cheung, Lian-Feng Li, Fang-Fang Sun, Si Qin, Ji-Cheng Huang, Gabriel M Leung, Edward C Holmes, Yan-Ling Hu, Yi Guan, Wu-Chun Cao

2020/ 7

coronavirus

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Proceedings of the National Academy of Sciences

Carla Mavian, Sergei Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne-Mieke Vandamme, Simon Dellicour, Samuel V Scarpino, Charlotte Houldcroft, Julian Villabona-Arenas, Taylor K Paisie, Nídia S Trovão, Christina Boucher, Yun Zhang, Richard H Scheuermann, Olivier Gascuel, Tommy Tsan-Yuk Lam, Marc A Suchard, Ana Abecasis, Eduan Wilkinson, Tulio de Oliveira, Ana I Bento, Heiko A Schmidt, Darren Martin, James Hadfield, Nuno Faria, Nathan D Grubaugh, Richard A Neher, Guy Baele, Philippe Lemey, Tanja Stadler, Jan Albert, Keith A Crandall, Thomas Leitner, Alexandros Stamatakis, Mattia Prosperi, Marco Salemi

2020/ 6

coronavirus

Sequencing and characterisation of complete mitochondrial DNA genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with phylogenetic consideration

Tropical life sciences research

Hung Hui Chung, Leonard Whye Kit Lim, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong

2020/ 4

genomics

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference—application to H5N1 spread in the Mekong region

Bioinformatics

Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie Von Dobschuetz, Filip Claes, Scott H Newman, Marc A Suchard, Guy Baele, Marius Gilbert

2020/ 4

influenza, bio/epi-informatics

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

Molecular biology and evolution

Li-Gen Wang, Tommy Tsan-Yuk Lam, Shuangbin Xu, Zehan Dai, Lang Zhou, Tingze Feng, Pingfan Guo, Casey W Dunn, Bradley R Jones, Tyler Bradley, Huachen Zhu, Yi Guan, Yong Jiang, Guangchuang Yu

2020/ 2

bio/epi-informatics

Sequencing and characterisation of complete mitogenome DNA for Rasbora hobelmani (Cyprinidae) with phylogenetic consideration

Journal of Ichthyology

HH Chung, CKA Kamar, LWK Lim, Y Liao, TT Lam, Yee Ling Chong

2020/ 1

genomics

Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia

New England journal of medicine

Qun Li, Xuhua Guan, Peng Wu, Xiaoye Wang, Lei Zhou, Yeqing Tong, Ruiqi Ren, Kathy SM Leung, Eric HY Lau, Jessica Y Wong, Xuesen Xing, Nijuan Xiang, Yang Wu, Chao Li, Qi Chen, Dan Li, Tian Liu, Jing Zhao, Man Liu, Wenxiao Tu, Chuding Chen, Lianmei Jin, Rui Yang, Qi Wang, Suhua Zhou, Rui Wang, Hui Liu, Yinbo Luo, Yuan Liu, Ge Shao, Huan Li, Zhongfa Tao, Yang Yang, Zhiqiang Deng, Boxi Liu, Zhitao Ma, Yanping Zhang, Guoqing Shi, Tommy TY Lam, Joseph T Wu, George F Gao, Benjamin J Cowling, Bo Yang, Gabriel M Leung, Zijian Feng

2020/ 1

coronavirus

Empirical transmission advantage of the D614G mutant strain of SARS-CoV-2

MedRxiv

Kathy Leung, Yao Pei, Gabriel M Leung, Tommy TY Lam, Joseph T Wu

2020/ 1

coronavirus

Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

MedRxiv

Kathy Leung, Marcus HH Shum, Gabriel M Leung, Tommy TY Lam, Joseph T Wu

2020/ 1

coronavirus

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. bioRxiv 2020.03. 30.015008

DOI

MF Boni, P Lemey, X Jiang, TTY Lam, B Perry, T Castoe, A Rambaut, DL Robertson

2020

coronavirus

Sequencing and characterization of complete mitogenome DNA for Rasbora myersi (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance

Gene Reports

Leonard Whye Kit Lim, Jill Sela Roja, Cynthia Keranti Anak Kamar, Hung Hui Chung, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong

2019/12

genomics

Transmitted and acquired oseltamivir resistance during the 2018–2019 influenza season

Journal of Infection

Julian W Tang, Matthew Kennedy, Angie Lackenby, Joanna Ellis, Tommy Lam

2019/12

influenza

Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015

Journal of Infection

Tommy T Lam, Julian W Tang, Florence Y Lai, Hassan Zaraket, Ghassan Dbaibo, Seweryn Bialasiewicz, Sarah Tozer, Jean-Michel Heraud, Steven J Drews, Todd Hachette, Paul KS Chan, Evelyn SC Koay, Hong Kai Lee, Kok Keng Tee, Yang Liu, Pieter LA Fraaij, Lance Jennings, Matti Waris, Mel Krajden, André Corriveau, Hamid Jalal, Hidekazu Nishimura, Pagbajabyn Nymadawa, Darmaa Badarch, Aripuana Watanabe, Alice Kabanda, Theo Sloots, Jen Kok, Dominic E Dwyer, Marion Koopmans

2019/10

influenza, other respiratory viruses, other viruses

Emergence of human infection with Jingmen tick virus in China: A retrospective study

EBioMedicine

Na Jia, Hong-Bo Liu, Xue-Bing Ni, Lesley Bell-Sakyi, Yuan-Chun Zheng, Ju-Liang Song, Jie Li, Bao-Gui Jiang, Qian Wang, Yi Sun, Ran Wei, Ting-Ting Yuan, Luo-Yuan Xia, Yan-Li Chu, Wei Wei, Lian-Feng Li, Jin-Ling Ye, Qing-Yu Lv, Xiao-Ming Cui, Yi Guan, Yi-Gang Tong, Jia-Fu Jiang, Tommy Tsan-Yuk Lam, Wu-Chun Cao

2019/ 5

arbovirus, ticks

Impact of a poorly performing point-of-care test during the 2017-2018 influenza season

Journal of Infection

Julian W Tang, Janice Blount, Carina Bradley, Bernadette Donaghy, Carol Shardlow, Srini Bandi, Caroline Baxter, Ann Hunter, Simon Range, Tommy TY Lam

2019/ 3

influenza

Genomic surveillance of avian-origin influenza A viruses causing human disease

Genome Medicine

Tommy T Lam, Oliver G Pybus

2018/12

influenza

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

Molecular biology and evolution

Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan

2018/12

bio/epi-informatics

Neuraminidase inhibitor susceptibility and evolutionary analysis of human influenza B isolates from three Asian countries during 2012–2015

Infection, Genetics and Evolution

Akinobu Hibino, Elie Massaad, Hiroki Kondo, Reiko Saito, Takashi Odagiri, Nobuhiro Takemae, Ryota Tsunekuni, Takehiko Saito, Yadanar Kyaw, Nay Lin, Yi Yi Myint, Htay Htay Tin, Nguyen Le Khanh Hang, Ren Yagami, Yugo Shobugawa, Tommy Lam, Hassan Zaraket, Japanese Influenza Collaborative Study Group

2018/ 8

influenza

Large-scale complete-genome sequencing and phylodynamic analysis of eastern equine encephalitis virus reveals source-sink transmission dynamics in the United States

Journal of virology

Yi Tan, Tommy Tsan-Yuk Lam, Lea A Heberlein-Larson, Sandra C Smole, Albert J Auguste, Scott Hennigan, Rebecca A Halpin, Nadia Fedorova, Vinita Puri, Timothy B Stockwell, Meghan H Shilts, Theodore Andreadis, Philip M Armstrong, Robert B Tesh, Scott C Weaver, Thomas R Unnasch, Alexander T Ciota, Laura D Kramer, Suman R Das

2018/ 6

arbovirus, mosquitoes

The impact of host genetic diversity on virus evolution and emergence

Ecology Letters

Cristina Rodríguez‐Nevado, Tommy T‐Y Lam, Edward C Holmes, Israel Pagan

2018/ 2

other viruses, genomics

Geographically weighted temporally correlated logistic regression model

Scientific reports

Yang Liu, Kwok-Fai Lam, Joseph T Wu, Tommy Tsan-Yuk Lam

2018/ 1

bio/epi-informatics

A cluster of Zika virus infection among travellers returning to China from Samoa: a case tracing study

Journal of Travel Medicine

Gang Wang, Wei Zheng, Sheng Zhu, Zhonghua Wu, Tommy Tsan-Yuk Lam, Yuanhua Tong, Runzi Qi

2018

other viruses

Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance

The Lancet Infectious Diseases

Julian W Tang, Tommy T Lam, Hassan Zaraket, W Ian Lipkin, Steven J Drews, Todd F Hatchette, Jean-Michel Heraud, Marion P Koopmans, Ashta Mary Abraham, Amal Baraket, Seweryn Bialasiewicz, Miguela A Caniza, Paul KS Chan, Cheryl Cohen, André Corriveau, Benjamin J Cowling, Marcela Echavarria, Ron Fouchier, Pieter LA Fraaij, Todd F Hachette, Hamid Jalal, Lance Jennings, Alice Kabanda, Herve A Kadjo, Mohammed Rafiq Khanani, Evelyn SC Koay, Mel Krajden, Hong Kai Lee, W Ian Lipkin, Julius Lutwama, David Marchant, Hidekazu Nishimura, Pagbajabyn Nymadawa, Benjamin A Pinsky, Sanjiv Rughooputh, Joseph Rukelibuga, Taslimarif Saiyed, Anita Shet, Theo Sloots, JJ Muyembe Tamfum, Stefano Tempia, Sarah Tozer, Florette Treurnicht, Matti Waris, Aripuana Watanabe, Emile Okitolonda Wemakoy

2017/10

other respiratory viruses

ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Methods in Ecology and Evolution

Guangchuang Yu, David K Smith, Huachen Zhu, Yi Guan, Tommy Tsan‐Yuk Lam

2017/ 1

bio/epi-informatics

Genomic analysis of the emergence, evolution, and spread of human respiratory RNA viruses

Annual Review of Genomics and Human Genetics

Tommy T-Y Lam, Huachen Zhu, Yi Guan, Edward C Holmes

2016/ 8

influenza, coronavirus, other respiratory viruses

Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015

Infection, Genetics and Evolution

Pei-Yu Huang, Chang-Chun David Lee, Chun-Hung Yip, Chung-Lam Cheung, Guangchuang Yu, Tommy Tsan-Yuk Lam, David K Smith, Huachen Zhu, Yi Guan

2016/ 3

influenza

Molecular evolution and intraclade recombination of enterovirus D68 during the 2014 outbreak in the United States

Journal of virology

Yi Tan, Ferdaus Hassan, Jennifer E Schuster, Ari Simenauer, Rangaraj Selvarangan, Rebecca A Halpin, Xudong Lin, Nadia Fedorova, Timothy B Stockwell, Tommy Tsan-Yuk Lam, James D Chappell, Tina V Hartert, Edward C Holmes, Suman R Das

2016/ 2

other viruses

Emergence and development of H7N9 influenza viruses in China

Current opinion in virology

Huachen Zhu, Tommy Tsan-Yuk Lam, David Keith Smith, Yi Guan

2016/ 2

influenza

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

Virus evolution

Andrew Rambaut, Tommy T Lam, Luiz Max Carvalho, Oliver G Pybus

2016/ 1

bio/epi-informatics

Infectivity and transmissibility of avian H9N2 influenza viruses in pigs

Journal of virology

Jia Wang, Maocai Wu, Wenshan Hong, Xiaohui Fan, Rirong Chen, Zuoyi Zheng, Yu Zeng, Ren Huang, Yu Zhang, Tommy Tsan-Yuk Lam, David K Smith, Huachen Zhu, Yi Guan

2016/ 1

influenza

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia

Science

Jamal SM Sabir, Tommy T-Y Lam, Mohamed MM Ahmed, Lifeng Li, Yongyi Shen, Salah EM Abo-Aba, Muhammd I Qureshi, Mohamed Abu-Zeid, Yu Zhang, Mohammad A Khiyami, Njud S Alharbi, Nahid H Hajrah, Meshaal J Sabir, Mohammed HZ Mutwakil, Saleh A Kabli, Faten AS Alsulaimany, Abdullah Y Obaid, Boping Zhou, David K Smith, Edward C Holmes, Huachen Zhu, Yi Guan

2016/ 1

coronavirus

Puzzling origins of the Ebola outbreak in the Democratic Republic of the Congo, 2014

Journal of virology

Tommy Tsan-Yuk Lam, Huachen Zhu, Yee Ling Chong, Edward C Holmes, Yi Guan

2015/10

other viruses

Epidemiological and evolutionary dynamics of influenza B viruses in Malaysia, 2012-2014

PloS one

Xiang Yong Oong, Kim Tien Ng, Tommy Tsan-Yuk Lam, Yong Kek Pang, Kok Gan Chan, Nik Sherina Hanafi, Adeeba Kamarulzaman, Kok Keng Tee

2015/ 8

influenza

Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013

Journal of virology

Simon J Watson, Pinky Langat, Scott M Reid, Tommy Tsan-Yuk Lam, Matthew Cotten, Michael Kelly, Kristien Van Reeth, Yu Qiu, Gaëlle Simon, Emilie Bonin, Emanuela Foni, Chiara Chiapponi, Lars Larsen, Charlotte Hjulsager, Iwona Markowska-Daniel, Kinga Urbaniak, Ralf Dürrwald, Michael Schlegel, Anita Huovilainen, Irit Davidson, Ádám Dán, Willie Loeffen, Stephanie Edwards, Michel Bublot, Thais Vila, Jaime Maldonado, Laura Valls, ESNIP3 Consortium, Ian H Brown, Oliver G Pybus, Paul Kellam

2015/ 7

influenza

Dissemination, divergence and establishment of H7N9 influenza viruses in China

Nature

Tommy Tsan-Yuk Lam, Boping Zhou, Jia Wang, Yujuan Chai, Yongyi Shen, Xinchun Chen, Chi Ma, Wenshan Hong, Yin Chen, Yanjun Zhang, Lian Duan, Peiwen Chen, Junfei Jiang, Yu Zhang, Lifeng Li, Leo Lit Man Poon, Richard J Webby, David K Smith, Gabriel M Leung, Joseph SM Peiris, Edward C Holmes, Yi Guan, Huachen Zhu

2015/ 6

influenza

Emergence and evolution of H10 subtype influenza viruses in poultry in China

Journal of virology

Chi Ma, Tommy Tsan-Yuk Lam, Yujuan Chai, Jia Wang, Xiaohui Fan, Wenshan Hong, Yu Zhang, Lifeng Li, Yongmei Liu, David K Smith, Richard J Webby, Joseph SM Peiris, Huachen Zhu, Yi Guan

2015/ 4

influenza

Occurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in China

Journal of virology

Wei Liu, Hang Fan, Jayna Raghwani, Tommy Tsan-Yuk Lam, Jing Li, Oliver G Pybus, Hong-Wu Yao, Ying Wo, Kun Liu, Xiao-Ping An, Guang-Qian Pei, Hao Li, Hong-Yu Wang, Jian-Jun Zhao, Tao Jiang, Mai-Juan Ma, Xian Xia, Yan-De Dong, Tong-Yan Zhao, Jia-Fu Jiang, Yin-Hui Yang, Yi Guan, Yigang Tong, Wu-Chun Cao

2014/11

influenza

Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China

Journal of virology

Huyi Liang, Tommy Tsan-Yuk Lam, Xiaohui Fan, Xinchun Chen, Yu Zeng, Ji Zhou, Lian Duan, Maying Tse, Chung-Hei Chan, Lifeng Li, Tak-Ying Leung, Chun-Hung Yip, Chung-Lam Cheung, Boping Zhou, David K Smith, Leo Lit-Man Poon, Malik Peiris, Yi Guan, Huachen Zhu

2014/ 9

influenza

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States

Infection, Genetics and Evolution

Matthew Scotch, Tommy Tsan-Yuk Lam, Kristy L Pabilonia, Theodore Anderson, John Baroch, Dennis Kohler, Thomas J DeLiberto

2014/ 8

influenza

Emergence and evolution of avian H5N2 influenza viruses in chickens in Taiwan

Journal of virology

Chang-Chun David Lee, Huachen Zhu, Pei-Yu Huang, Liuxia Peng, Yun-Cheng Chang, Chun-Hung Yip, Yao-Tsun Li, Chung-Lam Cheung, Richard Compans, Chinglai Yang, David K Smith, Tommy Tsan-Yuk Lam, Chwan-Chuen King, Yi Guan

2014/ 5

influenza

Increasing similarity in the dynamics of influenza in two adjacent subtropical Chinese cities following the relaxation of border restrictions

The Journal of General Virology

Yi Tan, Tommy Tsan-Yuk Lam, Chunli Wu, Shui-shan Lee, Cecile Viboud, Renli Zhang, Daniel M Weinberger

2014/ 3

influenza

Viral evolution explains the associations among hepatitis C virus genotype, clinical outcomes, and human genetic variation

Infection, Genetics and Evolution

Rebecca Rose, Peter V Markov, Tommy T Lam, Oliver G Pybus

2013/12

other viruses

Comparison of mutation patterns in full-genome A/H3N2 influenza sequences obtained directly from clinical samples and the same samples after a single MDCK passage

PLoS One

Hong Kai Lee, Julian Wei-Tze Tang, Debra Han-Lin Kong, Tze Ping Loh, Donald Kok-Leong Chiang, Tommy Tsan-Yuk Lam, Evelyn Siew-Chuan Koay

2013/11

influenza

Differing epidemiological dynamics of influenza B virus lineages in Guangzhou, southern China, 2009-2010

Journal of virology

Yi Tan, Wenda Guan, Tommy Tsan-Yuk Lam, Sihua Pan, Shiguan Wu, Yangqing Zhan, Cecile Viboud, Edward C Holmes, Zifeng Yang

2013/11

influenza

Migration and persistence of human influenza A viruses, Vietnam, 2001–2008

Emerging infectious diseases

Mai Quynh Le, Ha Minh Lam, Vuong Duc Cuong, Tommy Tsan-Yuk Lam, Rebecca A Halpin, David E Wentworth, Nguyen Tran Hien, Le Thi Thanh, Hoang Vu Mai Phuong, Peter Horby, Maciej F Boni

2013/11

influenza

The genesis and source of the H7N9 influenza viruses causing human infections in China

Nature

Tommy Tsan-Yuk Lam, Jia Wang, Yongyi Shen, Boping Zhou, Lian Duan, Chung-Lam Cheung, Chi Ma, Samantha J Lycett, Connie Yin-Hung Leung, Xinchun Chen, Lifeng Li, Wenshan Hong, Yujuan Chai, Linlin Zhou, Huyi Liang, Zhihua Ou, Yongmei Liu, Amber Farooqui, David J Kelvin, Leo LM Poon, David K Smith, Oliver G Pybus, Gabriel M Leung, Yuelong Shu, Robert G Webster, Richard J Webby, Joseph SM Peiris, Andrew Rambaut, Huachen Zhu, Yi Guan

2013/10

influenza

Effect of probiotic bacteria on the intestinal microbiota in irritable bowel syndrome

Journal of gastroenterology and hepatology

Siew Chien Ng, Emma FC Lam, Tommy TY Lam, Yawen Chan, Wendy Law, Pete CH Tse, Michael A Kamm, Joseph JY Sung, Francis KL Chan, Justin CY Wu

2013/10

microbiome

Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments

Infection, Genetics and Evolution

Tommy Tsan-Yuk Lam, Yee Ling Chong, Mang Shi, Chung-Chau Hon, Jun Li, Darren P Martin, Julian Wei-Tze Tang, Chee-Keng Mok, Shin-Ru Shih, Chi-Wai Yip, Jingwei Jiang, Raymond Kin-Hei Hui, Oliver G Pybus, Edward C Holmes, Frederick Chi-Ching Leung

2013/ 8

influenza

The rapidly expanding CRF01_AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s

AIDS (London, England)

Yi Feng, Xiang He, Jenny H Hsi, Fan Li, Xingguang Li, Quan Wang, Yuhua Ruan, Hui Xing, Tommy Tsan-Yuk Lam, Oliver G Pybus, Yutaka Takebe, Yiming Shao

2013/ 7

other viruses

Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission

Infection, Genetics And Evolution

Yee Ling Chong, Tommy Tsan-Yuk Lam, Oekyung Kim, Huaguang Lu, Patty Dunn, Mary Poss

2013/ 7

other viruses

Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus

Emerging infectious diseases

Matthew Cotten, Tommy T Lam, Simon J Watson, Anne L Palser, Velislava Petrova, Paul Grant, Oliver G Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul Kellam, Eleni Nastouli

2013/ 5

coronavirus

Molecular characterization of the fecal microbiota in patients with nonalcoholic steatohepatitis–a longitudinal study

PloS one

Vincent Wai-Sun Wong, Chi-Hang Tse, Tommy Tsan-Yuk Lam, Grace Lai-Hung Wong, Angel Mei-Ling Chim, Winnie Chiu-Wing Chu, David Ka-Wai Yeung, Patrick Tik-Wan Law, Hoi-Shan Kwan, Jun Yu, Joseph Jao-Yiu Sung, Henry Lik-Yuen Chan

2013/ 4

microbiome

Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus

Epidemics

Tommy Tsan-Yuk Lam, Wei Liu, Thomas A Bowden, Ning Cui, Lu Zhuang, Kun Liu, Yao-Yun Zhang, Wu-Chun Cao, Oliver G Pybus

2013/ 3

arbovirus, ticks

The evolutionary dynamics of influenza A virus adaptation to mammalian hosts

Philosophical Transactions of the Royal Society B: Biological Sciences

S Bhatt, TT Lam, SJ Lycett, AJ Leigh Brown, TA Bowden, EC Holmes, Y Guan, JLN Wood, IH Brown, P Kellam, Combating Swine Influenza Consortium, OG Pybus, Ian Brown, Sharon Brookes, Anna Germundsson, Alex Cook, Susanna Williamson, Stephen Essen, Fanny Garcon, George Gunn, Manuel Sanchez, Diogo Marques, James Wood, Dan Tucker, Ian McCrone, Julia Gog, Roberto Saenz, Meg Staff, Pablo Murcia, Wendy Barclay, Christl Donnelly, Ruth A Elderfield, Paul Kellam, Greg Baillie, Eve Coulter, Barbara Wieland, Alex Mastin, John McCauley, Andy Leigh Brown, Sam Lycett, Mark Woolhouse, Oliver Pybus, Samir Bhatt, Andrew Hayward, David Ishola, Alan Archibald, Tom Freeman, Bryan Charleston, Eric LeFevre, Mick Bailey, Charlotte Inman, Chris Stokes, Kin Chow Chang, Stephen Dunham, Gavin White, Jonathan Nguyen-Van-Tam, Joanne Enstone

2013/ 3

influenza

Epidemiological dynamics and phylogeography of influenza virus in southern China

The Journal of infectious diseases

Xiaowen Cheng, Yi Tan, Mingliang He, Tommy Tsan-Yuk Lam, Xing Lu, Cécile Viboud, Jianfan He, Shunxiang Zhang, Jianhua Lu, Chunli Wu, Shishong Fang, Xin Wang, Xu Xie, Hanwu Ma, Martha I Nelson, Hsiang-fu Kung, Edward C Holmes, Jinquan Cheng

2013/ 1

influenza

Phylodynamics of H5N1 avian influenza virus in Indonesia

Molecular ecology

TOMMY TSAN‐YUK LAM, CHUNG‐CHAU HON, Philippe Lemey, Oliver G Pybus, Mang Shi, Hein Min Tun, JUN Li, Jingwei Jiang, Edward C Holmes, FREDERICK CHI‐CHING LEUNG

2012/ 6

influenza

The recombinant origin of emerging human norovirus GII. 4/2008: intra-genotypic exchange of the capsid P2 domain

The Journal of general virology

Tommy Tsan-Yuk Lam, Huachen Zhu, David K Smith, Yi Guan, Edward C Holmes, Oliver G Pybus

2012/ 4

other viruses

Emergence and dissemination of a swine H3N2 reassortant influenza virus with 2009 pandemic H1N1 genes in pigs in China

Journal of virology

Xiaohui Fan, Huachen Zhu, Boping Zhou, David K Smith, Xinchun Chen, Tommy T-Y Lam, Leo LM Poon, Malik Peiris, Yi Guan

2012/ 2

influenza

Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

Ecology letters

Tommy Tsan‐Yuk Lam, Hon S Ip, Elodie Ghedin, David E Wentworth, Rebecca A Halpin, Timothy B Stockwell, David J Spiro, Robert J Dusek, James B Bortner, Jenny Hoskins, Bradley D Bales, Dan R Yparraguirre, Edward C Holmes

2012/ 1

influenza

Novel reassortment of Eurasian avian-like and pandemic/2009 influenza viruses in swine: infectious potential for humans

Journal of virology

Huachen Zhu, Boping Zhou, Xiaohui Fan, Tommy TY Lam, Jia Wang, Antony Chen, Xinchun Chen, Honglin Chen, Robert G Webster, Richard Webby, Joseph SM Peiris, David K Smith, Yi Guan

2011/10

influenza

Reassortment events among swine influenza A viruses in China: implications for the origin of the 2009 influenza pandemic

Journal of virology

Tommy Tsan-Yuk Lam, Huachen Zhu, Jia Wang, David K Smith, Edward C Holmes, Robert G Webster, Richard Webby, Joseph M Peiris, Yi Guan

2011/10

influenza

Genetic characterization and evolutionary analysis of 4 Newcastle disease virus isolate full genomes from waterbirds in South China during 2003–2007

Veterinary microbiology

Shaoxin Cai, Jun Li, Mabel Ting Wong, Peirong Jiao, Huiying Fan, Dawei Liu, Ming Liao, Jingwei Jiang, Mang Shi, Tommy Tsan-Yuk Lam, Tao Ren, Frederick Chi-Ching Leung

2011/ 8

other viruses

Spatial dynamics of human-origin H1 influenza A virus in North American swine

PLoS pathogens

Martha I Nelson, Philippe Lemey, Yi Tan, Amy Vincent, Tommy Tsan-Yuk Lam, Susan Detmer, Cécile Viboud, Marc A Suchard, Andrew Rambaut, Edward C Holmes, Marie Gramer

2011/ 6

influenza

Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States

Journal of virology

Martha I Nelson, Yi Tan, Elodie Ghedin, David E Wentworth, Kirsten St. George, Laurel Edelman, Eric T Beck, Jiang Fan, Tommy Tsan-Yuk Lam, Swati Kumar, David J Spiro, Lone Simonsen, Cecile Viboud, Edward C Holmes, Kelly J Henrickson, James M Musser

2011/ 1

influenza

Reassortment events between European Avian-like and American Triple-reassortant Swine Influenza Viruses in Southern China

Annual NIAID CEIRS Network Meeting

TY Lam, H Zhu, J Wang, DK Smith, EC Holmes, RG Webster, R Webby, JSM Peiris, Y Guan

2011

influenza

Pandemic H1N1/2009 virus in swine: prevalence and genesis of reassortants with the potential to infect humans

ESWI Influenza Conference

H Zhu, L Li, Y Zeng, J Zhou, Z Zheng, R Chen, R Zheng, L Duan, CH Yip, K Huang, TY Lam, J Wang, H Chen, RG Webster, R Webby, JSM Peiris, DK Smith, Y Guan

2011

influenza

History of Swine influenza viruses in Asia

Swine influenza

Huachen Zhu, Richard Webby, Tommy TY Lam, David K Smith, Joseph SM Peiris, Yi Guan

2011

influenza

Reassortants of the pandemic H1N1/2009 virus in swine and their potential to infect human

Annual NIAID CEIRS Network Meeting

H Zhu, DK Smith, TY Lam, L Li, Z Zheng, R Chen, R Zheng, Y Zeng, J Zhou, J Wang, H Chen, RG Webster, R Webby, JSM Peiris, Y Guan

2011

influenza

Detection of a novel swine influenza reassortant virus with human infectious potential and inter-species transmissibility from pigs to ferrets

40th Keystone Symposia on Molecular and Cellular Biology

H Zhu, L Duan, L Li, TY Lam, J Wang, DK Smith, JSM Peiris, Y Guan

2011

influenza

Molecular epidemiology of PRRSV: a phylogenetic perspective

Virus research

Mang Shi, Tommy Tsan-Yuk Lam, Chung-Chau Hon, Raymond Kin-Hei Hui, Kay S Faaberg, Trevor Wennblom, Michael P Murtaugh, Tomasz Stadejek, Frederick Chi-Ching Leung

2010/12

other viruses

The ever-expanding diversity of porcine reproductive and respiratory syndrome virus

Virus research

Michael P Murtaugh, Tomasz Stadejek, Juan E Abrahante, Tommy TY Lam, Frederick C-C Leung

2010/12

other viruses

Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses

Journal of virology

Mang Shi, Tommy Tsan-Yuk Lam, Chung-Chau Hon, Michael P Murtaugh, Peter R Davies, Raymond Kin-Hei Hui, Jun Li, Lina Tik-Wim Wong, Chi-Wai Yip, Jin-Wai Jiang, Frederick Chi-Ching Leung

2010/ 9

other viruses

Emerging, novel, and known influenza virus infections in humans

Infectious Disease Clinics

Julian W Tang, Nandini Shetty, Tommy TY Lam, KL Ellis Hon

2010/ 9

influenza

Features of the new pandemic influenza A/H1N1/2009 virus: virology, epidemiology, clinical and public health aspects

Current opinion in pulmonary medicine

Julian W Tang, Nandini Shetty, Tommy Tsan-Yuk Lam

2010/ 5

influenza

Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene

Journal of virology

Kok Keng Tee, Tommy Tsan-Yuk Lam, Yoke Fun Chan, Jon M Bible, Adeeba Kamarulzaman, CY William Tong, Yutaka Takebe, Oliver G Pybus

2010/ 4

other viruses

Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans

Journal of general virology

Junfa Yuan, Chung-Chau Hon, Yan Li, Dingming Wang, Gelin Xu, Huajun Zhang, Peng Zhou, Leo LM Poon, Tommy Tsan-Yuk Lam, Frederick Chi-Ching Leung, Zhengli Shi

2010/ 4

coronavirus

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Critical reviews in clinical laboratory sciences

Tommy Tsan-Yuk Lam, Chung-Chau Hon, Julian W Tang

2010/ 2

other viruses, bio/epi-informatics

The sequence and de novo assembly of the giant panda genome

Nature

Ruiqiang Li, Wei Fan, Geng Tian, Hongmei Zhu, Lin He, Jing Cai, Quanfei Huang, Qingle Cai, Bo Li, Yinqi Bai, Zhihe Zhang, Yaping Zhang, Wen Wang, Jun Li, Fuwen Wei, Heng Li, Min Jian, Jianwen Li, Zhaolei Zhang, Rasmus Nielsen, Dawei Li, Wanjun Gu, Zhentao Yang, Zhaoling Xuan, Oliver A Ryder, Frederick Chi-Ching Leung, Yan Zhou, Jianjun Cao, Xiao Sun, Yonggui Fu, Xiaodong Fang, Xiaosen Guo, Bo Wang, Rong Hou, Fujun Shen, Bo Mu, Peixiang Ni, Runmao Lin, Wubin Qian, Guodong Wang, Chang Yu, Wenhui Nie, Jinhuan Wang, Zhigang Wu, Huiqing Liang, Jiumeng Min, Qi Wu, Shifeng Cheng, Jue Ruan, Mingwei Wang, Zhongbin Shi, Ming Wen, Binghang Liu, Xiaoli Ren, Huisong Zheng, Dong Dong, Kathleen Cook, Gao Shan, Hao Zhang, Carolin Kosiol, Xueying Xie, Zuhong Lu, Hancheng Zheng, Yingrui Li, Cynthia C Steiner, Tommy Tsan-Yuk Lam, Siyuan Lin, Qinghui Zhang, Guoqing Li, Jing Tian, Timing Gong, Hongde Liu, Dejin Zhang, Lin Fang, Chen Ye, Juanbin Zhang, Wenbo Hu, Anlong Xu, Yuanyuan Ren, Guojie Zhang, Michael W Bruford, Qibin Li, Lijia Ma, Yiran Guo, Na An, Yujie Hu, Yang Zheng, Yongyong Shi, Zhiqiang Li, Qing Liu, Yanling Chen, Jing Zhao, Ning Qu, Shancen Zhao, Feng Tian, Xiaoling Wang, Haiyin Wang, Lizhi Xu, Xiao Liu, Tomas Vinar, Yajun Wang, Tak-Wah Lam, Siu-Ming Yiu, Shiping Liu, Hemin Zhang, Desheng Li, Yan Huang, Xia Wang, Guohua Yang, Zhi Jiang, Junyi Wang, Nan Qin, Li Li, Jingxiang Li, Lars Bolund, Karsten Kristiansen, Gane Ka-Shu Wong, Maynard Olson, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, Jun Wang

2010/ 1

genomics

Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses

Infection, Genetics and Evolution

Chi Wai Yip, Chung Chau Hon, Mang Shi, Tommy Tsan-Yuk Lam, Ken Yan-Ching Chow, Fanya Zeng, Frederick Chi-Ching Leung

2009/12

coronavirus

A phylogeny-based evolutionary, demographic and geographic dissection of north American type porcine reproductive and respiratory syndrome virus (NA-PRRSV)

International PRRS Symposium

M Shi, TY Lam, CC Hon, MP Murtaugh, P Davies, RKH Hui, J Li, TWL Wong, J Jiang, CW Yip, FCC Leung

2009

other respiratory viruses

Phylogenetic evidence for homologous recombination within the family Birnaviridae

Journal of General Virology

Chung-Chau Hon, Tommy Tsan-Yuk Lam, Chi-Wai Yip, Raymond Tsz-Yeung Wong, Mang Shi, Jingwei Jiang, Fanya Zeng, Frederick Chi-Ching Leung

2008/12

other viruses

Molecular epidemiology of H5N1 Avian Influenza Virus: Correlations between antigenic drift, geographical migration and expansion of viral diversity

International Journal of Infectious Diseases

TY Lam, OG Pybus, CC Hon, FC Leung

2008/12

influenza

Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia

PLoS pathogens

Tommy Tsan-Yuk Lam, Chung-Chau Hon, Oliver G Pybus, Sergei L Kosakovsky Pond, Raymond Tze-Yeung Wong, Chi-Wai Yip, Fanya Zeng, Frederick Chi-Ching Leung

2008/ 8

influenza

Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events

Virus research

Tsan-Yuk Lam, Chung-Chau Hon, Zhenggang Wang, Raymond Kin-Hi Hui, Fanya Zeng, Frederick Chi-Ching Leung

2008/ 2

influenza

Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus

Journal of virology

Chung-Chau Hon, Tsan-Yuk Lam, Zheng-Li Shi, Alexei J Drummond, Chi-Wai Yip, Fanya Zeng, Pui-Yi Lam, Frederick Chi-Ching Leung

2008/ 2

coronavirus

Comments to the predecessor of human SARS coronavirus in 2003–2004 epidemic

Veterinary microbiology

Tommy Tsan-Yuk Lam, Chung-Chau Hon, Pui-Yi Lam, Chi-Wai Yip, Fanya Zeng, Frederick Chi-Ching Leung

2008/ 1

influenza

Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China

Journal of general virology

Ching-Man Ma, Chung-Chau Hon, Tsan-Yuk Lam, Vince Yik-Yeung Li, Creany Ka-Wai Wong, Tulio de Oliveira, Frederick Chi-Ching Leung

2007/ 6

other viruses

Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B

Journal of virology

Chung-Chau Hon, Tsan-Yuk Lam, Alexei Drummond, Andrew Rambaut, Yiu-Fai Lee, Chi-Wai Yip, Fanya Zeng, Pui-Yi Lam, Patrick TW Ng, Frederick CC Leung

2006/ 9

other viruses

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