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  1. Article: Tracking the Genomic Footprints of SARS-CoV-2 Transmission.

    Lam, Tommy Tsan-Yuk

    Trends in genetics : TIG

    2020  Volume 36, Issue 8, Page(s) 544–546

    Abstract: 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 analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding ... ...

    Abstract 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 analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains.
    MeSH term(s) Betacoronavirus ; COVID-19 ; China ; Coronavirus Infections ; Genomics ; Humans ; Pandemics ; Pneumonia, Viral ; SARS Virus ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-05-28
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2020.05.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Editorial: Biomedical Data Visualization: Methods and Applications.

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

    Frontiers in genetics

    2022  Volume 13, Page(s) 890775

    Language English
    Publishing date 2022-04-27
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.890775
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Tracking the Genomic Footprints of SARS-CoV-2 Transmission

    Lam, Tommy Tsan-Yuk

    Trends in Genetics

    2020  Volume 36, Issue 8, Page(s) 544–546

    Keywords Genetics ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2020.05.009
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: Binding affinity between coronavirus spike protein and human ACE2 receptor.

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

    Computational and structural biotechnology journal

    2024  Volume 23, Page(s) 759–770

    Abstract: Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining ... ...

    Abstract Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (K
    Language English
    Publishing date 2024-01-17
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2024.01.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Tracking the Genomic Footprints of SARS-CoV-2 Transmission

    Lam, Tommy Tsan-Yuk

    Trends Genet

    Abstract: 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 analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding ... ...

    Abstract 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 analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #401257
    Database COVID19

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  6. Article ; Online: Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses

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

    Water Research. 2023 May, v. 235 p.119875-

    2023  

    Abstract: The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad ... ...

    Abstract The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.
    Keywords antibiotic resistance ; antibiotic resistance genes ; bioinformatics ; humans ; livestock ; metagenomics ; models ; research ; taxonomy ; wastewater ; wastewater treatment ; water
    Language English
    Dates of publication 2023-05
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 202613-2
    ISSN 1879-2448 ; 0043-1354
    ISSN (online) 1879-2448
    ISSN 0043-1354
    DOI 10.1016/j.watres.2023.119875
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses.

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

    Water research

    2023  Volume 235, Page(s) 119875

    Abstract: The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad ... ...

    Abstract The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.
    MeSH term(s) Humans ; Metagenome ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ecosystem
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-03-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 202613-2
    ISSN 1879-2448 ; 0043-1354
    ISSN (online) 1879-2448
    ISSN 0043-1354
    DOI 10.1016/j.watres.2023.119875
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Robust expansion of phylogeny for fast-growing genome sequence data.

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

    PLoS computational biology

    2024  Volume 20, Issue 2, Page(s) e1011871

    Abstract: 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. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ... ...

    Abstract 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. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ancestral sequences. It took about 21 seconds to insert 100 SARS-CoV-2 genomes into a 100k-taxa reference tree using 1.4 gigabytes. Benchmarking on four datasets, TIPars achieved the highest accuracy for phylogenies of moderately similar sequences. For highly similar and divergent scenarios, fully parsimony-based and likelihood-based phylogenetic placement methods performed the best respectively while TIPars was the second best. TIPars accomplished efficient and accurate expansion of phylogenies of both similar and divergent sequences, which would have broad biological applications beyond SARS-CoV-2. TIPars is accessible from https://tipars.hku.hk/ and source codes are available at https://github.com/id-bioinfo/TIPars.
    MeSH term(s) Phylogeny ; Likelihood Functions ; Genome ; Software ; SARS-CoV-2/genetics
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011871
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

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

    Vaccines

    2024  Volume 12, Issue 4

    Abstract: Background: Neutralizing antibody level wanes with time after COVID-19 vaccination. We aimed to study the relationship between baseline gut microbiota and immunogenicity after three doses of CoronaVac.: Methods: This was a prospective cohort study ... ...

    Abstract Background: Neutralizing antibody level wanes with time after COVID-19 vaccination. We aimed to study the relationship between baseline gut microbiota and immunogenicity after three doses of CoronaVac.
    Methods: This was a prospective cohort study recruiting three-dose CoronaVac recipients from two centers in Hong Kong. Blood samples were collected at baseline and one year post-first dose for virus microneutralization (vMN) assays to determine neutralization titers. The primary outcome was high immune response (defined as with vMN titer ≥ 40). Shotgun DNA metagenomic sequencing of baseline fecal samples identified potential bacterial species and metabolic pathways using Linear Discriminant Analysis Effect Size (LEfSe) analysis. Univariate and multivariable logistic regression models were used to identify high response predictors.
    Results: In total, 36 subjects were recruited (median age: 52.7 years [IQR: 47.9-56.4]; male: 14 [38.9%]), and 18 had low immune response at one year post-first dose vaccination.
    Conclusion: E. rectale,
    Language English
    Publishing date 2024-03-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines12040365
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Sequencing and Characterisation of Complete Mitochondrial DNA Genome for

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

    Tropical life sciences research

    2020  Volume 31, Issue 1, Page(s) 107–121

    Abstract: ... ...

    Abstract The
    Language English
    Publishing date 2020-04-07
    Publishing country Malaysia
    Document type Journal Article
    ZDB-ID 2607038-8
    ISSN 2180-4249 ; 1985-3718
    ISSN (online) 2180-4249
    ISSN 1985-3718
    DOI 10.21315/tlsr2020.31.1.7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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