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  1. Chew KS, Tan TW, Ooi YT
    Singapore Med J, 2011 Apr;52(4):252-6.
    PMID: 21552785
    In a multiethnic nation, it is not uncommon for doctors to encounter patients of different cultural backgrounds. Often, patients' cultural beliefs influence their perception of health and illnesses, and their treatment option. Many Chinese cultural beliefs are influenced by the Taoist concept of yin-yang balance.
  2. Ranganathan S, Gribskov M, Tan TW
    BMC Bioinformatics, 2008;9 Suppl 1(Suppl 1):S1.
    PMID: 18315840 DOI: 10.1186/1471-2105-9-S1-S1
    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.
  3. Tan TW, Tan HL, Chung YC
    PMID: 39572015 DOI: 10.1111/wvn.12756
    BACKGROUND: Breast cancer patients undergoing chemotherapy experience body composition changes impacting treatment outcomes. The role of resistance training in mitigating chemotherapy-induced sarcopenia in breast cancer patients is not well defined.

    AIMS: This study aims to assess the efficacy of resistance training in preventing sarcopenia among breast cancer patients undergoing chemotherapy.

    METHODS: A systematic search was conducted across PubMed, EMBASE, Medline, the Cochrane Library, and CINAHL until May 5, 2023. Selected literature focused on the effects of resistance training on body fat, muscle mass, muscle strength, and physical performance in breast cancer patients undergoing chemotherapy. Cochrane Risk of Bias tool version 2.0 was employed for quality assessment, and data were analyzed using Comprehensive Meta-Analysis version 2.0.

    RESULTS: Eleven randomized controlled trials (RCTs) showed that resistance training had a significant positive impact on reducing body fat (SMD = -0.250, 95% CI [-0.450, -0.050]), increasing lean body mass (SMD = 0.374, 95% CI [0.178, 0.571]), and enhancing handgrip strength at both the affected site (SMD = 0.326, 95% CI [0.108, 0.543]) and the nonaffected site (SMD = 0.276, 95% CI [0.059, 0.492]). Additionally, significant improvements were observed in leg press strength (SMD = 0.598, 95% CI [0.401, 0.796]) and overall physical performance (SMD = 0.671, 95% CI [0.419, 0.923]).

    LINKING EVIDENCE TO ACTION: Resistance training is a recommended intervention for reducing body fat, increasing muscle mass, muscle strength, and enhancing physical performance in breast cancer patients undergoing chemotherapy. Ideal low-intensity resistance training programs span 8-24 weeks, with 20-to-90-min sessions 2-4 times weekly. Regimens generally entail 8-12 repetitions at 40%-90% of one-repetition maximum test, with free-weight resistance training targeting major muscle groups yielding substantial benefits. Further research should explore outcomes across different chemotherapy phases and investigate long-term resistance training effects for a comprehensive view.

  4. Patro CP, Khan AM, Tan TW, Fu XY
    PLoS One, 2014;9(8):e104597.
    PMID: 25157689 DOI: 10.1371/journal.pone.0104597
    Signal transducers and activators of transcription (STAT) proteins are key signalling molecules in metazoans, implicated in various cellular processes. Increased research in the field has resulted in the accumulation of STAT sequence and structure data, which are scattered across various public databases, missing extensive functional annotations, and prone to effort redundancy because of the dearth of community sharing. Therefore, there is a need to integrate the existing sequence, structure and functional data into a central repository, one that is enriched with annotations and provides a platform for community contributions. Herein, we present STATdb (publicly available at http://statdb.bic.nus.edu.sg/), the first integrated resource for STAT sequences comprising 1540 records representing the known STATome, enriched with existing structural and functional information from various databases and literature and including manual annotations. STATdb provides advanced features for data visualization, analysis and prediction, and community contributions. A key feature is a meta-predictor to characterise STAT sequences based on a novel classification that integrates STAT domain architecture, lineage and function. A curation policy workflow has been devised for regulated and structured community contributions, with an update policy for the seamless integration of new data and annotations.
  5. Ranganathan S, Schönbach C, Nakai K, Tan TW
    BMC Genomics, 2010;11 Suppl 4:S1.
    PMID: 21143792 DOI: 10.1186/1471-2164-11-S4-S1
    The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InCoB), Sept. 26-28, 2010 in Tokyo, Japan. Initially, APBioNet created InCoB as forum to foster bioinformatics in the Asia Pacific region. Given the growing importance of interdisciplinary research, InCoB2010 included topics targeting scientists in the fields of genomic medicine, immunology and chemoinformatics, supporting translational research. Peer-reviewed manuscripts that were accepted for publication in this supplement, represent key areas of research interests that have emerged in our region. We also highlight some of the current challenges bioinformatics is facing in the Asia Pacific region and conclude our report with the announcement of APBioNet's 100 BioDatabases (BioDB100) initiative. BioDB100 will comply with the database criteria set out earlier in our proposal for Minimum Information about a Bioinformatics and Investigation (MIABi), setting the standards for biocuration and bioinformatics research, on which we will report at the next InCoB, Nov. 27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia.
  6. Ranganathan S, Eisenhaber F, Tong JC, Tan TW
    BMC Genomics, 2009;10 Suppl 3:S1.
    PMID: 19958472 DOI: 10.1186/1471-2164-10-S3-S1
    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.
  7. Tan TW, Chen BC, Tan HL, Chang CM
    JBI Database System Rev Implement Rep, 2017 Apr;15(4):862-872.
    PMID: 28398972 DOI: 10.11124/JBISRIR-2016-003034
    REVIEW QUESTION/OBJECTIVE: This review aims to determine the best available evidence related to the effectiveness of amylmetacresol and 2,4-dichlorobenzyl alcohol throat lozenges in patients with acute sore throat due to upper respiratory tract infection (URTI). The objective is to examine the analgesic properties of amylmetacresol and 2,4-dichlorobenzyl alcohol (AMC/DCBA) throat lozenge comparing with placebo for the relief of pain in patients with acute sore throat due to URTIs.The review question is:More specifically, the objectives are to.
  8. Ranganathan S, Hsu WL, Yang UC, Tan TW
    BMC Bioinformatics, 2008 Dec 12;9 Suppl 12(Suppl 12):S1.
    PMID: 19091008 DOI: 10.1186/1471-2105-9-S12-S1
    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.
  9. Hu Y, Tan PT, Tan TW, August JT, Khan AM
    PLoS One, 2013;8(4):e59994.
    PMID: 23593157 DOI: 10.1371/journal.pone.0059994
    The rapid mutation of human immunodeficiency virus-type 1 (HIV-1) and the limited characterization of the composition and incidence of the variant population are major obstacles to the development of an effective HIV-1 vaccine. This issue was addressed by a comprehensive analysis of over 58,000 clade B HIV-1 protein sequences reported over at least 26 years. The sequences were aligned and the 2,874 overlapping nonamer amino acid positions of the viral proteome, each a possible core binding domain for human leukocyte antigen molecules and T-cell receptors, were quantitatively analyzed for four patterns of sequence motifs: (1) "index", the most prevalent sequence; (2) "major" variant, the most common variant sequence; (3) "minor" variants, multiple different sequences, each with an incidence less than that of the major variant; and (4) "unique" variants, each observed only once in the alignment. The collective incidence of the major, minor, and unique variants at each nonamer position represented the total variant population for the position. Positions with more than 50% total variants contained correspondingly reduced incidences of index and major variant sequences and increased minor and unique variants. Highly diverse positions, with 80 to 98% variant nonamer sequences, were present in each protein, including 5% of Gag, and 27% of Env and Nef, each. The multitude of different variant nonamer sequences (i.e. nonatypes; up to 68%) at the highly diverse positions, represented by the major, multiple minor, and multiple unique variants likely supported variants function both in immune escape and as altered peptide ligands with deleterious T-cell responses. The patterns of mutational change were consistent with the sequences of individual HXB2 and C1P viruses and can be considered applicable to all HIV-1 viruses. This characterization of HIV-1 protein mutation provides a foundation for the design of peptide-based vaccines and therapeutics.
  10. Schönbach C, Tan TW, Kelso J, Rost B, Nathan S, Ranganathan S
    BMC Genomics, 2011 Nov 30;12 Suppl 3:S1.
    PMID: 22369160 DOI: 10.1186/1471-2164-12-S3-S1
    In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.
  11. Ranganathan S, Schönbach C, Kelso J, Rost B, Nathan S, Tan TW
    BMC Bioinformatics, 2011;12 Suppl 13:S1.
    PMID: 22372736 DOI: 10.1186/1471-2105-12-S13-S1
    The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB's goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.
  12. Ho CS, Chan YL, Tan TW, Tay GW, Tang TB
    J Psychiatr Res, 2022 Jan 12;147:194-202.
    PMID: 35063738 DOI: 10.1016/j.jpsychires.2022.01.026
    BACKGROUND: Given that major depressive disorder (MDD) is both biologically and clinically heterogeneous, a diagnostic system integrating neurobiological markers and clinical characteristics would allow for better diagnostic accuracy and, consequently, treatment efficacy.

    OBJECTIVE: Our study aimed to evaluate the discriminative and predictive ability of unimodal, bimodal, and multimodal approaches in a total of seven machine learning (ML) models-clinical, demographic, functional near-infrared spectroscopy (fNIRS), combinations of two unimodal models, as well as a combination of all three-for MDD.

    METHODS: We recruited 65 adults with MDD and 68 matched healthy controls, who provided both sociodemographic and clinical information, and completed the HAM-D questionnaire. They were also subject to fNIRS measurement when participating in the verbal fluency task. Using the nested cross validation procedure, the classification performance of each ML model was evaluated based on the area under the receiver operating characteristic curve (ROC), balanced accuracy, sensitivity, and specificity.

    RESULTS: The multimodal ML model was able to distinguish between depressed patients and healthy controls with the highest balanced accuracy of 87.98 ± 8.84% (AUC = 0.92; 95% CI (0.84-0.99) when compared with the uni- and bi-modal models.

    CONCLUSIONS: Our multimodal ML model demonstrated the highest diagnostic accuracy for MDD. This reinforces the biological and clinical heterogeneity of MDD and highlights the potential of this model to improve MDD diagnosis rates. Furthermore, this model is cost-effective and clinically applicable enough to be established as a robust diagnostic system for MDD based on patients' biosignatures.

  13. Tan TW, Tan HL, Hsu MF, Huang HL, Chung YC
    BMC Womens Health, 2023 Nov 14;23(1):606.
    PMID: 37964288 DOI: 10.1186/s12905-023-02749-7
    BACKGROUND: Sarcopenia is a chronic disease marked by gradual muscle system and functional decline. Prior research indicates its prevalence in those under 60 varies from 8 to 36%. There is limited evidence on the effectiveness of non-pharmacological interventions for sarcopenia prevention in menopausal women aged 40-60. This study examines the influence of such interventions for sarcopenia prevention on these women.

    METHODS: PubMed, EMBASE, Medline, Cochrane Library, CINAHL, PEDro, and Airiti Library were searched from inception until May 5, 2023. Randomized controlled trials that examined exercise, vitamin D and protein supplementation effects on muscle mass, strength, and physical function. Quality assessment used the Cochrane risk of bias tool, and analysis employed Comprehensive Meta-Analysis version 2.0.

    RESULTS: A total of 27 randomized controlled trials, involving 1,989 participants were identified. Meta-analysis results showed exercise improved lean body mass (SMD = 0.232, 95% CI: 0.097, 0.366), handgrip strength (SMD = 0.901, 95% CI: 0.362, 1.441), knee extension strength (SMD = 0.698, 95% CI: 0.384, 1.013). Resistance training had a small effect on lean body mass, longer exercise duration (> 12 weeks) and higher frequency (60-90 min, 3 sessions/week) showed small to moderate effects on lean body mass. Vitamin D supplementation improved handgrip strength (SMD = 0.303, 95% CI: 0.130, 0.476), but not knee extension strength. There was insufficient data to assess the impact of protein supplementation on muscle strength.

    CONCLUSIONS: Exercise effectively improves muscle mass, and strength in menopausal women. Resistance training with 3 sessions per week, lasting 20-90 min for at least 6 weeks, is most effective. Vitamin D supplementation enhances small muscle group strength. Further trials are needed to assess the effects of vitamin D and protein supplementation on sarcopenia prevention.

    REGISTRATION NUMBER: This review was registered on PROSPERO CRD42022329273.

  14. Tan TW, Tan HL, Chang MN, Lin WS, Chang CM
    PMID: 33810438 DOI: 10.3390/ijerph18073456
    (1) Background: The implementation of effective control measures in a timely fashion is crucial to control the epidemic outbreak of COVID-19. In this study, we aimed to analyze the control measures implemented during the COVID-19 outbreak, as well as evaluating the responses and outcomes at different phases for epidemic control in Taiwan. (2) Methods: This case study reviewed responses to COVID-19 and the effectiveness of a range of control measures implemented for epidemic control in Taiwan and assessed all laboratory-confirmed cases between 11 January until 20 December 2020, inclusive of these dates. The confirmation of COVID-19 infection was defined as the positive result of a reverse-transcriptase-polymerase-chain-reaction test taken from a nasopharyngeal swab. Test results were reported by the Taiwan Centers for Disease Control. The incidence rate, mortality rate, and testing rate were compiled, and the risk ratio was provided to gain insights into the effectiveness of prevention measures. (3) Results and Discussion: This study presents retrospective data on the COVID-19 incidence rate in Taiwan, combined with the vital preventive control measures, in a timeline of the early stage of the epidemic that occurred in Taiwan. The implementation of multiple strategy control measures and the assistance of technologies to control the COVID-19 epidemic in Taiwan led to a relatively slower trend in the outbreak compared to the neighboring countries. In Taiwan, 766 confirmed patients were included, comprised of 88.1% imported cases and 7.2% local transmission cases, within the studied period. The incidence rate of COVID-19 in Taiwan during the studied period was 32 per million people, with a mortality rate of 0.3 per million people. Our analysis showed a significantly raised incidence risk ratio in the countries of interest in comparison to Taiwan during the study period; in the range of 1.9 to 947.5. The outbreak was brought under control through epidemic policies and hospital strategies implemented by the Taiwan Government. (4) Conclusion: Taiwan's preventive strategies resulted in a drastically lower risk for Taiwan nationals of contracting COVID-19 when new pharmaceutical drug or vaccines were not yet available. The preventive strategies employed by Taiwan could serve as a guide and reference for future epidemic control strategies.
  15. Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS, et al.
    BMC Med Genomics, 2017 12 21;10(Suppl 4):78.
    PMID: 29322922 DOI: 10.1186/s12920-017-0301-2
    BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets.

    RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis.

    CONCLUSION: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

  16. Zeti AM, Shamsir MS, Tajul-Arifin K, Merican AF, Mohamed R, Nathan S, et al.
    PLoS Comput Biol, 2009 Aug;5(8):e1000457.
    PMID: 19714208 DOI: 10.1371/journal.pcbi.1000457
  17. Işık EB, Brazas MD, Schwartz R, Gaeta B, Palagi PM, van Gelder CWG, et al.
    Nat Biotechnol, 2023 Aug;41(8):1171-1174.
    PMID: 37568018 DOI: 10.1038/s41587-023-01891-9
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