Displaying publications 1 - 20 of 448 in total

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  1. Grand challenges in bioinformatics education and training
    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
    Matched MeSH terms: Computational Biology*
  2. Proceedings of the Asia Pacific Bioinformatics Network (APBioNet) Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011, November 30-December 2, 2011, Kuala Lumpur, Malaysia
    BMC Bioinformatics, 2011;12 Suppl 13:S1-25.
    PMID: 22893921
    Matched MeSH terms: Computational Biology*
  3. Fulltext Molecular medicine: the way forward
    Rahman AJA
    Med J Malaysia, 2004 Oct;59(4):441-2.
    PMID: 15779574
    Matched MeSH terms: Molecular Biology/trends*
  4. The cytology laboratory services in Malaysia
    Pillay B
    Malays J Pathol, 1982 Aug;5:7-9.
    PMID: 7187461
    Matched MeSH terms: Cell Biology*
  5. Computational Chemistry in Asia
    Wei GW, Soares TA, Wahab H, Wang R
    J Chem Inf Model, 2021 02 22;61(2):547.
    PMID: 33529020 DOI: 10.1021/acs.jcim.1c00081
    Matched MeSH terms: Computational Biology*
  6. Integrative Multi-Omics Through Bioinformatics
    Goh HH
    Adv Exp Med Biol, 2018 11 2;1102:69-80.
    PMID: 30382569 DOI: 10.1007/978-3-319-98758-3_5
    This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.
    Matched MeSH terms: Computational Biology*; Systems Biology*
  7. On ξ a -Quadratic Stochastic operators on 2-D Simplex
    Mukhamedov F, Izzat Qaralleh, Wan Nur Fairuz Alwani Wan Rozali
    Sains Malaysiana, 2014;43:1275-1281.
    A quadratic stochastic operator (Qso) is usually used to present the time evolution of differing species in biology. Some quadratic stochastic operators have been studied by Lotka and Volterra. The general problem in the nonlinear operator theory is to study the behavior of operators. This problem was not fully finished even for quadratic stochastic operators which are the simplest nonlinear operators. To study this problem, several classes of QSO were investigated. In this paper, we study the fri)-Qso defined on 2D simplex. We first classify 4-(a)-QS0 into 2 non-conjugate classes. Further, we investigate the dynamics of these classes of such operators.
    Matched MeSH terms: Biology
  8. Application of Reverse Vaccinology and Immunoinformatic Strategies for the Identification of Vaccine Candidates Against Shigella flexneri
    Leow CY, Chuah C, Abdul Majeed AB, Mohd Nor N, Leow CH
    Methods Mol Biol, 2022;2414:17-35.
    PMID: 34784029 DOI: 10.1007/978-1-0716-1900-1_2
    Reverse vaccinology (RV) was first introduced by Rappuoli for the development of an effective vaccine against serogroup B Neisseria meningitidis (MenB). With the advances in next generation sequencing technologies, the amount of genomic data has risen exponentially. Since then, the RV approach has widely been used to discover potential vaccine protein targets by screening whole genome sequences of pathogens using a combination of sophisticated computational algorithms and bioinformatic tools. In contrast to conventional vaccine development strategies, RV offers a novel method to facilitate rapid vaccine design and reduces reliance on the traditional, relatively tedious, and labor-intensive approach based on Pasteur"s principles of isolating, inactivating, and injecting the causative agent of an infectious disease. Advances in biocomputational techniques have remarkably increased the significance for the rapid identification of the proteins that are secreted or expressed on the surface of pathogens. Immunogenic proteins which are able to induce the immune response in the hosts can be predicted based on the immune epitopes present within the protein sequence. To date, RV has successfully been applied to develop vaccines against a variety of infectious pathogens. In this chapter, we apply a pipeline of bioinformatic programs for identification of Shigella flexneri potential vaccine candidates as an illustration immunoinformatic tools available for RV.
    Matched MeSH terms: Computational Biology
  9. A Q-marker screening strategy based on ADME studies and systems biology for Chinese herbal medicine, taking Qianghuo Shengshi decoction in treating rheumatoid arthritis as an example
    Wang J, Tao C, Xu G, Ling J, Tong J, Goh BH, et al.
    Mol Omics, 2023 Dec 04;19(10):769-786.
    PMID: 37498608 DOI: 10.1039/d3mo00029j
    Chinese herbal medicine (CHM) exhibits a broad spectrum of clinical applications and demonstrates favorable therapeutic efficacy. Nonetheless, elucidating the underlying mechanism of action (MOA) of CHM in disease treatment remains a formidable task due to its inherent characteristics of multi-level, multi-linked, and multi-dimensional non-linear synergistic actions. In recent years, the concept of a Quality marker (Q-marker) proposed by Liu et al. has significantly contributed to the monitoring and evaluation of CHM products, thereby fostering the advancement of CHM research. Within this study, a Q-marker screening strategy for CHM formulas has been introduced, particularly emphasising efficacy and biological activities, integrating absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification. As an illustrative case, the Q-marker screening of Qianghuo Shengshi decoction (QHSSD) for treating rheumatoid arthritis (RA) has been conducted. Consequently, from a pool of 159 compounds within QHSSD, five Q-markers exhibiting significant in vitro anti-inflammatory effects have been identified. These Q-markers encompass notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Furthermore, by employing an integrated analysis of network pharmacology and metabolomics, several instructive insights into pharmacological mechanisms have been gleaned. This includes the identification of key targets and pathways through which QHSSD exerts its crucial roles in the treatment of RA. Notably, the inhibitory effect of QHSSD on AKT1 and MAPK3 activation has been validated through western blot analysis, underscoring its potential to mitigate RA-related inflammatory responses. In summary, this research demonstrates the proposed strategy's feasibility and provides a practical reference model for the systematic investigation of CHM formulas.
    Matched MeSH terms: Systems Biology
  10. Fulltext Efficient feature selection and classification of protein sequence data in bioinformatics
    Iqbal MJ, Faye I, Samir BB, Said AM
    ScientificWorldJournal, 2014;2014:173869.
    PMID: 25045727 DOI: 10.1155/2014/173869
    Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth.
    Matched MeSH terms: Computational Biology/methods*
  11. First description of the tadpole of Kurixalus baliogaster (Inger, Orlov, and Darevsky, 1999) (Anura: Rhacophoridae) from Vietnam, with comments on reproductive biology
    Kropachev II, Vassilieva AB, Orlov NL, Rybaltovsky EM, Nguyen TT
    Zootaxa, 2021 Sep 14;5039(1):144-148.
    PMID: 34811091 DOI: 10.11646/zootaxa.5039.1.9
    To date, 20 species of Kurixalus Ye, Fei, and Dubois have been described, and all of these species are distributed throughout South and Southeast Asia, from eastern India, throughout Myanmar and the mountainous regions of southern China, to Indochina, western and northern peninsular Thailand, Malaysia, Sumatra, Borneo, and the Philippines (Frost 2021). Descriptions of the tadpoles of only 6 species have been published: K. berylliniris and K. wangi Wu, Huang, Tsai, Li, Jhang, Wu (Wu et al. 2016); K. eiffingeri (Boettger) (Kuramoto Wang 1987); K. idiootocus (Kuramoto Wang) (Kuramoto Wang 1987); K. cf. verrucosus (Boulenger) (Ziegler Vences 2002), and Kurixalus yangi Yu, Hui, Rao, Yang (Humtsoe et al. 2020). A description of the tadpoles of K. baliogaster (Inger, Orlov, Darevsky) is also given in the species description (Inger et al. 1999), but described larvae are assigned tentatively to this species in the published text. Additional studies on the identification of the conspecificity of the described tadpoles with K. baliogaster have not been conducted. Based on the much larger size of the tadpole body (TL up to 40.3 mm), as well as the labial tooth row formula 6(26)/5(1) given by Inger et al. (1999), we concluded that these described tadpoles cannot be larval K. baliogaster and most likely belong to some other species of rhacophorid frogs.
    Matched MeSH terms: Biology*
  12. Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae
    Ting TY, Li Y, Bunawan H, Ramzi AB, Goh HH
    J Biosci Bioeng, 2023 Apr;135(4):259-265.
    PMID: 36803862 DOI: 10.1016/j.jbiosc.2023.01.010
    Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.
    Matched MeSH terms: Synthetic Biology*
  13. Fulltext Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference
    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.
    Matched MeSH terms: Computational Biology*; Systems Biology
  14. Functional Genomics
    Goh HH, Ng CL, Loke KK
    Adv Exp Med Biol, 2018 11 2;1102:11-30.
    PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2
    Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
    Matched MeSH terms: Computational Biology*; Systems Biology
  15. Fulltext Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)
    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.
    Matched MeSH terms: Computational Biology/methods; Computational Biology/trends*; Systems Biology
  16. Fulltext New recursive circular algorithm for listing all permutations
    Sharmila Karim, Zurni Omar, Haslinda Ibrahim, Khairil Iskandar Othman, Mohamed Suleiman
    Pertanika Journal of Science & Technology, 2014;22(1):25-33.
    MyJurnal
    Linear array of permutations is hard to be factorised. However, by using a starter set, the process of listing the permutations becomes easy. Once the starter sets are obtained, the circular and reverse of circular operations are easily employed to produce distinct permutations from each starter set. However, a problem arises when the equivalence starter sets generate similar permutations and, therefore, willneed to be discarded. In this paper, a new recursive strategy is proposed to generate starter sets that will not incur equivalence by circular operation. Computational advantages are presented that compare the results obtained by the new algorithm with those obtained using two other existing methods. The result indicates that the new algorithm is faster than the other two in time execution.
    Matched MeSH terms: Computational Biology
  17. Fulltext Adaptation of sensor morphology: an integrative view of perception from biologically inspired robotics perspective
    Iida F, Nurzaman SG
    Interface Focus, 2016 Aug 06;6(4):20160016.
    PMID: 27499843 DOI: 10.1098/rsfs.2016.0016
    Sensor morphology, the morphology of a sensing mechanism which plays a role of shaping the desired response from physical stimuli from surroundings to generate signals usable as sensory information, is one of the key common aspects of sensing processes. This paper presents a structured review of researches on bioinspired sensor morphology implemented in robotic systems, and discusses the fundamental design principles. Based on literature review, we propose two key arguments: first, owing to its synthetic nature, biologically inspired robotics approach is a unique and powerful methodology to understand the role of sensor morphology and how it can evolve and adapt to its task and environment. Second, a consideration of an integrative view of perception by looking into multidisciplinary and overarching mechanisms of sensor morphology adaptation across biology and engineering enables us to extract relevant design principles that are important to extend our understanding of the unfinished concepts in sensing and perception.
    Matched MeSH terms: Biology
  18. Fulltext Solution for nonlinear Duffing oscillator using variable order variable stepsize block method
    Ahmad Fadly Nurullah Rasedee, Mohammad Hasan Abdul Sathar, Norizarina Ishak, Irneza Ismail, Musab Sahrim, Nur Ainna Ramli, et al.
    MATEMATIKA, 2017;33(2):165-175.
    MyJurnal
    Real life phenomena found in various fields such as engineering, physics,
    biology and communication theory can be modeled as nonlinear higher order ordinary
    differential equations, particularly the Duffing oscillator. Analytical solutions for these
    differential equations can be time consuming whereas, conventional numerical solutions
    may lack accuracy. This research propose a block multistep method integrated with a
    variable order step size (VOS) algorithm for solving these Duffing oscillators directly.
    The proposed VOS Block method provides an alternative numerical solution by reducing
    computational cost (time) but without loss of accuracy. Numerical simulations
    are compared with known exact solutions for proof of accuracy and against current
    numerical methods for proof of efficiency (steps taken).
    Matched MeSH terms: Biology
  19. Fulltext Whole-exome sequencing and bioinformatic analyses revealed differences in gene mutation profiles in papillary thyroid cancer patients with and without benign thyroid goitre background
    Eng ZH, Abdullah MI, Ng KL, Abdul Aziz A, Arba'ie NH, Mat Rashid N, et al.
    Front Endocrinol (Lausanne), 2022;13:1039494.
    PMID: 36686473 DOI: 10.3389/fendo.2022.1039494
    BACKGROUND: Papillary thyroid cancer (PTC) is the most common thyroid malignancy. Concurrent presence of cytomorphological benign thyroid goitre (BTG) and PTC lesion is often detected. Aberrant protein profiles were previously reported in patients with and without BTG cytomorphological background. This study aimed to evaluate gene mutation profiles to further understand the molecular mechanism underlying BTG, PTC without BTG background and PTC with BTG background.

    METHODS: Patients were grouped according to the histopathological examination results: (i) BTG patients (n = 9), (ii) PTC patients without BTG background (PTCa, n = 8), and (iii) PTC patients with BTG background (PTCb, n = 5). Whole-exome sequencing (WES) was performed on genomic DNA extracted from thyroid tissue specimens. Nonsynonymous and splice-site variants with MAF of ≤ 1% in the 1000 Genomes Project were subjected to principal component analysis (PCA). PTC-specific SNVs were filtered against OncoKB and COSMIC while novel SNVs were screened through dbSNP and COSMIC databases. Functional impacts of the SNVs were predicted using PolyPhen-2 and SIFT. Protein-protein interaction (PPI) enrichment of the tumour-related genes was analysed using Metascape and MCODE algorithm.

    RESULTS: PCA plots showed distinctive SNV profiles among the three groups. OncoKB and COSMIC database screening identified 36 tumour-related genes including BRCA2 and FANCD2 in all groups. BRAF and 19 additional genes were found only in PTCa and PTCb. "Pathways in cancer", "DNA repair" and "Fanconi anaemia pathway" were among the top networks shared by all groups. However, signalling pathways related to tyrosine kinases were the most significantly enriched in PTCa while "Jak-STAT signalling pathway" and "Notch signalling pathway" were the only significantly enriched in PTCb. Ten SNVs were PTC-specific of which two were novel; DCTN1 c.2786C>G (p.Ala929Gly) and TRRAP c.8735G>C (p.Ser2912Thr). Four out of the ten SNVs were unique to PTCa.

    CONCLUSION: Distinctive gene mutation patterns detected in this study corroborated the previous protein profile findings. We hypothesised that the PTCa and PTCb subtypes differed in the underlying molecular mechanisms involving tyrosine kinase, Jak-STAT and Notch signalling pathways. The potential applications of the SNVs in differentiating the benign from the PTC subtypes requires further validation in a larger sample size.

    Matched MeSH terms: Computational Biology
  20. Fulltext A bioinformatics potpourri
    Schönbach C, Li J, Ma L, Horton P, Sjaugi MF, Ranganathan S
    BMC Genomics, 2018 01 19;19(Suppl 1):920.
    PMID: 29363432 DOI: 10.1186/s12864-017-4326-x
    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.
    Matched MeSH terms: Computational Biology*; Systems Biology/methods*
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