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KHAN, MOHAMMAD ASİF

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MOHAMMAD ASİF
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KHAN
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Item Type: Publication × Author: Tan, Tin Wee ×

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Now showing 1 - 9 of 9
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    T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
    (2010-10-01T00:00:00Z) Tay, Daniel Ming Ming; Govindarajan, Kunde Ramamoorthy; KHAN, MOHAMMAD ASİF; Ong, Terenze Yao Rui; Samad, Hanif M.; Soh, Wei Wei; Tong, Minyan; Zhang, Fan; Tan, Tin Wee; KHAN, MOHAMMAD ASİF
    Background: Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding virulence. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to collate and annotate existing effector sequences in public databases to enable systematic analyses of these sequences for development of models for screening and selection of putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments.
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    Dissecting the Dynamics of HIV-1 Protein Sequence Diversity
    (2013-04-01T00:00:00Z) Hu, Yongli; Tan, Paul ThiamJoo; Tan, Tin Wee; August, J. Thomas; KHAN, MOHAMMAD ASİF; KHAN, MOHAMMAD ASİF
    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.
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    Analysis of viral diversity for vaccine target discovery
    (2017-12-01T00:00:00Z) Khan, Asif M.; Hu, Yongli; Miotto, Olivo; Thevasagayam, Natascha M.; Sukumaran, Rashmi; Raman, Hadia Syahirah Abd; Brusic, Vladimir; Tan, Tin Wee; August, J. Thomas; KHAN, MOHAMMAD ASİF
    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.
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    West Nile Virus T-Cell Ligand Sequences Shared with Other Flaviviruses: a Multitude of Variant Sequences as Potential Altered Peptide Ligands
    (2012-07-01T00:00:00Z) Jung, Keun-Ok; KHAN, MOHAMMAD ASİF; Tan, Benjamin Yong Liang; Hu, Yongli; Simon, Gregory G.; Nascimento, Eduardo J. M.; Lemonnier, Francois; Brusic, Vladimir; Miotto, Olivo; Tan, Tin Wee; Marques, Ernesto T. A.; Dhalia, Rafael; Salmon, Jerome; August, J. Thomas; KHAN, MOHAMMAD ASİF
    Phylogenetic relatedness and cocirculation of several major human pathogen flaviviruses are recognized as a possible cause of deleterious immune responses to mixed infection or immunization and call for a greater understanding of the inter-Flavivirus protein homologies. This study focused on the identification of human leukocyte antigen (HLA)-restricted West Nile virus (WNV) T-cell ligands and characterization of their distribution in reported sequence data of WNV and other flaviviruses. H-2-deficient mice transgenic for either A2, A24, B7, DR2, DR3, or DR4 HLA alleles were immunized with overlapping peptides of the WNV proteome, and peptide-specific T-cell activation was measured by gamma interferon (IFN-gamma) enzyme-linked immunosorbent spot (ELISpot) assays. Approximately 30% (137) of the WNV proteome peptides were identified as HLA-restricted T-cell ligands. The majority of these ligands were conserved in similar to >= 88% of analyzed WNV sequences. Notably, only 51 were WNV specific, and the remaining 86, chiefly of E, NS3, and NS5, shared an identity of nine or more consecutive amino acids with sequences of 64 other flaviviruses, including several major human pathogens. Many of the shared ligands had an incidence of >50% in the analyzed sequences of one or more of six major flaviviruses. The multitude of WNV sequences shared with other flaviviruses as interspecies variants highlights the possible hazard of defective T-cell activation by altered peptide ligands in the event of dual exposure to WNV and other flaviviruses, by either infection or immunization. The data suggest the possible preferred use of sequences that are pathogen specific with minimum interspecies sequence homology for the design of Flavivirus vaccines.
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    STATdb: A Specialised Resource for the STATome
    (2014-08-01T00:00:00Z) Patro, C. Pawan K.; Khan, Asif M.; Tan, Tin Wee; Fu, Xin-Yuan; KHAN, MOHAMMAD ASİF
    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.
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    Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines
    (2010-06-01T00:00:00Z) Gomes, Ana Lisa V.; Wee, Lawrence J. K.; KHAN, MOHAMMAD ASİF; Gil, Laura H. V. G.; Marques, Ernesto T. A.; Calzavara-Silva, Carlos E.; Tan, Tin Wee; KHAN, MOHAMMAD ASİF
    Background: Symptomatic infection by dengue virus (DENV) can range from dengue fever (DF) to dengue haemorrhagic fever (DHF), however, the determinants of DF or DHF progression are not completely understood. It is hypothesised that host innate immune response factors are involved in modulating the disease outcome and the expression levels of genes involved in this response could be used as early prognostic markers for disease severity.
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    APBioNet-Transforming Bioinformatics in the Asia-Pacific Region
    (2013-10-01T00:00:00Z) KHAN, MOHAMMAD ASİF; Tan, Tin Wee; Schoenbach, Christian; Ranganathan, Shoba; KHAN, MOHAMMAD ASİF
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    Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)
    (2010-12-01T00:00:00Z) Tan, Tin Wee; Tong, Joo Chuan; KHAN, MOHAMMAD ASİF; de Silva, Mark; Lim, Kuan Siong; Ranganathan, Shoba; KHAN, MOHAMMAD ASİF
    The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources.
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    Simple re-instantiation of small databases using cloud computing
    (2013-10-01T00:00:00Z) Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C. Pawan K.; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; KHAN, MOHAMMAD ASİF; KHAN, MOHAMMAD ASİF
    Background: Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress.