tag:blogger.com,1999:blog-91201388922340640762011-11-28T08:07:56.750+08:00Asif M. KhanMy ResearchAsif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.comBlogger271100tag:blogger.com,1999:blog-9120138892234064076.post-45265153715503829052042-08-15T02:01:00.000+08:002009-01-25T18:37:43.610+08:00My research interestsThis page provides a list of all peer-reviewed journal and conference articles that I have authored or co-authored. A summary view of this page is available here.Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.comtag:blogger.com,1999:blog-9120138892234064076.post-28753182180772675942011-05-25T01:31:00.000+08:002011-05-25T01:31:31.559+08:0026) Highly conserved influenza A sequences as T cell epitopes-based vaccine targets to address the viral variabilityTan PT, Khan AM, August JT.
Hum Vaccin. 2011 Apr 1;7(4)
PUBMED PMID: 21471731
Out link: Full-text
Impact Factor Year 2009: 1.94
No. of Citations: ?
ABSTRACT
Vaccines are the only proven effective method for prevention of human infectious diseases. Almost all traditional vaccines require activating immunological memory B cells to secrete neutralizing antibodies against invading pathogens. The Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-86812558184828341042010-08-10T01:54:00.005+08:002011-05-25T01:29:39.714+08:0025) T3SEdb: Data warehousing of virulence effectors secreted by the bacterial Type III Secretion SystemTay DMM*, Govindarajan KR*, Khan AM, Ong TYR, Samad HM, Soh WW, Tong M, Zhang F, Tan TW
BMC Bioinformatics. 2010; 11 Suppl 7:S4.
PUBMED PMID: 21106126
Out link: Full-text
Impact Factor Year 2009: 3.428
No. of Citations: ?
* Contributed equally
ABSTRACT
Background
Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-61017112687736418522010-08-10T01:47:00.007+08:002011-05-25T01:38:03.964+08:0024) Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domainKothapalli R, Khan AM, Basappa, Gopalsamy A, Chong YS and Annamalai L
PLoS One. 2010 (In Press).
PUBMED PMID: 20824169
Out link: Full-text
Impact Factor Year 2009: 4.351
No. of Citations: 0
ABSTRACT
Background
MMP-13, a zinc dependent protease which catalyses the cleavage of type II collagen, is expressed in osteoarthritis (OA) and rheumatoid arthritis (RA) patients, but not in normal adult Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-83094739329228136852010-08-10T01:34:00.004+08:002010-08-10T02:04:58.369+08:0023) Classification of dengue fever patients based on gene expression data using support vector machines.Gomes AL*, Wee LJ*, Khan AM, Gil LH, Marques ET Jr, Calzavara-Silva CE, Tan TW.PLoS One. 2010 Jun 23;5(6):e11267.PUBMED PMID: 20585645Out link: Full-textImpact Factor Year 2009: 4.351No. of Citations: 0*Contributed equallyABSTRACTBackgroundSymptomatic infection by dengue virus (DENV) can range from dengue fever (DF) to dengue haemorrhagic fever (DHF), however, the determinants of DF or DHF Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-25140717621382407562010-01-10T22:45:00.005+08:002010-08-10T01:22:10.913+08:0022) Dendritic cell mediated delivery of plasmid DNA encoding LAMP/HIV-1 Gag fusion immunogen enhances T cell epitope responses in HLA DR4 Tg miceSimon GG, Hu Y, Khan AM, Zhou J, Salmon J, Chikhlikar PR, Jung KO, Marques ET, August JT.PLoS One. 2010 Jan 5;5(1):e8574.PUBMED PMID: 20052293Out link: Full-textImpact Factor Year 2009: 4.351No. of Citations: 0BackgroundThis report describes the identification and bioinformatics analysis of HLA-DR4-restricted HIV-1 Gag epitope peptides, and the application of dendritic cell mediated immunization Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-28475458171117183602010-01-10T22:42:00.007+08:002010-08-10T02:11:35.282+08:0021) The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: a case study in the Nat. Uni. of SingaporeLim SJ, Khan AM, De Silva M, Lim KS, Hu Y, Tan CH, Tan TW.BMC Bioinformatics. 2009 Dec 3;10 Suppl 15:S12.PUBMED PMID: 19958511Out link: Full-textImpact Factor Year 2009: 3.428No. of Citations: 1ABSTRACTBackground The rapid advancement of computer and information technology in recent years has resulted in the rise of e-learning technologies to enhance and complement traditional classroom teaching Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-46300500557821195582010-01-10T22:39:00.005+08:002010-08-10T02:13:32.114+08:0020) A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era.Tan TW, Lim SJ, Khan AM, Ranganathan S.BMC Genomics. 2009 Dec 3;10 Suppl 3:S36.PUBMED PMID: 19958501Out link: Full-textImpact Factor Year 2009: 3.759No. of Citations: 1ABSTRACT BackgroundThe development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular and molecular phenomena pose Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-62767245155333179212009-06-20T09:27:00.008+08:002010-08-10T02:38:26.838+08:0019) Conservation and variability of West Nile virus proteinsKoo QY, Khan AM, Jung KO, Ramdas S, Miotto O, Tan TW, Brusic V, Salmon J, August JT.PLoS One. 2009;4(4):e5352. Epub 2009 Apr 29.PUBMED PMID: 19401763Out link: Full-textImpact Factor Year 2009: 4.351No. of Citations: 0ABSTRACTBackgroundWest Nile virus (WNV) has emerged globally as an increasingly important pathogen for humans and domestic animals. Studies of the evolutionary diversity of the virusAsif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-3489160194424051412009-01-25T18:30:00.005+08:002010-08-10T02:19:37.706+08:0018) Conservation and variability of dengue virus proteins: implications for vaccine designKhan AM, Miotto O, Nascimento EJ, Srinivasan KN, Heiny AT, Zhang GL, Marques ET, Tan TW, Brusic V, Salmon J, August JT. Virus Reviews and Research, 2008, 13 Supp 1, 74-75 & Proceedings of First Pan American Dengue Research Network Meeting, Recife, Brazil, July 2008PUBMED PMID: N.AOut link: N.AImpact Factor Year 2009: N.ANo. of Citations: 0ABSTRACTBackgroundGenetic variation and rapid evolution Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-45006851373000141872008-08-13T10:58:00.012+08:002010-08-10T02:24:54.800+08:0017) Conservation and variability of dengue virus proteins: implications for vaccine designKhan AM, Miotto O, Nascimento EJ, Srinivasan KN, Heiny AT, Zhang GL, Marques ET, Tan TW, Brusic V, Salmon J, August JT. PLoS Negl Trop Dis. 2008 Aug 13;2(8):e272.PUBMED PMID: 18698358Out link: Full-textImpact Factor Year 2009: 4.693No. of Citations: 7 (total): 5 (non-self) & 2 (self)ABSTRACTBackgroundGenetic variation and rapid evolution are hallmarks of RNA viruses, the result of high mutation Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-65339778557317510782008-01-12T13:23:00.008+08:002010-08-10T01:26:35.492+08:0016) Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomesZhang GL*, Khan AM*, Srinivasan KN, Heiny AT, Lee KX, Kwoh CK, August JT, Brusic V.BMC Bioinformatics. 2008, 9(Suppl 1):S19* Contributed equallyPUBMED PMID: In ProcessOut link: Full-textImpact Factor Year 2009: 3.428No. of Citations: 6 (total): 4 (non-self) & 2 (self)ABSTRACT :BACKGROUND : T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-10053333119810246592007-12-08T14:45:00.010+08:002010-08-10T01:27:11.139+08:0015) Automatic Synchronization and Distribution of Biological Databases and Software over Low-Bandwidth Networks among Developing Countries.Sangket U, Phongdara A, Chotigeat W, Nathan D, Kim WY, Bhak J, Ngamphiw C, Tongsima S, Khan AM, Lin H, Tan TW.Bioinformatics. 2008 Jan 15;24(2):299-301. Epub 2007 Nov 23.PUBMED PMID: 18037613Out link: Full-textImpact Factor Year 2009: 4.926No. of Citations: 2 (total): 0 (non-self) & 2 (self)ABSTRACT :Bioinformatics involves the collection, organization, and analysis of large amounts of Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-78328579910175879702007-12-08T14:39:00.006+08:002010-08-10T01:27:40.089+08:0014) Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets.Heiny AT, Miotto O, Srinivasan KN, Khan AM, Zhang GL, Brusic V, Tan TW, August JT.PLoS ONE. 2007 Nov 21;2(11):e1190.PUBMED PMID: 18030326Out link: Full-textImpact Factor Year 2009: 4.351No. of Citations: 33 (total): 28 (non-self) & 5 (self)ABSTRACT :BACKGROUND: Influenza A viruses generate an extreme genetic diversity through point mutation and gene segment exchange, resulting in many new Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-72284356323374569242007-07-07T12:31:00.002+08:002010-08-10T01:27:58.657+08:0013) Temporal and antigenic analysis of dengue virus serotype 1 genome polyprotein sequencesRajapakse M, Veeramani A, Gopalakrishnan K, Ananthanarayan S, Srinivasan KN, August JT, Khan AM, Brusic V.International Conference on Biomedical and Pharmaceutical Engineering, 2006. Singapore, December 11, 2006.Out link: Full-textImpact Factor Year 2009: NANo. of Citations: 0ABSTRACT :Dengue virus poses a significant health threat. The new emerging strains continue to cause annual epidemics. InAsif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-67042435549805336182007-06-03T13:32:00.006+08:002010-08-10T00:35:42.844+08:0012) A systematic bioinformatics approach for selection of epitope-based vaccine targetsKhan AM, Miotto O, Heiny AT, Salmon J, Srinivasan KN, Nascimento EJ, Marques ET, Brusic V, Tan TW, August JT.Cell Immunol. 2006 Dec;244(2):141-147. Epub 2007 Apr 16.PUBMED PMID: 17434154Out link: Full-textImpact Factor Year 2009: 2.698No. of Citations: 15 (total): 9 (non-self) & 6 (self)ABSTRACT :Epitope-based vaccines provide a new strategy for prophylactic and therapeutic application of Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-35064491785288052382007-01-28T16:44:00.007+08:002010-08-10T01:32:59.504+08:0011) Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.Khan AM, Heiny A, Lee KX, Srinivasan K, Tan TW, August JT, Brusic V.BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S4.PUBMED PMID: 17254309Out link: Full-textImpact Factor Year 2009: 3.428No. of Citations: 16 (total): 8 (non-self) & 8 (self)ABSTRACT :BACKGROUND : Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-47144695371712887742007-01-28T16:09:00.007+08:002010-08-10T00:40:48.636+08:0010) Neural models for predicting viral vaccine targets.Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V.J Bioinform Comput Biol. 2005 Oct;3(5):1207-25.PUBMED PMID: 16278955.Out link: Full-text Impact Factor Year 2009: NANo. of Citations: 16 (total): 5 (non-self) & 11 (self)ABSTRACT :We applied artificial neural networks (ANN) for the prediction of targets of immune responses that are useful for study of vaccine formulations against viral Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-63512156262739690742007-01-28T16:08:00.007+08:002010-08-10T00:53:13.883+08:009) MULTIPRED: a computational system for prediction of promiscuous HLA binding.Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V.Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W172-9.PUBMED PMID: 15980449Out link: Full-textImpact Factor Year 2009: 7.479No. of Citations: 70 (total): 51 (non-self) & 19 (self)ABSTRACT :MULTIPRED is a web-based computational system for the prediction of peptide binding to multiple molecules (proteins) belonging to human leukocyte Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-78607026487642125682007-01-28T16:07:00.007+08:002010-08-10T00:54:09.704+08:008) BioWare: A framework for bioinformatics data retrieval, annotation and publishing.Koh JLY, Krishnan SPT, Seah SH, Tan PT, Khan AM, Lee ML, Brusic V.27th Annual International ACM SIGIR Conference on Research and Development in IR. Sheffield, UK, July 29, 2004.Out link: Full-textImpact Factor Year 2009: NANo. of Citations: 10 (total): 3 (non-self) & 7 (self)ABSTRACT :In-depth analysis about a specific subject in molecular biology, specifically those associated with the Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-51191914137413819512007-01-28T16:06:00.004+08:002010-08-10T00:56:55.295+08:007) Duplicate Detection in Biological Data using Association.Koh JLY, Lee ML, Khan AM, Tan PTJ, Brusic V2nd European Workshop on Data Mining and Text Mining for Bioinformatics.Pisa, Italy, September 24, 2004.Out link: Full-textImpact Factor Year 2009: NANo. of Citations: 19 (total): 16 (non-self) & 3 (self)ABSTRACT :Recent advancement in biotechnology has produced a massive amount of raw biological data which are accumulating at an exponential rate. ErrorsAsif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-51828814075388812352007-01-28T16:05:00.006+08:002010-08-10T00:59:30.230+08:006) Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.Siew JP, Khan AM, Tan PT, Koh JL, Seah SH, Koo CY, Chai SC, Armugam A, Brusic V, Jeyaseelan K.Bioinformatics. 2004 Dec 12;20(18):3466-80. Epub 2004 Jul 22.PUBMED PMID: 15271784Out link: Full-textImpact Factor Year 2009: 4.926No. of Citations: 9 (total): 5 (non-self) & 4 (self)ABSTRACT:MOTIVATION: Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-55235007788194274542007-01-28T16:04:00.005+08:002010-08-10T01:02:46.733+08:005) Prediction of class I T-cell epitopes: evidence of presence of immunological hotspots inside antigens.Srinivasan KN, Zhang GL, Khan AM, August JT, Brusic V.Bioinformatics. 2004 Aug 4;20 Suppl 1:I297-I302.PUBMED PMID: 15262812Out link: Full-textImpact Factor Year 2009: 4.926No. of citations: 30 (total): 14 (non-self) & 16 (self)ABSTRACT:MOTIVATION: Processing and presentation of major histocompatibility complex class I antigens to cytotoxic T-lymphocytes is crucial for immune surveillance against Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-12811103538216721852007-01-28T16:03:00.006+08:002010-08-10T02:34:02.482+08:004) CysView: protein classification based on cysteine pairing patterns.Lenffer J, Lai P, El Mejaber W, Khan AM, Koh JL, Tan PT, Seah SH, Brusic V.Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W350-5.PUBMED PMID: 15215409Out link: Full-textImpact Factor Year 2009: 7.479No. of Citations: 11 (total): 7 (non-self) & 4 (self)ABSTRACT :CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-31085840050206402412007-01-28T16:02:00.009+08:002010-08-10T01:09:26.268+08:003) ANTIMIC: a database of antimicrobial sequences.Brahmachary M, Krishnan SP, Koh JL, Khan AM, Seah SH, Tan TW, Brusic V, Bajic VB.Nucleic Acids Res. 2004 Jan 1;32(Database issue):D586-9.PUBMED PMID: 14681487Out link: Full-textImpact Factor Year 2009: 7.479No. of Citations: 86 (t0tal): 84 (non-self) & 2 (self)ABSTRACT :Antimicrobial peptides (AMPs) are important components of the innate immune system of many species. These peptides are found in Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-53172338447397971772007-01-28T16:00:00.006+08:002010-08-10T01:19:03.521+08:002) Molecular evolution and phylogeny of elapid snake venom three-finger toxins.Fry BG, Wuster W, Kini RM, Brusic V, Khan A, Venkataraman D, Rooney AP.J Mol Evol. 2003 Jul;57(1):110-29.PUBMED PMID: 12962311Out link: Full-textImpact Factor Year 2009: 2.128No. of Citations: 81 (total): 55 (non-self) & 26 (self)Award won: Zuckerkandl prizeABSTRACT :Animal venom components are of considerable interest to researchers across a wide variety of disciplines, including molecular Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-9120138892234064076.post-12043140433928009902007-01-28T15:50:00.005+08:002010-08-10T01:21:25.828+08:001) Bioinformatics for venom and toxin sciences.Tan PT, Khan AM, Brusic V.Brief Bioinform. 2003 Mar;4(1):53-62. Review.PUBMED PMID: 12715834Out link: Full-textImpact Factor Year 2009: 7.329No. of Citations: 19 (total): 10 (non-self) & 9 (self)ABSTRACT :Venomous animals produce a myriad of important pharmacological components. The individual components, or venoms (toxins), are used in ion channel and receptor studies, drug discovery, and Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0