Shoba Ranganathan

Summary

Affiliation: Macquarie University
Country: Australia

Publications

  1. pmc Xpro: database of eukaryotic protein-encoding genes
    Vivek Gopalan
    Department of Biochemistry, National University of Singapore, Singapore 119260
    Nucleic Acids Res 32:D59-63. 2004
  2. ncbi request reprint The hand, foot and mouth disease virus capsid: sequence analysis and prediction of antigenic sites from homology modelling
    Shoba Ranganathan
    Bioinformatics Centre, Department of Biochemistry, National University of Singapore, Singapore
    Appl Bioinformatics 1:43-52. 2002
  3. pmc ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
    Shivashankar H Nagaraj
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    Nucleic Acids Res 35:W143-7. 2007
  4. pmc InCoB2012 Conference: from biological data to knowledge to technological breakthroughs
    Christian Schonbach
    Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820 8502, Japan
    BMC Bioinformatics 13:S1. 2012
  5. doi request reprint Functional annotation of the human chromosome 7 "missing" proteins: a bioinformatics approach
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia
    J Proteome Res 12:2504-10. 2013
  6. pmc InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia
    Christian Schonbach
    Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820 8502, Japan
    BMC Genomics 12:S1. 2011
  7. pmc Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
    BMC Bioinformatics 12:S1. 2011
  8. pmc Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)
    Tin Wee Tan
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 11:S27. 2010
  9. pmc A multi-factor model for caspase degradome prediction
    Lawrence J K Wee
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 10:S6. 2009
  10. pmc Flanking signal and mature peptide residues influence signal peptide cleavage
    Khar Heng Choo
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
    BMC Bioinformatics 9:S15. 2008

Collaborators

Detail Information

Publications67

  1. pmc Xpro: database of eukaryotic protein-encoding genes
    Vivek Gopalan
    Department of Biochemistry, National University of Singapore, Singapore 119260
    Nucleic Acids Res 32:D59-63. 2004
    ..Xpro is updated for each new GenBank release and is freely available via the internet at http://origin.bic. nus.edu.sg/xpro...
  2. ncbi request reprint The hand, foot and mouth disease virus capsid: sequence analysis and prediction of antigenic sites from homology modelling
    Shoba Ranganathan
    Bioinformatics Centre, Department of Biochemistry, National University of Singapore, Singapore
    Appl Bioinformatics 1:43-52. 2002
    ..From the model, we have identified two putative immunogenic regions, one of which is unique to EV71. The hydrophobic pocket within VP1, found in bovine enterovirus, poliovirus and rhinovirus, is also conserved in EV71...
  3. pmc ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
    Shivashankar H Nagaraj
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    Nucleic Acids Res 35:W143-7. 2007
    ..ESTExplorer runs on a Linux cluster and is freely available for the academic community at http://estexplorer.biolinfo.org...
  4. pmc InCoB2012 Conference: from biological data to knowledge to technological breakthroughs
    Christian Schonbach
    Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820 8502, Japan
    BMC Bioinformatics 13:S1. 2012
    ..Other highlights included sessions organized by the Pan-Asian Pacific Genome Initiative and a Machine Learning in Immunology competition. InCoB2013 is scheduled for September 18-21, 2013 at Suzhou, China...
  5. doi request reprint Functional annotation of the human chromosome 7 "missing" proteins: a bioinformatics approach
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia
    J Proteome Res 12:2504-10. 2013
    ..Proteotypic peptides have been computationally generated to facilitate rapid identification of these proteins. Four of the "missing" chromosome 7 proteins have been substantiated by the ENCODE proteogenomic peptide data...
  6. pmc InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia
    Christian Schonbach
    Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820 8502, Japan
    BMC Genomics 12:S1. 2011
    ..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...
  7. pmc Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
    BMC Bioinformatics 12:S1. 2011
    ....
  8. pmc Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)
    Tin Wee Tan
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 11:S27. 2010
    ..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...
  9. pmc A multi-factor model for caspase degradome prediction
    Lawrence J K Wee
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 10:S6. 2009
    ....
  10. pmc Flanking signal and mature peptide residues influence signal peptide cleavage
    Khar Heng Choo
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
    BMC Bioinformatics 9:S15. 2008
    ....
  11. pmc Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors
    Lesheng Kong
    Computational Biology Group, Temasek Life Sciences Laboratory, 1 Reseach Link National University of Singapore, Singapore 117604
    BMC Bioinformatics 9:S22. 2008
    ....
  12. pmc InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010
    Christian Schonbach
    Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820 8502, Japan
    BMC Bioinformatics 11:S1. 2010
    ....
  13. pmc Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage
    Khar Heng Choo
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    BMC Bioinformatics 9:S15. 2008
    ..We report here a structure-based model for Escherichia coli DsbA 13-25 in complex with its endogenous type I SPase...
  14. pmc A comprehensive assessment of N-terminal signal peptides prediction methods
    Khar Heng Choo
    Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis, Singapore
    BMC Bioinformatics 10:S2. 2009
    ..Of the myriad software prediction tools developed to automate the task of assigning the SP cleavage site of these new sequences, we review here, the performance and reliability of commonly used SP prediction tools...
  15. pmc Bioinformatics education--perspectives and challenges
    Shoba Ranganathan
    Macquarie University, Sydney, Australia
    PLoS Comput Biol 1:e52. 2005
  16. pmc Emerging strengths in Asia Pacific bioinformatics
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
    BMC Bioinformatics 9:S1. 2008
    ..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...
  17. pmc Bioinformatics research in the Asia Pacific: a 2007 update
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and Biotechnology Research Institute, Macquarie University, Sydney NSW 2109, Australia
    BMC Bioinformatics 9:S1. 2008
    ..We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours...
  18. pmc Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
    BMC Genomics 11:S1. 2010
    ..27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia...
  19. pmc A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
    BMC Genomics 8:311. 2007
    ..In this study, we provide first insights into the transcriptome of the adult stage of D. viviparus through the analysis of expressed sequence tags (ESTs)...
  20. doi request reprint Advanced in silico analysis of expressed sequence tag (EST) data for parasitic nematodes of major socio-economic importance--fundamental insights toward biotechnological outcomes
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and Australian Research Council ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia
    Biotechnol Adv 27:439-48. 2009
    ....
  21. pmc Structural diversity of biologically interesting datasets: a scaffold analysis approach
    Varun Khanna
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
    J Cheminform 3:30. 2011
    ..abstract:..
  22. pmc A comparative structural bioinformatics analysis of inherited mutations in β-D-Mannosidase across multiple species reveals a genotype-phenotype correlation
    Thi Huynh
    Department of Chemistry and Biomolecular Sciences and ARC center of excellence in Bioinformatics, Macquarie University, NSW 2109, Australia
    BMC Genomics 12:S22. 2011
    ..Accordingly, the pathology and clinical manifestations of the disease could be correlated to the genotypic modifications...
  23. pmc Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse
    Elsa Chacko
    Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
    BMC Genomics 10:S5. 2009
    ..This classification quantifies the variation in transcript diversity in the three species...
  24. pmc TranSeqAnnotator: large-scale analysis of transcriptomic data
    Ranjeeta Menon
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW 2109, Australia
    BMC Bioinformatics 13:S24. 2012
    ..With the advent of large-scale sequencing projects and generation of sequence data at protein and cDNA levels, automated analysis pipeline is necessary to store, organize and annotate ESTs...
  25. pmc Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs)
    Shivashankar H Nagaraj
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
    PLoS Negl Trop Dis 2:e301. 2008
    ..Mining the entire expressed sequence tag (EST) data available from parasitic nematodes represents an approach to discover such ES targets...
  26. pmc CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge
    Jitendra Gaikwad
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    BMC Bioinformatics 9:S25. 2008
    ..We have developed the Customary Medicinal Knowledgebase (CMKb), an integrated multidisciplinary resource, to document, conserve and disseminate this knowledge...
  27. doi request reprint MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures
    Javed Mohammed Khan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia
    Bioinformatics 27:1192-3. 2011
    ....
  28. pmc Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs)
    Gagan Garg
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
    BMC Genomics 13:S8. 2012
    ..Furthermore, predictions have, in the main, focussed on classical secretory pathways while it is well established that helminth parasites also utilise non-classical secretory pathways...
  29. pmc An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications
    Ranjeeta Menon
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
    BMC Genomics 13:S10. 2012
    ..circumcincta, there is some potential for the development of a vaccine against this parasite. Hence, we infer excretory/secretory molecules for T. circumcincta as possible immunogens and vaccine candidates...
  30. pmc In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches
    Shivashankar H Nagaraj
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    BMC Bioinformatics 9:S10. 2008
    ..In this study, we evaluated EST data analysis for the parasitic nematode Trichostrongylus vitrinus (order Strongylida) using ESTExplorer, compared with database matching alone...
  31. pmc Advances in translational bioinformatics and population genomics in the Asia-Pacific
    Shoba Ranganathan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW 2109, Australia
    BMC Genomics 13:S1. 2012
    ....
  32. pmc In silico secretome analysis approach for next generation sequencing transcriptomic data
    Gagan Garg
    Dept of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia
    BMC Genomics 12:S14. 2011
    ..However, none of transcriptomic studies have extensively covered ES protein prediction for identifying novel therapeutic targets, especially as parasites adopt non-classical secretion pathways...
  33. ncbi request reprint A hitchhiker's guide to expressed sequence tag (EST) analysis
    Shivashankar H Nagaraj
    Department of Chemistry and Biomolecular Sciences and Biotechnology Research Institute, Macquarie University, Sydney, Australia
    Brief Bioinform 8:6-21. 2007
    ..An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping...
  34. pmc In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance
    Varun Khanna
    Dept of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
    BMC Bioinformatics 12:S25. 2011
    ..In this study we propose to build robust machine learning model to classify and screen compounds active against parasitic nematodes...
  35. doi request reprint An ethnobotanical study of medicinal plants used by the Yaegl Aboriginal community in northern New South Wales, Australia
    Joanne Packer
    Indigenous Bioresources Research Group, Macquarie University, North Ryde, Sydney 2109, Australia
    J Ethnopharmacol 139:244-55. 2012
    ..This collaboration between the Yaegl Aboriginal community in northern New South Wales (NSW), Australia and an academic institution, demonstrates an effective means of preserving and adding value to this information...
  36. pmc Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases
    Elsa Chacko
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW 2109, Australia
    BMC Genomics 10:S11. 2009
    ..Of the 94 human inherited disease genes, a protein domain analysis was carried out for the transcript sequences of 12 human genes that have orthologous genes and have been characterised in cow...
  37. pmc An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host
    Mark W Robinson
    Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Ultimo, Sydney, New South Wales 2007, Australia
    Mol Cell Proteomics 8:1891-907. 2009
    ..hepatica are secreted into the parasite gut via a classical endoplasmic reticulum/Golgi pathway, we speculate that the antioxidants, which all lack a signal sequence, are released via a non-classical trans-tegumental pathway...
  38. doi request reprint Unlocking the Puzzling Biology of the Black Périgord Truffle Tuber melanosporum
    Mohammad Tawhidul Islam
    Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
    J Proteome Res 12:5349-56. 2013
    ..This study has resulted in the functional characterization of novel proteins to increase our biological understanding of this organism and to uncover potential biomarkers of authenticity, freshness, and perfume maturation. ..
  39. pmc ASGS: an alternative splicing graph web service
    Durgaprasad Bollina
    Department of Chemistry and Biomolecular Sciences and Biotechnology Research Institute, Macquarie University, Sydney, NSW 2109, Australia
    Nucleic Acids Res 34:W444-7. 2006
    ..This freely available web service can be accessed at http://asgs.biolinfo.org...
  40. ncbi request reprint A practical guide to structure-based prediction of MHC-binding peptides
    Shoba Ranganathan
    Department of Chemistry, Macquarie University, New South Wales, Australia
    Methods Mol Biol 409:301-8. 2007
    ..This chapter introduces the use of structural models as a predictive method to determine whether a peptide sequence can bind to a specific MHC allele...
  41. doi request reprint Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome
    Mohammad T Islam
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW 2109, Australia
    J Proteome Res 13:76-83. 2014
    ..The chromosome-wise functional annotation of all "missing" proteins is freely available to the scientific community through our web server ( http://biolinfo.org/protannotator ). ..
  42. pmc Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
    Gaurav Kumar
    ARC Centre of Excellence in Bioinformatics and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    BMC Syst Biol 7:12. 2013
    ....
  43. ncbi request reprint In silico prediction of immunogenic T cell epitopes for HLA-DQ8
    Javed M Khan
    Department of Chemistry and Biomolecular Sciences and ARC center of excellence in Bioinformatics, Macquarie University, NSW 2109, Australia
    Immunome Res 8:14. 2012
    ..This combined approach provides a set of sensitive and specific computational tools to facilitate high-throughput screening of peptides for immunotherapeutic applications such as controlling allergic and autoimmune responses...
  44. pmc A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation
    Javed Mohammed Khan
    Department of Chemistry and Biomolecular Sciences and ARC center of excellence in Bioinformatics, Macquarie University, NSW 2109, Australia
    BMC Genomics 10:S33. 2009
    ....
  45. pmc Physiochemical property space distribution among human metabolites, drugs and toxins
    Varun Khanna
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
    BMC Bioinformatics 10:S10. 2009
    ....
  46. pmc Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one
    Javed Mohammed Khan
    Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
    PLoS ONE 6:e17194. 2011
    ....
  47. ncbi request reprint Delineation of modular proteins: domain boundary prediction from sequence information
    Lesheng Kong
    Biotechnology Research Institute, Macquarie University, NSW 2109, Australia
    Brief Bioinform 5:179-92. 2004
    ..Finally, we will review existing domain boundary prediction methods and discuss their strengths and weaknesses...
  48. pmc Network analysis of human protein location
    Gaurav Kumar
    ARC Centre of Excellence in Bioinformatics and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia
    BMC Bioinformatics 11:S9. 2010
    ..A comprehensive analysis of protein SCL in human PPI and metabolic networks for various subcellular compartments is necessary for developing a robust SCL prediction methodology...
  49. doi request reprint The transcriptome of Echinostoma caproni adults: further characterization of the secretome and identification of new potential drug targets
    Gagan Garg
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, SW 2109, Australia
    J Proteomics 89:202-14. 2013
    ..Of the 3415 predicted excretory/secretory proteins compiled (including non-classical secretory proteins), 180 different proteins were confirmed by proteomic analysis. Potential drug targets were also identified...
  50. pmc OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI
    Johann Lenffer
    Biotechnology Research Institute and Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
    Nucleic Acids Res 34:D599-601. 2006
    ..ncbi.nlm.nih.gov/entrez/query.fcgi?db=omia). Curation of OMIA data by researchers working on particular species and disorders has also been enabled...
  51. pmc pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes
    Javed Mohammed Khan
    Department of Chemistry and Biomolecular Sciences and ARC center of excellence in Bioinformatics, Macquarie University, NSW 2109, Australia
    Immunome Res 6:S2. 2010
    ....
  52. ncbi request reprint APBioNet: the Asia-Pacific regional consortium for bioinformatics
    Shoba Ranganathan
    Department of Biochemistry and Bioinformatics Centre, National University of Singapore, Singapore
    Appl Bioinformatics 1:101-5. 2002
    ..Recent milestones achieved include hosting an international bioinformatics symposium in Asia and setting up large-scale regional grid-computing projects...
  53. pmc MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences
    Bernett T K Lee
    Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
    Nucleic Acids Res 31:3533-6. 2003
    ..The server also permits the alignment to be saved in several forms, both graphical and text, suitable for further processing and analysis by other programs...
  54. doi request reprint Critical technologies for bioinformatics
    Vladimir Brusic
    Brief Bioinform 9:261-2. 2008
  55. ncbi request reprint MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Institute for Infocomm Research, Singapore
    Appl Bioinformatics 5:111-4. 2006
    ....
  56. pmc SPdb--a signal peptide database
    Khar Heng Choo
    Department of Biochemistry, National University of Singapore, Singapore
    BMC Bioinformatics 6:249. 2005
    ..To support this understanding, we present SPdb signal peptide database http://proline.bic.nus.edu.sg/spdb, a repository of experimentally determined and computationally predicted signal peptides...
  57. ncbi request reprint A workflow for mutation extraction and structure annotation
    Rajaraman Kanagasabai
    Department of Data Mining, Institute for Infocomm Research, Singapore, Singapore
    J Bioinform Comput Biol 5:1319-37. 2007
    ..The ontology and visualization tool are available at (http://datam.i2r.a-star.edu.sg/mstrap)...
  58. ncbi request reprint CASVM: web server for SVM-based prediction of caspase substrates cleavage sites
    Lawrence J K Wee
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    Bioinformatics 23:3241-3. 2007
    ..We have also included a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity. AVAILABILITY: http://www.casbase.org/casvm/index.html..
  59. ncbi request reprint Genomic characterization of Tv-ant-1, a Caenorhabditis elegans tag-61 homologue from the parasitic nematode Trichostrongylus vitrinus
    Min Hu
    Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
    Gene 397:12-25. 2007
    ..elegans using the parasite homologue/orthologue Tv-ant-1. This first insight into an ANT of T. vitrinus provides a foundation for exploring its role in developmental and/or survival processes of trichostrongylid nematodes...
  60. ncbi request reprint XdomView: protein domain and exon position visualization
    Gopalan Vivek
    Department of Biochemistry, National University of Singapore, Singapore 119260
    Bioinformatics 19:159-60. 2003
    ..The association of sequence signals to 3D structure in XdomView provides a valuable visualization environment for eukaryotic gene organization, gene evolution, protein folding and protein structure classification...
  61. ncbi request reprint Oesophagostomum dentatum: potential as a model for genomic studies of strongylid nematodes, with biotechnological prospects
    Robin B Gasser
    Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
    Biotechnol Adv 25:281-93. 2007
    ..dentatum - pig system provides an attractive model for exploring molecular developmental and reproductive processes in strongylid nematodes, leading toward new intervention methods and biotechnological outcomes...
  62. pmc Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
    BMC Bioinformatics 7:S7. 2006
    ..We report here a structure-based model for the prediction of peptide binding to DRB1*0402 and DQB1*0503. The scoring functions were rigorously trained, tested and validated using experimentally verified peptide sequences...
  63. pmc SVM-based prediction of caspase substrate cleavage sites
    Lawrence J K Wee
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Bioinformatics 7:S14. 2006
    ..As the support vector machines (SVM) algorithm has been shown to be useful in several biological classification problems, we have implemented an SVM-based method to investigate its applicability to this domain...
  64. ncbi request reprint Accurate prediction of scorpion toxin functional properties from primary structures
    Paul T J Tan
    Laboratories for Information Technology, Knowledge Discovery Department, Institute for Infocomm Research, Singapore 119613, Singapore
    J Mol Graph Model 24:17-24. 2005
    ....
  65. pmc SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
    Lesheng Kong
    Department of Biochemistry, National University of Singapore, 8 Medical Drive, 117597, Singapore
    Nucleic Acids Res 32:W356-9. 2004
    ..Furthermore, the web service provides model stereochemical quality evaluation using PROCHECK. SDPMOD is freely accessible to academic users via the web interface at http://proline.bic.nus.edu.sg/sdpmod...
  66. pmc DEDB: a database of Drosophila melanogaster exons in splicing graph form
    Bernett T K Lee
    Department of Biochemistry, National University of Singapore, Singapore
    BMC Bioinformatics 5:189. 2004
    ..The splicing graph then serves as the basis for the classification of the various types of alternative splicing events...
  67. ncbi request reprint SCORPION2: a database for structure-function analysis of scorpion toxins
    Paul T J Tan
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore, Singapore 119613
    Toxicon 47:356-63. 2006
    ..The SCORPION2 database is available at http://sdmc.i2r.a-star.edu.sg/scorpion/...