Prof. Shoba Ranganathan

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Contact details

Shoba Ranganathan

Professor of Bioinformatics

Dept. of Chemistry and Biomolecular Sciences & Biotechnology Research Institute

Telephone: +61-2-9850-6262 Fax: +61-2-9850-8313

Email: shoba.ranganathan@mq.edu.au

Location: Building F7B, Room 233

Address:

Dept. of Chemistry and Biomolecular Sciences

Macquarie University

NSW 2109, Australia

Biography

  • Professor Shoba Ranganathan has studied and worked in the field of bioinformatics for 24 years, when the field was known as theoretical biochemistry and subsequently as biocomputing. She collaborated with pioneers in this discipline at the Institut de Biologie Physico-Chimique in Paris, funded by the Rothschild Foundation, and has continued to be a leading player in bioinformatics throughout her career.
  • Shoba served as the first Australian Director of the International Society for Computational Biology (2003-5) and is currently the President of the Asia-Pacific Bioinformatics Network. She is also Chairperson of the S* Life Science Informatics Alliance, established with a view to encouraging international students and multi-disciplinary collaboration in bioinformatics. She has established a new bioinformatics group at Macquarie under the auspices of the Biotechnology Research Institute.

Research interests

  • Shoba’s research interests are in computational structural biology and comparative genome sequence analysis. Specific examples of her recent research are outlined below.

Parasitic Nematode Genomics:

  • We are seeking novel genes for a gene-based parasitic nematode intervention strategy, in collaboration with Prof. Robin Gasser, University of Melbourne. Our White Paper for whole genome sequencing of strongylid parasites has been accepted by the National Human Genome Research Institute, for sequencing at the Washington University Genome Sequencing Center.

Immunoinformatics:

  • This research aims to explore the structural principles involved in T-cell mediated vaccine development. Shoba is approaching this analysis of immune systems from a structural perspective with a view to determining how they function by understanding their molecular structure. Shoba will inquire into how and why vaccines work selectively on the basis of the inheritance of certain receptors in our immune defense system.

Genome-Phenome Mapping:

  • This research explores the apparent simplicity of the human genome in order to explain the complexity of higher organisms. Shoba is working on the development of a new methodology for RNA and DNA sequence alignments in the study of alternative splicing in eukaryotic genomes. Through the innovative use of comparative genome sequence analysis, she hopes to generate a new algorithm addressing this phenomenon.

Transcriptomics:

  • We are analyzing alternate transcript diversity arising from splice variants for entire genomes, using a graph theoretical approach.
  • Shoba’s work has significant application in the development of software systems and as a methodology for vaccine development. Its greatest potential is in target identification and drug design for the pharmaceutical and biotechnology industries. Her research is also highly relevant to the creation of tools for proteomic and genomic studies.
  • Curriculum Vitae click here for Shoba's CV


Publications

2007 2006 2005 2000-2004 1990s 1980s

2007

  • L.W.K. Wee, T.W. Tan, S. Ranganathan (2007): CASVM: web server for SVM-based prediction of caspase sub-strates cleavage sites. Bioinformatics, accepted.
  • M. Hu, B.E. Campbell, M. Pellegrino, A. Loukas, I. Beveridge, S. Ranganathanm R.B. Gasser (2007): Genomic characterization of Tv-ant-1, a Caenorhabditis elegans tag-613 homologue from the parasitic nematode Trichostrongylus vitrinus. Gene, in press, online: doi:10.1016/j.gene.2007.03.011.
  • H.N. Shivashankar, N. Deshpande, R.B. Gasser, S. Ranganathan (2007): ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.. Nucl. Acids Research, in press, online: doi:10.1093/nar/gkm378.
  • H.N. Shivashankar, R.B. Gasser, S. Ranganathan (2007): A hitchhiker's guide to expressed sequence tags (ESTs) and their bioinformatics analysis. Briefings Bioinf, 8, 6-21; online: doi:10.1093/bib/bbl015.
  • R.B. Gasser, P. Cottee, A.J. Nisbet, B. Ruttkowski, S. Ranganathan, A. Joachim (2007): Oesophagostomum dentatum – potential as a model for genomic studies of strongylid nematodes, with biotechnological prospect. Biotechnol Adv, 25, 281-293.
  • M.T. Islam, D. Bollina, A. Nayak, S. Ranganathan (2007): Towards an Agent-based Information Retrieval System for Computational Biomarker Discovery, in the International Conference on Information and Communication Technology (ICICT 2007), March 7-9, 2007, Dhaka, Bangladesh, pp.57-63..
  • J.C. Tong, T.W. Tan, S. Ranganathan (2007): Methods and Protocols for Prediction of Immunogenic Epitopes. Briefings Bioinf, 8, 96-108; online: doi:10.1093/bib/bbl038.
  • J.C. Tong, T.W. Tan, S. Ranganathan (2007): In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. Bioinformatics, 23, 177-183; doi:10.1093/bioinformatics/btl563.
  • S. Ranganathan, J.C. Tong, T.W. Tan (2007) Structural Immunoinformatics, in Immunoinformatics:, eds. C. Schoenbach, S. Ranganathan and V. Brusic, Springer, Immunomics Reviews (vol. 1), in press.
  • S. Ranganathan, J.C. Tong (2007) A Practical Guide to Structure-based Prediction of MHC Binding Peptides, ed. D.R. Flower, Human Press, Methods in Molecular Biology: Immunoinformatics: predicting immunogenicity in silico, Vol. 409, chap. 22, pp.297-305.

2006

  • S. Ranganathan, M. Tammi, M. Gribskov, T.W. Tan (2006): Establishing Bioinformatics Research in the Asia Pacific. BMC Bioinformatics, 7 Suppl 5, S1.
  • L.W.K. Wee, T.W. Tan, S. Ranganathan (2006): SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics, 7 Suppl 5, S14.
  • J.C. Tong, T.W. Tan, A.A. Sinha, S. Ranganathan (2007): Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated Pemphigus vulgaris. BMC Bioinformatics, 7 Suppl 5, S7.
  • D. Bollina, B.T.K. Lee, T.W. Tan, S. Ranganathan (2006): ASGS: An alternative splicing graph web service. Nucl. Acids Research, 34, W444-W447.
  • S. Ranganathan, S. Wongsai, H. Nevalainen (2006). Comparative genomic analysis of glycosylation pathways in yeast, plants and higher eukaryotes. Applied Mycology and Biotechnology, Vol. 6, pp.227-248.
  • J.C. Tong, G.L. Zhang, T.W. Tan, J.T. August, V. Brusic, S. Ranganathan (2006): Prediction of HLA-DQ3.2(beta) Ligands: Evidence of Multiple Registers in Class II Binding Peptides, Bioinformatics, 22, 1232-1238.
  • J.C. Tong, L. Kong, T.W. Tan, S. Ranganathan (2006): MPID-T: database for sequence-structure-function information on TCR-peptide-MHC interactions. Applied Bioinformatics, 5, 111-114.
  • J. Lenffer, F.W. Nicholas, K. Castle, A. Rao, S. Gregory, M. Poidinger, M.D. Mailman, S. Ranganathan (2006): OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. Nucl. Acids Research, 34, D599-D601.
  • P.T.J. Tan, A. Veeramani, K.N. Srinivasan, S. Ranganathan, V. Brusic (2006): SCORPION2: A database for structure-function analysis of scorpion toxins. Toxicon, 47, 356-363.
  • P.T.J. Tan, A. Veeramani, K.N. Srinivasan, S. Ranganathan, V. Brusic (2006): Extraction of functional peptide motifs in scorpion toxins. J. Pept. Sci., 12, 420-427.

2005

  • S. Ranganathan (2005): Bioinformatics Education - Perspectives and Challenges. PLoS Comp. Biol., 1:e52.
  • D. Bollina, B.T.K. Lee, S. Ranganathan (2005) MVC Architecture in Bioinformatics web applications and its Java implementation, in The seveth International Conference on Information Integration and Web-based Applications and Services (iiWAS2005), Sept. 19-21, 2005, Kuala Lumpur, Malaysia, G. Kotsis, D. Tanier, S. Bressan, I.K. Ibrahim and S. Mokhtar (eds), Austrian Computer Society, Vol. 2, pp. 759-764.
  • D. Bollina, B.T.K. Lee, S. Ranganathan (2005) SGS: Splicing Graph Server, in BioInfo2005, Proceedings of the 2005 International Joint Conference of InCoB, AASBi and KSBi, Sept. 22-24, 2005, Busan, Korea, D. Lee, L. Wong, S. Kim, D.W. Kim, T.W. Tan and K.H. Lee (eds.), pp. 47-50.
  • K.H. Choo, T.W. Tan, S. Ranganathan (2005): SPdb – A Signal Peptide Database. BMC Bioinformatics, 6, 249.
  • J.C. Tong, J. Bramson, D. Kanduc, S. Chow, A.A. Sinha, S. Ranganathan (2005): Modeling the Bound Conformation of Pemphigus Vulgaris-associated Peptides to MHC Class II DR and DQ Alleles, Immunome Research, 2, 1.
  • H.C. Ng, S. Ranganathan, K.L. Chua, H.E. Khoo (2005): Cloning and molecular characterization of the first aquatic hyaluronidase, SFHYA1, from the venom of stonefish (Synanceja horrida). Gene, 346, 71-81.
  • P.T.J. Tan, K.N. Srinivasan, S.H Seah, J.L.Y. Koh, T.W. Tan, S. Ranganathan, V. Brusic (2005): Accurate prediction of scorpion toxin functional properties from primary structures. J. Mol. Graph. Model. 24, 17-24.

2000-2004

  • B.T.K. Lee, T.W. Tan, S.Ranganathan (2004) DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics 5,189.
  • E. Tng, S.M. Tan, S. Ranganathan, M. Cheng, S.K.A. Law (2004) The integrin (alpha)L(beta)2 hybrid domain serves as a link for the propagation of activation signal from its stalk regions to the I-like domain. J. Biol. Chem. 279, 54334–54339.
  • L. Kong, B.T.K. Lee, J.C. Tong, T.W. Tan, S. Ranganathan (2004) SDPMOD: an automated comparative modelling server for small disulfide-bonded proteins. Nucleic Acids Res 32,W356-W359.
  • L. Kong, S. Ranganathan (2004) Delineation of Modular Proteins: Domain Boundary Prediction from Sequence Information. Briefings Bioinf 5,179-192.
  • J.C. Tong, T.W. Tan, S. Ranganathan (2004) Modeling the Structure of Bound Peptide Ligands to Major Histocompatibility Complex. Protein Sci 13:2523-2532.
  • V. Gopalan, B.T.K Lee, T.W. Tan, S. Ranganathan (2004) Xpro: A Genome-wide Resource for all Eukaryotic Protein-encoding Genes. Nucleic Acids Res 32, D59-D63.
  • S.Ranganathan, G.S. Ong, T.W. Tan (2003) APBioBox – an Asia Pacific Bioinformatics grid software suite. Genome Informatics 14, 717-718.
  • B.T.K. Lee, T.W. Tan, S. Ranganathan S (2003) MGAlign, a reduced search space approach to the alignment of mRNA sequences to genomic sequences. Genome Informatics 14, 474-475.
  • P.P. Kumar, B.D. Kumar, S. Ranganathan (2003) Antisense suppression of a cytokininbinding protein from petunia causes excessive branching and reduces adventitious shoot bud induction in vitro. I. K. Vasil (ed.), Plant Biotechnology 2002 and Beyond, Kluwer Academic, Netherlands, pp. 285-287.
  • B.T.K. Lee, T.W. Tan, S. Ranganathan (2003): MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequence. Nucleic Acids Res., 31, 3533-3536.
  • S. Ranganathan (2003) Molecular Modeling on the web, Biocomputing: Computer Tools for Biologists, ed. Stuart M. Brown, Biotechniques Press, Eaton Publishing, Westborough, USA, chap. 49, pp. 411-417.
  • G. Vivek, T.W. Tan, S. Ranganathan (2003): Xdom: A graphical Tool for Visualizing Intron Positions mapped to Protein Domains. Bioinformatics 19, 159-160.
  • K.R. Govindarajan, P. Kanguane, T.W. Tan, S. Ranganathan (2003): MPID: MHC-Peptide Interaction Database. Bioinformatics, 19, 309-310.
  • E. Giannakis, T.S. Jokiranta, R.J. Ormsby, S. Ranganathan, D.A. Male, V.A. Fischetti, C. Mold, D.L. Gordon (2003): A common site within factor H SCR 7 responsible for binding heparin, C-reactive protein and streptococcal M protein. Eur. J. Immunol., 33, 962-969.
  • Y.P. Lim, J.O. Höög, P. Gardner, S. Ranganathan, S. Andersson, S. Subbiah, T.W. Tan, W. Hide, A.S. Weiss (2003): The S-Star Trial Bioinformatics Course: An On-Line Learning Success. Biochem. Mol. Biol. Edu., 31, 20-23.
  • P.R. Boag, S. Ranganathan, S.E. Newton, R.B. Gasser (2002): A male-specific (cysteine-rich) protein of Oesophagostomum dentatum (Strongylida) with structural characteristics of a serine protease inhibitor containing two trypsin inhibitor-like domains. Parasitology. 125, 445-455.
  • K.N. Srinivasan, V. Sivaraja, I. Huys, T. Sasaki, B. Cheng, T.K.S. Kumar, K. Sato, J. Tytgat, C. Yu, B.C.S. Chia, S. Ranganathan, J.H. Bowie, R.M. Kini, P. Gopalakrishnakone (2002): (kappa)-Hefutoxins, a Novel Class of Potassium Channel Toxins with Unique Structure and Activity. J. Biol. Chem., 277, 30040-30047.
  • S. Ranganathan, S. Singh, C.L. Poh, V.T.K. Chow (2002): The hand, foot and mouth disease virus capsid: sequence analysis and prediction of antigenic sites from homology modelling. Applied Bioinformatics, 1, 43-52.
  • S. Ranganathan, S. Subbiah, T.W. Tan (2002): APBioNet: The Asia-Pacific Regional Consortium for Bioinformatics. Applied Bioinformatics, 1, 101-105.
  • S. Ranganathan, K.R. Govindarajan, P. Kanguane, T.W. Tan (2002): MHC-Peptide Interaction Database. Nucl Acids Res Online, www3.oup.co.uk/nar/database/summary/107.
  • S. Miyano, S. Ranganathan (2001): The Asia-Pacific Regional Perspective on Bioinformatics. IEEE Intelligent Systems, 16, 19-61.
  • S. Ranganathan (2001): Molecular Modeling on the web. Biotechniques, 30, 50-52.
  • S.G. Dove, O. Hoegh-Guldberg, S. Ranganathan (2001): Major colour patterns of reef-building corals are due to family of GFP-like proteins. Coral Reefs, 19, 197-204.
  • E. Giannakis, D.A. Male, R.J. Ormsby, C. Mold, T. S. Jokiranta, S. Ranganathan, D.L. Gordon (2001): Multiple Ligand Binding Sites on Domain Seven of Human Complement Factor H. International Immunopharm.1, 433-443.
  • S. Ranganathan, D.A. Male, R.J. Ormsby, E. Giannakis, D.L. Gordon (2000): Pinpointing the putative heparin/sialic acid-binding residues in the ‘sushi’ domain 7 of factor H: a molecular modeling study. Pacific Symposium on Biocomputing, 5, 155-167.
  • K.J. Simpson, S. Ranganathan, J. Fischer, P.A. Janssens, D.C. Shaw, K.R. Nicholas (2000): Molecular characterisation and differential regulation of the tammar wallaby Whey Acidic Protein Gene. J. Biol. Chem., 275, 23074-23081.
  • D.A. Male, R.J. Ormsby, S. Ranganathan, E. Giannakis, D.L. Gordon (2000): Complement factor H: sequence analysis of 221kb of human genomic DNA containing the entire fH, fHR-1 and fHR-3 genes. Mol. Immun., 37, 41-52.

1990s

  • S. Ranganathan, K.J. Simpson, D.C. Shaw, K. Nicholas, (1999): The Whey Acidic Protein (WAP) family: a New Signature Motif and Three-Dimensional Structure by Comparative Modeling. J. Mol. Graphics Model. 17, 106-113.
  • S. McDowall, A. Argentaro, S. Ranganathan, P. Weller, S. Mertin, S. Mansour, J. Tomlie, V. Harley (1999): Functional and Structural studies of wild type SOX9 and mutations causing Campomelic Dysplasia. J. Biol. Chem. 274, 24023-24030.
  • E. Giannakis, D.A. Male, S. Ranganathan, D.A. Bourne, T.K. Blackmore, D.L. Gordon Conserved Residues in factor H SCR7 implicated in heparin binding (1998) Gordon Molec. Immunol. 35, 353.
  • J.E. Gready, S. Ranganathan, P.L. Cummins (1998): Reaction Mechanisms in Enzyme Active Sites using a “Divide and Conquer” Approach: Hybrid Quantum and Molecular Mechanics (QM/MM), in Proceedings of the 2nd CSIRO Symposium on Computational Challenges in Life Sciences, Eds. M.T. Michalewicz and M. Witten, CSIRO, Melbourne, pp. 201-212.
  • S. Ranganathan, J.E. Gready (1997): Hybrid Quantum and Molecular Mechanical (QM/MM) Studies on the Pyruvate to L-Lactate Interconversion in L-Lactate Dehydrogenase. J. Phys. Chem B 101, 5614-5618.
  • J.E. Gready, S. Ranganathan, P.R. Schofield, Y. Matsuo, K. Nishikawa (1997): Predicted Structure of the Extracellular Region of Ligand-Gated Ion-Channel Receptors shows SH2-like and SH3-like Domains forming the Ligand-Binding Site. Protein Sci. 6, 983-998.
  • S. Ranganathan, J.E. Gready (1994): Mechanistic Aspects of Biological Redox Reactions involving NADH 5. AM1 Transition State Studies for the Pyruvate - L-lactate interconversion in L- lactate dehydrogenase. Farad. Trans. 90, 2047-56.
  • P. Politzer, J.S. Murray, M.E. Grice, T. Brinck, S. Ranganathan (1991): Radial Behavior of the Average Local Ionization Energies of Atoms, J. Chem. Phys., 95, 6699-6704.
  • J.S. Murray, S. Ranganathan, P. Politzer (1991): Correlations between the Hydrogen Bond Accepting Parameter and the calculated Electrostatic Potential. J. Org. Chem.56, 3734-3737.
  • S. Ranganathan (1991): Substituent Effects on Carbonyl Bond Orders. J. Mol. Struct. Theochem. 233, 83-87.
  • J.S. Murray, N. Sukumar, S. Ranganathan, P. Politzer (1990): A Computational Analysis of the Electrostatic Potentials and relative Bond Strengths of Hydrazine and some of its 1,1-Dimethyl derivatives. Int. J. Quant. Chem., 37, 611-629.

1980s

  • P. Politzer, N. Sukumar, K. Jayasuriya, S. Ranganathan (1988): A Computational Evaluation and Comparison of Nitramine Properties. J. Am. Chem. Soc., 110, 3425-3430.
  • P. Politzer, S. Ranganathan (1986): Bond-Order - Bond-Energy Correlations. Chem. Phys. Lett., 124, 527-530.
  • A.S.N. Murthy, S. Ranganathan (1985): Compliant Fields for Molecular Interactions II: Water Dimer and Formic Acid Dimer. Int. J. Quant. Chem., 27, 547-557.
  • C. Etchebest, A. Pullman, S. Ranganathan (1985): The Gramicidin A Channel: Theoretical Energy profiles computed for Single Occupancy by a Divalent Cation Ca2+. Biochim. Biophys. Acta (Memb.) 818, 23-30.
  • C. Etchebest, S. Ranganathan, A. Pullman (1984): The Gramicidin A Channel: Comparison of Energy Profiles of Na+, K+ and Cs+. FEBS Lett. 173, 301-306.
  • A. Pullman, H. Sklenar, S. Ranganathan (1984): An ab initio study of the binding of N2 to Na+ and K+. Chem. Phys. Lett. 110, 346-350.
  • A. Pullman, S. Ranganathan (1984): Ab Initio study of the Stepwise Hydration of NO+. Chem. Phys. Lett. 107, 107-111.
  • A.S.N. Murthy, S. Ranganathan, A.P. Bharadwaj (1984): Quantum Chemical Investigations of Ion-Molecule Interactions - Low Frequency Vibrations, Geometry and Energetics. Ind. J. Pure Appl. Phys. 22, 393-397.
  • A.S.N. Murthy, S. Ranganathan (1983): Compliant fields for Formic Acid and Formamide. Farad. Trans. II 79, 1699-1706.
  • A.S.N. Murthy, S. Ranganathan (1983): The Use of CNDO/Force and Compliance Constants Methods in the evaluation of Quadratic Potential Functions for Carbonyl and Formyl Fluorides. J. Comput. Chem. 4, 175-180.
  • A.S.N. Murthy, S. Ranganathan (1983): Compliant fields for Water, Ammonia and Methane. J. Mol. Struct. Theochem 104, 1-8.
  • A.S.N. Murthy, S. Ranganathan (1982): Compliant Fields for Molecular Interactions I: Lithium Cation and Carbonyl Donors. Proc. Ind. Acad. Sci. (Chem. Sci.), 91, 535-545.
  • A.S.N. Murthy, S. Ranganathan (1982): Force Field of Carbon Suboxide. J. Mol. Struct. Theochem 90, 219-226.
  • A.S.N. Murthy, S. Ranganathan (1980): Semi-empirical Molecular Orbital Studies on the Problem of Nonclassical Resonance in the Homoallylic Cation. Int. J. Quant. Chem. 18,1479-1482.
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