Prof. Shoba Ranganathan

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Contact details

Shoba Ranganathan

Professor of Bioinformatics

Address: Dept. of Chemistry and Biomolecular Sciences
Macquarie University
Sydney NSW 2109, Australia
Telephone: +61-2-9850-6262 Fax: +61-2-9850-8313
Email: shoba.ranganathan@mq.edu.au

Location: Building F7B, Room 121


Latest news


  • Professor Shoba Ranganathan has studied and worked in the field of bioinformatics since 1983, 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 associated to CNRS, and has continued to be a leading player in bioinformatics throughout her career.
  • Shoba Ranganathan the first Chair in Bioinformatics in Australia, at Macquarie University and is Adjunct Professor at the National University of Singapore (since 2004). Her research interests include genome annotation, transcriptome analysis, structural bioinformatics, immunoinformatics, genome-phenome analysis, biological networks, biodiversity informatics and cheminformatics. Shoba’s achievements include the development of graph-theoretical methods for alternative splicing analysis, a rapid and accurate docking protocol for vaccine design, pipelines for assembly and annotation of transcriptomic data, especially from helminth parasites and network approaches for large scale data mining.
  • 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. Shoba serves on the editorial boards of several bioinformatics journals including PLoS One and BMC Bioinformatics, and contributes to the organisation and scientific program of several international bioinformatics conferences. She is a steering committee member of the International Immunomics Society and of Bioinformatics Australia. She is also a Bioinformatics and Biostatistics expert advisory panel member to the National Health & Medical Research Council, Australia since 2012.
  • Shoba recently hosted InCoB2014 at Sydney, Australia

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Curriculum Vitae with full list of publications

CV


Research interests

Shoba’s research interests are in the area of computational biology and bioinformatics. Specific examples of her recent research are outlined below.

Alternative splicing:

  • Alternative pre-mRNA splicing is an important mechanism for controlling gene expression in higher eukaryotes. A single gene produces several functionally diverse proteins by alternative usage of exons or introns within pre-mRNA transcripts. These gene products can be specific to tissue, developmental stage, and disease state. We have pioneered the use of graph theory for genome-wide analysis of alternative splicing in the fruitfly, chicken compared to mouse and human and more recently, the cow, contributing to the annotation of the bovine genome as well as where the cow can be used as a model for human diseases.

Immunoinformatics:

  • Major histocompatibility complexes (MHC) play a vital role for antigen presentation and recognition by binding immunogenic peptide epitopes (p) and forming peptide-MHC (pMHC) complexes, for recognition by T cell receptors (TR), culminating in T cell activation. For efficient vaccine design and to minimize experimental T cell binding assays, advanced computational strategies for predicting strong MHC-binding epitopes with high propensity to activate T cells are required. By developing a fast accurate method for pMHC binding and analysing the physicochemical basis of TR binding to pMHC, we can accurately predicted T cell epitopes amongst high-binders for disease-implicated human MHC alleles.

Protein interaction networks:

  • Biological processes are governed by generic rules embedded in the complex connectivity or networks. Systematic studies over the past few years have unveiled how these rules maintain cellular complexity by coordinating a large number of biological processes and their molecular components. Integrating data from protein-protein and metabolite-linked protein interaction networks, we have compared, contrasted and analysed the statistical properties across different subcellular compartments. Our results indicate that the metabolic network adds value to the information in the protein interaction network for the localisation process of proteins in human subcellular compartments.

Transcriptomics:

  • Parasitic nematodes infect humans, other animals and plants, and impose a significant public health and economic burden worldwide due to the diseases that they cause. A better understanding of parasite genomes, host-parasite relationships and the molecular biology of parasites themselves will enable the rational development of diagnostic tests and/or safe anti-parasitic compounds, following the functional annotation of parasite genomic sequences. With only a few completely sequenced nematode genomes, expressed sequence tag (EST) data-sets provide a low-cost alternative (“poor man’s genome”) to whole genome sequences and a glimpse of the transcriptome of an organism. EST data require a number of computational methods for their pre-processing, clustering, assembly and annotation to yield biologically relevant information. We have developed semi-automated bioinformatic pipelines, ESTExplorer and EST2Secretome to identify molecules involved in key biological processes or pathways that might serve as targets for new drugs or vaccines.

Biodiversity and Chem Informatics:

  • Biodiversity informatics is emerging as a discipline focusing on the collection, digitisation, collation, dissemination and analysis of species-level data. We have applied biodiversity informatics tools and resources to conserve and protect customary Aboriginal medicinal plants (CMP) and their associated indigenous knowledge. In collaboration with Aboriginal communities, a web-based multidisciplinary customary medicinal knowledgebase (CMKb) was developed as a unique Australian resource. GIS and ecological niche modeling techniques were used to identify CMP species-rich areas and evaluate the cultural worth of the habitats. Further, to understand the likely impacts of climate change on the areas of highest cultural worth, predictive models were developed for current and future climate scenarios, based on spatial distributions of select CMP species.
  • Bioactive compounds from natural sources are lead compounds for many therapeutic agents. Starting from the bioactive compounds in CMKb, we have carried out cheminformatics analysis of large public datasets as well as used machine learning methdos to predict novel lead molecules.

Publications (from 2009; for full list organized as themes, pl. see CV)

2014

  • Tong, JC, Tan TW, Ranganathan S (2014) Structure-based clustering of MHC proteins for broad-based T-cell vaccine design. In: De RK, Tomar N (Eds.) Immunoinformatics, Springer, Methods in Molecular Biology, in press.
  • Khanna V, Ranganathan S (2014) Chemogenomics approach to computer-aided drug discovery. In: Sakharkar K, Sakharkar MK, Chandra R (Eds.) Genomics and Drug Discovery, River Publishers, in press.
  • Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X, Bhonagiri-Palsikar V, Minx P, Warren WC, Zhan B, Hotez PJ, Sternberg PW, Dougall A, Gaze ST, Bethony J, Mulvenna J, Ranganathan S, Rabelo EM, Wilson RW, Felgner PL, Hawdon JM, Gasser RB, Loukas A, Mitreva M (2014) Genome of the human hookworm Necator americanus. Nature Genetics, 46, 261-269.
  • Sowmya G, Khan JM, Anand S, Ahn SB, Baker MS, Ranganathan S (2014) A site for direct integrin αvβ6•uPAR interaction from structural modelling and docking. J Struct Biol, 185, 327-335.
  • Krajaejun T, Lerksuthirat T, Garg G, Lowhnoo T, Yingyong W, Khositnithikul R, Tangphatsornruang S, Suriyaphol P, Ranganathan S, Sullivan TD (2014) Transcriptome Analysis Reveals Pathogenicity and Evolutionary History of the Pathogenic Oomycete Pythium insidiosum. Fungal Biol, accepted 27 Jan. 2014
  • Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S (2014) Protannotator: A Semiautomated Pipeline for Chromosome-Wise Functional Annotation of the "Missing" Human Proteome. J Proteome Res. 13, 76-83.
  • Sowmya G, Ranganathan S (2014) Protein-protein interactions and prediction: a comprehensive overview. Peptide & Protein Letters, 21, 779-789 (invited)

2013

  • Tong JC, Ranganathan S (2013) Computer-aided vaccine design, Woodhead Publishing Series in Biomedicine No. 23, Woodhead, Cambridge, UK, pp 1-164.
  • Ranganathan S (2013) Adaptive Immune System. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306219.html
  • Ranganathan S (2013) T cell Signaling. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306227.html
  • Ranganathan S (2013) T Cell Activation. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306225.html
  • Ranganathan S (2013) Structural Immunoinformatics. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306224.html
  • Ranganathan S (2013) Reverse Vaccinology. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306223.html
  • Ranganathan S (2013) T Cell Epitopes. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306226.html
  • Ranganathan S (2013) TR Germline Bias. In: Dubitzky W., Wolkenhauer O., Cho K., Yokota H. (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306229.html
  • Ranganathan S (2013) pMHC epitope. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. URL: http://www.springerreference.com/docs/html/chapterdbid/306228.html
  • Khan J, Ranganathan S (2013) TR recognition of MHC-peptide complexes. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H (Ed.) Encyclopedia of Systems Biology. Springer-Verlag Berlin Heidelberg. ISBN: 9781441998637. DOI: 10.1007/SpringerReference_306267
  • Garg G, Ranganathan S (2013) High-throughput functional annotation and data mining of fungal genomes to identify therapeutic targets. In: Eds. Gupta VK, Tuohy M, Ayyachamy M, Turner KM, O’Donovan A. Laboratory protocols in fungal biology: current methods in fungal biology. Springer, New York, USA. ISBN 978-1-4614-2355-3, Invited book chapter, pp.559-564.
  • Kumar G, Ranganathan S (2013) Biological data integration using network models. In: Elloumi M, Zomaya AY (Eds). Biological Knowledge Discovery Handbook: Prepossessing, Mining and Postprocessing of Biological Data, Wiley Series in Bioinformatics. John Wiley & Sons, New Jersey. ISBN: 978-1-1181-3273-9, pp.155-173, invited chapter.
  • Islam MT, Mohamedali A, Garg G, Khan JM, Gorse AD, Parsons J, Marshall P, Ranganathan S*, Baker MS* (2013) Unlocking the Puzzling Biology of the Black Périgord Truffle Tuber melanosporum. J Proteome Res. 12, 5349-56. (joint corresponding authors)
  • Khan AM, Tan TW, Schönbach C, Ranganathan S (2013) APBioNet – transforming bioinformatics in the Asia-Pacific Region. PLoS Comput Biol, invited editorial, 9, e1003317.
  • Schönbach C, Shen B, Tan TW, Ranganathan S (2013) InCoB2013 introduces Systems Biology as a major conference theme. BMC Systems Biology, 7(Suppl 3), S1.
  • Tan TW, Xie C, De Silva M, Lim KS, Patro CPK, Lim SJ, Govindarajan KR, Tong JC, Choo KH, Ranganathan S, Khan AM (2013) Simple re-instantiation of small databases using cloud computing. BMC Genomics, 14(Suppl 5), S13
  • Garg G, Bernal B, Trelis M, Forment J, Ortiz J, Valero ML, Pedrola L, Martinez-Blanch J, Esteban JG, Ranganathan S, Toledo R, Marcilla A (2013) The transcriptome of Echinostoma caproni adults: further characterization of the secretome and identification of new potential drug targets. J Proteomics, 8, 202-214.
  • Kumar G, Breen EJ, Ranganathan S (2013) Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. BMC Systems Biology, 7, 12.

Ranganathan S, Khan JM, Garg G, Baker MS (2013) Functional Annotation of the Human Chromosome 7 “Missing” Proteins: A Bioinformatics Approach. J Proteome Res, 12, 2504-2510.

2012

  • Ranganathan S, Schönbach C, Tongsima S, Chan J, Tan TW (2012) Advances translational bioinformatics and population genomics in the Asia-Pacific. BMC Genomics, 13 (Suppl 8), S1.
  • Schönbach C, Ranganathan S, Tongsima S, Chan J, Tan TW (2012) Defining Computational Biology and Bioinformatics. BMC Bioinformatics, 13 (Suppl 17), S1.
  • Garg G, Ranganathan S (2012) Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs), BMC Genomics, 13 (Suppl 8):S8.
  • Menon R, Gasser RB, Mitreva M, Ranganathan S (2012) An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications, BMC Genomics, 13 (Suppl 8):S10.
  • Menon R, Garg G, Gasser RB, Ranganathan S (2012) TranSeqAnnotator: Large-scale analysis of transcriptomic data, BMC Bioinformatics, 13 (Suppl 17), S24.
  • Packer J,* Gaikwad J,* Harrington D, Ranganathan S, Vemulpad S, Jamie J (2012): Medicinal Plants of New South Wales, in Genetic Resources, Chromosome Engineering and Crop Improvement Series: Medicinal Crops, ed. Singh RJ, CRC Press, Taylor & Francis Group, USA. Invited book chapter, 259-296. (*joint first authors)
  • Young ND, Jex AR, Li B, Shiping L, Linfeng Y, Zijun X, Cantacessi C, Xun X, Fangyuan C, Wu X, Hall RS, Campbell BE, Loukas A, Ranganathan S, Rollinson D, Wang J, Yang H, Rinaldi G, Brindley PJ, Gasser RB (2012). The Schistosoma haematobium genome, in response to the wake-up call, Nature Genetics, 44, 221–225.
  • Packer J, Brouwer N, Harrington D, Gaikwad J, Heron R, Yaegl Community Elders, Ranganathan S, Vemulpad S, Jamie J (2012) An ethnobotanical study of medicinal plants used by the Yaegl Aboriginal community in northern New South Wales, Australia. J Ethnopharmacol, 139, 244-255.
  • Marcilla A, Garg G, Bernal D, Ranganathan S, Forment J, Muñoz-Antolí C, Dominguez MV, Pedrola L, Martinez J, Sotillo J, Trelis M, Toledo R, Esteban JG (2012) The transcriptome analysis of Strongyloides stercoralis L3i larvae reveals targets for invention in a neglected disease. PLoS Negl. Trop. Dis., 6, e1513.
  • Khan JM, Kumar G, Ranganathan S (2012) In silico prediction of immunogenic T cell epitopes for HLA-DQ8. Immunome Res, 8, 1.
  • Cantacessi C, Campbell BE, Jex AR, Young ND, Hall RS, Ranganathan S, Gasser RB (2012) Bioinformatics meets parasitology. Parasite Immunol., 34, 265–275.

2011

  • Jex AR, Li B, Young ND, Hall RS, Yang L, Liu S, Xun X, Xiong Z, Chen F, Wu X, Zhou G, Fang X, Campbell BE, Cantacessi C, Schwarz EM, Ranganathan S, Geldhof P, Nejsum P, Sternberg P, Wang J, Yang H, Gasser RB (2011) The Ascaris suum genome. Nature, 479, 529–533.
  • Ranganathan S, Schönbach C, Kelso J, Rost B, Nathan S, Tan TW (2011) Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia. BMC Bioinformatics, 12(Suppl 13), S1.
  • Schönbach C, Tan TW, Kelso J, Rost B, Nathan S, Ranganathan S (2011) InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Genomics, 12 (Suppl 3):S1.
  • Garg G, Ranganathan S (2011) In silico secretome analysis approach for next generation sequencing transcriptomic data. BMC Genomics, 12(Suppl 3), S14.
  • Hyunh T,* Khan JM,* Ranganathan S (2011) A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-Mannosidase reveals a genotype-phenotype correlation. BMC Genomics, 12(Suppl 3), S22 (*joint first authors).
  • Khanna V, Ranganathan S (2011) In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance. BMC Bioinformatics, in press.
  • Cantacessi C, Campbell BE, Jex AR, Young ND, Hall RS, Ranganathan S, Gasser RB (2011) Parasite Immunol., 12 (Suppl 13), S25.
  • Gaikwad J, Wilson PD, Ranganathan S (2011) Ecological niche modeling of customary medicinal plant species used by Australian Aborigines to identify species-rich and culturally valuable areas for conservation. Ecol. Model. 222, 3437–3443.
  • Khanna V, Ranganathan S (2011) Scaffold analysis and fragment co-occurrence studies on public datasets of biological interest. J Cheminformatics, 3, 30.
  • Khanna V, Ranganathan S (2011) Molecular Similarity and Diversity Approaches in Chemoinformatics. Drug Devel Res, 72, 74-84.
  • Indigenous Bioresources Research Group (Packer J, Gaikwad J, Harrington D, Ranganathan S, Vemulpad S, Jamie J) and Yaegl Aboriginal Elders (2011): Yaegl Medicinal and Plant Resources Handbook 2011, Edition 1, Macquarie University, Sydney, 978-1-74138-361-4, pp.1-72.
  • Cantacessi C, Gasser RB, Strube C, Schnieder T, Jex AR, Hall RS, Campbell BE, Young ND, Ranganathan S, Sternberg PW, Mitreva M (2011) Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention. Biotechnol. Adv., 29, 261-271.
  • Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group (2011) Towards BioDBcore: a community-defined information specification for biological databases. Database, 2011:baq027 (editorial).
  • Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group (2011) Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res., 39, D7–D10.
  • Khan JM, Cheruku HR, Tong JC, Ranganathan S (2011) MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures. Bioinformatics, 27:1192-1193.
  • Khan JM, Ranganathan S (2011) Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one. PLoS ONE, 6(2): e17194.
  • Garg G, Ranganathan S (2011) High-throughput functional annotation and data mining of fungal genomes to identify therapeutic targets: Laboratory protocols in fungal biology: current methods in fungal biology. Editors: Vijai Kumar Gupta, Maria Tuohy, Manimaran Ayyachamy, Kevin M. Turner, Anthonia O’Donovan. Springer, New York, USA. Invited book chapter, in press, ISBN 978-1-4614-2355-3.
  • Chacko E, Ranganathan S (2011): Graphs in Bioinformatics, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, eds. M. Elloumi and A.Y. Zomaya, Wiley, pp.193-219.
  • Kumar G, Ranganathan S (2011): Untangling Biological Networks Using Bioinformatics, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, eds. M. Elloumi and A.Y. Zomaya, Wiley, pp.867-892.
  • Khanna V, Ranganathan S (2011): In Silico Methods for the Analysis of Metabolites and Drug Molecules, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, eds. M. Elloumi and A.Y. Zomaya, Wiley, pp.363-383.
  • Gaikwad J, Wilson K, Kohen J, Vemulpad S, Jamie J, Ranganathan S (2011): Combining Ethnobotany and Informatics to Discover Knowledge from Data, in Ethnomedicinal Plants: Revitalization of Traditional Knowledge of Herbs, eds. Rai M, Acharya D and Rios JL, Science Publishers, USA, pp.444-457.

2010

  • Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL (2010) Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci., 3:259-66.
  • Tan TW, Tong JC, Khan AM, de Silva M, Lim KS, Ranganathan S. (2010) Advancing Standards for Bioinformatics Activities: Persistence, Reproducibility, Disambiguation and Minimum Information About a Bioinformatics investigation (MIABi). BMC Genomics, 11 Suppl 4, S27.
  • Ranganathan S, Schönbach C, Nakai K, Tan TW (2010) Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB2010). BMC Genomics, 11 Suppl 4, S1.
  • Schönbach C, Nakai K, Tan TW, Ranganathan S (2010) InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinformatics, 11 Suppl 7, S1.
  • Cantacessi C, Mitreva M, Campbell BE, Hall RS, Young ND, Jex AR, Ranganathan S, Gasser RB (2010) First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach. Infect Genet Evol. 10, 1199-1207.
  • Cantacessi C, Mitreva M, Jex AR, Young ND, Campbell BE, Hall RS, Doyle MA, Ralph SA, Rabelo EM, Ranganathan S, Sternberg PW, Loukas A, Gasser RB (2010) Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome. PLoS Negl. Trop. Dis., 4, e684.
  • Cantacessi C, Jex AR, Hall RS, Young ND, Campbell BE, Joachim A, Nolan MJ, Abubucker S, Sternberg PW, Ranganathan S, Mitreva M, Gasser RB (2010) A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. Nucleic Acids Res., 38, e171.
  • Chacko E, Ranganathan S (2010): Graphs in Bioinformatics, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, eds. M. Elloumi and A.Y. Zomaya, Wiley, pp.193-219.
  • Khan JM, Ranganathan S (2010) pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. Immunome Res., 6 Suppl 1, S2.
  • Davies MN, Ranganathan S, Flower DR (eds.) (2010) Bioinformatics for Immunomics, Springer, New York.
  • Khan JM, Tong JC, Ranganathan S (2010) Structural Immunoinformatics: understanding MHC-Peptide-TR binding, in Bioinformatics for Immunomics, eds. Dr .N Davies, Ranganathan S and D.R. Flower, Springer, New York, pp.77-93.
  • Kumar G, Ranganathan S (2010): Network analysis of human protein location. BMC Bioinformatics, 11 Suppl 7, S9.
  • Kumar G, Ranganathan S (2010): Untangling Biological Networks Using Bioinformatics, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, eds. M. Elloumi and A.Y. Zomaya, Wiley, pp.867-892.
  • Gaikwad J, Wilson K, Kohen J, Vemulpad S, Jamie J, Ranganathan S (2010): Combining Ethnobotany and Informatics to Discover Knowledge from Data, in Ethnomedicinal Plants: Revitalization of Traditional Knowledge of Herbs, eds. Rai M, Acharya D and Rios JL, Science Publishers, USA, pp.444-457.
  • Packer J,* Gaikwad J,* Harrington D, Ranganathan S, Vemulpad S, Jamie J (2010): Medicinal Plants of New South Wales, in Genetic Resources, Chromosome Engineering and Crop Improvement Series: Medicinal Crops, ed. Singh RJ, CRC Press, Taylor & Francis Group, USA. Invited book chapter, in press. (*joint first authors)
  • Khanna V, Ranganathan S (2010): In Silico Methods for the Analysis of Metabolites and Drug Molecules, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, eds. M. Elloumi and A.Y. Zomaya, Wiley, pp.363-383.
  • Islam MT, Shaikh M, Nayak A, Ranganathan S (2010) Biomarker Information Extraction Tool (BIET) Development using Natural Language Processing and Machine Learning, Proc. International Conference and Workshop on Emerging Trends in Technology in 2010 (ICWET 2010) Mumbai, India, ACM Digital Library, pp.121-126.
  • Islam MT, Shaikh M, Nayak A, Ranganathan S (2010) Extracting Biomarker Information applying Natural Language Processing and Machine Learning, Proc. 2010 IEEE 4th Int'l Conference on Bioinformatics and Biomedical Engineering (iCBBE 2010), Chengdu, China, pp. 1-4. doi: 10.1109/ICBBE.2010.5514717.

2009

  • Ranganathan S (2009) Towards a career in bioinformatics. BMC Bioinformatics, 10 Suppl 15, S1.
  • Ranganathan S, Eisenhaber F, Tong JC, Tan TW (2009) Extending Asia Pacific bioinformatics into new realms in the “-omics” era. BMC Genomics, 10 Suppl 3, S1.
  • Ranganathan S, G. Garg (2009) Secretome: clues into pathogen infection and clinical applications. Genome Medicine, 1,113.
  • Ranganathan S, Menon R, Gasser RB (2009) Advanced in silico analysis of expressed sequence tag (EST) data for parasitic nematodes of major socio-economic importance - Fundamental insights toward biotechnological outcomes. Biotechnol. Adv., 27, 439-448.
  • Robinson MW, Menon R, Donnelly SM, Dalton JP, Ranganathan S (2009) An integrated transcriptomic and proteomic analysis of the secretome of the helminth pathogen, Fasciola hepatica: proteins associated with invasion and infection of the mammalian host. Mol. Cell Proteomics, 8, 1891–1907.
  • Rabelo EM, Hall RS, Loukas A, Cooper L, Hu M, Ranganathan S, Gasser RB (2009) Improved insights into the transcriptomes of the human hookworm Necator americanus--fundamental and biotechnological implications. Biotechnol. Adv., 27, 122-132.
  • Cantacessi C, Zou FC, Hall RS, Zhong W, Jex AR, Campbell BE, Ranganathan S, Sternberg PW, Zhu XQ, Gasser RB (2009) Bioinformatic analysis of abundant gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform. Mol. Cell Probes, 23, 205-217.
  • Chacko E, Ranganathan S (2009) Genome-wide analysis of alternative splicing in cow: implications for bovine as a model for human diseases. BMC Genomics, 10 Suppl 3, S11.
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