• 5255 Citations
  • 37 h-Index
1980 …2021
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Research Outputs 1980 2019

2014

Transcriptome analysis reveals pathogenicity and evolutionary history of the pathogenic oomycete Pythium insidiosum

Krajaejun, T., Lerksuthirat, T., Garg, G., Lowhnoo, T., Yingyong, W., Khositnithikul, R., Tangphatsornruang, S., Suriyaphol, P., Ranganathan, S. & Sullivan, T. D., 2014, In : Fungal Biology. 118, 7, p. 640-653 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Pythium insidiosum
Pythium
Oomycetes
pathogenicity
Gene Expression Profiling
2013

Adaptive immune system

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 10-11 2 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

Analysis and comparison of γ-retroviral vector integration behaviour in human CD34+cells transduced under conditions employed in the French and English SCID-X1 clinical trials

Hallwirth, C. V., Garg, G., Malani, N. V., Peters, T., Hetherington, N., Hyman, J., Kramer, B., Ginn, S. L., Ruan, X., Ranganathan, S., Buckley, M., Bushman, F. D. & Alexander, I. E., Aug 2013, In : Journal of Gene Medicine. 15, 8-9, p. 315-316 2 p.

Research output: Contribution to journalMeeting abstractResearch

APBioNet-transforming bioinformatics in the Asia-Pacific Region

Khan, A. M., Tan, T. W., Schönbach, C. & Ranganathan, S., 31 Oct 2013, In : PLoS Computational Biology. 9, 10, p. 1-3 3 p., e1003317.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Computer-Aided Vaccine Design

Tong, J. C. & Ranganathan, S., 2013, Oxford: Elsevier. 135 p.

Research output: Book/ReportBookResearchpeer-review

Computer-Aided Design
Vaccines
Informatics
B-Lymphocytes
Databases

Functional annotation of the human chromosome 7 "missing" proteins: A bioinformatics approach

Ranganathan, S., Khan, J. M., Garg, G. & Baker, M. S., 2013, In : Journal of Proteome Research. 12, 6, p. 2504-2510 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Chromosomes, Human, Pair 7
Staphylococcal Protein A
Human Chromosomes
Bioinformatics
Chromosomes

High-throughput functional annotation and data mining of fungal genomes to identify therapeutic targets

Garg, G. & Ranganathan, S., 2013, Laboratory protocols in fungal biology: current methods on fungal biology. Gupta, V. K., Tuohy, M. G., Ayyachamy, M., Turner, K. M. & O'Donovan, A. (eds.). New York: Springer, Springer Nature, p. 559-564 6 p. (Fungal biology).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Fungal Genome
Data Mining
Proteins
Cryptococcus gattii
Molecular Sequence Annotation

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework

Kumar, G., Breen, E. J. & Ranganathan, S., 6 Feb 2013, In : BMC Systems Biology. 7, p. 1-14 14 p., 12.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Ovarian Cancer
Neoplasm Genes
Ovarian Neoplasms
Genes
Gene

InCoB2013 introduces Systems Biology as a major conference theme

Schönbach, C., Shen, B., Tan, T. W. & Ranganathan, S., 4 Nov 2013, In : BMC Systems Biology. 7, Supplement 3, p. 1-3 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Systems Biology
Bioinformatics
Computational Biology
North America
Systems Analysis

pMHC epitope

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 1718-1719 2 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

Simple re-instantiation of small databases using cloud computing

Tan, T. W., Xie, C., De Silva, M., Lim, K. S., Patro, C. P. K., Lim, S. J., Govindarajan, K. R., Tong, J. C., Choo, K. H., Ranganathan, S. & Khan, A. M., 2013, In : BMC Genomics. 14, Suppl 5, p. 1-4 4 p., S13.

Research output: Contribution to journalConference paperResearchpeer-review

Open Access
File
Databases
Computational Biology
Cloud Computing
Online Systems
Publications

Structural immunoinformatics

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 2022-2023 2 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

T cell activation

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). Springer, Springer Nature, p. 2115-2115 1 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

T cell epitopes

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 2118-2119 2 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

T cell signalling

Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 2119-2119 1 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

The transcriptome of Echinostoma caproni adults: Further characterization of the secretome and identification of new potential drug targets

Garg, G., Bernal, D., Trelis, M., Forment, J., Ortiz, J., Valero, M. L., Pedrola, L., Martinez-Blanch, J., Esteban, J. G., Ranganathan, S., Toledo, R. & Marcilla, A., 26 Aug 2013, In : Journal of Proteomics. 89, p. 202-214 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Echinostoma
Transcriptome
Helminths
Pharmaceutical Preparations
Proteins

TR Germline Bias

Ranganathan, S., 2013, Encyclopedia of Systems Biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 2212-2212 1 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

TR recognition of MHC-peptide complexes

Khan, J. & Ranganathan, S., 2013, Encyclopedia of systems biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). New York: Springer, Springer Nature, p. 2212-2218 7 p.

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference bookResearch

Unlocking the puzzling biology of the Black Périgord truffle Tuber melanosporum

Islam, M. T., Mohamedali, A., Garg, G., Khan, J. M., Gorse, A. D., Parsons, J., Marshall, P., Ranganathan, S. & Baker, M. S., 6 Dec 2013, In : Journal of Proteome Research. 12, 12, p. 5349-5356 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Perfume
Fragrances
Proteins
Proteomics
Biochemistry
2012

Advances in translational bioinformatics and population genomics in the Asia-Pacific

Ranganathan, S., Tongsima, S., Chan, J., Tan, T. W. & Schönbach, C., 2012, In : BMC Genomics. 13, Suppl 7, p. 1-4 4 p., S1.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Metagenomics
Computational Biology
Precision Medicine
Thailand
Genomics

An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications

Menon, R., Gasser, R. B., Mitreva, M. & Ranganathan, S., 2012, In : BMC Genomics. 13, Suppl 7, p. 1-17 17 p., S10.

Research output: Contribution to journalArticleResearchpeer-review

Gene Expression Profiling
Proteins
Expressed Sequence Tags
Parasites
Cysteine Proteases

An ethnobotanical study of medicinal plants used by the Yaegl Aboriginal community in northern New South Wales, Australia

Packer, J., Brouwer, N., Harrington, D., Gaikwad, J., Heron, R., Yaegl Community Elders, C. E., Ranganathan, S., Vemulpad, S. & Jamie, J., 6 Jan 2012, In : Journal of Ethnopharmacology. 139, 1, p. 244-255 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
South Australia
New South Wales
Medicinal Plants
Plant Preparations
Health Services Research

Bioinformatics meets parasitology

Cantacessi, C., Campbell, B. E., Jex, A. R., Young, N. D., Hall, R. S., Ranganathan, S. & Gasser, R. B., May 2012, In : Parasite Immunology. 34, 5, p. 265-275 11 p.

Research output: Contribution to journalReview articleResearchpeer-review

Parasitology
Computational Biology
Parasites
Technology
Transcriptome

Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs)

Garg, G. & Ranganathan, S., 2012, In : BMC Genomics. 13, p. 1-11 11 p., S8.

Research output: Contribution to journalConference paperResearchpeer-review

Open Access
File
Helminths
Expressed Sequence Tags
Databases
Parasitic Diseases
Helminth Proteins

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs

Schönbach, C., Tongsima, S., Chan, J., Brusic, V., Tan, T. W. & Ranganathan, S., 2012, In : BMC Bioinformatics. 13, Suppl 17, p. 1-6 6 p., S1.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Bioinformatics
Computational Biology
Knowledge
Immunology
Biotechnology

In silico prediction of immunogenic T cell epitopes for HLA-DQ8

Khan, J. M., Kumar, G. & Ranganathan, S., 2012, In : Immunome Research. 8, 1, p. 1-9 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Epitopes
T-Lymphocyte Epitopes
T-cells
Computer Simulation
Peptides

Medicinal plants of New South Wales, Australia

Packer, J., Gaikwad, J., Harrington, D., Ranganathan, S., Jamie, J. & Vemulpad, S., 2012, Genetic Resources, chromosome engineering, and crop improvement: Volume 6 : medicinal plants. Singh, R. J. (ed.). Boca Raton ; London ; New York: CRC Press, Taylor & Francis Group, Vol. 6. p. 259-296 38 p. (Genetic Resources, chromosome engineering, and crop improvement series).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

non-vascular plants
Orchards
South Australia
New South Wales
Biodiversity

The transcriptome analysis of strongyloides stercoralis L3i larvae reveals targets for intervention in a neglected disease

Marcilla, A., Garg, G., Bernal, D., Ranganathan, S., Forment, J., Ortiz, J., Muñoz-Antolí, C., Dominguez, M. V., Pedrola, L., Martinez-Blanch, J., Sotillo, J., Trelis, M., Toledo, R. & Esteban, J. G., Feb 2012, In : PLoS Neglected Tropical Diseases. 6, 2, p. 1-9 9 p., e1513.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Strongyloides stercoralis
Neglected Diseases
Gene Expression Profiling
Larva
Transcriptome

TranSeqAnnotator: large-scale analysis of transcriptomic data.

Menon, R., Garg, G., Gasser, R. B. & Ranganathan, S., 2012, In : BMC Bioinformatics. 13, Suppl 17, p. 1-7 7 p., S24.

Research output: Contribution to journalConference paperResearchpeer-review

Expressed Sequence Tags
Proteins
Protein
Pipelines
Computational Biology

Whole-genome sequence of Schistosoma haematobium

Young, N. D., Jex, A. R., Li, B., Liu, S., Yang, L., Xiong, Z., Li, Y., Cantacessi, C., Hall, R. S., Xu, X., Chen, F., Wu, X., Zerlotini, A., Oliveira, G., Hofmann, A., Zhang, G., Fang, X., Kang, Y., Campbell, B. E., Loukas, A. & 8 othersRanganathan, S., Rollinson, D., Rinaldi, G., Brindley, P. J., Yang, H., Wang, J., Wang, J. & Gasser, R. B., Feb 2012, In : Nature Genetics. 44, 2, p. 221-225 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Schistosoma haematobium
Genome
Parasites
Neglected Diseases
Schistosoma
2011

A comparative structural bioinformatics analysis of inherited mutations in b-D-Mannosidase across multiple species reveals a genotype-phenotype correlation

Huynh, T., Khan, J. M. & Ranganathan, S., 2011, 10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). Schoenbach, C., Nathan, S., Tan, T. W. & Ranganathan, S. (eds.). United Kingdom: Springer, Springer Nature, Vol. 12, Suppl. 3. p. 1-13 13 p. S22

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contributionResearchpeer-review

Mannosidases
mannosidases
Genetic Association Studies
Bioinformatics
Computational Biology

Ascaris suum draft genome

Jex, A. R., Liu, S., Li, B., Young, N. D., Hall, R. S., Li, Y., Yang, L., Zeng, N., Xu, X., Xiong, Z., Chen, F., Wu, X., Zhang, G., Fang, X., Kang, Y., Anderson, G. A., Harris, T. W., Campbell, B. E., Vlaminck, J., Wang, T. & 10 othersCantacessi, C., Schwarz, E. M., Ranganathan, S., Geldhof, P., Nejsum, P., Sternberg, P. W., Yang, H., Wang, J., Wang, J. & Gasser, R. B., 24 Nov 2011, In : Nature. 479, 7374, p. 529-533 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Ascaris suum
Ascaris
Genome
Ascariasis
Necator

Combining ethnobotany and informatics to discover knowledge from data

Gaikwad, J., Wilson, K., Kohen, J., Vemulpad, S., Jamie, J. & Ranganathan, S., 2011, Ethnomedicinal plants: revitalization of traditional knowledge of herbs. Rai, M., Acharya, D. & Ríos, J. L. (eds.). 1st ed. Enfield, NH: Science Publishers, p. 444-457 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention

Cantacessi, C., Gasser, R. B., Strube, C., Schnieder, T., Jex, A. R., Hall, R. S., Campbell, B. E., Young, N. D., Ranganathan, S., Sternberg, P. W. & Mitreva, M., May 2011, In : Biotechnology Advances. 29, 3, p. 261-271 11 p.

Research output: Contribution to journalReview articleResearchpeer-review

Dictyocaulus
Transcriptome
Protein-Serine-Threonine Kinases
Proteins
Nucleoplasmins

Ecological niche modeling of customary medicinal plant species used by Australian Aborigines to identify species-rich and culturally valuable areas for conservation

Gaikwad, J., Wilson, P. D. & Ranganathan, S., 24 Sep 2011, In : Ecological Modelling. 222, 18, p. 3437-3443 7 p.

Research output: Contribution to journalArticleResearchpeer-review

medicinal plant
modeling
habitat
herbarium
niche

Generation and analysis of a highly complex γ-retroviral vector integration site dataset from human CD34+ cells using illumina next-generation sequencing

Hallwirth, C. V., Hyman, J., Garg, G., Ruan, X., Veeravalli, L., Kramer, B., Shahab, A., Ong, C. T., Liddle, C., Ranganathan, S., Russell, D. W., Wei, C-L. & Alexander, I. E., 2011, In : Journal of Gene Medicine. 13, 7-8, p. 430-431 2 p.

Research output: Contribution to journalMeeting abstractResearch

Graphs in bioinformatics

Chacko, E. & Ranganathan, S., 2011, Algorithms in computational molecular biology: Techniques, approaches and applications. Elloumi, M. & Zomaya, A. Y. (eds.). Oxford: John Wiley & Sons, p. 192-219 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia

Schönbach, C., Tan, T. W., Kelso, J., Rost, B., Nathan, S. & Ranganathan, S., 30 Nov 2011, In : BMC Genomics. 12, 3, p. 1-4 4 p., S1.

Research output: Contribution to journalArticleResearch

Open Access
File
Anniversaries and Special Events
Bioinformatics
Computational Biology
bioinformatics
Joints

In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance

Khanna, V. & Ranganathan, S., 30 Nov 2011, In : BMC Bioinformatics. 12, Suppl 13, p. 1-12 12 p., S25.

Research output: Contribution to journalConference paperResearchpeer-review

Computer Simulation
Anthelmintics
Economics
Developing Countries
Support vector machines

In silico methods for the analysis of metabolites and drug molecules

Khanna, V. & Ranganathan, S., 2011, Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications. Elloumi, M. & Zomaya, A. Y. (eds.). Hoboken, NJ: John Wiley & Sons, p. 361-381 21 p. (Bioinformatics: Computational Techniques and Engineering).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

In silico secretome analysis approach for next generation sequencing transcriptomic data

Garg, G. & Ranganathan, S., 2011, 10th International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology. Schoenbach, C., Nathan, S., Tan, T. W. & Ranganathan, S. (eds.). Piscataway, N.J.: Institute of Electrical and Electronics Engineers (IEEE), Vol. 12, Suppl. 3. p. 1-10 10 p. S14

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contributionResearchpeer-review

transcriptomics
Computer Simulation
Proteins
proteins
Helminth Proteins

Molecular similarity and diversity approaches in chemoinformatics

Khanna, V. & Ranganathan, S., Feb 2011, In : Drug Development Research. 72, 1, p. 74-84 11 p.

Research output: Contribution to journalReview articleResearchpeer-review

Libraries
Digital Libraries
Drug Discovery
Computer Simulation
Pharmacokinetics

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures

Khan, J. M., Cheruku, H. R., Tong, J. C. & Ranganathan, S., Apr 2011, In : Bioinformatics. 27, 8, p. 1192-1193 2 p., btr104.

Research output: Contribution to journalArticleResearchpeer-review

Structure-function
Peptides
Databases
Interaction
TR-2 mycotoxin

Structural diversity of biologically interesting datasets: A scaffold analysis approach

Khanna, V. & Ranganathan, S., Aug 2011, In : Journal of Cheminformatics. 3, p. 1-14 14 p., 30.

Research output: Contribution to journalArticleResearchpeer-review

metabolites
Metabolites
Scaffolds
Biological Products
Lead

Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference

Ranganathan, S., Schönbach, C., Kelso, J., Rost, B., Nathan, S. & Tan, T. W., 30 Nov 2011, In : BMC Bioinformatics. 12, SUPPL. 13, p. 1-4 4 p., S1.

Research output: Contribution to journalEditorialResearchpeer-review

Open Access
File
Computational Biology
Bioinformatics
Joints
Genome
Genes

Towards BioDBcore: A community-defined information specification for biological databases

Gaudet, P., Bairoch, A., Field, D., Sansone, S. A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G. & 18 othersImanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Mizrachi, I. K., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O. & Yamasaki, C., 2011, In : Database. 2011, p. 1-6 6 p., baq027.

Research output: Contribution to journalArticleResearchpeer-review

Databases
Specifications
Syntactics
Semantics
Interoperability

Towards BioDBcore: a community-defined information specification for biological databases

Gaudet, P., Bairoch, A., Field, D., Sansone, S. A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G. & 18 othersImanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Karsch-Mizrachi, I., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O. & Yamasaki, C., Jan 2011, In : Nucleic acids research. 39, SUPPL. 1, p. D7-D10 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Databases
Semantics

Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one

Khan, J. M. & Ranganathan, S., 2011, In : PLoS ONE. 6, 2, p. 1-12 12 p., e17194.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
T-Cell Antigen Receptor
T-lymphocytes
peptides
Peptides
receptors

Untangling biological networks using bioinformatics

Kumar, G., Cootes, A. P. & Ranganathan, S., 2011, Algorithms in computational molecular biology: Techniques, approaches and applications. Elloumi, M. & Zomaya, A. Y. (eds.). Oxford: Wiley-Blackwell, Wiley, p. 867-892 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

2010

Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

Tan, T. W., Tong, J. C., Khan, A. M., de Silva, M., Lim, K. S. & Ranganathan, S., 2 Dec 2010, In : BMC Genomics. 11, Supplement 4, p. 1-7 7 p., S27.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Bioinformatics
Computational Biology
bioinformatics
reproducibility
compliance