• 5506 Citations
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1980 …2019

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Article
2019

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCϵ

Hardianto, A., Khanna, V., Liu, F. & Ranganathan, S., 4 Feb 2019, In : BMC Bioinformatics. 19, Suppl. 13, p. 1-11 11 p., 342.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
8 Downloads (Pure)
5 Citations (Scopus)

Prediction of novel mouse TLR9 agonists using a random forest approach

Khanna, V., Li, L., Fung, J., Ranganathan, S. & Petrovsky, N., 20 Dec 2019, In : BMC Molecular and Cell Biology. 20, Suppl 2, p. 1-14 14 p., 56.

Research output: Contribution to journalArticle

Open Access
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3 Downloads (Pure)
2018

Molecular dynamics pinpoint the global fluorine effect in balanoid binding to PKCϵ and PKA

Hardianto, A., Liu, F. & Ranganathan, S., 26 Feb 2018, In : Journal of Chemical Information and Modeling. 58, 2, p. 511-519 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

PhoglyStruct: prediction of phosphoglycerylated lysine residues using structural properties of amino acids

Chandra, A., Sharma, A., Dehzangi, A., Ranganathan, S., Jokhan, A., Chou, K-C. & Tsunoda, T., 18 Dec 2018, In : Scientific Reports. 8, p. 1-11 11 p., 17923.

Research output: Contribution to journalArticle

Open Access
File
15 Citations (Scopus)
31 Downloads (Pure)

Role of solvent accessibility for aggregation-prone patches in protein folding

Mishra, A., Ranganathan, S., Jayaram, B. & Sattar, A., 27 Aug 2018, In : Scientific Reports. 8, p. 1-13 13 p., 12896.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
7 Downloads (Pure)
2017

Divergent response of homologous ATP sites to stereospecific ligand fluorination for selectivity enhancement

Patel, A. R., Hardianto, A., Ranganathan, S. & Liu, F., 21 Feb 2017, In : Organic and Biomolecular Chemistry. 15, 7, p. 1570-1574 5 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Human Prestin: a candidate PE1 protein lacking stringent mass spectrometric evidence?

Mohamedali, A., Ahn, S. B., Sreenivasan, V. K. A., Ranganathan, S. & Baker, M. S., 1 Dec 2017, In : Journal of Proteome Research. 16, 12, p. 4531-4535 5 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Prediction of interface residue based on the features of residue interaction network

Jiao, X. & Ranganathan, S., 7 Nov 2017, In : Journal of Theoretical Biology. 432, p. 49-54 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)
2016
Open Access
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76 Downloads (Pure)
2015

A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes' stages A-D colorectal cancers

Mahboob, S., Ahn, S. B., Cheruku, H. R., Cantor, D., Rennel, E., Fredriksson, S., Edfeldt, G., Breen, E. J., Khan, A., Mohamedali, A., Muktadir, M. G., Ranganathan, S., Tan, S. H., Nice, E. & Baker, M. S., 2015, In : Clinical Proteomics. 12, 1, p. 1-12 12 p., 10.

Research output: Contribution to journalArticle

Open Access
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18 Citations (Scopus)
19 Downloads (Pure)

Coherence analysis discriminates between retroviral integration patterns in CD34+ cells transduced under differing clinical trial conditions

Hallwirth, C. V., Garg, G., Peters, T. J., Kramer, B. A., Malani, N. V., Hyman, J., Ruan, X., Ginn, S. L., Hetherington, N. A., Veeravalli, L., Shahab, A., Ranganathan, S., Wei, C. L., Liddle, C., Thrasher, A. J., Bushman, F. D., Buckley, M. J. & Alexander, I. E., 29 Apr 2015, In : Molecular Therapy - Methods and Clinical Development. 2, p. 1-10 10 p., 15015.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
8 Downloads (Pure)

Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock

Tyagi, R., Joachim, A., Ruttkowski, B., Rosa, B. A., Martin, J. C., Hallsworth-Pepin, K., Zhang, X., Ozersky, P., Wilson, R. K., Ranganathan, S., Sternberg, P. W., Gasser, R. B. & Mitreva, M., 1 Nov 2015, In : Biotechnology Advances. 33, 6 Pt 1, p. 980-991 12 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Discrete structural features among interface residue-level classes

Sowmya, G. & Ranganathan, S., 9 Dec 2015, In : BMC Bioinformatics. 16, p. 1-8 8 p., S8.

Research output: Contribution to journalArticle

Open Access
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4 Citations (Scopus)
5 Downloads (Pure)

GIW and InCoB are advancing bioinformatics in the Asia-Pacific

Schönbach, C., Horton, P., Yiu, S. M., Tan, T. W. & Ranganathan, S., 18 Dec 2015, In : BMC Bioinformatics. 16, 18, p. 1-5 5 p., I1.

Research output: Contribution to journalArticle

Open Access
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Linking structural features of protein complexes and biological function

Sowmya, G., Breen, E. J. & Ranganathan, S., Sep 2015, In : Protein Science. 24, 9, p. 1486-1494 9 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)
2014

A site for direct integrin αvβ6·uPAR interaction from structural modelling and docking

Sowmya, G., Khan, J. M., Anand, S., Ahn, S. B., Baker, M. S. & Ranganathan, S., Mar 2014, In : Journal of Structural Biology. 185, 3, p. 327-335 9 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Characterization of the interaction between heterodimeric αvβ6 integrin and urokinase plasminogen activator receptor (uPAR) using functional proteomics

Ahn, S. B., Mohamedali, A., Anand, S., Cheruku, H. R., Birch, D., Sowmya, G., Cantor, D., Ranganathan, S., Inglis, D. W., Frank, R., Agrez, M., Nice, E. C. & Baker, M. S., 5 Dec 2014, In : Journal of Proteome Research. 13, 12, p. 5956-5964 9 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Genome of the human hookworm Necator americanus

Tang, Y. T., Gao, X., Rosa, B. A., Abubucker, S., Hallsworth-Pepin, K., Martin, J., Tyagi, R., Heizer, E., Zhang, X., Bhonagiri-Palsikar, V., Minx, P., Warren, W. C., Wang, Q., Zhan, B., Hotez, P. J., Sternberg, P. W., Dougall, A., Gaze, S. T., Mulvenna, J., Sotillo, J. & 9 others, Ranganathan, S., Rabelo, E. M., Wilson, R. K., Felgner, P. L., Bethony, J., Hawdon, J. M., Gasser, R. B., Loukas, A. & Mitreva, M., 2014, In : Nature Genetics. 46, 3, p. 261-269 9 p.

Research output: Contribution to journalArticle

110 Citations (Scopus)

InCoB2014: bioinformatics to tackle the data to knowledge challenge

Ranganathan, S., Tan, T. W. & Schönbach, C., 8 Dec 2014, In : BMC Bioinformatics. 15, 16, p. 1-3 3 p., I1.

Research output: Contribution to journalArticle

Open Access
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5 Downloads (Pure)

InCoB2014: systems biology update from the Asia-Pacific

Ranganathan, S., Tan, T. W. & Schönbach, C., 8 Dec 2014, In : BMC Systems Biology. 8, Suppl. 4, p. 1-2 2 p., I1.

Research output: Contribution to journalArticle

Open Access
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InCoB2014: mining biological data from genomics for transforming industry and health

Schönbach, C., Tan, T. W. & Ranganathan, S., 8 Dec 2014, In : BMC Genomics. 15, S9, p. 1-4 4 p., I1.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
7 Downloads (Pure)

Protannotator: A semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome

Islam, M. T., Garg, G., Hancock, W. S., Risk, B. A., Baker, M. S. & Ranganathan, S., 3 Jan 2014, In : Journal of Proteome Research. 13, 1, p. 76-83 8 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Protein-protein interactions and prediction: A comprehensive overview

Sowmya, G. & Ranganathan, S., 2014, In : Protein and peptide letters. 21, 8, p. 779-789 11 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

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 journalArticle

17 Citations (Scopus)
2013

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 journalArticle

Open Access
File
3 Citations (Scopus)
19 Downloads (Pure)

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 journalArticle

14 Citations (Scopus)

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 journalArticle

Open Access
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8 Citations (Scopus)
5 Downloads (Pure)

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 journalArticle

Open Access
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2 Citations (Scopus)
4 Downloads (Pure)

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 journalArticle

12 Citations (Scopus)

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 journalArticle

14 Citations (Scopus)
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 journalArticle

Open Access
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2 Citations (Scopus)
2 Downloads (Pure)

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 journalArticle

13 Citations (Scopus)

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 journalArticle

Open Access
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30 Citations (Scopus)
1540 Downloads (Pure)

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 journalArticle

Open Access
File
1 Citation (Scopus)

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 journalArticle

Open Access
File
4 Citations (Scopus)
12 Downloads (Pure)

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 journalArticle

Open Access
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22 Citations (Scopus)
25 Downloads (Pure)

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 others, Ranganathan, 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 journalArticle

278 Citations (Scopus)
2011

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 others, Cantacessi, 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 journalArticle

186 Citations (Scopus)
17 Citations (Scopus)

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 journalArticle

Open Access
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3 Citations (Scopus)

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 journalArticle

13 Citations (Scopus)

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 journalArticle

24 Citations (Scopus)

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 others, Imanishi, 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 journalArticle

Open Access
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27 Citations (Scopus)
3 Downloads (Pure)

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 others, Imanishi, 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 journalArticle

16 Citations (Scopus)

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 journalArticle

Open Access
File
8 Citations (Scopus)
10 Downloads (Pure)
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 journalArticle

Open Access
File
20 Citations (Scopus)

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Cantacessi, C., Jex, A. R., Hall, R. S., Young, N. D., Campbell, B. E., Joachim, A., Nolan, M. J., Abubucker, S., Sternberg, P. W., Ranganathan, S., Mitreva, M. & Gasser, R. B., 1 Sep 2010, In : Nucleic Acids Research. 38, 17, p. e171 1 p.

Research output: Contribution to journalArticle

58 Citations (Scopus)

First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach

Cantacessi, C., Mitreva, M., Campbell, B. E., Hall, R. S., Young, N. D., Jex, A. R., Ranganathan, S. & Gasser, R. B., Dec 2010, In : Infection, Genetics and Evolution. 10, 8, p. 1199-1207 9 p.

Research output: Contribution to journalArticle

45 Citations (Scopus)