• 5510 Citations
  • 37 h-Index
1980 …2019

Research output per year

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Research Outputs

2019

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018

Ahmad, S., Gromiha, M. M., Raghava, G. P. S., Schönbach, C. & Ranganathan, S., 18 Apr 2019, In : BMC Genomics. 19, Suppl. 9, 4 p., 266.

Research output: Contribution to journalConference paper

Open Access
File
4 Downloads (Pure)

Applications of machine learning in GPCR bioactive ligand discovery

Jabeen, A. & Ranganathan, S., Apr 2019, In : Current Opinion in Structural Biology. 55, p. 66-76 11 p.

Research output: Contribution to journalReview article

4 Citations (Scopus)

Bioinformatics approaches for improving seminal plasma proteome analysis

Noor, Z. & Ranganathan, S., 1 Oct 2019, In : Theriogenology. 137, p. 43-49 7 p.

Research output: Contribution to journalConference paper

Open Access
File
7 Citations (Scopus)
149 Downloads (Pure)

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)

Editorial overview: theory and simulation: demystifying GPCRs – structure, function and drug design

Ranganathan, S. & Blundell, T. L., Apr 2019, In : Current Opinion in Structural Biology. 55, p. vi-viii 3 p.

Research output: Contribution to journalEditorial

Encyclopedia of bioinformatics and computational biology

Ranganathan, S. (ed.), Gribskov, M. (ed.), Nakai, K. (ed.) & Schönbach, C. (ed.), 2019, Amsterdam; Oxford; Cambridge: Elsevier. 3346 p.

Research output: Book/ReportEdited Book/Anthology

Genome databases and browsers

Southwood, D. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Ranganathan, S., Gribskov, M., Nakai, K. & Schönbach, C. (eds.). Amsterdam: Elsevier, Vol. 2. p. 251-256 6 p.

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

Host-pathogen interactions

Southwood, D. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Ranganathan, S., Gribskov, M., Nakai, K. & Schönbach, C. (eds.). Amsterdam: Elsevier, Vol. 3. p. 103-112 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Identification of proteins from proteomic analysis

Noor, Z., Mohamedali, A. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Cannataro, M., Gaeta, B. & Asif Khan, M. (eds.). Amsterdam; Oxford; Cambridge: Elsevier, Vol. 3. p. 855-870 16 p.

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

5 Citations (Scopus)

Looking for missing proteins

Jabeen, A., Mohamedali, A. & Ranganathan, S., 2019, Reference module in life sciences. Roitberg, B. D., Cotter, P. D., Dixon, B., Giordano, A., Mayor, R., O'Neill, S., Pentimalli, F., Ranganathan, S., Sharfstein, S. T., Vitale, I., Wilson, K., Zaragoza, O. & Zhou, H-X. (eds.). Elsevier, p. 1-15 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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
File
3 Downloads (Pure)

Protocol for protein structure modelling

Jabeen, A., Mohamedali, A. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Cannataro, M., Gaeta, B. & Asif Khan, M. (eds.). Amsterdam; Oxford; Cambridge: Elsevier, Vol. 3. p. 252-272 21 p.

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

1 Citation (Scopus)

Quantification of proteins from proteomic analysis

Noor, Z., Adhikari, S., Ranganathan, S. & Mohamedali, A., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Cannataro, M., Gaeta, B. & Asif Khan, M. (eds.). Amsterdam; Oxford; Cambridge: Elsevier, Vol. 3. p. 871-890 20 p.

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

Rational structure-based drug design

Khanna, V., Ranganathan, S. & Petrovsky, N., 2019, Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. Ranganathan, S., Gribskov, M., Nakai, K. & Schönbach, C. (eds.). Amsterdam: Elsevier, Vol. 2. p. 585-600 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Structural bioinformatics analysis of variants on GPCR function

Syed Haneef, S. A. & Ranganathan, S., Apr 2019, In : Current Opinion in Structural Biology. 55, p. 161-177 17 p.

Research output: Contribution to journalReview article

1 Citation (Scopus)
2018

A bioinformatics potpourri

Schönbach, C., Li, J., Ma, L., Horton, P., Sjaugi, M. F. & Ranganathan, S., 19 Jan 2018, In : BMC Genomics. 19, Suppl 1, 6 p., 920.

Research output: Contribution to journalEditorial

Open Access
File
15 Downloads (Pure)

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses

Zhou, X., Zheng, J., Ivan, F. X., Yin, R., Ranganathan, S., Chow, V. T. K. & Kwoh, C-K., 9 May 2018, In : BMC Genomics. 19, Suppl 2, p. 1-10 10 p., 88.

Research output: Contribution to journalConference paper

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

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
2 Citations (Scopus)
7 Downloads (Pure)
2017

Accelerating the search for the missing proteins in the human proteome

Baker, M. S., Ahn, S. B., Mohamedali, A., Islam, M. T., Cantor, D., Verhaert, P. D., Fanayan, S., Sharma, S., Nice, E. C., Connor, M. & Ranganathan, S., 24 Jan 2017, In : Nature Communications. 8, p. 1-13 13 p., 14271.

Research output: Contribution to journalReview article

Open Access
File
48 Citations (Scopus)
28 Downloads (Pure)

A systematic bioinformatics approach to identify high quality mass spectrometry data and functionally annotate proteins and proteomes

Islam, M., Mohamedali, A., Ahn, S. B., Nawar, I., Baker, M. S. & Ranganathan, S., 2017, Proteome bionformatics. Keerthikumar, S. & Mathivanan, S. (eds.). New York: Humana Press Inc., p. 163-176 14 p. (Methods in Molecular Biology; vol. 1549).

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Citations (Scopus)

De novo peptide sequencing: deep mining of high-resolution mass spectrometry data

Islam, M. T., Mohamedali, A., Fernandes, C. S., Baker, M. S. & Ranganathan, S., 2017, Proteome bioinformatics: Methods in molecular biology. Keerthikumar, S. & Mathivanan, S. (eds.). 1st ed. New York: Humana Press Inc., p. 119-134 16 p. (Methods in Molecular Biology; vol. 1549).

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

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)

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases

Hardianto, A., Yusuf, M., Liu, F. & Ranganathan, S., 28 Dec 2017, In : BMC Bioinformatics. 18, Suppl 16, p. 19-30 12 p., 572.

Research output: Contribution to journalConference paper

Open Access
File
6 Citations (Scopus)
9 Downloads (Pure)

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

2016 update on APBioNet's annual international conference on bioinformatics (InCoB)

Schönbach, C., Verma, C., Wee, L. J. K., Bond, P. J. & Ranganathan, S., 22 Dec 2016, In : BMC Genomics. 17, Suppl.13, p. 1-4 4 p., 1036.

Research output: Contribution to journalEditorial

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

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016)

Schönbach, C., Verma, C., Bond, P. J. & Ranganathan, S., 22 Dec 2016, In : BMC Bioinformatics. 17, Suppl.19, p. 1-4 4 p., 524.

Research output: Contribution to journalEditorial

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

Systems proteomics view of the endogenous human claudin protein family

Liu, F., Koval, M., Ranganathan, S., Fanayan, S., Hancock, W. S., Lundberg, E. K., Beavis, R. C., Lane, L., Duek, P., McQuade, L., Kelleher, N. L. & Baker, M. S., 5 Feb 2016, In : Journal of Proteome Research. 15, 2, p. 339-359 21 p.

Research output: Contribution to journalReview article

11 Citations (Scopus)
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
File
18 Citations (Scopus)
19 Downloads (Pure)

Chemogenomics approach to computer aided drug discovery

Khanna, V. & Ranganathan, S., 2015, Post-genomic approaches in drug and vaccine development. Sakharkar, K. R., Sakharkar, M. K. & Chandra, R. (eds.). Aalborg, Denmark: River Publishers, p. 93-114 22 p. (River Publishers Series in Research and Business Chronicles-Biotechnology and Medicine; vol. 5).

Research output: Chapter in Book/Report/Conference proceedingChapter

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
File
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
File
4 Citations (Scopus)
5 Downloads (Pure)

GIW and InCoB, two premier bioinformatics conferences in Asia with a combined 40 years of history

Schonbach, C., Horton, P., Yiu, S-M., Tan, T. W. & Ranganathan, S., 9 Dec 2015, In : BMC Genomics. 16, Supplement 12, p. 1-4 4 p., I1.

Research output: Contribution to journalEditorial

Open Access
File
3 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
File

Introduction to selected papers from GIW/InCoB 2015

Horton, P., Schönbach, C., Ranganathan, S. & Yiu, S. M., 1 Oct 2015, In : Journal of Bioinformatics and Computational Biology. 13, 5, 2 p., 1502003.

Research output: Contribution to journalEditorial

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)

Quest for missing proteins: update 2015 on chromosome-centric human proteome project

Horvatovich, P., Lundberg, E. K., Chen, Y. J., Sung, T. Y., He, F., Nice, E. C., Goode, R. J., Yu, S., Ranganathan, S., Baker, M. S., Domont, G. B., Velasquez, E., Li, D., Liu, S., Wang, Q., He, Q. Y., Menon, R., Guan, Y., Corrales, F. J., Segura, V. & 34 others, Casal, J. I., Pascual-Montano, A., Albar, J. P., Fuentes, M., Gonzalez-Gonzalez, M., Diez, P., Ibarrola, N., Degano, R. M., Mohammed, Y., Borchers, C. H., Urbani, A., Soggiu, A., Yamamoto, T., Salekdeh, G. H., Archakov, A., Ponomarenko, E., Lisitsa, A., Lichti, C. F., Mostovenko, E., Kroes, R. A., Rezeli, M., Végvári, Á., Fehniger, T. E., Bischoff, R., Vizcaíno, J. A., Deutsch, E. W., Lane, L., Nilsson, C. L., Marko-Varga, G., Omenn, G. S., Jeong, S. K., Lim, J. S., Paik, Y. K. & Hancock, W. S., 4 Sep 2015, In : Journal of Proteome Research. 14, 9, p. 3415-3431 17 p.

Research output: Contribution to journalReview article

50 Citations (Scopus)
2014

Advanced in silico analysis of expressed sequence tag (EST) data for parasitic nematodes of major socio-economic importance

Ranganathan, S., 2014, Bioinformatics in systems biology and cryopreservation in agrobiodiversity. Noor, N. M. (ed.). Selangor: Penerbit Universiti Kebangsaan Malaysia, p. 35-57 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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)

Biological data integration using network models

Kumar, G. & Ranganathan, S., 2014, Biological knowledge discovery handbook: preprocessing, mining and postprocessing of biological data. Elloumi, M. & Zomaya, A. Y. (eds.). Hoboken, New Jersey: John Wiley & Sons, p. 155-173 19 p. (Wiley series on bioinformatics : Computational techniques and engineering.).

Research output: Chapter in Book/Report/Conference proceedingChapter

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: 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
File