• 5268 Citations
  • 37 h-Index
1980 …2021
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Research Outputs 1980 2019

2015

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 journalEditorialResearch

Linking structural features of protein complexes and biological function

Sowmya, G., Breen, E. J. & Ranganathan, S., 1 Sep 2015, In : Protein Science. 24, 9, p. 1486-1494 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteins
Solvation
Nonparametric Statistics
Genomics
Binding energy

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 othersCasal, 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 articleResearchpeer-review

Human Chromosomes
Proteome
Chromosomes
Posters
Proteins
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 journalEditorialResearchpeer-review

Open Access
File
Computational Biology
Genomics
Systems Biology
Manuscripts
Singapore
Open Access
File
Protease Inhibitors
Edetic Acid
Blood
Plasmas
Electrophoresis

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 journalEditorialResearchpeer-review

Open Access
File
Systems Biology
Bioinformatics
Computational Biology
Update
Genomics

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 articleResearchpeer-review

Claudins
Proteomics
Proteins
Tissue
Tight Junction Proteins
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 articleResearchpeer-review

Open Access
File
proteome
Proteome
proteins
Proteins
genome

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 proceedingChapterResearchpeer-review

Workflow
Proteome
Computational Biology
Proteomics
Mass Spectrometry

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 proceedingChapterResearchpeer-review

High-Throughput Nucleotide Sequencing
Mass Spectrometry
Peptides
Proteome
Proteomics

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 journalArticleResearchpeer-review

Fluorination
fluorination
Fluorine
adenosine triphosphate
Halogenation

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 paperResearchpeer-review

Open Access
File
Adenosinetriphosphate
Inhibitor
Fluorine
Phosphotransferases
Adenosine Triphosphate

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 journalArticleResearchpeer-review

Mass spectrometry
Mass Spectrometry
Proteins
Peptides
Chromosomes, Human, Pair 7

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 journalArticleResearchpeer-review

Biological Phenomena
prediction
Prediction
Interaction
Proteins
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 journalEditorialResearchpeer-review

Open Access
File
Computational Biology
Genomics
Metagenomics
Posters
Precision Medicine

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 paperResearchpeer-review

Open Access
File
H7N9 Subtype Influenza A Virus
Influenza A virus
Viruses
Orthomyxoviridae
Human Influenza

Imaginative order from reasonable chaos: conformation-driven activity and reactivity in exploring protein-ligand interactions

Moore, A. F., Newman, D. J., Ranganathan, S. & Liu, F., 2018, In : Australian Journal of Chemistry. 71, 12, p. 917-930 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Biological Products
Chaos theory
Conformations
Ligands
Proteins

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

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

Research output: Contribution to journalArticleResearchpeer-review

Fluorine
Protein Kinases
Molecular dynamics
Proteins
Protein Kinase C

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 journalArticleResearchpeer-review

Open Access
File
Lysine
Amino Acids
Biological Phenomena
Benchmarking
Neural Networks (Computer)

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 journalArticleResearchpeer-review

Open Access
File
Protein Folding
Proteins
Area Under Curve
Amino Acids
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 paperResearchpeer-review

Open Access
File
Computational Biology
India
Genomics
Public Opinion
Indonesia

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 articleResearchpeer-review

Odorant Receptors
Ligands
Drug Discovery
Chemical Databases
Drug Industry

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 paperResearchpeer-review

seminal plasma
Proteome
proteome
Semen
Computational Biology

Clinically relevant post-translational modification analyses: maturing workflows and bioinformatics tools

Pascovici, D., Wu, J. X., McKay, M. J., Joseph, C., Noor, Z., Kamath, K., Wu, Y., Ranganathan, S., Gupta, V. & Mirzaei, M., 1 Jan 2019, In : International Journal of Molecular Sciences. 20, 1, p. 1-30 30 p., 16.

Research output: Contribution to journalReview articleResearchpeer-review

Open Access
File
Workflow
Post Translational Protein Processing
Bioinformatics
Computational Biology
Proteins

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, 11 p., 342.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Protein Kinase C
Selectivity
Isoenzymes
Adenosinetriphosphate
Analogue

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 journalEditorialResearchpeer-review

Encyclopedia of bioinformatics and computational biology

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

Research output: Book/ReportEdited Book/AnthologyResearchpeer-review

Genome databases and browsers

Southwood, D. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology. 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 bookResearchpeer-review

Host-pathogen interactions

Southwood, D. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology. 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 proceedingChapterResearchpeer-review

Identification of proteins from proteomic analysis

Noor, Z., Mohamedali, A. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology. 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 bookResearchpeer-review

Proteins
Biomarkers
Mass spectrometers
Bioinformatics
Fruits

iSwathX: an interactive web-based application for extension of DIA peptide reference libraries

Noor, Z., Wu, J. X., Pascovici, D., Mohamedali, A., Molloy, M. P., Baker, M. S. & Ranganathan, S., 1 Feb 2019, In : Bioinformatics. 35, 3, p. 538-539 2 p.

Research output: Contribution to journalArticleResearchpeer-review

Peptide Library
Peptides
Web-based
Libraries
Mass Spectrometry

Protocol for protein structure modelling

Jabeen, A., Mohamedali, A. & Ranganathan, S., 2019, Encyclopedia of bioinformatics and computational biology. 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 bookResearchpeer-review

Proteins

Quantification of proteins from proteomic analysis

Noor, Z., Adhikari, S., Ranganathan, S. & Mohamedali, A., 2019, Encyclopedia of bioinformatics and computational biology. 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 bookResearchpeer-review

Proteins
Mass spectrometry
Proteomics
Experiments

Rational structure-based drug design

Khanna, V., Ranganathan, S. & Petrovsky, N., 2019, Encyclopedia of bioinformatics and computational biology. 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 proceedingChapterResearchpeer-review

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 articleResearchpeer-review

Cannabinoid Receptors
G-Protein-Coupled Receptors
Computational Biology
Endocannabinoids
Precision Medicine