• 5216 Citations
  • 37 h-Index
1980 …2021
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Research Outputs 1980 2019

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

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

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
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
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
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
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 journalArticleResearchpeer-review

Open Access
File
Carcinoembryonic Antigen
Interleukin-8
Immunoassay
Prolactin
Colorectal Neoplasms

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 proceedingChapterResearchpeer-review

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 journalArticleResearchpeer-review

Open Access
File
Clinical Trials
Genetic Therapy
Hematopoietic System
Insertional Mutagenesis
Paris

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, p. 980-991 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Strongyloidea
Livestock
Biotechnology
Agriculture
Parasites

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 journalArticleResearchpeer-review

Open Access
File
Proteins
Protein
Polarity
Class
Protein-protein Interaction

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 journalEditorialResearchpeer-review

Open Access
File

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 journalArticleResearchpeer-review

Informatics
Bioinformatics
Computational Biology
Genome
Genes

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
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 proceedingChapterResearchpeer-review

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 journalArticleResearchpeer-review

Plasminogen
Urokinase-Type Plasminogen Activator
Integrins
Integrin alpha Chains
Immunoprecipitation

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 proceedingChapterResearchpeer-review

Proteins
Data Mining
Information Storage and Retrieval
Computational Biology
Databases

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 journalArticleResearchpeer-review

Urokinase Plasminogen Activator Receptors
Integrins
Proteomics
Ligation
Assays

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 othersRanganathan, 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 journalArticleResearchpeer-review

Necator americanus
Ancylostomatoidea
Human Genome
Genome
Growth Disorders

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 journalArticleResearchpeer-review

Open Access
File
Systems Biology
Gene Regulatory Network
Computational Biology
Network Analysis
Bioinformatics

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 journalArticleResearchpeer-review

Open Access
File
Bioinformatics
Computational Biology
Informatics
Proteins
Breadth

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 journalArticleResearchpeer-review

Open Access
File
Data Mining
Genomics
Computational Biology
Industry
Health

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 journalArticleResearchpeer-review

Proteome
Chromosomes
Pipelines
Proteins
Human Chromosomes

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 journalArticleResearchpeer-review

Proteins
Association reactions
Databases
Catalysis
Documentation

Structure-based clustering of major histocompatibility complex (MHC) proteins for broad-based T-cell vaccine design

Tong, J. C., Tan, T. W. & Ranganathan, S., 2014, Immunoinformatics. De, R. K. & Tomar, N. (eds.). 2nd ed. New York: Humana Press, p. 503-511 9 p. (Methods in Molecular Biology; vol. 1184).

Research output: Chapter in Book/Report/Conference proceedingChapterResearch

Major Histocompatibility Complex
Cluster Analysis
Vaccines
T-Lymphocytes
Proteins