Data Mining and Text Mining Laboratory
Department of Bioinformatics
Bharathiar University

    Peer Reviewed Journal Papers

  1. Abdulkadhar S, Bhasuran B, Natarajan J. Multiscale Laplacian graph kernel combined with lexico-syntactic patterns for biomedical event extraction from literature. Knowledge and Information Systems. 2020 Oct 24:1-31. ISSN:0219-1377 (IF-2.963)
  2. Nath AR, Natarajan J. Network analysis of MicroRNA transcripts revealed relevant MicroRNAs and gene candidates for angiogenesis in gastric cancer. Gene Reports. 2020 Oct 5:100903.
  3. Ganapathy S, Shafna Asmy VS, Natarajan J, Selvaraj U, Thirugnanasambandam S. Invitro And Insilico Analysis Of The Marine Seaweed-Derived Compound Fucoidan Against EMT Markers. International Journal Of Scientific & Technology Research Volume 9, Issue 04, April 2020.
  4. Raja K, Subramanian D, Abdulkadhar S, Natarajan J. hPP Corpus: A Tagged Biomedical Corpus for Automatic Extraction of Human Protein Phosphorylation for Understanding Cellular Functions. Journal of Embryology & Stem Cell Research (2020):1-12.
  5. Maroli N, Kalagatur NK, Bhasuran B, Jayakrishnan A, Manoharan RR, Kolandaivel P, Natarajan J, Kadirvelu K. Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation. Journal of chemical information and modeling. 2019 Oct 23;59(11):4942-58.ISSN: 1549-9596 (IF 3.96)
  6. Subramanian D, Natarajan J. RNA-seq analysis reveals resistome genes and signalling pathway associated with vancomycin-intermediate Staphylococcus aureus. Indian journal of medical microbiology. 2019 Apr 1;37(2):173.ISSN:0255-0857 (IF 0.95)
  7. Samykannu G, Vijayababu P, Antonyraj CB, Perumal P, Narayanan S, Basheer Ahamed SI, Natarajan J. In silico characterization of B cell and T cell epitopes for subunit vaccine design of Salmonella typhi PgtE: a molecular dynamics simulation approach. Journal of Computational Biology. 2019 Feb 1;26(2):105-16.ISSN: 1066-5277 (IF-1.191)
  8. Subramanian, D., Bhasuran, B., & Natarajan, J. (2018). Genomic analysis of RNA-Seq and sRNA-Seq data identifies potential regulatory sRNAs and their functional roles in Staphylococcus aureus. Genomics.ISSN: 0888-7543 (IF 3.1)
  9. Bhasuran, B., Subramanian, D., & Natarajan, J. (2018). Text mining and network analysis to find functional associations of genes in high altitude diseases. Computational biology and chemistry, 75, 101-110. ISSN: 1476-9271 (IF 1.581)
  10. Bhasuran, B., & Natarajan, J. (2018). Automatic extraction of gene-disease associations from literature using joint ensemble learning. PloS one, 13(7), e0200699. ISSN: 1932-6203 (IF 2.7)
  11. Raja, K., & Natarajan, J. (2018). Mining protein phosphorylation information from biomedical literature using NLP parsing and Support Vector Machines. Computer methods and programs in biomedicine, 160, 57-64. ISSN: 0169-2607 (IF 3.4).
  12. Samykannu, G., Vijayababu, P., & Natarajan, J. (2018). Substrate specificities in Salmonella typhi outer membrane protease (PgtE) from omptin family–An in silico proteomic approach. Informatics in Medicine Unlocked.ISSN: 2352-9148.
  13. Murugesan, G., Abdulkadhar, S., & Natarajan, J. (2017). Distributed smoothed tree kernel for protein-protein interaction extraction from the biomedical literature. PloS one, 12(11), e0187379. ISSN: 1932-6203 (IF 2.7).
  14. Abdulkadhar, S., Murugesan, G., & Natarajan, J. (2017). Classifying protein-protein interaction articles from biomedical literature using many relevant features and context-free grammar. Journal of King Saud University-Computer and Information Sciences.ISSN: 1319-1578.
  15. Chakkyarath, V, and Natarajan, J. Identification of Ideal Multitargeting Bioactive Compounds Against Mur Ligases of Enterobacter aerogenes and Its Binding Mechanism in Comparison with Chemical Inhibitors, Interdiscip Sci Comput Life Sci (2017) (DOI 10.1007/s12539-017-0261-4) ISSN:1913-2751 (IF 1.4)
  16. Subramanian, D., & Natarajan, J. (2017). Phylogeny and domain examination of two-component regulatory systems across staphylococcal species. ISSN:0972-5849.
  17. Murugesan, G., Abdulkadhar, S., Bhasuran, B., and Natarajan, J., BCC-NER: Bidirectional, Contextual Clues Named Entity Tagger for Gene/Protein Mention Recognition, EURASIP Journal on Bioinformatics and Systems Biology (1), 7 (2017)ISSN: 1687-4153.
  18. Prabahar A, Natarajan J., ImmunemiR - a database of prioritized immune miRNA disease associations and its interactome, MicroRNA, 7:1 (2017)ISSN: 2211-5366.
  19. Prabahar A, Natarajan J., MicroRNA mediated network motifs in autoimmune diseases and its crosstalk between genes, functions and pathways, Jr. of Immu. methods, 440, 19–26, (2017)ISSN: 0022-1759 (IF 2.1)
  20. Prabahar A, Natarajan J., Prediction of microRNAs involved in immune system diseases through network based features, J Biomed Inform. 65,34-45 (2017)ISSN: 1532-0464 (IF 2.95).
  21. Bhasuran, B., Murugesan, G., Abdulkadhar, S., and Natarajan, J., Stacked ensemble combined with fuzzy matching for biomedical named entity recognition of diseases, J Biomed Inform. 64, 1-9, (2016) ISSN: 1532-0464 (IF 2.95).
  22. Jayapalan, S., Devika, S., and Natarajan, J., Computational Identification and Analysis of Neurodegenerative Disease Associated Protein Kinases in Hominids, Genes & Diseases, 3(3), 228–237, (2016)ISSN: 2352-3042.
  23. Arighi, C. N., Carterette, B., … Natarajan, J.,… Wu, C., Overview of the interactive task in BioCreative V, Database (Oxford). Sep 1;2016. pii: baw119. doi: 10.1093/database/baw119 (2016) ISSN: 1758-0463 (IF 3.9).
  24. Gnanendra, S., Mohamed, S., and Natarajan, J., 2D and 3D-QSAR study of acyl homoserine lactone derivatives as potent inhibitors of quorum sensor, SdiA in Salmonella typhimurium, Int. Jr. BioAutomation, 20(4), 441-456, (2016)ISSN:1314-1902.
  25. Jayapalan, S., and Natarajan, J., Classification and Domain Analysis of Protein Kinases in Hominids, Current Science 110, 5, 828-838, (2016) ISSN: 0011-3891 (IF 0.992).
  26. Devika, S., and Natarajan, J., Network Analysis of S. aureus Response to Ramoplanin Reveals Modules for Virulence Factors and Resistance Mechanisms and Characteristic Novel Genes, Gene, 574(1),149-62, (doi 2015.08.006) (ISSN: 0378-1119) (2015) (IF 2.638).
  27. Subramani, S., Kalpana, R., Monickaraj, P.M. and Natarajan, J., HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways, Journal of Biomedical Informatics 54, 121–13, (2015) ISSN: 1532-0464 (IF 2.95).
  28. Archana, P., and Natarajan, J., Prediction of miRNA in Human MHC that Encodes Different Immunological Function Using Support Vector Machines , Curr. Bioinfo., Vol 9, (2014) ISSN: 1574-8936 (IF 2.0).
  29. Anusuya, S., and Natarajan, J., Combination of site directed mutagenesis and secondary structure analysis predicts the amino acids essential for stability of M. leprae MurE, Inter. discip Sci., 6(1), 40-47, (2014) ISSN: 1913-2751 (IF-1.4).
  30. Raja, K., Subramani, S., and Natarajan, J., A hybrid named entity tagger for tagging human proteins/genes, Int. J. Data Mining and Bioinformatics, Vol 10, 3, 315-328 (2014) ISSN: 1748-5673 (IF 0.789).
  31. Subramani, S., Kalpana, R., and Natarajan, J., ProNormz – An integrated approach for human proteins and protein kinases normalization, Jr. of Biomedical Appl., 47, 131-138 (2013) ISSN: 1532-0464 (IF 2.95).
  32. Natarajan, J., Text Mining Perspectives in Microarray Data Mining, ISRN Comp. Biology, Volume 2013, Article ID 159135 (2013) (doi:10.1155/2013/159135) ISSN 2314-4165.
  33. Anusuya, S., and Natarajan, J, The eradication of leprosy: molecular modeling techniques for novel drug discovery, Expert Opin. Drug Discov., (2013) ISSN: 1746-0441 (IF 4.421).
  34. Selvaraj, S., and Natarajan J., Expression-Based Network Biology Identifies High Score Sub-networks and Their Roles in Rett Syndrome, Int. Jr. of Pharma & Bio Sciences, In Press (2013) ISSN: 0975-6299.
  35. Gnanendra, S., Mohamed, S., and Natarajan, J, Identification of Potent Inhibitors for Salmonella Typhimurium Quorum Sensing via Virtual Screening and Pharmacophore Modeling, Comb. Che. & High Throughput Screen., 16(10):826-39, (2013) ISSN: 1386-2073 (IF 2.1).
  36. Subramani, S., Jayapalan, S., Kalpana, R., and Natarajan, J., , HomoKinase: A Curated Database of Human Protein Kinases, ISRN Comp. Biology, Vol. 2013, ID 417634, (2013) (doi: 10.1155/2013/417634) ISSN:2314-4165.
  37. Arighi, C. N., Carterette, B., … Natarajan, J., , … ,Wu, C., An overview of the BioCreative 2012 Workshop Track III: interactive text mining task, Database, Vol.2013:bas056 (2013) (doi:10.1093/ database/bas056) ISSN: 1758-0463 (IF 3.9).
  38. Raja, K., Subramani, S., and Natarajan, J., PPInterFinder—a mining tool for extracting causal relations on human proteins from literature, Database, Vol.2013:bas052 (2013) (doi:10.1093/ database/bas052) ISSN: 1758-0463 (IF 3.9).
  39. Anusuya, S., Anbazhagan, V., and Natarajan, J, Virtual screening studies of phenylsulfonamido-3-morpholinopropan-2-yldihydrogen phosphate derivatives as novel inhibitors of MurC–MurF ligases from Mycobacterium leprae, Med Chem Res, 21(12):4341-4351 (2012) ISSN: 1054-2523 (IF 1.42).
  40. Balakrishnan, IK., Rangasamy, S, and Natarajan J., A Parkinson’s disease mitochondrial dysfunction pathway with gene hubs, Online J Bioinform., 13(3):375-381 (2012) ISSN:1443-2250.
  41. Devaraj, S., and Natarajan, J., miRNA-mRNA network detects hub mRNAs and cancer specific miRNAs in lung cancer, In Silico Biol 11(5): 281-295 (2012) ISSN:1386-6338.
  42. Anusuya, S., and Natarajan, J, Multi-Targeted Therapy for Leprosy: Insilico Strategy to Overcome Multi Drug Resistance and to Improve Therapeutic Efficacy, Infection, Genetics and Evolution 12(8):1899-910 (2012) ISSN: 1567-1348 (IF 3.1).
  43. Gnanendra S, Anusuya, S., and Natarajan, J, Molecular modeling and active site analysis of SdiA homolog, a putative quorum sensor for Salmonella typhimurium pathogenecity revels specific binding patterns of AHL transcriptional regulators, Journal of Molecular Modeling, 18(10):4709-4719 (2012) ISSN: 1610-2940 (IF 2.0).
  44. Anusuya, S., and Natarajan, J, Homology modeling and docking analyses of M. leprae Mur ligases reveals the common binding residues for structure based drug designing to eradicate leprosy, Journal of Molecular Modeling, 18(6): 2659-2672 (2012) ISSN: 1610-2940 (IF 2.0).
  45. Anusuya, S., and Natarajan, J, Comparative modeling of UDP-N-acetylmuramoyl-glycyl-D-glutamate-2, 6-diaminopimelate ligase from Mycobacterium leprae and analysis of its binding features through molecular docking studies, Journal of Molecular Modeling, 18(1):115-125 (2012) ISSN: 1610-2940 (IF 2.0).
  46. Selvaraj, S., and Natarajan J., Microarray data analysis and mining tools, Bioinformation, 6(3): 392-395 (2011) ISSN: 0973-8894.
  47. Gnanendra, T. S., Geethu, G., Arjunan, S., Sharmila, B., Zahir Hussain, M. I., Moorthy, K., and Natarajan J., Theoretical models of quorum sensing dependent regulation of transcriptional activators of pseudomonas aeruginosa, International Journal of Biological Technology, 1(3):43-49 (2010) ISSN: 0976 – 4313.
  48. Ravichandran, S., and Natarajan J., Brain tumor biomarker identification via differential gene expression analysis of microarray data using CGAP, On line Journal of Bioinformatics, 11(1), 83-89, (2010)ISSN:1443-2250.
  49. Anusuya1, S., and Natarajan, J., Differential genome analyses of metabolic enzymes in Mycobacterium leprae for drug target identification, Bioinformation, 4(9): 392-395 (2010) ISSN:0973-8894 (IF 1.2).
  50. Rajendran S. and Natarajan J., A Comparative study of differentially expressed gene selection programs for microarray data mining, The Internet Journal of Genomics and Proteomics, 5 (2) (2010) ISSN: 1540-2630.
  51. Vishalini K., Nicy Sweety I and Natarajan J., Computational identification of Alzheimer’s disease specific transcription factors using microarray gene expression data, Journal of Proteomics and Bioinformatics 2: 505-508, (2009) ISSN: 0974-276X.
  52. Natarajan, J. and Jawahar G., Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature, Bioinformation 2(5): 185-193 (2007) ISSN 0973-8894 (IF 1.2).
  53. Natarajan, J., Berrar D., Dubitzky W., Hack C. J, Zhang Y., Desesa C., Van Brocklyn J. R., Bremer E. G. "Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell", BMC Bioinformatics, Aug 10;7(1):373, (2006) ISSN:1471-2105 (IF 3.0).
  54. Natarajan J., Berrar D., Hack C.J., Dubitzky W., "Knowledge discovery in biology and biotechnology texts: A review of techniques, evaluation strategies, and applications", Critical Reviews in Biotechnology, Vol. 25, 31-52, (2005) ISSN: 0738-8551 (IF 2.8).

  55. Book Chapters

  56. Raja K, Natarajan J, Kuusisto F, Steill J, Ross I, Thomson J, Stewart R. Automated Extraction and Visualization of Protein–Protein Interaction Networks and Beyond: A Text-Mining Protocol. In Protein-Protein Interaction Networks 2020 (pp. 13-34). Humana, New York, NY. ISBN:978-1-4939-9872-2.
  57. Bhasuran B, Natarajan J. Distant Supervision for Large-Scale Extraction of Gene–Disease Associations from Literature Using DeepDive. InInternational Conference on Innovative Computing and Communications 2019 (pp. 367-374). Springer, Singapore. ISBN: 978-981-13-2353-9.
  58. Jayapalan, S., and Natarajan, J., Kinome wide evolutionary analysis on hominoids, In: Below Ground Biodiversity, P. Katheiswari (Ed.), Research India Publications, 77-86 (2015) ISBN: 978-93-84443-28-3.
  59. Raja, K., Subramani, S., and Natarajan, J., Template Filling in Text Mining, Book Chapter in Encyclopedia of Systems Biology, Dubitzky, W., Wolkenhauer, O., Yokota, H., Cho, K.-H. (Eds.) (2013) ISBN: 978-1-4419-9862-0.
  60. Natarajan, J., Haines, C, Berglund, B, et al., GetItFull - A tool for downloading and pre-processing full-text journal articles LNCS 3886: Knowledge Discovery in Life Science Literature,139-145 (2006) ISBN-13: 978-3540328094.
  61. Natarajan, J., Mulay, N, DeSesa, C, et al., A grid infrastructure for text mining of full text articles and creation of a knowledge base of gene relations LNCS 3745: Biological and Medical Data Analysis, 101-108, (2005) ISBN: 978-3-540-68063-5.
  62. Bremner,E.G., Natarajan, J., Zhang,Y., DeSesa,C., Hack,C.J. and Dubitzky,W., Text mining of full text articles and creation of a knowledge base for analysis of microarray data LNAI 3303: Knowledge Exploration in Life Science Informatics, 84-95, (2004) ISBN: 978-3-540-23927-7.

  63. Conferences Symposia Proceedings

  64. Ramasamy M, Abdulkadhar S, Natarajan J. Deep Neural Network for the Automatic Classification of Vertebral Column Disorders. (IEEE-2020).
  65. Bhasuran B., Natarajan J. (2019) Distant Supervision for Large-Scale Extraction of Gene–Disease Associations from Literature Using DeepDive. In: Bhattacharyya S., Hassanien A., Gupta D., Khanna A., Pan I. (eds) International Conference on Innovative Computing and Communications. Lecture Notes in Networks and Systems, vol 56. Springer, SingaporeISBN:978-981-13-2354-6.
  66. Abdulkadhar, S., Murugesan, G., & Natarajan, J. (2017, November). Recurrent convolution neural networks for classification of protein-protein interaction articles from biomedical literature. In Research in Computational Intelligence and Communication Networks (ICRCICN), 2017 Third International Conference on (pp. 192-197). IEEE.ISBN: 978-1-5386-1932-2.
  67. Raja, K., Abdulkadhar, S., Tsoi, LC., Natarajan, J., A hybrid text mining system for chemical entity recognition and classification using dictionary look-up and pattern matching @ BeCalm challenge evaluation workshop, Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 81-88 (2017).
  68. Bhasuran, B. and Natarajan, J., Text mining and network analysis to identify genes related to high altitude diseases, Proc. third Int. Conf. on Comp. Biology, Bharathiar University, Coimbatore, 43-51 (2016).
  69. Devika, S., and Natarajan, J., Interaction analysis of vancomycin-resistome from RNA-seq data using Galaxy and functional examination of sRNA241 in S. aureus, Galaxy Community Conference,(2016).
  70. Subramani, S., and Natarajan, J., An integrated text mining system based on network analysis for knowledge discovery of human gene-disease associations (GenDisFinder), Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 427-434 (2015).
  71. Wang, Q., et. al., Natarajan, J., et. al., Arighi, C., Overview of the Interactive Task in BioCreative V, Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 364-383 (2015).
  72. Raja, K., Subramani, S., and Natarajan, J., A comparative study and performance evaluation of three named entity taggers for tagging human proteins and protein kinases names in biomedical text, Proc. of the Nat. Conf. Comp. Biology, Bharathair University, Coimbatore, 72-82, (2013).
  73. Natarajan, J., and Dey, A., Text Mining Applications in Computational Biology, Proc. of the Nat. Conf. Comp. Biology, Bharathair University, Coimbatore, 65-71, (2013).
  74. Kaplana, R, Suresh, S, Natarajan J, PPInterFinder – A Web Server for Mining Human Protein ‐ Protein Interactions, Proc. of the BioCreative workshop, Georgetown University, Washington DC, April 8-9, (2012).
  75. Natarajan J., Text searching and mining methods for biological data analysis, Proceedings of Nat. Conf. on Bioinfo. and Comp. Biology, Jodhpur, India 58-63 (2011).
  76. Madhuvanthi, K., Selvaraj, S., and Natarajan J., Data mining in Microarray Data Analysis, Proceedings of Indo-US Workshop on Biocomputing, (ISB 2011), Calicut, India, 121-124 (2011).
  77. Kurup, K., and Natarajan J., Analysis of disordered regions in Protein kinase subfamilies of Homo sapiens and Coenorhabditis elegans, ACM Proceedings of International Symposium on Biocomputing, (ISB 2010), Calicut, Kerala, (2010) ( 1722024.1722028) ISBN:978-1-60558-722-6.