Plant University
Resume:
Ms. Kalpana Raja
Opp: Sankara Narayana Mahal,
Bharathiar Univ. PO, Coimbatore –641046,
Tamilnadu, India.
Tele: 0091 422-***-****, Mobile: 0091 994-***-****
E-mail : *******.*****@*****.***
Profile
Having an excellent knowledge in biology and software programming, I am looking
forward to achieve more in research b y contributing m y skills, knowledge, abilities and personal
commitments to science.
Educational Qualification
Oct 2010 – Dec 2013 Bharathiar Universit y, PhD Bioinformatics,
Coimbatore, India. Broad field of research - Computational
Biology and Bioinformatics
Thesis Title: Text Mining Approaches to Identify and Extract Human
Protein - Protein Interaction Information with a special reference to
Human Protein Phosphorylation.
Jun 2009 - May 2011 Bharathiar Universit y, MSc Bioinformatics,
75.6 % - First Class.
Coimbatore, India.
Jan 2001 - Jul 2002 The Robert Gordon MSc Computing: Software Technology,
University, Aberdeen, 68% - Aggregate
Scotland, UK.
Jun 1999 – May 2000 Bharathiar Universit y, PGDCA (Post Graduate Diploma in
Coimbatore, India. Computer Application),
80% - First Class
Jun 1998 – Dec 2000 CMC Ltd. (A Govt. of DAST (Diploma in Advanced Software
Technology), Grade “A” – Excellent
India enterprise), India.
Jul 1992 - May 1998 Tamilnadu Dr. M. G. R. Bachelor of Pharmacy,
Medical University, 73% - Aggregate
Chennai, India.
1992 Board of Higher Secondary Higher Secondary Course Certificate,
Examination, Tamilnadu, 81%
India.
1990 Board of Higher Secondary Secondary School Leaving Certificate,
Education, Tamilnadu, 88.4%
India.
Employment
Research Scholar – Computational Biology and Bioinformatics (Oct 2010 to Dec 2013)
Data Mining and Text Mining Laborator y, Department of Bioinformatics, School of Life
Sciences, Bharathiar University, Coimbatore, Tamilnadu, India.
Computer Programmer (May 2010 to Apr 2013)
Data Mining and Text Mining Laborator y, Department of Bioinformatics, School of Life
Sciences, Bharathiar University, Coimbatore, Tamilnadu, India.
Senior Research Fellow – Bioinformatics (March 2008 to May 2010)
Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology,
Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India.
Course Associate – Bioinformatics & Biotechnology (March 2008 to May 2010)
Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology,
Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India.
Assistant Professor (Nov 2002 to Feb 2008)
KMR College of Pharmacy, Perundurai, Tamilnadu, India.
Technical skills
Software Skills: Specialization - Java, JDBC, J2EE
Languages : Java, J2EE, VB, Perl, C, C++.
RDBMS / DBMS : SQL Server, Oracle, MS SQL, M ySQL
Operating S ystem : Linux, Unix, Windows 98/2000/XP, Windows NT
Web design/development : PHP, HTML, XML, Java Script, VB Script
Statistics / Machine learning tool: Weka, SVMLight, LibSVM
Bioinformatics Skills:
Alignment tools : BLAST, FASTA, ClustalW
Visualization software : RASMOL, PYMOL, SwissPdv Viewer
Biological Databases : NCBI, EMBL, DDBJ, SWISSPROT, PDB etc
Metabolic Pathway Database : Kyoto Encyclopedia of Genes and Genomes (KEGG)
Gene Prediction : GENSCAN, ORF-FINDER, EXPASY-TRANSLATE
Protein modeling tools : Discovery Studio, Modeller
Docking tool : Autodock, Schrodinger
Miscellaneous : CORINA, Convert
Computer Aided Drug Designing Skills:
Pharmacogenomics Databases : PharmGKB, CTD
Drug related Databases : DrugBank, PubChem, eMolecules
Chemicals Drawing Tools : ChemSketch, ISISDraw, MarvinSketch, Molinspiration
Toxicity Prediction Tool : Lazar Toxicity Predictions, ADME-Tox, FAF Drugs
Human genetic disorder Database : Online Mendelian Inheritance in Man (OMIM)
Coordinates Converting Tool : Prodrg Server
Research Grants/Projects
Text Mining and Data Warehousing of Human Protein Kinases Relationships and
Pathways (May 2010 to Apr 2013)
Department of Information Technology, Government of India, New Delhi, India.
Supervisor: Dr. N. Jeyakumar, PhD (UK)
Research Area: Information Extraction / Natural Language Processing / Text Mining
Objectives achieved:
1. NAGGNER – An integrated named entit y tagger for extracting and normalizing human
protein kinases in biomedical literature. URL: http://www.biominingbu.org:8080/NAGGNER/
2. ProNormz – Web tool for human gene/protein and protein kinases normalization with
synon yms dictionar y. URL: http://www.biominingbu.org/pronormz/index.html
3 HomoKinase – A database for human protein kinases.
.
URL: http://www.biominingbu.org/homokinase/index.html
4 PPInterFinder - A mining tool for extracting causal relations on human proteins from
.
literature. URL: http://www.biominingbu.org/ppinterfinder/index.html
5. HPIMiner – A text mining s ystem for visualizing protein interactions and pathways.
URL: http://www.biominingbu.org/HPIminer/
6. hPP corpus – A biomedical corpus on human protein phosphorylation
7. Mining protein phosphorylation information from biomedical literature using NLP parsing
and Support Vector Machine (SVM)
8. Direct Comparison of Support Vector Machines, Bayesian Network, Naïve Bayes, Decision
Tree and Random Forest classifiers on mining Phosphorylation Information from Biomedical
Literature
Consortium of Agricultural Biotechnology (Mar 2008 to May 2010)
Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology,
Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India.
Supervisor: Dr. L. Arul, PhD
Research Area: Data Mining
Objectives achieved:
1. PrebZIP – A tool to identify basic zipper transcription factors in eukar yotes.
2. Evolution of bZIP transcription factors across organisms using PrebZIP.
3. Database of basic zipper transcription factors in eukaryotes.
4. Computational approaches to identify NBS-LRR in plants.
Course associate:
1. Java Programming and BioJava for B.Tech. (Bioinformatics)
2. Programming with Perl for B.Tech. (Bioinformatics)
3. Pharmacogenomics and Toxicogenomics for B.Tech. (Bioinformatics)
4. Cheminformatics and Drug Discover y for B.Tech. (Bioinformatics)
5. Biopharmaceutical Technology for B.Tech. (Biotechnology)
ProfileSkim –An Intelligent Document Browser (Jun 2001 to Dec 2001)
School of Computing, Faculty of Science and Technology, The Robert Gordon University, Aberdeen,
Scotland, UK.
Supervisor: Dr. David J Harper, PhD
Research Area: Information Retrieval / Text Mining
Award: The Universit y patented ProfileSkim in 2005. The ProfileSkim has won a medal of the
British Computer Society's Technology Awards 2005!
Paper Publications
Publications from PhD work
Journal Papers (*IF – Impact Factor)
1. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. PPInterFinder - A mining tool
for extracting causal relations on human proteins from literature. DATABASE: The
Journal of Biological Database and Curation. 2013, Vol. 2013, Article ID bas052. (IF:
3.179).
2. Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John
Wilbur, Petra Fe y, Robert Dodson, Laurel Cooper, Ceri Van Sl yke, WasilaDahdul, Paula
Mabee, Donghui Li, Bethan y Harris, Marc Gillespie, Silvia Jimenez, Phoebe Roberts,
Lisa Matthews, Kevin Becker, Harold Drabkin, Susan Bello, Luana Licata, Andrew
Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa Haendel, Kimberly Van Auken,
Hans-Michael Muller, Hong M Cui, Jim Balhoff, Johnny Chi-Yang Wu, Zhi yong Lu,
Oana Catalina Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan
Miguel Cejuela, Pratibha Dubey, Cath y Wu. An Overview of the BioCreative
Workshop 2012 Track III: Interactive Text Mining Task. DATABASE: The Journal of
Biological Database and Curation. 2013, Vol. 2013, Article ID bas056. (IF: 3.179).
3. Suresh Subramani, Kalpana Raja, Jeyakumar Natarajan. ProNormz - Web tool for
Human Gene/Protein and Protein Kinases Normalization with Synonyms Dictionary.
Journal of Biomedical Informatics. (In press) (IF: 2.131).
4. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. A hybrid named entity tagger
for tagging human proteins/genes. International Journal of Data Mining and
Bioinformatics. (In press) (IF: 0.393).
5. Suresh Subramani, Saranya Jayapalan, Kalpana Raja, Jeyakumar Natarajan. HomoKinase –
A curated database for human protein kinases. ISRN Computational Biology. 2013, Vol.
2013, Article ID 417634.
6. Kalpana Raja, Jeyakumar Natarajan. Mining protein phosphorylation information from
biomedical literature using NLP parsing and Support Vector Machines (SVM).
Bioinformatics (Communicated) (IF: 5.323)
7. Subramani Suresh, Kalpana Raja, Jeyakumar Natarajan. HPIMiner - A text mining
system for visualizing Human Protein Interactions and Pathways. (Communicated) (IF:
2.131).
Conference Papers
8. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. A comparative study and
performance evaluation of three named entity taggers for tagging human proteins
and protein kinases names in biomedical text. In Proceedings of the National Conference
on Computational Biology (NCCB) 2013, Coimbatore, India, February 15-16, 2013, 72-82.
9. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. PPInterFinder – A web server for
mining human protein-protein interactions. In Proceedings of BioCreative Workshop
2012, Washington DC, USA, April 2012, 151-164.
Book Chapter
10. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. Template Filling in Text Mining.
Springer Encyclopedia of Systems Biology. 2013, Article ID 173.
Manuscripts to be submitted
11. Kalpana Raja, Jeyakumar Natarajan. Human Protein Phosphorylation (hPP) Corpus: A
tagged corpus for human protein phosphorylation relation available in biomedical
literature. BMC Bioinformatics. (IF: 3.02).
12. Kalpana Raja, Jeyakumar Natarajan. Direct Comparison of Support Vector Machines,
Bayesian Network, Naïve Bayes, Decision Tree and Random Forest classifiers on mining
Phosphorylation Information from Biomedical Literature. Journal of American Medical
Informatics Association. (IF: 3.571).
13. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. NAGGNER – A hybrid named
entity tagger for tagging human proteins/genes. (Manuscript under preparation).
Publications from employment as Senior Research Fellow
Journal Papers (*IF – Impact Factor) ( Equal contribution)
14. Kalpana Raja, Vellingiri Srividhya, Prabahar Archana, Govindasamy Vanitha. Identification
of disease resistance R-genes in plants through in silico analysis for domain
recognition and pattern matching algorithm for domain prediction. International Journal
of Interdisciplinary Research and Reviews, 2013, 1(2): 9-16.
15. Archana Prabahar, Srividhya Vellingiri, Sathishkumar Natarajan, Kalpana Raja, Renganathan
Gandhimeyyan, Bharathi Nathan. Ajocin (Allicin+Ajoene) can inhibit the enzymatic
activity of aflatoxin biosynthesis in peanuts and prevent human carcinogenic
exposure. International Journal of Agricultural and Food Science, 2012, 2(3): 77-85.
16. Kalpana Raja. Bio-programming prospects of Java: A computational move towards the
understanding of the biological aspects of genes and proteins. Indian Journal of
Computer Science and Engineering, 2011, 2(6): 949-956.
17. Vichangal P. Santhanakrishnan, Kalpana Raja, Natarajan Sathishkumar, Srinivasan
Narasimhan, Chandrasekar Balakumaran. Molecular Docking Study on the anti-
inflammatory effect of Osthol and its derivatives towards human p38alpha MAP
kinase. International Journal of Bioinformatics, 2011, 4(1): 1-7.
18. Kalpana Raja, Loganathan Arul, Vellingiri Srividhya, Dhandapani Vignesh, Ponnusam y
Balasubramanian. PrebZIP: A computational tool to identify bZIP transcription
factor in eukaryotes. Pattern Recognition. (Communicated). (IF: 2.292)
19. Kalpana Raja, Archana Prabahar, Sugan ya Selvakumar, Thingalur K Raja. In silico
analysis to compare the effectiveness of assorted drugs prescribed for Swine -flu in
diverse medicine systems. Indian Journal of Pharmaceutical Sciences. (Manuscript under
revision). (IF: 0.338)
20. Archana Prabahar, Subashini Swaminathan , Kalpana Raja , Srividh ya Vellingiri, Bharathi
Nathan, Nagarajan Pothi. Discovery of novel inhibitors targeting movement protein for
controlling the transmission of Banana Bunchy Top Virus (BBTV) infection in plantain
by structure-based virtual screening. International Journal of Bioinformatics Research and
Applications. (Communicated).
Book Chapter
21. Kalpana Raja, Vanitha Govind. BioJava, 2008, 1-50. Tamil Nadu Agricultural University,
Coimbatore –641 003, Tamilnadu, India.
Practical Manual
22. Kalpana Raja, Vanitha Govind. Java Programming and BioJava, 2009. Tamil Nadu
Agricultural University, Coimbatore –641 003, Tamilnadu, India.
23. Archana Prabahar, Kalpana Raja, Raja Natarajan. Programming with Perl, 2009. Tamil
Nadu Agricultural University, Coimbatore –641 003, Tamilnadu, India.
24. Kalpana Raja. Cheminformatics and Drug Discovery, 2009. Tamil Nadu Agricultural
University, Coimbatore –641 003, Tamilnadu, India.
25. Kalpana Raja. Biopharmaceutical Technology, 2008. Tamil Nadu Agricultural University,
Coimbatore –641 003, Tamilnadu, India.
26. Kalpana Raja. Pharmacogenomics and Toxicogenomics, 2008. Tamil Nadu Agricultural
University, Coimbatore –641 003, Tamilnadu, India.
Awards / Grants
1. International Travel Grant from Department of Science and Technology, Govt. of
India (2012) – For paper presentation (poster) at APBC 2012, Melbourne, Australia.
2. Computer Programmer (May 2010 – Apr 2013). PhD Fellowship by Department of
Information Technology, Govt. of India.
3. British Computer Society's Technology Awards 2005 for MSc thesis work on
ProfileSkim – An Intelligent Document Browser.
4. RGU Reward for ProfileSkim (2006) by The Robert Gordon University, Aberdeen,
Scotland, UK.
5. Partial Scholarship on tuition fee (£ 1,000.00) (2001) by The Robert Gordon
University, Aberdeen, Scotland, UK.
Invited speaker
1. “Extraction of protein-protein interaction information from biomedical literature by pattern
matching” on 15 Feb 2013 at DRDO-BU-Centre for life sciences, Bharathiar University,
Coimbatore, India.
2. “Insilico Drug Designing and the role of Next Generation Sequencing in Drug Development”
on 22 Sep 2012 at J.S.S. College of Pharmac y, Oot y, India.
3. “Protein structure prediction and docking” on 16 Feb 2009 at Centre for Plant Molecular
Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
Professional Membership
1. International Association of Engineers (IAENG) Membership, Hong Kong, China. (Life
member).
2. Registered Pharmacist, Tamil Nadu Pharmacy Council, Chennai, India. (Life member).
Conferences / Symposia / Workshop organized / attended
Paper presentation
1. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. PPInterFinder – A web server for
mining human protein-protein interactions. Biocreative Workshop’12, Washington DC,
USA. 2012.
2. Boobalan Chinnathambi, Kalpana Raja, Archana Prabahar. SpliceSiter – A tool to RNA
Splicing. National Level technical Symposium, Pratyarth, Sastra University, Tanjavur, India.
2009.
3. Kalpana Raja, Arul Loganathan, Srividhya Velliangiri, Vignesh Dhandabani,
Balasubramaniam Ponnuswamy. PrebZIP – A tool to identify bZIP class of transcription
factors. National Level Symposium, MOTIF, Bharathiar University, Coimbatore, India. 2008.
Poster presentation
4. Archana Prabahar, Subashini Swaminathan, Kalpana Raja, Loganathan Arul, P
Nagarajan, P Sivasubramanian, Jagadish Ramalingam. CDR Pred – A tool for CDR
prediction. In BTIS annual meeting, New Delhi, India. 2013.
5. Suresh Subramani, Kalpana Raja, Jeyakumar Natarajan. A Suit of Text Mining Tools for
Human Literature Mining. BioCreative Workshop 2012, Washington DC, USA. 2012.
6. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. NAGGNER – A hybrid named
entity tagger for tagging human proteins/genes. Asia Pacific Bioinformatics Conference
(APBC2012), Melbourne, Australia. 2012.
7. Suresh Subramani, Kalpana Raja, Jeyakumar Natarajan. ProNormz - Web tool for human
Gene/Protein and Protein Kinases Normalization with Synonyms Dictionary. INCOBS
2nd International Conference on Bioinformatics and Systems Biology, Annamalai University,
Chidambaram, India. 2011.
8. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. An integrated named entity
tagger for extracting and normalizing human protein kinases in biomedical literature.
National Level Symposium on Structural Bioinformatics and Computer Aided Drug Design,
Alagappa University, Karaikudi, India. 2010.
Participation
9. AICTE sponsored National Seminar on Probability, Random Process and their
applications, Coimbatore Institute of Engineering and Technology, Coimbatore, India,
2012.
10. CSIR Sponsored National Workshop on Computational Intelligence Applications in
Bioinformatics, Dr. M.G.R. Educational and Research Institute – University, Chennai,
India, 2011.
11. MOTIF – National S ymposium, Bharathiar University, Coimbatore, India, 2010.
Workshop organized (Team work)
12. DBT Sponsored Workshop on Protein Structure Prediction and Docking, Tamil Nadu
Agricultural Universit y, Coimbatore, India. 2009 and 2010.
13. State Level workshop on Management and Monitoring of Field Trials of Genetically
Engineered Crops in State Agricultural Universities, Tamil Nadu Agricultural Universit y,
Coimbatore, India. 2009.
14. Summer Training on Biotechnology, Tamil Nadu Agricultural University, Coimbatore,
India. 2009.
References
Dr. N. Jeyakumar, PhD, Associate Professor, Department of Bioinformatics, Bharathiar
University, Coimbatore - 641 046, Tamilnadu, India
Telephone: 0091 422-***-**** Mobile: 0091 944-***-****
Email: n.jeyakumar@ yahoo.co.in
Dr. L. Arul, PhD, Associate Professor, Department of Plant Molecular Biology and
Bioinformatics, Centre for Plant Molecular Biology, Tamil Nadu Agricultural Universit y,
Coimbatore -641003, Tamilnadu, India
Telephone: 0091 422-***-**** Mobile: 0091 944-***-****
Email: *******@*****.***
Dr. V. P. Santhana Krishnan PhD, Assistant Professor, Department of Biotechnology, Centre for
Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore -641003, Tamilnadu,
India
Telephone: 0091 422-***-**** Mobile: 0091 948-***-****
Email: *********@*****.**.**
Personal Details
Date of Birth: 27 May 1975
Sex: Female
Marital status: Single
Nationality: India
Languages known: English and Tamil
Hobbies: Yoga and Meditation, fashion jewellery designing, travelling and cooking
Skype ID: kalpana.rajaa
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