Plant University

Ms. Kalpana Raja

*, ***** *****,

Opp: Sankara Narayana Mahal,

Bharathiar Univ. PO, Coimbatore –641046,

Tamilnadu, India

Tele: 0091 422-***-****, Mobile: 0091 994-***-****

E-mail : *******.*****@*****.***, ********@*****.***

Age: 37 years DOB: 27/05/1975

Profile

Having an excellent knowledge in biology and software programming, I am now

pursuing PhD in Computational Biology and Bioinformatics at a reputed university. I am

looking forward to achieve more in research by contributing my skills, knowledge, abilities and

personal commitments to science.

Educational Qualification

Oct 2010 – Bharathiar University, PhD Computational Biology and

Coimbatore, India.

Sep 2013 Bioinformatics

Bharathiar University, MSc Bioinformatics, 75.6 % - First Class.

Jun 2009 -

Coimbatore, India.

May 2011

The Robert Gordon University,

Jan 2001 - MSc Computing: Software Technology,

Aberdeen, Scotland, UK 68% - Aggregate

Jul 2002

Jun 1999 – Bharathiar University, PGDCA (Post Graduate Diploma in

Coimbatore, India. Computer Application), 80% - First Class

May 2000

Jun 1998 – CMC Ltd. (A Govt. of India DAST (Diploma in Advanced Software

Technology), Grade A – Excellent

enterprise), India

Dec 2000

Tamilnadu Dr. M. G. R. Medical Bachelor of Pharmacy, 73% - Aggregate

Jul 1992 -

University, Chennai, India

May 1998

Board of Higher Secondary Higher Secondary Course Certificate, 81%

1992

Examination, Tamilnadu, India

Board of Higher Secondary

1990 Secondary School Leaving Certificate,

Education, Tamilnadu, India 88.4%

Employment: Research Experience

Research Scholar – Computational Biology and Bioinformatics

Fellowship - Computer Programmer - Specialization in Java/J2EE

Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University,

Coimbatore, Tamilnadu, India. (May 2010 to Apr 2013).

Research Area: Information Extraction / Text Mining

Supervisor: Dr. N. Jeyakumar, PhD(UK)

Project: “Text Mining and Data Warehousing of Human Protein Kinases Relationships and

Pathways”

Objectives achieved:

1. NAGGNER – An integrated named entity tagger for extracting and normalizing human

protein kinases in biomedical literature.

2. ProNormz – Web tool for Human Gene/Protein and Protein Kinases Normalization with

Synonyms Dictionary.

3. HomoKinase – A database for human protein kinases

4. PPInterFinder - A mining tool for extracting causal relations on human proteins from

literature

5. HPIMiner – A text mining system for visualizing protein interactions and pathways

6. Mining protein phosphorylation information from biomedical literature using NLP

parsing and Support Vector Machine (SVM)

7. Corpus on human protein phosphorylation – Current research

Senior Research Fellow – Bioinformatics

Programming specialization in Java/JDBC/J2EE

Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology,

Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India. (March 2008 to May 2010).

Research Area: Data Mining, Pattern Recognition and Structural Biology

Supervisor: Dr. L. Arul, PhD

Project: “Consortium of Agricultural Biotechnology”

Objectives achieved:

1. PrebZIP – A tool to identify basic zipper transcription factors in eukaryotes.

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.

5. In-silico drug design with osthol compounds.

6. Comparative analysis on drugs prescribed for Swine-flu.

Research (Whilst Education in UK)

Programming specialization in Java

Research Area: Information Retrieval / Text Mining

Supervisor: Dr. David Harper, PhD

Project: ProfileSkim –An Intelligent Document Browser

Award: The University patterned ProfileSkim in 2005. The ProfileSkim has won a medal of the

British Computer Society's Technology Awards 2005!

Employment: Teaching Experience

Course Associate – Bioinformatics & Biotechnology

Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University,

Coimbatore, Tamilnadu, India (March 2008 to May 2010).

Responsibilities: Taught the following courses and prepared practical manuals.

Java Programming and BioJava for B.Tech. (Bioinformatics)

Programming with Perl for B.Tech. (Bioinformatics)

Pharmacogenomics and Toxicogenomics for B.Tech. (Bioinformatics)

Cheminformatics and Drug Discovery for B.Tech. (Bioinformatics)

Biopharmaceutical Technology for B.Tech. (Biotechnology)

Assistant Professor

KMR College of Pharmacy, Perundurai, Tamilnadu, India. (Nov 2002 to Feb 2008).

Responsibilities: Taught the following courses during various semesters.

Pharmacology and Toxicology

Pharmacogenomics

Molecular Biology

Pharmaceutical biotechnology

Biochemistry

Computer Aided Drug Design

Introduction to Bioinformatics and biological databases.

Technical Skills

Software Skills:

Specialization - Java, JDBC, J2EE

Languages : Java, J2EE, VB, Perl, C, C++.

RDBMS / DBMS : SQL Server, Oracle, MS SQL, MySQL

Operating System : 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 Tools:

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 modelling tools : Discovery Studio, Modeller

Docking tool : Autodock, Schrodinger, Discovery Studio

Miscellaneous : CORINA, Convert

Paper Publication

Publications from PhD work (*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 Fey, Robert Dodson, Laurel Cooper, Ceri Van Slyke, WasilaDahdul, Paula

Mabee, Donghui Li, Bethany 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, Zhiyong Lu,

Oana Catalina Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan

Miguel Cejuela, Pratibha Dubey, Cathy 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. 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.

4. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. Template Filling in Text

Mining. Springer Encyclopedia of Systems Biology. (In press).

5. Kalpana Raja, Jeyakumar Natarajan. Mining protein phosphorylation information

from biomedical literature using NLP parsing and Support Vector Machines

(SVM). 19th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

(KDD-2013). (Manuscript submitted).

6. 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.

7. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. A hybrid named entity

recognition for tagging human proteins/genes. International Journal of Data Mining

and Bioinformatics. (In press).

8. Subramani Suresh, Kalpana Raja, Jeyakumar Natarajan. HPIMiner - A Text mining

system for visualizing Human Protein Interactions and Pathways. ISMB 2013

(Manuscript submitted).

9. 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.

10. Suresh Subramani, Kalpana Raja, Jeyakumar Natarajan. ProNormz - Web tool for

Human Gene/Protein and Protein Kinases Normalization with Synonyms

Dictionary. Journal of Biomedical Informatics. (Manuscript submitted).

Publications from employment as Senior Research Fellow

11. Raja Kalpana, 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.

12. Kalpana Raja, Loganathan Arul, Vellingiri Srividhya, Dhandapani Vignesh, Ponnusamy

Balasubramanian. PrebZIP: A computational tool to identify bZIP transcription

factor in eukaryotes. Pattern Recognition. (Manuscript submitted).

13. 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.

14. Kalpana Raja. Bio-programming prospects of Java: A computational move towards

the understanding of the biological aspects of genes and p roteins. Indian Journal of

Computer Science and Engineering, 2011, 2(6): 949-956.

15. Kalpana Raja, Archana Prabahar, Suganya Selvakumar, Thingalur K Raja. Efficacy of

assorted drugs prescribed for Swine-flu in diverse medical systems. Indian Journal of

Pharmaceutical Sciences. (Manuscript submitted).

16. Vichangal P. Santhanakrishnan, Raja Kalpana, 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.

Book / Book Chapter Publication

1. Kalpana Raja, Vanitha Govind. BioJava, 2008. Tamil Nadu Agricultural University,

Coimbatore –641 003, Tamilnadu, India.

Invited Guest Lecture

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 Pharmacy, Ooty, India.

Conferences / Symposia / Workshop organized / attended

Paper presentation

1. Boobalan C, Kalpana R, Archana P. SpliceSiter – A tool to RNA Splicing. In

Proceedings of National Level technical Symposium, Pratyarth, Sastra University,

Tanjavur, India. 2009.

2. Kalpana R, Arul L, Srividhya V, Vignesh D, Balasubramaniam P. PrebZIP – A tool to

identify bZIP class of transcription factors. In Proceedings of National Level

Symposium, MOTIF, Bharathiar University, Coimbatore, India. 2008.

Poster presentation

1. 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, 10 Feb 2013.

2. Suresh Subramani, Kalpana Raja, Jeyakumar Natarajan. A Suit of Text Mining Tools

for Human Literature Mining. In Proceedings of BioCreative Workshop 2012,

Washington DC, USA, 4-5 April 2012.

3. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. NAGGNER – A hybrid named

entity tagger for tagging human proteins/genes. In Proceedings of Asia Pacific

Bioinformatics Conference (APBC2012), Melbourne, Australia, 17-19 Jan 2012.

4. Suresh Subramani, Kalpana Raja, Jeyakumar Natarajan. ProNormz - Web tool for

Human Gene/Protein and Protein Kinases Normalization with Synonyms

Dictionary. In Proceedings of INCOBS 2nd International Conference on Bioinformatics

and Systems Biology, Annamalai University, Chidambaram, India. 2011.

5. Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. An integrated named entity

tagger for extracting and normalizing human protein kinases in biomedical

literature. In Proceedings of National Level Symposium on Structural Bioinformatics

and Computer Aided Drug Design, Alagappa University, Karaikudi, India. 2010.

Participation

1. AICTE sponsored National Seminar on Probability, Random Process and their

applications, Coimbatore Institute of Engineering and Technology, Coimbatore, India,

2012.

2. CSIR Sponsored National Workshop on Computational Intelligence Applications in

Bioinformatics, Dr. M.G.R. Educational and Research Institute – University, Chennai,

India, 2011.

3. MOTIF – National Symposium, Bharathiar University, Coimbatore, India, 2010.

Workshop organized (Team work)

1. DBT Sponsored Workshop on Protein Structure Prediction and Docking, Tamil Nadu

Agricultural University, Coimbatore, India. 2009, 2010.

2. State Level workshop on Management and Monitoring of Field Trials of Genetically

Engineered Crops in State Agricultural Universities, Tamil Nadu Agricultural

University, Coimbatore, India. 2009.

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. Partial Scholarship on tuition fee (£ 1,000.00) (2001) by The Robert Gordon

University, Aberdeen, Scotland, UK.

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).

References

Dr. N. Jeyakumar, PhD, Associate Professor, Department of Bioinformatics, Bharathiar

University, Coimbatore - 641 046, Tamilnadu, India

Telephone: 0091 422-***-**** Mobile: 0091 944-***-****

Email: *.*********@*****.**.**

Dr. L. Arul, PhD, Associate Professor, Department of Plant Molecular Biology and

Bioinformatics, Centre for Plant Molecular Biology, Tamil Nadu Agricultural University,

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: *********@*****.**.**

Dr. R. Narayanan, PhD, Professor, Department of Agricultural Microbiology, Tamil Nadu

Agricultural University, Coimbatore -641003, Tamilnadu, India

Telephone: (R) 0091 422-***-****, (O) 0091 422-***-****

Email: ****************@*****.***

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