AREA OF INTEREST Microarray data, Deep sequencing data analysis and integration.

CURRENT STATUS

Working as a PhD candidate in the field of Systems Biology under supervision of Prof Martin Kuiper, Dept. Of Biology, NTNU, Norway.

PHD PROJECTS

1) Systems biology model for Arabidopsis defence response mechanism.

In this Project I have analysed Affymetrics microarray data obtained from systemic samples of control, mock and Oilseed Rape Mosaic Virus treated Arabidopsis plants. With the help of Bioconductor packages, R and Python programming I also analysed the smallRNA deep sequencing data. The work included further integration of the Mass Spectrometry Protein data for studying the combined defence mechanism of Arabidopsis against the viral attack, I am in the final stage of this work and manuscript is in preparation.

2) Hypothesis Knowledge management.

My second project included the analyses of Gene expression data to study response of cancer cells to the stomach hormone Gastrin, and was produced by Bruland et al (manuscript in preparation). Briefly, a time series experiment was performed in the Rat cell line AR42J, two biological replicates were analyzed to yield a data set based on 156 Illumina microarray hybridizations. Genes were selected for differential expression relative to the control, throughout the time series and are being used for further hypothesis generation for Transcription factors involved. The analyses involved the use of R with lumi and genefilter packages of Bioconductor.

3) Gene correlation network in cancer cells.

I am also working on time series microarray experiment based on human genes from the MCF-7 Breast Cancer cells stimulated by the growth hormone ‘epidermal growth factor' (EGF) and 'Heregulin' (HRG). The data is normalised , filtered for genes with varying profiles, and used for calculating Pearson correlation and further analyses.

PROJECT EXPERIENCE

 

2011: Worked on Biological Validation of the clustering method developed by a Wim de Mulder, This also included analyses of gene expression data for three datasets and then obtaining GO terms for the clustered genes for calculation of Mutual Information. I worked with R and Biomart and genefilter package of Bioconductor for the same. The paper has been submitted in Dec 2011.

 

2009: Zifbase, A database of Zinc finger proteins and related resources

Development of online database and tool for research on Zinc finger proteins under the supervision of  Dr. D.Sundar at Indian Institute of Technology, Delhi available at http://web.iitd.ac.in/~sundar/zifbase/. Here I learned to work on Linux; Mysql for Database construction; PhP and HTML for development of web interface.

 

2008: A Distributed Information Sub centre (DISC) Project of Department of Biotechnology, Govt. of India, titled "Essential oil database for highly invasive weeds in India." at National Institute of Plant Genomic Research, JNU campus, New Delhi under Dr. Gitanjali Yadav. It included creation of a database and simultaneous building of user friendly web pages for retrieval of data available on NIPGR website.

 

2007: A project on "Web Retrieving Genome Annotation: Case Example Candida dubliniensis        Chromosome 7" at IISc and JNCASR, Bangalore under Dr. Debnath Pal during summer research fellowship offered by Indian Academy of Science, Bangalore, INSA (New Delhi) and NASI (Allahabad). It included creating a database, finding homologs using web tools and making a web page.

2005: A Project on "The real time stability of biochemistry, ELISA, and serological and immunological kits at expiry and three months after expiry", at RANBAXY, diagnostic division Okhla New Delhi under Mr. Inder Singh Bargali, Quality Assurance Officer.

Minor Project: Completed report on "Compare Molecular Dynamics and Monte Carlo   techniques for simulations of this system under different solvent/dielectric conditions using villin headpiece (PDB Code: 1VII)". (M.Sc. 2nd semester).  

SCHOLARSHIPS

Studentship by Department of Biotechnology, Government of India, at NIPGR, 2008.

Indian Academy of Sciences Summer Research Fellowship in 2007.

COMPUTATIONAL SKILLS

Linux -Ubuntu and Windows

Languages       

R and Bioconductor: Packages like limma , affy, lumi, ArrayQualitymetrics , genefilter , biomart, clust , shortread, biostrings etc.

Other Languages: Python, Matlab, PERL for bioinformatics, PhP, HTML

Database management systems

MySQL, Postgresql

Network modelling and analyses Tools:

Cytoscape , Cell Designer

Others: Array express, Bowtie, SamTools, Anova, Integrated genomic browser

EDUCATION AND TRAINING

Succesfully conducted the course Statistical analysis of gene expression data with R and Bioconductor , 2009.

M.Sc Bioinformatics, Dept. Of Computer Science, Jamia Millia Islamia, New Delhi, India. 80 % marks.

B.sc (H) Biotechnology, Amity institute of biotechnology, Amity University, Noida, UP, India, CGPA 8.69 /10 .

Teaching experience for the courses

Systems Biology and

Bioinformatics and sequence analyses

PUBLICATIONS

1) Mannu Jayakanthan, Jayaraman Muthukumaran, Sanniyasi Chandrasekar, Konika Chawla, Ankita Punetha, and Durai Sundar. ZifBASE: a database of zinc finger proteins and associated resources. BMC genomics, 10(1):421+, September 2009.

BOOK CHAPTERS

1) Konika Chawla, P.Barah, Martin Kuiper and Atle M. Bones, "Systems Biology: a Promising Tool to Study Abiotic Stress Responses", in "Omics and Plant Abiotic Stress Tolerence", N. Tuteja and S.S.Gill and R. Tuteja, Editors. 2011, Betham eBooks: International Centre for Genetic Engineering and Biotechnology, India.

http://www.benthamscience.com/ebooks/9781608050581/contents.htm