User:Ramuigib

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Current revision

Recent topics Computational analysis of Genomes and Proteomes, Twins, Systems Biology of M. tuberculosis, characterizing important pathways of pathogens

Present position Srinivasan Ramachandran, Ph.D. Scientist E I Born, Chennai, April 14, 1963

Present address Type IV(18), CRRI New Colony, Maharani Bagh, New Delhi 110 065

Education After completing my B.Sc. degree in Chemistry Honours from St. Xavier’s College, University of Calcutta, I joined Jawaharlal Nehru University for M.Sc. in Biotechnology. During this time I had an aptitude for computers that flowed automatically. I completed my Ph.D. in 1993.

Research Interests After completing my M.Sc., even though I had 2 job offers, I declined because my attraction to research was very strong. I enjoyed both experimental and computer work and I continue that tempo even today. Primarily, I enjoy doing science and research. My research tack follows the doublet principle of Innovation followed by Consolidation. My group has contributed to algorithm development, tackling biological important problems using modern technology, preparing Web servers and software products that have won global acclaim. My group is interested in Genome wide analysis, Twins, Systems Biology platform preparation, characterizing important pathways of pathogens. We do both experimental science and computer analysis.

We follow the motto

“Whatever we do, we do it thoroughly and describe it in such a way that it is reproduced as such in others hands”

Prize, Awards Won

• Faculty 1000 Biology prize on global competition in 2006

• Best Teacher Appraisal for 2006

• National Bioscience Award for Career Development 2007by Deptt. Of Biotechnology, Govt. of India

Word Class Products developed

• SEAPATH for prediction of virulence factors in bacterial pathogens and integrated into GenoCluster in partnership with M/s. Jalaja Technolgies, Bangalore.

Some recent Publications,Patents and Book Chapters:

Kaushal Kumar, Gaurav Sachdeva, Preti Jain, Brahmachari, S.K., Ramachandran, S. Computational Method for identifying adhesin and adhesin-like proteins of therapeutic potential Patent Filed (Notice of acceptance issued 2008).

To our knowledge, a first report on this unique protein with such a beautiful biophysical behavior in M. tuberculosis

Kumar N, Shukla S, Kumar S, Suryawanshi, A, Chaudhry U, Ramachandran S, Maiti S (2007) An Intrinsically Disordered Protein From A Pathogenic Mesophile Mycobacterium tuberculosis Adopts Structured Conformation At High Temperature. Proteins: Structure, Function, and Bioinformatics Proteins. 2008 May 15;71(3):1123-33

Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F.(2008) Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol. 2008 Apr;26(4):190-200.

Brahmachari, Samir Kumar; (Delhi, IN) ; Ramachandran, Srinivasan; (Delhi, IN) ; Nandi, Tannistha; (Delhi, IN) ; Bhimarao, Chandrika; (Delhi, IN) A computational method for the identification of candidate proteins useful as anti-infectives. Application No. 09/820,843 Accepted USPTO

Functional role of all dinucleotide repeats in the Human Genome

Sharma VK, Kumar N, Brahmachari SK, Ramachandran S. (2007) Abundance of Dinucleotide Repeats and Gene Expression are Inversely Correlated: a role for gene function in addition to intron length. Physiol. Genomics (in press).

Identify and check virulence proteins in Malaria

Ansari, F.A., Kumar, N., Subramanyam, M.B., Gnanamani M., Ramachandran S.

     (2007) MAAP: Malarial Adhesins and Adhesin-like proteins Predictor. Proteins: 
    Structure, Function, and Bioinformatics (in press).

 Obtain integrative perspective on your data

Gnanamani, M. Kumar, N., Ramachandran, S. (2007) ARC: Automated Resource Classifier for agglomerative functional classification of prokaryotic proteins using annotation texts. J. Biosc. (in press, special August Issue).

Functional role of (TG/CA)n repeats in Human Genome

Sharma V.K., Sharma, A., Kumar, N., Khandelwal, M., Kumar Mandapati, K., Horn-Saban, S., Strichman-Almashanu, L., Lancet, D., Brahmachari, S.K., Ramachandran S. (2006) Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats. BMC Genomics. 7(1):258

First analytical description of simple proteins from more than 240 prokaryotes

Subramanyam, M.B., Gnanamani, M., Ramachandran, S. (2006) Simple sequence proteins in prokaryotic proteomes. BMC Genomics. 8;(7):141.

First analytical description of simple repeats form entire Human genome

Sharma, V.K., Brahmachari, S.K., Ramachandran, S. (2005) (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length. BMC Genomics. 6(1):83

First report on analysis of monozygotic twins using microarrays --- Charles Auffray, Faculty 1000 Biology Member

Sharma A., Sharma, V.K., Horn-Saban, S., Lancet, D., Ramachandran, S. Brahmachari SK. (2005) Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays. Physiol. Genomics. 21(1):117-23.

First Original Bioinformatics research and product on surface adhesions – Editorial classification

Sachdeva, G., Kumar, K., Jain, P., Ramachandran, S. (2005) SPAAN: A Software for Prediction of Adhesins and Adhesin-like proteins using Neural networks, Bioinformatics 21(4):483-91.

A software, first of its kind for microarray design

Sharma, A., Srivastava, G.P., Sharma, V.K. , Ramachandran, S. (2004) ArrayD: A general purpose software for Microarray design. BMC Bioinformatics 5:142.

Book Chapters Ramachandran, S., Bandhyopadhyay, A. (2005) “Computational and Experimental proteomics: Opening new horizons in microbial research”. Advances in Biotechnology, Ed: P.C. Trivedi, Agrobios (India) Publishers, Jodhpur

Ramachandran, S., Jain, P., Kumar, K., Sachdeva, G. (2005) Mining from complete proteomes to identify adhesins and adhesin-like proteins: a rapid aid to experimental researchers, Bioinformatics Of Genome Regulation And Structure 2004 (The Second Biennial Volume), Kluwer-Springer Publishing House, Netherlands.

Vineet K. Sharma, Anu Sharma, Samir K. Brahmachari and Srinivasan Ramachandran (2005) (TG/CA)n Repeats in Human Genome: In silico analysis of the distribution and functional role of these repeats as cis modulators of transcription Mathematical Biology: Recent trends Peeyush Chandra and B.V. Rathish Kumar (Eds) Anamaya Publishers, New Delhi, India

Personal

I regularly subscribe and read Reader’s Digest. I like music, especially soft pop and Smooth Jazz. I have one son and a loving and caring wife. I learnt from other’s experience that one who enjoys working and delivering without clinging is true leadership. The Thiruvalluvar Kural is very appropriate here:

Cling to the one who does not cling Then Clinging ceases to cling

Here is my own prayer I offer,

How many secrets you have locked in, My Lord As I dig, I find more and more and more, It never seems to end, pulling me into infinitum Such is the vastness of your creation, My Lord It is beautiful, it is ugly, it is rough, it is smooth, It is big, it is small, it is all in ONE

Alas! My life is so short That I can only do a tiny bit Of size equal to a grain of sand Then, why My Lord I should stake a claim? I therefore, shed the ’I’ in me and submit to Thee

Other links If you are interested in my full Biodata then click here. [[Media:Media:Example.ogg[[Media:Media:Example.ogg[[Media:Image:Example.ogg[[Image:

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