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Srinivasan Ramachandran, Ph.D.


Senior Principal Scientist

Room 130,

CSIR-Institute of Genomics and Integrative Biology (CSIR), Mathura Road, New Delhi-110 025. Tel: 091-11-29879130. Email: ramu@igib.res.in; ramuigib@gmail.com


Current Interests: Integrative Bioinformatics and molecular biology, data analytics.


Education:

M.Phil. dissertation :" Application of Nucleic Acid Hybridization to the diagnosis of Tuberculosis"

This work is an extension of the previous work published by Bhattacharya et al. In Ind. J. Med Res., 87, pp 144-150. My work confirmed the previous results and showed that the whole genomic DNA hybridization technique could be used to differentiate typical from atypical mycobacteria. Additionally, I extended the non-isotopic method for applications in Clinical Centres.

Ph.D. Thesis: " Organization and structure of ribosomal ribonucleic acid genes in Entamoebae histolytica. "

This work represents sequencing, rRNA gene mapping using homology approach, Secondary structure models and phylogenetic analysis. The structural models - aside from providing basic information on rRNAs - will serve as a basis for identifying reagents (drugs) that might interfere with ribosomal function in Entamoebae and to generate probes for diagnostic applications.

Post-Doctoral Fellowship: I spent a few years at The National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA. I joined a laboratory to work on a intestinal nematode parasite of humans called Strongyloides stercoralis. I developed markers for differentiating these group of parasites using rDNA internal transcribed spacers analysis, prepared cDNA library from the L3 infective stage and identified several clones for sero-diagnosis. The recombinant proteins were produced by the His-tagged fusion and developed for ELISA. Further, a few recombinant antigens were identified with potential to develop recombinant skin test antigens. During this time I also extended my Bioinformatics experience by analyzing newly sequenced microbial genomes and helped in improved annotation.

The Genomics Programme: After my brief post-doctoral period I returned to India to join the then Centre for Biochemical Technology now re-christened Institute of Genomics and Integrative Biology to join the genomics programme. It was a new and exciting venture. I assisted in the upgradation of computational facilities. I also set up the Microarray facility with assistance from the Director. The computational facilities have now grown to become recognized as a ‘World Class’ Center. The center is now called as G.N. Ramachandran Knowledge Centre for Genome Informatics in honour of the famous Prof. G.N. Ramachandran who pioneered Computational Biophysical work on protein structure more than 4 decades ago. The Microarray facility has become country wide recognized and researchers from various parts including the Indian Institute of Science have used the facility for their research. We have developed several microarrays that are classified as Theme Chips, which have been used by various users in their research investigations. The achievements of both these arms of genomics involving me directly are listed below under various headings.


Awards and other Recognitions

1. Faculty 1000 Biology Prize on Global competition, 2006.

2. Best teacher of the year 2006-2007 (evaluated by Ph.D. students of IGIB).

3. National Bioscience Award for Career Development 2007 by Deptt. Of Biotechnology.


Supervision of M. Tech and Ph.D. Thesis:

Janga Sarath Chandra (2003) Student IIT, Delhi. Study of gene order conservation in S. cerevisiae. Dissertation submitted towards 5-year dual degree M. Tech in Biochemical engineering and Biotechnology, Indian Istitute of Technology, Delhi

Co-Supervisor: Dr. S. Ramachandran

Tannistha Nandi (2005) Student IGIB, CSIR Computational studies of protein sequences across various genomes. Thesis towards Ph..D. in Bioinformatics, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi

Co-Supervisor: Dr. S. Ramachandran

Vineet K. Sharma (2006) Student IGIB, CSIR Analysis and understanding of repetitive sequence in the genome. Thesis towards Ph..D. in Bioinformatics, Delhi University, Delhi

Co-Supervisor: Dr. S. Ramachandran

Chandra Shekhar Prasad (2006) Student IIT Delhi Comparative study of alcohol producing pathways of yeast and bacteria: A genomic perspective. Deptt. Of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi

Co-Supervisor: Dr. S. Ramachandran

Anu Sharma (2008) Student IGIB, CSIR Differential expression in selected humans using microarrays. Thesis towards Ph..D., Delhi University, Delhi

Co-Supervisor: Dr. S. Ramachandran

Anannya Bandhyopadhyay (2010) Student IGIB, CSIR Characterization of the nitrogen regulation pathway protein PII of Mycobacterium tuberculosis. Thesis towards Ph..D., Pune University, Pune Supervisor: Dr. S. Ramachandran

Rupanjali Chaudhuri (2014) Analysis of virulence factors from selected pathogens using Bioinformatics approach. Thesis towards Ph.D., Pune University, Pune. Supervisor: Dr. S. Ramachandran

Sanjiv Kumar (2014) Computational identification of novel potential adhesins of Mycobacterium tuberculosis H37Rv and their experimental validation. Thesis towards Ph.D., Pune University, Pune. Supervisor: Dr. S. Ramachandran

Sriyans Jain (2014) Molecular characterization of protein – protein interaction and protein – nulceotide interaction in M. tuberculosis PII. Thesis towards Ph.D., Pune University, Pune. Supervisor: Dr. S. Ramachandran

Bhanwar Lal Puniya (2015) In silico chemical reactions modeling of pathways of Mycobacterium tuberculosis using transcriptomics data. Thesis towards Ph.D. Pune University, Pune. Supervisor: Dr. S. Ramachandran


BIBLIOGRAPHY (Reverse Chronological):

(63) Rani J, Mittal I, Pramanik A, Singh N, Dube N, Sharma S, Puniya BL,Raghunandanan MV, Mobeen A, Ramachandran S. T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders. Sci Rep. 2017 Jul 31;7(1):6892. doi: 10.1038/s41598-017-07238-0.

(62) Chaudhuri R, Ramachandran S. Immunoinformatics as a Tool for New Antifungal Vaccines. Methods Mol Biol. 2017;1625:31-43. doi: 10.1007/978-1-4939-7104-6_3.

(61) Shrivastava P, Navratna V, Silla Y, Dewangan RP, Pramanik A, Chaudhary S, Rayasam G, Kumar A, Gopal B, Ramachandran S. Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues. Sci Rep. 2016 Aug 9;6:30827. doi: 10.1038/srep30827. PubMed

PMID: 27501775; PubMed Central PMCID: PMC4977564.

(60) Puniya BL, Kulshreshtha D, Mittal I, Mobeen A, Ramachandran S. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. Sci Rep. 2016 Mar 22;6:23440. doi: 10.1038/srep23440. PubMed PMID: 27000948; PubMed Central PMCID: PMC4802306.

(59) Ahirwar R, Nahar S, Aggarwal S, Ramachandran S, Maiti S, Nahar P. In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen responsive elements as aptamer alike sequences. Scientific Reports, 2016, 6, 21285.

(58) Bhattacharya S, Aggarwal R, Singh VP, Ramachandran S, Datta M. Down-regulation of miRNAs during delayed wound healing in diabetes: Role of Dicer. Mol Med. 2015 Nov 19. doi: 10.2119/molmed.2014.00186. [Epub ahead of print]

(57) Vats A, Gourie-Devi M, Verma M, Ramachandran S, Taneja B, Kukreti R, Taneja V. Identification of L84F mutation with a novel nucleotide change c.255G‚Äâ>‚ÄâT in the superoxide dismutase gene in a North Indian family with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2015 Dec 2:1-7. [Epub ahead of print]

(56) Rani J, Shah AR, Ramachandran S (2015) pubmed.mineR: An R package with text-mining algorithms to analyse PubMed abstracts. J. Biosci. 40(4), 671-682.

(55) Jalali S, Kohli S, Latka C, Bhatia S, Vellarikal SK, Sivasubbu S, Scaria V,Ramachandran S. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. PLoS One. 2015 Jun 2;10(6):e0128711.

(54) Latka C, Dey SS, Mahajan S, Prabu R, Jangir PK, Gupta C, Das S, Ramachandran VG, Bhattacharya SN, Pandey R, Sharma R, Ramachandran S, Taneja B. Genome sequence of a clinical isolate of dermatophyte, Trichophyton rubrum from India. FEMS Microbiol Lett. 2015 Apr;362(8):fnv039.

(53) Chaudhuri R, Ramachandran S. Prediction of virulence factors using bioinformatics approaches. Methods Mol Biol. 2014;1184:389-400. doi:10.1007/978-1-4939-1115-8_22.

(52) Chaudhuri R, Kulshreshtha D, Raghunandanan MV, Ramachandran S. Integrative immunoinformatics for Mycobacterial diseases in R platform. Syst Synth Biol. 2014 Mar;8(1):27-39. doi: 10.1007/s11693-014-9135-9. Epub 2014 Feb 15.

(51) Kumar A, Kumar S, Kumar D, Mishra A, Dewangan RP, Shrivastava P, Ramachandran S, Taneja B. The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis. Acta Crystallogr D Biol Crystallogr. 2013 Dec;69 (Pt 12):2543-54. doi: 10.1107/S0907444913026371. Epub 2013 Nov 19.

(50) Jain S, Mandal RS, Anand S, Maiti S, Ramachandran S. Probing the amino acids critical for protein oligomerisation and protein-nucleotide interaction in Mycobacterium tuberculosis PII protein through integration of computational and experimental approaches. Biochim Biophys Acta. 2013 Dec;1834(12):2736-49. doi: 10.1016/j.bbapap.2013.10.006. Epub 2013 Oct 12.

(49) Bhanwar Lal Puniya, Deepika Kulshreshtha, Srikant Prasad Verma, Sanjiv Kumar and Srinivasan Ramachandran Integrated gene co-expression network analysis in the growth phase of Mycobacterium tuberculosis reveals new potential drug targets Integrated gene co-expression network analysis in the growth phase of Mycobacterium tuberculosis reveals new potential drug targets. Mol. BioSyst., 2013 Nov;9(11):2798-815. doi: 10.1039/c3mb70278b.

(48) Sanjiv Kumar, Bhanwar Lal Puniya, Shahila Parween, Pradip Nahar, Srinivasan Ramachandran. Identification of novel adhesins of M. tuberculosis H37Rv using integrated approach of multiple computational algorithms and experimental analysis. PLoS One. 2013 Jul 29;8(7):e69790. doi: 10.1371/journal.pone.0069790. Print 2013.

(47) Sharma S, Jain S, Nair GN, Ramachandran S. Capsicum annuum enhances l-lactate production by Lactobacillus acidophilus:Implication in curd formation. J Dairy Sci. 2013 May 6. pii: S0022-0302(13)00320-2. doi: 10.3168/jds.2012-6243.

(46) Somkuti J, Jain S, Ramachandran S, Smeller L (2013) Folding–unfolding transitions of Rv3221c on the pressure–temperature plane. High Pressure Research, An International Journal, Volume 33, Issue 2, DOI: 10.1080/08957959.2013.780055

(45) Sachdeva Gaurav, Kumar Kaushal, Jain Preti, Brahmachari, Samir Kumar, Ramachandran, Srinivasan, Notice of Allowance, Korean Patent Application No. 10-2006-7018206, No. of claims 15, Korean Intellectual Property Office. 2012

(44) Shachi Gahoi, Rahul Shubhra Mandal, Nikita Ivanisenko, Priyanka Shrivastava, Sriyans Jain, Ashish Kumar Singh, Muthukurrusi Varieth , Raghunandanan, Swarna Kanchan, Bhupesh Taneja, Chhabinath Mandal, Vladimir A. Ivanisenko, Anil Kumar, Rita Kumar, [Open Source Drug Discovery Consortium], Srinivasan Ramachandran* (2013) Computational Screening for New Inhibitors of M. tuberculosis Mycolyltransferases Antigen 85 Group of Proteins as Potential Drug Targets. J Biomol Struct Dyn. 31:.30-43

(43) Pintus SS, Ivanisenko NV, Demenkov PS, Ivanisenko TV, Ramachandran S, Kolchanov NA, Ivanisenko VA. (2013) The substitutions G245C and G245D in the Zn2+-binding pocket of the p53 protein result in differences of conformational flexibility of the DNA-binding domain. J Biomol Struct Dyn. 31:.78-86.

(42) Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics. 2011 Dec;10(12):M111.011627. Epub 2011 Oct 3. PubMed PMID: 21969609; PubMed Central PMCID: PMC3275902.

(41) Chaudhuri R, Verma S, Shah AR, Paul C, Chakraborty S, Puniya BL, Mandal RS, Ramachandran S. (2011) Biological Data Modelling and Scripting in R. in Bioinformatics - Computational Biology and Modeling (ISBN 979-953-307-280-6), Ed: Dr. Ning-Sun Yang, Institute of BioAgricultural Sciences, National Taiwan University, Taipei, Taiwan, InTech Open Access Publishers. { accessed 3000 times. Top downloads are from the following five countries: United States of America, India, China, Germany, United Kingdom}

(40) Bhardwaj A, Scaria V, Raghava GPS, Lynn AM,Chandra N, Banerjee S, Raghunandanan MV, Pandey V,Taneja B, Yadav J, Dash D, Bhattacharya J, Misra A, Kumar A,Ramachandran S, Thomas Z, Brahmachari SK. (2011) Open source drug discoverye A new paradigm of collaborative research in tuberculosis drug development. Tuberculosis, 91:479-486.

(39) Ramachandran S, Chaudhuri R, Verma R, Shah AR, Sen R, Paul C. 2012 Chapter 105: Systems Immunology: Data modeling and scripting in R. W. Dubitsky, O. Wolkenhauer, K. Cho, & H. Yokota (eds.) Encyclopedia of Systems Biology, Springer Science + Business Media, LLC.

(38) Chaudhuri R, Ansari FA, Raghunandanan MV, Ramachandran S. FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens. BMC Genomics. 2011 Apr 15;12(1):192.

(37) Bandyopadhyay A, Arora A, Jain S, Laskar A, Mandal C, Ivanisenko VA, Fomin ES, Pintus SS, Kolchanov NA, Maiti S, Ramachandran S. Expression and molecular characterization of the Mycobacterium tuberculosis PII protein. J Biochem. 2010 Feb;147(2):279-89.

(36) Srinivasan Ramachandran*, Amit Katiyar, Amit Sinha, Anshu Bharadwaj, Anirban Dutta, Ayush Raman, Archana Pan, Balwant Kishen Malik, Balvinder Singh, Beena Pillai, Bharati Dutta, Bhanot Priyamwada Sinha, Bhupesh Taneja, Chhabinath Mandal, Charu Kapil Richa, Chitra Dutta, Debasis Dash, Debaprasad Mukherjee, Debdas Paul, Debojyoti Chakraborty, Faraz Alam Ansari, Gajinder Pal Singh, Gajendra Pal Singh Raghava, Gargi Guhathakurtha, Imran Siddiqui, Manish Kumar, Manoj Hariharan, Mekapati Bala Subramanyam, Monika Joon, Mridula Bose, Mudgal Haymanti, Muthiah Gnanamani, Muthukurussi Varieth Raghunandanan, Nanda Ghoshal, Nitin Kumar Singh, Pallavi Sarmah, Ramaswamy Suyambu Kesava Vijayan, Rajni Verma, Rakesh Sharma, Ravishankar Ramachandran, Rupanjali Chaudhuri, Sabyasachi Das, Samir Kumar Brahmachari, Sandip Paul, Sanjib Chatterjee, Savita Bhutoria, Shantanu Chowdhury, Simone Gupta, Souvik Maiti, Subhagata Ghosh, Suchir Arora, Sudipto Saha, Sumit K. Bag, Sumit Deb, Vani Brahmachari, Vanika Gupta, Vikram Kumar, Vinod Scaria, Yasha Bhasin, Yogendra Singh, [OSDD Consortium], Mycobacterium tuberculosis systems biology data in R, Biobytes, Vol.5, ISSN 0971 3271, 2009, 40-48.

(35) Chaudhuri R, Ahmed S, Ansari FA, Singh HV, Ramachandran S. (2008) MalVac: database of malarial vaccine candidates. Malar J. 2008 Sep 23;7:184.

(34) Kaushal Kumar, Gaurav Sachdeva, Preti Jain, Brahmachari, S.K., Ramachandran, S. Computational Method for identifying adhesin and adhesin-like proteins of therapeutic potential Patent. 7,424,370, September 9, 2008 (granted USPTO)

(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.

(32) 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. 7,363,166, April 22, 2008 (granted USPTO)

(31) 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

(30) 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 31(1):96-103.

(29) 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 ;70(3):659-666.

(28) Gnanamani, M. Kumar, N., Ramachandran, S. (2007) ARC: Automated Resource Classifier for agglomerative functional classification of prokaryotic proteins using annotation texts. J. Biosc. 32(5), 937-945.

(27) 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 [Epub ahead of print]

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

(25) Ramachandran, S. (2006) Compositional Analysis of Proteins: An Old Theme Revisited. (Review) Proc. Ind. Natl. Sci. Acad. B71, No.1, 9-18.

(24) 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 [Epub ahead of print]

(23) 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.

(22) 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.

(21) Nandi T, Brahmachari SK, Kannan K, Ramachandran S.(2004) Clusters of proteins in archaeal and bacterial proteomes using compositional analysis. In Silico Biol.;4(4):573-91.

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

(19) Sharma, V.K., B-Rao, C., Sharma, A., Brahmachari, S.K., Ramachandran, S. (2003) (TG/CA)n repeats in housekeeping genes. J. Biomol. Str. Dyn. Vol. 21, 303-310.

(18) Nandi, T., Kannan, K. Ramachandran, S. (2003) Species and strain specific patterns of low complexity proteins in Escherichia and Mycobacteria. Curr. Sci. Vol. 85, 185-187.

(17) Nandi, T. Kannan, K., Ramachandran, S. (2003) The low complexity proteins from enteric pathogenic bacteria: Taxonomic parallels embedded in diversity. In Silico Biology, Vol. 3, 277-285.

(16) Nandi T., Dash, D., Ghai, R., B-Rao, C., Kannan, K., Brahmachari, S.K., Ramakrishnan, C., Ramachandran S. (2003) A Novel Complexity Measure for Comparative Analysis of Protein Sequences from Complete Genomes. J. Biomolec. Str. Dyn., Vol. 20, 657-667.

(15) Chopra, P., Singh, A., Koul, A., Ramachandran, S., Drlica, K., Tyagi, A.K., Singh, Y. (2003) Cytotoxic activity of Nucleoside diphosphate kinase secreted from M. tuberculosis. Eur. J. Biochem., Vol. 270, 625-634.

(14) Ravi, V., Ramachandran, S., Tompson, R.W., Andersen, J.F., Neva, F.A. (2002) Characterization of a recombinant immunodiagnostic antigen (NIE) from Strongyloides stercoralis L3-stage larvae. Mol. Biochem Parasitol., Vol. 125, 73-81.

(13) M. Majumdar, A. Bharadwaj, Ilora Ghosh, S. Ramachandran and K. Datta (2002) Evidence for the presence of HABP1 pseudogene in multiple locations of mammalian genome. DNA & Cell Biology, Vol. 21, 727-735.

(12) Nandi, T., B-Rao, C., Ramachandran, S. (2002) Comparative genomics using data mining tools. Journal of Biosciences. Vol 27, No.1, 15-25.

(11) Bhattacharya, A., Bhattacharya, S., Joshi, A., Ramachandran, S., Ramaswamy, R. (2000) Identification of parasitic genes by computational methods. Parasitol. Today, Vol. 16, No. 3, 127-31.

(10) Ramachandran, S., Dash, D., Brahmachari, S.K. (1999) The multitude of Omics and Omes: Evolution of scientific terms in molecular biology in the new millennium, Curr. Sci. Vol. 77, No. 7, 846-847.

(9) Ramachandran, S., (1999) A new curriculum , Curr. Sci., Vol. 76, No. 3, 263.

(8) Ramachandran, S., and Ramaswamy R.(1999) Gene identification in bacterial and organellar genomes using GeneScan. Computers and Chemistry, Vol. 23, No. 2, 165-174.

(7) Ramachandran, S., Thompson, R.W., Gam, A.A. and Neva, F.A. (1998) Recombinant cDNA clones for immunodiagnosis of Strongylodiasis. J. Infect. Dis., Vol. 177, 196-203.

(6) Tiwari, S., Ramachandran, S., Bhattacharya, A., Bhattacharya, S., and Ramaswamy, R. (1997) Prediction of probable genes by fourier analysis of genomic sequences. Comp. Appl. Biosc., Vol. 13, 263-170.

(5) Ramachandran,S., Gam, A.,A., and Neva, F.A. (1997) Molecular differences between several species of Strongyloides and comparison of selected isolates of Strongyloides stercoralis using a PCR linked RFLP approach . Am. J. Trop. Med. Hyg., Vol. 56(1), 61-65.

(4) Moore, T.A., Ramachandran, S., Gam, A.A., Neva, F.A., Lu, W., Saunders, L., Williams, S.A., and Nutman, T.B. (1996) Identification of novel sequences and codon usage in Strongyloides stercoralis. Mol. Biochem. Parasitol., Vol. 79, 243-248.

(3) Sehgal, D., Mittal, V.,Ramachandran, S., Dhar, S.K., Bhattacharya, A. and Bhattacharya, S. (1994) Nucleotide sequence organisation and analysis of the nuclear ribosomal DNA circle of the protozoan parasite Entamoeba histolytica. Mol.Biochem.Parasitaol., Vol. 67,205-214.

(2) Ramachandran, S., Bhattacharya,, A. and Bhattacharya,, s. (1993) Nucleotide sequence analysis of the rRNA transcription unit of a pathogenic Entamoeba histolytica strain HM-1:IMSS. Nucleic Acids Research, Vol. 21,2011.

(1) Mittal, V., Ramachandran, S., Sehgal, D., Bhattacharya, A. and Bhattacharya,,S. (1991). Sequence analysis of a DNA fragment with yeast autonomously replicating sequence activity from the extrachromosomal ribosomal DNA circle of Entamoeba histolytica. Nucleic Acids Research, Vol. 19, 2777.

Books & Book Chapters:


1. S. Ramachandran as contributor for a Chapter on Bioinformatics in the text book of Biotechnology for Class XII, Central Board of Secondary Education, Preet Vihar, Delhi, March 2003.

2. Sharma, A., Taneja, K.K., Rembhotkar, G.W., Mugasimangalam, R., Ramachandran, S. (2003) Hu-1536, Hu-2304, and Hu-800 Human Arrays for Discovery. In Current Trends in Laboratory Medicine (Section 1), Trends Clinical Biochemistry Laboratory Medicine, Association of Clinical Biochemists of India, 58-65.

3. Nandi, T. Ramachandran, S. (2003) Low Complexity Sequences in Proteins: New Perspectives for Sequence and Structure from Comparative Genomics. Book of Abstracts: Albany 2003, J. Biomol. Str. Dyn.

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

5. 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

6. 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

7. Preti Jain, Gaurav Sachdeva, Srinivasan Ramachandran (2005) Computational Approach for the Analysis of Genomic Information from Pathogenic Microbes to Guide Development of Novel Therapeutics. Mathematical Biology: Recent trends Peeyush Chandra and B.V. Rathish Kumar (Eds) Anamaya Publishers, New Delhi, India.

8. Book reviews Basic Bioinformatics by S. Ignacimuthu

Narosa Publishing House, 22 Daryaganj, New Delhi 110 002 (2005), 190 pp Current Science, (2005) Vol. 88, No.10, pp1690

INVITED LECTURES (Reverse Chronological):

111) Computer representation of molecules and searching libraries using ChemmineR. Bioinformatics Seminar-cum-Hands-on Training 2017 on “R Language and Drug Development” October 30-31, 2017 at BIF, Jamia Hamdard.

110) Integration of Text Data Mining and Genomic data Analytics : A case application for Type 2 Diabetes associated complications, 27th June, 2017 Bioinformatics workshop Supercomputing Facility for Bioinformatics & Computational Biology,3rd floor, Synergy Building (above Staff Canteen),Indian Institute of Technology Delhi,Hauz Khas, New Delhi - 110016, India.

109) Gene atlas of T2D associated Complications. Non coding RNA and Modern Biology, 18th March, 2017, JNU convention Centre, New Delhi

108) The DapA target of M. tuberculosis. Emerging Trends in Biotechnology & Drug Discovery, 10th February, 2017, CSIR-Institute of Genomics & Integrative Biology, Mall Road, Delhi University North Campus, Delhi-110007

107) Text mining of biomedical texts from PubMed using PubMed.mineR. Bioinformatics Centre, Savitribai Phule Pune University, Workshop on “Algorithms in Bioinformatics” January 9-12, 2017

106) Delivered a talk and chaired a session “T2DiACoD:A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders”, National Symposium on Bioinformatics and Computational Systems Biology, Central University Himachal Pradesh, TAB-Shahpur, Kangra, 12-14 November 2016.

105) Resource Person in practical workshop, Databases, Sequence alignment, Multiple sequence alignment and Phylogenetic trees, Bhaskaracharya College, Delhi, Feb 21, 28, March 6, 2016.

104) Algorithmic approaches to mining from biomedical texts for integrative data analytics. Silver Jubilee Celebration of Bioinformatics and computational biology at JNU, March 1, 2016.

103) Pubmed.mineR - Algorithmic approaches to biomedical text mining: Application to Gene mining. International Conference on Translational Biotechnology "BioSangam 2016", MNNIT, Allahabad, Feb 4-6, 2016.

102) Resource Person, Gene Expression Analysis: Hands-on using Microarray and Next Generation Sequencing Data, Acharya Narendra Dev College, Delhi, March 7-9, 2015

101) Reaching beyond 3 Vs of ‘Big Data’: using R 20th Refresher course Course in Life Sciences, UGC Academic Staff College, JNU, Feb 4, 2015

100) Using integrative approaches combining bioinformatics and experiments for new advances. 4th August 2014 UGC Academic Staff College, Biotechnology Faculty development program, Jawaharlal Nehru University, New Delhi.

99) Integrative Bioinformatics approaches for Novel Discoveries. 2nd August 2014 JIIT University, Noida.

98) Integrative Approaches in Bioinformatics useful for Novel Discoveries. Genomics & Proteomics Research June 12, 2014 SELECTBIO, Radisson Blu Plaza, New Delhi

97) Integration of gene expression and metabolic reactions models provides insights into robustness and drug target points in M. tuberculosis. Seminar -Cum-Workshop on "Evolutionary Genomics” Tezpur University, Tezpur, Feb 14 – 17, 2014

96) Integrative Bioinformatics Approaches: Immunoinformatics, December 11, 2013, Computational Tools for Animal Genome Resource Data Analysis (2nd December to 13th December 2013), National Bureau of Animal Genetic Resources, Karnal

95) Integrative Bioinformatics: A few case examples of infectious diseases, National Medical Biochemistry conference (AMBICON-2013) from 14 November 2013 at Christian Medical College, Ludhiana

94) Integrated Bioinformatics approaches reveal new insights: a case study of Mycobacterium tuberculosis,CEP Course Defence Institute of Physiology and Allied Sciences (DIPAS), Delhi, September 25, 2013

93) Gene Co-expression analysis as another approach for identifying potential drug targets in M. tuberculosis, 5th workshop on Bioinformatics and molecular modeling in Drug design, March 21-23, 2013, ACBR, University of Delhi.

92) Identification of novel adhesins of M. tuberculosis H37Rv using integrated approach of multiple algorithms and experimental analysis. Kolkata International School cum Conference on Systems Biology, Kolkata, December 28, 2012 – January 3, 2013, Saha Institute of Nuclear Physics & Bose Institute, Kolkata.

91) Case examples of Cheminformatics, integrated immunoinformatics, and Single Nucleotide Variations. Kolkata International School cum Conference on Systems Biology, Kolkata, December 28, 2012 – January 3, 2013, Saha Institute of Nuclear Physics & Bose Institute, Kolkata.

90) Introduction to Quantitative analysis for Biologists. Kolkata International School cum Conference on Systems Biology, Kolkata, December 28, 2012 – January 3, 2013, Saha Institute of Nuclear Physics & Bose Institute, Kolkata.

89) Multiple Sequence Alignment and Phylogenetic Analysis. December 24, 2012. Add on Course, Bhaskaracharya College, Delhi University, Dwarka, Delhi.

88) Development of new algorithms for analysis of genomics data from pathogens. Bioinformatics Workshop, October 11, 2012, IIT Delhi,

87) Sequence Databases and alignments and finding Orthologs October 5, 2012. Add on Course, Bhaskaracharya College, Delhi University, Dwarka, Delhi.

86) Analysis of Genomics Data from Pathogens, September 26 2012, Indian Science Congress Association, Shillong Chapter, NEHU, Shillong

85) Bioinformatics Workshop on Recent trends in Genomics and Databases, September 24 – 27, 2012, NEHU, Shillong

84) Shachi Gahoi, Rahul Shubhra Mandal, Nikita Ivanisenko, Priyanka Shrivastava, Sriyans Jain, Ashish Kumar Singh, Muthukurrusi Varieth Raghunandanan, Swarna Kanchan, Bhupesh Taneja, Chhabinath Mandal, Vladimir A. Ivanisenko, Anil Kumar, Rita Kumar [Open Source Drug Discovery Consortium], Srinivasan Ramachandran, Computational screening for new inhibitors of M. tuberculosis mycolyltransferases antigen 85 group of proteins as potential drug targets February 22-25, 2012, International Conference on Open Source for Computer-Aided Translational Medicine, Institute of Microbial Technology, Chandigarh, India

83) Srinivasan Ramachandran, Rupanjali Chaudhuri, Srikant Prasad Verma, Sequence analysis: Biological Data Modelling and Scripting in R December 14-16, 2011, Conference on Informatics & Integrative Biology" (CIIB-2011) at Kolkata during Bose Institute, Kolkata

82) Using the R platform for Systems Biology work. In Bioinformatics: Unravelling Genes and Proteins, a workshop for teachers from 10 to 15 May 2010, Miranda House, Delhi University, Delhi.

81) M. tuberculosis SysBorg R: An interoperable and reliable platform for analysis for systems biology. Indo-US Workshop on Informatics in Molecular Virology and Genetics, Pune, India, April 20-23, 2010.

80) Bioinformatics analysis for useful Biotechnological leads, Mizoram University, Aizawl November 27, 2009.

79) Bioinformatics analysis of pathogen genomes, National Workshop on Functional Genomics and Proteomics Institute of Life Sciences, Bhubaneswar, November 18-20, 2009.

78) Processes in open source drug discovery as a multiagency project, Symposium on Inhaled Tuberculosis Therapies, 3-5 Nov, 2009, IHC, New Delhi.

77) Datamining and Rational Drug Discovery: A case study, Rational Approaches in Drug Designing: Application of tools and techniques of Bioinformatics, Central Drug Research Institute, October 30, 2009.

76) Orientation Lecture for Open Source Drug Discovery, Deptt. Of Chemistry, Saurashtra University, Rajkot June 16, 2009.

75) Open Source model for Drug Discovery: A new concept, International Symposium on Biotechnology, Education, Research and Industrialization, School of Biotechnology, WhiteHouse College, Lalitpur, Nepal June 14, 2009.

74) New Approaches to Drug Discovery for combating Tuberculosis: the Open Source Concept UPE- lecture series at NEHU, Shillong, May 9, 2009.

73) Invited attended the System biology and Proteomics in Biomedical Science, IICB Kolkata, March 27-29, 2009 as part of CSIR Systems Biology core groups member.

72) New Approaches to Drug Discovery for combating Tuberculosis: The Open Source Concept, National Conference on Antimicrobial Resistance: From Emerging Threat to reality, March 25, 2009

71) Surface Adhesins of microbial pathogens, Open Source for Computer Aided Drug Discovery, March 22-23, 2009

70) Introduction to Machine Learning, IIT Short Term Course, March 12-13, 2009

69) High Throughput Biology & Microarrays, Training Workshop at North East Hill University, Shillong February 10-12, 2009.

68) Today's Bioinformatics, CPDHE, University of Delhi, February 6, 2009.

67) Attended the National Drug Discovery Conference 2009, January 21-23, 2009 at University of Delhi (South Campus), Delhi.

66) The Mycobacterium tuberculosis SysBorg Joint Indo-Russian Workshop "Systems Biology and Genome Informatics of M. tuberculosis and other infectious diseases" Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia October 12-14, 2008

65) "Application Bioinformatics for infectious diseases" The BGRS'2008 International Summer School for Young Scientists "Evolution, Systems Biology and High Performance Computing Bioinformatics" Novosibirsk, Russia, June 29-July 2, 2008.

64) Intrinsically Disordered Proteins in Pathogens: The case of Rv3221c of Mycobacterium tuberculosis National WorkShop "Protein folding and bioinformatics" at Bose Institute, Kolkata March 4-5, 2008.

63) "M. tuberculosis SysBorg: how it got made and where is it leading to?" Recent Trends in Bioinformatics, Biotechnology and Metabolic pathway engineering MGM Institute Aurangabad, Feb 3, 2008.

62) Microarrays II, , in the workshop" inferring biological relationships Bioinformatics Centre, North East Hill University, Shillong, Dec 1, 2007

61) Microarrays I, in the workshop" inferring biological relationships, Bioinformatics Centre, North East Hill University, Shillong, Dec 1, 2007.

60) Introduction to Bioinformatics, Refresher course in Botany, Deptt. Of Botany, North East Hill University, Shillong Nov. 30, 2007

59) "Genome sequence databases", in the workshop" inferring biological relationships, Bioinformatics Centre, North East Hill University, Shillong, Nov. 30, 2007

58) "Genome Analysis", Bioinformatics Centre, in the workshop" inferring biological relationships, North East Hill University, Shillong, Nov. 30, 2007

57) "M. tuberculosis SysBorg: A Systems Biology platform leading to a bigger drug discovery platform" in Science of Life Symposium, Miranda House, Delhi University, Nov. 22, 2007

56) " Bioinformatics as the first step of Biotechnology in the future", National Workshop on Bioinformatics, Meerut Institute of Engineering and Technology, Nov. 18, 2007, Meerut.

55) "Genome sequencing and Molecular mapping", in Workshop on Biotechnology Education, Dehradun, Uttarakhand, October 6, 2007.

54) "Inaugural address on Bioinformatics", Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, October 3, 2007.

53) "Using machine learning methods for developing algorithms to predict virulence factors in pathogens" DST Sponsored SERC School on Machine Learning and Pattern Evolution methods in Chemo and Bioinformatics, , Jointly organized by National Chemical Laboratory (NCL), Pune Centre for Development of Advanced Computing (C-DAC), Pune 26-29 June 2007.

52) "High-throughput Biology & Microarrays" Bioinformatics course in AIIMS (Biotechnology), March 21, 2007.

51) "The merit of Bioinformatics in Genomics era" Bioinformatics course in AIIMS (Biotechnology), March 20, 2007.

50) "Mining the Genomic Information for Biotechnological Applications" in National Seminar on "Frontiers in Biotechnology and Bioinformatics" Feb. 3, 2007.

49) "Bioinformatics approaches for Infectious Pathogens: Development of novel algorithms, platforms and applications with reference to Mycobacterium tuberculosis. Knowledge Discovery in Life Sciences: Tools & Techniques in Bioinformatics January29-February 2, 2007 University of Pune

48) "Development of novel algorithms and in silico analysis of proteomes" International conference on current trends in Industrial and Applied Mathematics(ICCTIAM07) from 16-18 January 2007, MS University, Vadodara

47) "Application of machine learning and statistical methods for analyzing complete sequences of genomes and proteomes" International Conference on Bioinformatics, INCOB 2006 December 18-20, 2006, New Delhi

46) "Genomics@IGIB" Second ASEAN-INDIA BIOINFORMATICS HRD PROGRAMME, Ashok Hotel, Dec. 14, 2006, New Delhi

45) "Systems Biology of Mycobacterium tuberculosis:mtb SysBorg Society of Biological Chemists(India)" 75th Annual Meeting, Dec. 9, 2006, Jawaharlal Nehru University, New Delhi

44) "Bioinformatics to Systems Biology: CSIR-IGIB concepts and efforts" at The First CUBIC-CDFD workshop on Bioinformatics and Genome Analysis, April 21-23, 2006, Cologne, Germany.

43) "Genomics, Bioinformatics and Integrative Biology: A tale of twins, repeats, virulence factors", Genomics and Proteomics Approaches for Drug Development" November 21-25, 2005, Biotech Park, Lucknow.

42) "Bioinformatics analysis of pathogenic Microbial surface proteins in virulence", IGIB Wednesday Forum discussion, Nov. 9, 2005.

41) "Prediction of Surface Proteins from Pathogens using Artificial Intelligence", Indo- Russian Seminar on Recent Trends in Applied Bioinformatics & Medi-informatics, IIIT, Allahabad, Nov. 6-7, 2005.

40) "Systems Biology of Mycobacterium tuberculosis: The CSIR In Silico Biology Networked Team Effort & Private-Public Partnership", Indo-Taiwan Joint Workshop on Functional Genomics, IGIB, Delhi, October 21, 2005.

39) "Bioinformatics Analysis of Surface Proteins", Machine Learning Techniques in Functional Proteomics, Institute of Microbial Technology, Chandigarh, October 19. 2005.

38) "Sequence Analysis, Multiple Sequence Analysis and Gene Identification", Lecture for Add-On course in Bioinformatics, Ramjas College, Delhi University, September 26, 2005.

37) "Identification of microbial adherence proteins using artificial intelligence as a new approach for drug targets and vaccine candidates" , Indo-Brazil-South Africa Trilateral Workshop on Functional Genomics, Life Science, GM Food and Agriculture July 18-19, 2005, IGIB, Delhi.

36) "Developing INDO-EU project on Systems Biology for Human Health, Paris, June 22-24, 2005.

35) "Identifying new candidates for vaccine development using Artificial Intelligence", Asian Regional Workshop on Intracellular Pathogens, ITREID and JNU, March 8-11, 2005, India Habitat Centre, New Delhi.

34) "A crusade against infectious pathogens: Development of anti-infectives using in silico approaches based on artificial pathogens", Vaccines and Drugs against Mycobacterial infections, February 10-11, 2005, Indian Institute of Technology, Kharagpur.

33) "A value added annotation system for fresh genome sequences from pathogenic organisms", Sino-India Workshop on Genome Informatics, Hangzhou, Shanghai, China October 27-30, 2004.

32) "Extracting useful leads from complete proteomes for Biotechnological Applications", Bioinformatics tools and their applications, October 20, NIIT campus at Indian Institute of Technology, Delhi.

31) "A neural network based approach for developing anti-infectives" at Techniche 2004, September 3-5, 2004, Indian Institute of Technology, Guwahati.

30) "Mining from complete proteomes to identify adhesins and adhesin-like proteins: A rapid aid to experimental researchers", July 25-30, Bioinformatics of Genome Regulation and Structure (BGRS 2004), Novosibirsk, Russia.

29) "Extracting useful leads from complete proteomes for Biotechnological Applications", Bioinformatics tools and their applications, July 15, Indian Institute of Technology, Delhi.

28) "Extracting useful leads from complete proteomes using Bioinformatics approaches", Training Programme in Bioinformatics, Biotech Park, Biotechnology City, Lucknow, July 13-15, 2004

27) "Blending Compositional Analysis with Artificial neural networks: A New Application to the Identification of Adhesins, Department of Computer Science, Technion Israel Institute of Technology, Haifa, Israel (summer 2004)

26) "Blending Compositional Analysis with Artificial neural networks: A New Application to the Identification of Adhesins, Institute of Evolution, University of Haifa, Haifa, Israel (summer 2004)

25) "Blending Compositional Analysis with Artificial neural networks: A New Application to the Identification of Adhesins, BigRoc Seminar, The Weizmann Institute of Science, Rehovot, Israel (summer 2004)

24) "Organizational Development Programme", CSIR India, IGIB, Delhi, April 26-27, 2004.

23) "Bioinformatics Applications" at "New generation veterinary vaccines & molecular techniques in animal disease diagnosis", National Biotechnology Centre, Indian Veterinary Research Institute, Izatnagar, Bareilly, 29th March 2004.

22) "Bioinformatics for beginners and in silico Proteomics of Microbial proteomes" at the Daulat Ram College, Delhi University, Delhi (2004)

21) "In silico Proteomics of Microbial proteomes" at the Swami Shraddanand College, Delhi University, Delhi. (2004)

20) "A multi-pronged approach to Tuberculosis" at The Indo-UK Tuberculosis meeting, CDFD, Hyderabad (January 12-13, 2004).

19) "Bioinformatics, Microarrays and Molecular Biology" at the CSIR-Pharma Industry Interaction, CDRI, Lucknow (November 27-28, 2003).

18) "Bioinformatics approaches to analysis of genomic information" at the Indo-French Interactive Seminar on Bioinformatics and Proteomics, CCMB, Hyderabad (December 15-16, 2003).

17) "Simple sequences in proteins and in the DNA: Structural and functional roles" at the 10th FAOBMB symposium, IISc, Bangalore (December 7-11, 2003).

16) "Gene Expression variation in natural population: A perspective from (TG/CA)n repeats" at International Symposium On Molecular Toxicology And Environmental Health, ITRC, Lucknow (November 5-8 2003).

15) "Mining genomic sequences and microarray data using novel computational approaches", at The Max Planck Institute of Genetics, Berlin (September 18-19, 2003). Sponsored by The Department of Biotechnology, Govt. of India.

14) "Bioinformatics analysis of genomic and microarray data" at Tata Energy Research Institute, on DNA based marker technologies and its applications, July 21-31, 2003.

13) "Bioinformatics for Class XII" At the Biotechnology workshop held at Army School, CBSE, Ferozepur Cantt. Ferozepur, June 2003.

12) "Comparative analysis of microbial sequences using complexity analysis" At the Bioinformatics Workshop, Industrial Toxicology Research Centre, Lucknow (January 2003)

11) "Differential gene expression analysis using microarrays" At the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi (Feb. 2003)

10) "Comparative analysis of E. coli and M. tuberculosis genomes" as a special invitee to The Guha Research Conference (2002)

9) "Bioinformatics and Microarrays" At The Consultancy Development Centre, India Habitat Centre (2002)

8) "Computational analysis of Microbial genomes" At The Society of Young Scientists meeting in AIIMS (2002)

7) "Sequence metrics & RNA secondary structure from comparative analysis" At Workshop on Computational Genomics held in Indian Statistical Institute, Barrackpore trunk road, Kolkata (Dec. 2001).

6) "A course on Comparative genomics" As part of Advanced diploma in Bioinformatics, Jawaharlal Nehru University, New Delhi 110 067 (Nov. 2001)

5) "Basics of Bioinformatics" At Delhi University Teachers training workshop lecture cum demonstration in Bioinformatics (2001)

4) "Basics of Bioinformatics" As part of M.Sc. course in Dr. B.R. Ambedkar Centre for Biomedical Research, Delhi University (2000)

3) "Biotechnology and the new biology emerging from Genomics research" At School of Biotechnology, Indraprastha University. (1999)

2) "Bioinformatics softwares: The GCG package" At BIOINFORMATICS Workshop held in Delhi University, South Campus (1993).

1) "Bioinformatics softwares: The GCG package" At BIOINFORMATICS Workshop held in Jawaharlal Nehru University (1993).

Courses conducted and Teaching Experience:

  1. “Bioinformatics 3 credit course and practicals” as part of B. Tech. In Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi.
  2. “Comparative genomics with practicals” as part of the Advanced diploma in Bioinformatics, Jawaharlal Nehru University, New Delhi.
  3. “Higher order Comparative genomics with practicals and discussion” as part of Post-Graduate diploma in Bioinformatics, EduTech, South Extension, Delhi.
  4. Summer lectures in Bioinformatics as part of training, Institute of Genomics and Integrative Biology, CSIR, Delhi
  5. Guest Lectures in Bioinformatics for the M.Tech programme of Indian Institute of Technology, Hauz Khas, Delhi.
  6. Guest Lectures in Bioinformatics for Delhi University Teachers and M.Sc. in Biomedical Sciences, Dr. B.R. Ambedkar Centre, Delhi University, Delhi.
  7. Basic of Bioinformatics, Ph.D. course work, IGIB every year
  8. Summer lectures series in Bioinformatics, IGIB, 2003.
  9. Ph.D. course work, IGIB, since 2004.

Articles in the ‘Open’

  1. http://sysborgtb.osdd.net/bin/view/OpenBookmarks/NationalConferenceOnDrugDiscoveryDevelopment. Prepared lecture notes and list of references including abstracts as teaching material.
  2. http://crdd.osdd.net/indipedia/index.php/Incentives_for_working_in_Open_Source_Drug_Discovery Prepared notes for describing the incentives for participating members of Open Source Drug Discovery
  3. http://crdd.osdd.net/indipedia/index.php/Issues_Faced_While_Working_in_Open_Source_Drug_Discovery Prepared notes for responding to the issues of concern to participating members of Open Source Drug Discovery. The CRDD site is part of the conglomerate sites under Open Source Drug Discovery.
  4. http://crdd.osdd.net/indipedia/index.php/Issues_Faced_While_Working_in_Open_Source_Drug_Discovery_II In continuation, part II, Prepared notes for responding to the issues of concern to participating members of Open Source Drug Discovery. The CRDD site is part of the conglomerate sites under Open Source Drug Discovery.
  5. Ramesh Ummanni, S. Ramachandran, OSDD consortium, Anuradha kumar, Geetha Vani Rayasam Innovation at OSDD – Unconventional vs Conventional approaches Science Reporter, Vol 51 No. 4 2014 20-23
  6. Geetha Sugumaran, Prasun Dutta, S. Ramachandran, David Wild, Tom L. Blundell, Anshu Bhardwaj, OSDD Predictive Sciences Team. Predictive Sciences for Drug discovery. Science Reporter, Vol 51 No. 4 2014 32- 36.

Students Presentation Awards in Symposia (reverse Chronological):

  1. Smriti Sharma (2013) Best Poster Award “Capsicum annum enhances L-lactate production by Lactobacillus acidophilus: implication in curd formation”. In 7th Asian Conference on Lactic Acid Bacteria, Sept 6-8, 2013, India Habitat Centre, New Delhi, India.
  2. Anannya Bandhopadhyay (2007) Best Poster Award”Molecular Characterization of Mycobacterium tuberculosis PII protein” in Society of Biological Chemists 76th annual meeting, Tirupathi 2007
  3. Vineet K. Sharma (2005) Student award for oral presentation on “Examining the role of (TG/CA)n repeats from a genome wide perspective using human microarray expression datasets” HUGO’s 10th Human Genome Meeting, Kyoto, Japan, 18-21, April 2005
  4. Tannistha Nandi (2003) Finn Wold award for poster on “Comparative analysis of protein sequences from complete genomes using a novel tool ScanCom” at the 17th Symposium of The Protein Society, Boston, Massachusetts, USA.
  5. Vineet K. Sharma (2003) 1st prize for poster on “Probing the functional role of the abundant (TG/CA)n repeats in human genome” at Fourth Annual symposium on frontiers in biomedical research, Dr. B.R. Ambedkar centre for Biomedical Research, Delhi University.
  6. Anu Sharma (2002) 2nd prize for poster on “Simple repeats and differential gene expression at the genome level” at Annual symposium in Biomedical Sciences, Dr. B.R. Ambedkar centre for Biomedical Research, Delhi University
  7. Tannistha Nandi (2002) 3rd prize for poster on “A novel complexity measure for comparative analysis of protein sequences from complete genome sequences: sequence features and implications for structure” at Annual symposium in Biomedical Sciences, Dr. B.R. Ambedkar centre for Biomedical Research, Delhi University

Students placed in India

1. Dr. Vineet Sharma,

Assistant Professor

Metagenomics and Systems Biology Laboratory

Dept. of Biological Sciences,

Indian Institute of Science Education and Research, Bhopal, India

2. Dr. Anu Sharma

Assistant Professor,

Mount Carmel College, Bengluru, India



Organization of National & International Symposia and Workshops:

1. S. Ramachandran as Secretary of GenoMeet 2000 : An Interactive Meet on Genomics Research in the New Millennium: Emerging Concepts, Paradigms and Technologies, February 23-25, 2000

2. S. Ramachandran as organizing, preparation of reagents, hands on demonstration on the bench, lecture and assisted in overall coordination in National Workshop on Microarrays, March 10-12, 2003: A hands on workshop organized under the Task force on Toxicogenomics.

3. S. Ramachandran as member of publication committee and preparation of posters for advertising & assisted in overall co-ordination for Satellite symposium to the 10th FAOBMB symposium on Genome Informatics, December 5-6, 2003.

4. S. Ramachandran as Co-ordinator, Indian side of DST-RFBR Joint Indo-Russian Workshop "Systems Biology and Genome Informatics of M. tuberculosis and other infectious diseases"October 12-14, 2008, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

5. S. Ramachandran as Joint Co-ordinator (CSIR-IGIB & CSIR-IMTECH) Indian side, of the Indo-Russia workshop on "Predictive Biology using Systems and Integrative analysis and Methods"at CSIR-IMTECH, Chandigarh in November 15-19, 2010 under DST-RFBR

Membership of scientific bodies:

1. Life Member, Society of Biological Chemists (India) Member No. 1332 (2001).

2. Life Member, Indian Biophysical Society Member No. IBS/L-435.

3. Member Computer Society of India N0050303

Reviewer & Examiner for journals, M. Tech Thesis, Ph.D. Thesis & grants:

1. Proceedings of The Indian National Science Academy

2. Current Science

3. Bioinformatics

4. Microbes and Infections

5. Biotechniques

6. External Examiner for International Centre for Genetic Engineering and

Biotechnology, Delhi

7. External Examiner for Indian Institute of Technology, Delhi

8. External Examiner for Dr. Ambedkar Centre for Biomedical Research, University of

Delhi, Delhi.

9. External Examiner for Guru Gobind Singh Indraprastha University, Kashmere gate,

Delhi

10. Reviewer of grant proposals submitted to CSIR ExtraMural, DBT and ICMR.

11. Academic committee member, School of Computational and Integrative Sciences, Jawaharlal Nehru University.

Additional responsibilites delivered:

1. Assistance in the maintenace of computational facilities, IGIB.

2. Maintenance and co-ordination of Microarray facility, IGIB.

3. Students recruitment committee, IGIB

4. Faculty recruitment in Universities

4. Country wide Advisor for Microarray facilities

5. Bioinformatics Consultant

Human resource Achievements

Students trained in M.Sc. Projects:

Genome Informatics

  1. Mahesh Kumar, G.D. (1999) “Comparative study of Word (peptide) complexity between Escherichia coli and Mycobacterium tuberculosis”. Summer project report submitted. Deptt. Of Marine Sciences & Biotechnology, University of Goa, Goa.
  2. Raj Kumar Kurupati (2002) “Analysis of simple and complex repeats in selected genes”. Dissertation submitted. Dr. B.R. Ambedkar Centre for Biomedical research, University of Delhi, Delhi.
  3. Hemant Ritturaj Kushwaha (2002) “Assembly of chromosome 18 sequence from given sequence files”. Dissertation submitted. Center for Biotechnology, University of Allahabad, Allahabad.
  4. Kavita Gakhar (2002) “Recognition of promoter consensus sequence”. Dissertation submitted. School of Information Technology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi.
  5. Srivastava, G.P. Sharma, A. Ramachandran, S. (2002) “Spotdesigner: A simple software for microarray designining independent of systems”. Indian Institute of Technology, Kanpur.
  6. Jasmine Ahluwalia (2003) “Comparative analysis of protein sequences from viral genomes using ScanCom”. Dissertation submitted.
  7. Swati Shukla (2003) Towards characterization of hypothetical gene Rv3221c of Mycobacterium tuberculosis. Dissertation submitted. Dr. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi
  8. Prettina Anto Louis (2004) Comparative moleculat economics of Mycobacterium tuberculosis and Escherichia coli. Bharathiar University, Coimbatore.
  9. Hardeep S. Gambhir (2004) Sequence evolution of RNA polymerase, a high cost protein. Deptt. Of Biotechnology, Guru Ghasidas University, Bilaspur.
  10. Swagatika Rath (2004) In silico analysis of drug resistance mutations in Mycobacterium tuberculosis, Deptt. Of Bioinformatics, Centre for Post-Graduate Studies, Orissa University of Agriculture and Technology, Bhubaneshwar.
  11. Pranita Bhatele (2005) Prediction of adhesin and adhesin-like proteins in Entamoeba histolytica. Biological Science Deptt., Rani Durgawati University, Jabalpur
  12. Naveen Kumar (2005) Web Technology Development For Genome Analysis Using Automation. DOEACC, Chandigarh (Delhi sub-Branch).
  13. Raghavan Bhavia (2006) In silico functional characterization of adhesin proteins in mycobacteria. Deptt. Of Life Sciences, IASE deemed university
  14. Ayush Raman (2006) Host Protein Mimicry of M. tuberculosis proteins Vellore Institute of Technology, Vellore
  15. Ruchi Chourisia (2006) Functional testing of EXPOLDB and analysis of (TG/CA)n repeats in exon-intron boundaries in molecular pathways using EXPOLDB and algorithm development for finding distance attributes of proteins. Sikkim Manipal University
  16. Rajesh Kumar (2006) Analyzing the (TG/CA)n repeats and expression variability in pathways of humans using EXPOLDB. University of Pune.
  17. Ishan Chaturvedi (2006) “Probing the presence of Type III secretion system apparatus in Mycobacteria using Support Vector Machine”. Indian Institute of Technology, Kharagpur.
  18. Priyanka Dhingra (2006) Retrieval of antigenic T cell epitopes for M. tuberculosis H37Rv adhesins. Banasthali Vidyapith
  19. Nidhi Yadav (2006) Recombinant protein expression, purification, and identification. Dr. B.R. Ambedkar University, Agra.
  20. Gargi Guhathakurta (2006) Bioinformatic analyses of genetic and phenotypic polymorphisms (SNPs and In-Dels) in different strains of Mycobacterium tuberculosis. Banasthali Vidyapith University for Women
  21. Shruti Bhatnagar (2006) Host Mimicry Of Mycobacterium Tuberculosis Proteins In Selected Functional Classes Of Secreted , Surface And Intermediary Metabolism. JayPee Institute of Bioinformatics, Solan, Himachal Pradesh.
  22. Ritesh Jain (2006) Prediction of human miRNA targets in Adhesins of Mycobacterium tuberculosis H37Rv. Indian Institute of Technology, Chennai.
  23. Thauseef Mohammed (2007) Towards making efforts in preparing an in insilico platform for the prediction of Vaccine Database. Indian Institute of Technology, Guwahati.
  24. Latika Bhonsle (2008) An analysis of host molecular mimicry and the effect of insertion sequence elements on the Mycobacterium tuberculosis H37Rv genome. Dr. Ambedkar Centre for Biomedical Research, Delhi University.
  25. Vanika Gupta (2008) Examining antigens of Mycobacterium tuberculosis for evidence of protection using literature search. Jamia Hamdard University on Indian Academy of Sciences Fellowship.
  26. Rajni Verma (2008) M. tuberculosis SysBorg Data collection and structuring on mtb persistence. Institute of Genomics and Integrative Biology.
  27. Santosh Maharana (2008) M. tuberculosis SysBorg, LINUX version data uploading and check. Institute of Genomics and Integrative Biology.
  28. Nayani Nasa (2008) Comparative genomics studies in Mycobacterial starins using Automated Resource Classifier. Jaipur Engineering College and Research Centre.
  29. Varun Gupta (2008) Bioinformatics & Softwares. Career Institute of Technology, Faridabad.
  30. Rubina Chongtham (2008) Finding the shortest pathway for the microbial degradation of plant polysaccharides to biofuels. Department of Botany, Delhi University.
  31. Neha Bhargava (2010) Developing user friendly functions for SysBorg R, Department of Bioinformatics, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Akrudi, Pune
  32. Jyoti Rani (2011) Text mining in R for Bioinformatics. Banasthali Vidyapith, Rajasthan
  33. Deepika Kulshreshtha (2012) Genome analysis using R and Bioconductor, Banasthali Vidyapith, Rajasthan.
  34. Priyanka Kumari. (2014) Analysis of Growth pattern of recombinant mutants for PII protein in Mycobacterium smegmatis. Deptt. Of Biotechnology, Loyola Academy and PG college, Hyderabad.
  35. Nawras T. Jassim (2014) Bioinformatics Sequence analysis of CD59 stem cells proteins. Deptt. Of Computer Science, Jamia Hamdard University
  36. Mahboubeh Mehmankhah (2014) Predicting probable ligands to inhibit HER1 and HER2 in gastric cancer. Deptt. Computer Science, Jamia Hamdard University.
  37. Anasuya Bhargav (2014) Building biomedical concepts on malaria from pubmed literature texts. Deptt. Of Biotechnology, Tezpur University.
  38. Ishita Ghai (2015) A gene centric approach to the susceptibility to Tuberculosis among diabetics using integrated data mining. School of Biosciences and Technology, VIT University.
  39. Pritam Borah (2015) Therapeutic trends in diabetic neuropathies: A literature mining, cheminformatics and genomic approach. Deptt. Of Molecular Biology and Biotechnology, Tezpur Central University.
  40. Shalini Rawat (2015) To clone the fragments of genes of M. tuberculosis coding for moon lighting proteins and testing their binding propensities to extracellular matrix proteins. Deptt. Of Biosciences ad Bioengineering, IIT Bombay.
  41. Vandana (2016). Expression of N-terminal domain of Rv2599 and Rv3909 of Mycobacterium tuberculosis for their binding propensities to extracellular matrix proteins. Central University South Bihar.
  42. Mr. Digvijay Dheer (2017) MAP 2 CONNECT : FROM SCIENTIFIC TEXT 2 INDUSTRY, B.TECH BIOTECH project, AMITY INSTITUTE OF BIOTECHNOLOGY AMITY UNIVERSITY, NOIDA
  43. Ms.Richa Rashmi (2016) Integrated Gene Expression Analysis of Controls Across Datasets Available of The Genes Implicated In Type 2 Diabetes Mellitus Complications, M.Tech Thesis, Indraprastha Institute of Technology, Delhi
  44. Mr. Deepanshu Malhotra (2017) Recent trends in gene disease association in Type 2 Diabetes Mellitus (T2DM) complications using literature mining approach, B.Tech Industry practice training, NIIT University, Neemrana.
  45. Mr. Keshav Bhojak (2017), Gene expression analysis of the nutrients for type 2 diabetes, M.Tech Thesis, Indraprastha Institute of Technology, Delhi

Microarrays

  1. Dorey Benjamin (2000) A Experience with Microarray Procedures. Summer project report submitted. The American College, Madurai Kamaraj University, Madurai
  2. Teena Pasrija (2001) An Experiment with DNA Microarray: Towards preparing Test DNA Chips. Summer project report submitted. Department of Experimental Medicine and Biotechnology, PIGMER, Chandigarh.
  3. Madhu Singh (2002) Duplication of Human EST Library for Microarrays. Dissertation submitted. Centre for Biotechnology, University of Allahabad, Allahabad. Co-supervisor – Dr. K.K. Taneja.
  4. PadmaPriya (2002) Towards preparing Blood Expressed Microarrays. Dissertation submitted. Deptt. Of Biotechnology, Bharatidasan University, Thiruchirapalli. Co-supervisor – Dr. K.K. Taneja.
  5. Ramya, R.G.(2002) Blood Expressed Microarrays for differential gene expression profiling. Dissertation submitted Bharatidasan University, Thiruchirapalli. Co-supervisor – Dr. K.K. Taneja.
  6. Gazalla Sheikh (2002) PCR amplification and purification of cDNA clones for preparation of Custom Arrays. Summer project report submitted. Deptt. Of Biotechnology, University of Calicut, Calicut
  7. Shruti Sharma (2002) Mass scale PCR amplification and purification for fabrication of metabolic arrays- I. Summer project submitted. Deptt. Of Biochemistry, Benares Hindu University, Varanasi.
  8. Smriti Sharma (2002) Mass scale PCR amplification and purification for fabrication of metabolic arrays- II. Summer project submitted. Deptt. Of Biochemistry, Benares Hindu University Varanasi.
  9. Vivek Kumar Maurya (2002) Preparation of DNA microarray slide of Human ESTs. Dissertation submitted. Deptt. Of Biotechnology, V.B.S. Purvanchal University, Jaunpur. Co-supervisor – Dr. K.K. Taneja.
  10. Ashu Shah (2003) Preparation of DNA microarray slide of Human ESTs. Dissertation submitted. School of Biotechnology, Benares Hindu University, Varanasi. Co-supervisor – Dr. K.K. Taneja.
  11. Avanika Mahajan (2003) “Gene Expression profiling in HeLa cell line using DNA microarrays. Summer Project submitted. School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi.
  12. Namrata Bhatanagar (2003) “Gene Expression profiling in human blood using DNA microarrays. Summer project submitted. College of Pharmacy, University of Delhi, Delhi.

Copyrights and Patents filed

  1. Ramachandran, S., Makkar, V. (2000) Method for partitioning protein sequences of probable specialized functions using a distance method and several physico-chemical properties of amino acids (Accepted)
  2. Ramachandran, S., Makkar, V. (2000) Method for computing complexity of protein sequences using a dimer word count approach (Accepted)
  3. Tannistha Nandi., Ramachandran, S. (2001) ProCom Database: A database of protein sequences classified on the basis of sequence complexity and linked with functional information. (Submitted)
  4. Goel, A., Anand, A., Sharma, A., Ramachandran, S. (2002) Array-annotator. A simple and flexible algorithm for microarray spot annotation. (Submitted)
  5. Sharma, V.K., Sharma, A., Khandelwal, M., Ramachandran, S., Brahmachari, S.K. (2002) EXPOLDB database: A database to correlate differentially expressing genes with TG/CAn repeats
  6. Sharma, V.K., Bhatnagar, P., Ramachandran, S. (2002) Collective algorithms for repeat detection and analysis.
  7. Kaushal Kumar, Gaurav Sachdeva, Preti Jain, Ramachandran, S. (2003) Adhesin proteins database. (CR 6/2003)

Students of the following Universities/Institutes have carried out projects under my supervision:

Indian Institute of Technology, Kanpur, Indian Institute of Technology, Delhi, University of Delhi, Bharatidasan University, Guru Gobind Singh Indraprastha University, Benares Hindu University, PGIMER, Chandigarh, Bansthali Vidyapith.