Everyone in this World is special
Srinivasan Ramachandran, Ph.D.
Senior Principal Scientist
CSIR-Institute of Genomics and Integrative Biology (CSIR), Mathura Road, New Delhi-110 025. Tel: 091-11-29879130. Email: email@example.com; firstname.lastname@example.org
Current Interests: Integrative Bioinformatics and molecular biology, data analytics.
Education: <- click here for details
M.Phil. dissertation :" Application of Nucleic Acid Hybridization to the diagnosis of Tuberculosis"
Ph.D. Thesis: " Organization and structure of ribosomal ribonucleic acid genes in Entamoebae histolytica. "
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.
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.
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: <- click here for details
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
Sriyans Jain (2014) Molecular characterization of protein – protein interaction and protein – nucleotide interaction in M. tuberculosis PII. 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
Rupanjali Chaudhuri (2014) Analysis of virulence factors from selected pathogens using Bioinformatics approach. Thesis towards Ph.D., Pune University, Pune. 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
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
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
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
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
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
BIBLIOGRAPHY (Reverse Chronological): <- Click here for details
(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
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
113) Gene Atlas of Type 2 Diabetes associated comorbidities. International Conference on " Innovations and Translational Dimensions: Food, Health and Environmental Biotechnology” [Biosangam-2018] during March 09 - 11, 2018
112) Text mining of biomedical literature in R and its applications. 24/3/2018. BT2 - Bioinformatics Training for Trainers, 20th to 24th March, 2018, CSIR-IMTECH, Chandigarh
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.
Courses conducted and Teaching Experience:
- “Bioinformatics 3 credit course and practicals” as part of B. Tech. In Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi.
- “Comparative genomics with practicals” as part of the Advanced diploma in Bioinformatics, Jawaharlal Nehru University, New Delhi.
- “Higher order Comparative genomics with practicals and discussion” as part of Post-Graduate diploma in Bioinformatics, EduTech, South Extension, Delhi.
- Summer lectures in Bioinformatics as part of training, Institute of Genomics and Integrative Biology, CSIR, Delhi
- Guest Lectures in Bioinformatics for the M.Tech programme of Indian Institute of Technology, Hauz Khas, Delhi.
- Guest Lectures in Bioinformatics for Delhi University Teachers and M.Sc. in Biomedical Sciences, Dr. B.R. Ambedkar Centre, Delhi University, Delhi.
- Basic of Bioinformatics, Ph.D. course work, IGIB every year
- Summer lectures series in Bioinformatics, IGIB, 2003.
- Ph.D. course work, IGIB, since 2004.
Articles in the ‘Open’
- http://sysborgtb.osdd.net/bin/view/OpenBookmarks/NationalConferenceOnDrugDiscoveryDevelopment. Prepared lecture notes and list of references including abstracts as teaching material.
- 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
- 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.
- 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.
- 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
- 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):
- 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.
- Anannya Bandhopadhyay (2007) Best Poster Award”Molecular Characterization of Mycobacterium tuberculosis PII protein” in Society of Biological Chemists 76th annual meeting, Tirupathi 2007
- 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
- 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.
- 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.
- 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
- 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,
Metagenomics and Systems Biology Laboratory
Dept. of Biological Sciences,
Indian Institute of Science Education and Research, Bhopal, India
2. Dr. Anu Sharma
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
4. Microbes and Infections
6. External Examiner for International Centre for Genetic Engineering and
7. External Examiner for Indian Institute of Technology, Delhi
8. External Examiner for Dr. Ambedkar Centre for Biomedical Research, University of
9. External Examiner for Guru Gobind Singh Indraprastha University, Kashmere gate,
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:
- 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.
- 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.
- Hemant Ritturaj Kushwaha (2002) “Assembly of chromosome 18 sequence from given sequence files”. Dissertation submitted. Center for Biotechnology, University of Allahabad, Allahabad.
- Kavita Gakhar (2002) “Recognition of promoter consensus sequence”. Dissertation submitted. School of Information Technology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi.
- Srivastava, G.P. Sharma, A. Ramachandran, S. (2002) “Spotdesigner: A simple software for microarray designining independent of systems”. Indian Institute of Technology, Kanpur.
- Jasmine Ahluwalia (2003) “Comparative analysis of protein sequences from viral genomes using ScanCom”. Dissertation submitted.
- Swati Shukla (2003) Towards characterization of hypothetical gene Rv3221c of Mycobacterium tuberculosis. Dissertation submitted. Dr. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi
- Prettina Anto Louis (2004) Comparative moleculat economics of Mycobacterium tuberculosis and Escherichia coli. Bharathiar University, Coimbatore.
- Hardeep S. Gambhir (2004) Sequence evolution of RNA polymerase, a high cost protein. Deptt. Of Biotechnology, Guru Ghasidas University, Bilaspur.
- 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.
- Pranita Bhatele (2005) Prediction of adhesin and adhesin-like proteins in Entamoeba histolytica. Biological Science Deptt., Rani Durgawati University, Jabalpur
- Naveen Kumar (2005) Web Technology Development For Genome Analysis Using Automation. DOEACC, Chandigarh (Delhi sub-Branch).
- Raghavan Bhavia (2006) In silico functional characterization of adhesin proteins in mycobacteria. Deptt. Of Life Sciences, IASE deemed university
- Ayush Raman (2006) Host Protein Mimicry of M. tuberculosis proteins Vellore Institute of Technology, Vellore
- 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
- Rajesh Kumar (2006) Analyzing the (TG/CA)n repeats and expression variability in pathways of humans using EXPOLDB. University of Pune.
- Ishan Chaturvedi (2006) “Probing the presence of Type III secretion system apparatus in Mycobacteria using Support Vector Machine”. Indian Institute of Technology, Kharagpur.
- Priyanka Dhingra (2006) Retrieval of antigenic T cell epitopes for M. tuberculosis H37Rv adhesins. Banasthali Vidyapith
- Nidhi Yadav (2006) Recombinant protein expression, purification, and identification. Dr. B.R. Ambedkar University, Agra.
- 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
- 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.
- Ritesh Jain (2006) Prediction of human miRNA targets in Adhesins of Mycobacterium tuberculosis H37Rv. Indian Institute of Technology, Chennai.
- Thauseef Mohammed (2007) Towards making efforts in preparing an in insilico platform for the prediction of Vaccine Database. Indian Institute of Technology, Guwahati.
- 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.
- Vanika Gupta (2008) Examining antigens of Mycobacterium tuberculosis for evidence of protection using literature search. Jamia Hamdard University on Indian Academy of Sciences Fellowship.
- Rajni Verma (2008) M. tuberculosis SysBorg Data collection and structuring on mtb persistence. Institute of Genomics and Integrative Biology.
- Santosh Maharana (2008) M. tuberculosis SysBorg, LINUX version data uploading and check. Institute of Genomics and Integrative Biology.
- Nayani Nasa (2008) Comparative genomics studies in Mycobacterial starins using Automated Resource Classifier. Jaipur Engineering College and Research Centre.
- Varun Gupta (2008) Bioinformatics & Softwares. Career Institute of Technology, Faridabad.
- Rubina Chongtham (2008) Finding the shortest pathway for the microbial degradation of plant polysaccharides to biofuels. Department of Botany, Delhi University.
- Neha Bhargava (2010) Developing user friendly functions for SysBorg R, Department of Bioinformatics, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Akrudi, Pune
- Jyoti Rani (2011) Text mining in R for Bioinformatics. Banasthali Vidyapith, Rajasthan
- Deepika Kulshreshtha (2012) Genome analysis using R and Bioconductor, Banasthali Vidyapith, Rajasthan.
- 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.
- Nawras T. Jassim (2014) Bioinformatics Sequence analysis of CD59 stem cells proteins. Deptt. Of Computer Science, Jamia Hamdard University
- Mahboubeh Mehmankhah (2014) Predicting probable ligands to inhibit HER1 and HER2 in gastric cancer. Deptt. Computer Science, Jamia Hamdard University.
- Anasuya Bhargav (2014) Building biomedical concepts on malaria from pubmed literature texts. Deptt. Of Biotechnology, Tezpur University.
- 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.
- Pritam Borah (2015) Therapeutic trends in diabetic neuropathies: A literature mining, cheminformatics and genomic approach. Deptt. Of Molecular Biology and Biotechnology, Tezpur Central University.
- 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.
- 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.
- Mr. Digvijay Dheer (2017) MAP 2 CONNECT : FROM SCIENTIFIC TEXT 2 INDUSTRY, B.TECH BIOTECH project, AMITY INSTITUTE OF BIOTECHNOLOGY AMITY UNIVERSITY, NOIDA
- 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
- 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.
- Mr. Keshav Bhojak (2017), Gene expression analysis of the nutrients for type 2 diabetes, M.Tech Thesis, Indraprastha Institute of Technology, Delhi
- Dorey Benjamin (2000) A Experience with Microarray Procedures. Summer project report submitted. The American College, Madurai Kamaraj University, Madurai
- 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.
- 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.
- PadmaPriya (2002) Towards preparing Blood Expressed Microarrays. Dissertation submitted. Deptt. Of Biotechnology, Bharatidasan University, Thiruchirapalli. Co-supervisor – Dr. K.K. Taneja.
- Ramya, R.G.(2002) Blood Expressed Microarrays for differential gene expression profiling. Dissertation submitted Bharatidasan University, Thiruchirapalli. Co-supervisor – Dr. K.K. Taneja.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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)
- Ramachandran, S., Makkar, V. (2000) Method for computing complexity of protein sequences using a dimer word count approach (Accepted)
- 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)
- Goel, A., Anand, A., Sharma, A., Ramachandran, S. (2002) Array-annotator. A simple and flexible algorithm for microarray spot annotation. (Submitted)
- 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
- Sharma, V.K., Bhatnagar, P., Ramachandran, S. (2002) Collective algorithms for repeat detection and analysis.
- 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.