User:Ramuigib

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Recent topics of Research

This is the times of thousands of genomes. We are interested in comprative genomics to unravel the mysteries of varying tropism in pathogens, host-pathogen dynamics and disease modelling in complex diseases. We will be using open source platforms like R although we are not entirely glued to it.

Email: ramu@igib.res.in

Present position

Srinivasan Ramachandran, Ph.D. Principal Scientist

Born, Chennai, April 14, 1963

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

We follow the motto

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


Personal

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

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

Here is my own prayer I offer,

How many secrets you have locked in, My Lord

As I dig, I find more and more and more,

It never seems to end, pulling me into infinitum

Such is the vastness of your creation, My Lord

It is beautiful, it is ugly, it is rough, it is smooth,

It is big, it is small, it is all in ONE

Alas! My life is so short

That I can only do a tiny bit

Of size equal to a grain of sand

Then, why My Lord I should stake a claim?

I therefore, shed the ’I’ in me and submit to Thee


INVITED LECTURES :

INVITED LECTURES (Reverse Chronological):

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. November 14, 2013, CMC Ludhiana, Ludhiana.

94) Integrated Bioinformatics approaches reveal new insights: a case study of Mycobacterium tuberculosis, September 25, 2013, CEP, DIPAS, Delhi,

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).


Publications Online

On the Issues faced in Open Source Drug Discovery

http://crdd.osdd.net/indipedia/index.php/Issues_Faced_While_Working_in_Open_Source_Drug_Discovery

On the Incentives for working in Open Source Drug Discovery

http://crdd.osdd.net/indipedia/index.php/Incentives_for_working_in_Open_Source_Drug_Discovery

Publications in Journals

(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.

(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.


(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.

(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.

(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.

(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.

(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.

(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.

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

(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.

(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.

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

(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.

(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.

(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.

(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

(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.

(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.

(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.

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

(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.

(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.

(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.

(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]

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

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

(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]

(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.

(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.

(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.

(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

(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)

(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.

(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)

(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.

(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.

(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. 2009 Nov 2. [Epub ahead of print].

(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.

(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. 2084-2089

(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 xxx 1-8.

(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.

(42) Genomics, Proteomics and Bioinformatics, Book Chapter New Edition (2011), CBSE Class XII book on Biotechnology.

(43) 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.

(44) Pintus SS, Ivanisenko NV, Demenkov PS, Ivanisenko TV, Ramachandran S, Kolchanov NA, Ivanisenko VA. 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. Journal of Biomolecular Structure and Dynamics (accepted)


(45) 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. Journal of Biomolecular Structure and Dynamics J Biomol Struct Dyn. 2012 Jul 18.

(46) 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

(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, DOI: 10.1080/08957959.2013.780055

(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.

(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.

(49) Bhanwar Lal Puniya, Deepika Kulshreshtha, Srikant Prasad Verma, Sanjiv Kumar Srinivasan Ramachandran. Integrated gene co-expression network analysis in the growth phase of Mycobacterium tuberculosis reveals new potential drug targets. Mol. BioSyst., 2013, Accepted Manuscript DOI: 10.1039/C3MB70278B. http://pubs.rsc.org/en/content/articlelanding/2013/mb/c3mb70278b

(50) Kumar A*, Kumar S*, Kumar D, Mishra A, Dewangan RP, Shrivastava P, Ramachandran S and Taneja B (2013). Crystal structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis. Acta Crystallographica Section D.

(51) 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 Oct 12.

(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. PubMed PMID: 24592289; PubMed Central PMCID: PMC3933634.

(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. PubMed PMID: 25048137.


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

Students Presentation Awards in Symposia:

1. Smriti Sharma (2013) Best Poster Award "Capsicum annum enhances L-lactate production by Lactobacillus acidophilus; implication in curd formation". 7th Asian Conference on Lactic acid bacteria, India Habitat Centre, New Delhi, September 6-8, 2013.

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

Organization of National & International Symposia: 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.

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

Supervision of M. Tech and Ph.D. Thesis: 1.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

2.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

3.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

4.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

5.Anu Sharma (2008) Student IGIB, CSIR Differential expression in selected humans using microarrays. Co-Supervisor: Dr. S. Ramachandran

6.Anannya Bandhyopadhyay (2010) Student IGIB, CSIR Characterization of the nitrogen regulation pathway protein PII of Mycobacterium tuberculosis. Supervisor: Dr. S. Ramachandran