Publication list

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.