Publications



2010
  1. Shashank Hambarde, Ragothaman M. Yennamalli , Naidu Subbarao , Sudhir Chandna; "Predictive inference on cytoplasmic and mitochondrial thioredoxin peroxidases in the highly radioresistant Lepidopteran insect Spodoptera frugiperda", Bioinformation 4: 399-404, 2010
  2. Mobashar Hussain Urf Turabe Fazil, Sunil Kumar, Naidu Subbarao , Haushila Prasad Pandey, Durg Vijai Singh, "Homology modelling of a sensor histidine kinase from Aeromonas hydrophila", Journal of Molecular Modeling 16:1003–1009, 2010
  3. Ankita Varshney, Priyankar Sen, Ejaz Ahmad, Mohd. Rehan, Naidu Subbarao , Rizwan Hasan Khan, "Ligand binding strategies of human serum albumin: How can the cargo be utilized?", Chirality 22:77-87, 2010
  4. Vaz C, Ahmad H M, Sharma P, Gupta R, Kumar L, Kulshreshtha R, Bhattacharya A.Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood.BMC Genomics 2010, 11:288.
  5. Agarwal S, Vaz C, Bhattacharya A, Srinivasan A.Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM).BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S29.


2009
  1. Das S, Vishnoi A, and Bhattacharya A ; ABWGAT: Anchor Based Whole Genome Analysis Tool . Bioinformatics Advance Access published on October 14, 2009. doi:10.1093/bioinformatics/btp587
  2. Agarwal M, Kushwaha HR and Chakravarty C “ Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides ” . J. Phys. Chem. (Accepted) 2009
  3. Singh P, Bandyopadhyay P, Bhattacharya S, Krishnamachari A and Sengupta S “ Riboswitch detection using profile Hidden Markov Models ” . BMC Bioinformatics 2009, 10:325
  4. Vinekar R and Ghosh I “Determination of Phosphorylation Sites for NADP-specific Isocitratedehydrogenase from Mycobacterium tuberculosis”. Journal of Biomolecular Structure & Dynamics, Volume 26, Issue Number 6, p 663-895 (June 2009)
  5. Kampmann T, Yennamalli R , Campbell P, Stoermer MJ,Fairlie DP, Kobe B and Young PR. “ In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses” , Antiviral Res. (2009).
  6. Das S*, Yennamalli RM*, Vishnoi A*,Gupta P and Bhattacharya A. “Single nucleotide variations associated with Mycobacterium tuberculosis KZN strains” , Journal of Biosciences, 2009 (Accepted for publication) (* Equal contribution)
  7. Banerji A, Ghosh I. “A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in Proteins”, European Biophysics Journal, 2009(Feb.)
  8. Vishnoi A, Srivastava A, Roy R,  Bhattacharya A. “MGDD: Mycobacterium tuberculosis genome diversity database”, BMC Genomics  9:373, (2009) doi:10.1186/1471-2164-9-373
  9. Prasad A, Agrawal M and Ramaswamy R. “ Strange nonchaotic attractors in driven delay–dynamics in Nonlinear Dynamics”, ( Chapters in Book) Eds. M. Daniel and S. Rajasekar (Narosa, New Delhi 2009) pp 299–304.
  10. Bandyopadhyay P, Kuntz ID. “Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction ”Biopolymers, 91, 68, (2009)
  11. Meher BR, Kumar MVS, Bandyopadhyay P. “Molecular Dynamics simulation of HIV-protease with polarizable and non-polarizable force fields” . Indian Journal of Physics, 2009,83, 81(invited article).
  12. Vashist J,Vishvanath, Kapoor R, Kapil A, Yennamalli R, Subbarao N , Rajeswari MR.“Interaction of nalidixic acid and ciprofloxacin with wild type and mutated quinolone-resistance-determining region of DNA gyrase A” . Indian J Biochem. Biophys., 2009,46(2):147-53.
  13. Nandi A, Vaz C, Bhattacharya A and Ramaswamy R . “ miRNA regulated dynamics in circadian oscillator models” . BMC Systems Biology 2009, 3:45
  14. Kushwaha HR, Singh AK, Sopory SK, Singla-Pareek SL and Pareek A. “Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa  L.  reveals their developmental and stress regulation” .BMC Genomics 2009, 28;10:200.
  15. Sabharwal KS VP, Kushwaha HR, Sopory SK, Singla-Pareek SL, Pareek A. “Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. ” . Funct Integr Genomics. 2009 Feb;9(1):109-23. Epub 2008 Jul 2.
  16. Yennamalli R, Subbarao N, Kampmann T, McGeary RP, Young PR, Kobe B.“Identification of novel target sites and an inhibitor of the dengue virus E protein” . J Comput. Aided Mol. Des., 2009, (pub ahead of print)..
  17. Sahni NS,Piepel GF, and Naes T. “Product and Process Improvement Using Mixture-Process Variable Methods and Robust Optimization Techniques ”.Journal of Quality Technology. 2009,41(2).
  18. Kelkar A, Vivek T, Ramaswamy R, Deobagkar D. “Characterisation of inactivation domains and evolutionary strata in Human X chromosome through Markov segmentation”.PloS One,2009.
  19. Banerji A, and Ghosh I. “Revisiting the Myths of Protein Interior: Studying Proteins with Mass-Fractal Hydrophobicity-Fractal and Polarizability-Fractal Dimensions”. PLoS One, 4(10).


2008

  1. Lyakhov IG., Krishnamachari A , and Thomas D. Schneider (2008). “Discovery of novel tumor suppressor p53 response elements using information theory Nucleic Acids Research 36(11):3828-33
  2. Hosseini A., Ranade SH., Ghosh I., Khandekar P. “Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes”, DNA Seq. 2008, 19(3):167-76.
  3. Khan SN, Islam B, Yennamalli R, Zia Q, Subbarao N, Khan AU."Characterization of doxorubicin binding site and drug induced alteration in the functionally important structural state of oxyhemoglobin", J Pharm Biomed Anal. 2008, 48(4):1096-104(Dec).
  4. Khan SN, Islam B, Yennamalli R, Sultan A, Subbarao N, Khan AU, "Interaction of mitoxantrone with human serum albumin: spectroscopic and molecular modeling studies", European Journal of Pharmaceutical Sciences, 2008, 35(5):371-82 (Dec).
  5. Oswal N, Sahni NS, Bhattacharya A, Komath SS. and Muthuswami R “Unique motifs identification of A proteins from glycosyltransferases of the GT4 family” , BMC Evolutionary Biology.
  6. Tyagi S, Vaz C,Gupta V, Bhatia R, Maheswari S, Srinivasan A and Bhattacharya A “CID-miRNA: A web server for prediction of novel miRNA precursors in human genome.” Biochemical and Biophysical Research Communications (2008).
  7. Singh A, Hemant R. Kushwaha and Sharma P. “Molecular modelling and comparative structural account of aspartyl beta-semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv)” . J Mol Model. 2008 Apr;14(4):249-63.
  8. Mueller DS, kampmann T, Yennamalli R, Young PR and Kobe B and Mark AE (2008).“Histidine protonation and the activation of viral fusion proteins”. Biochemical Society Transactions 36, 43-45
  9. Bandyopadhyay P. “Assessment of Two Surface Monte Carlo (TSMC) method to find stationary points of (H2O)15 and (H2O)20 clusters” . Theoretical Chemistry Accounts 120(1), 307-312. (2008)
  10. Bandyopadhyay P. (2008). “Two-surface Monte Carlo with basin hopping: Quantum mechanical trajectory and multiple stationary points of water cluster”. The journal of chemical physics 128, 134103.
  11. Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy K R , Kuntz ID, and Gibson BW(2008) “Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking”. Analytical Chemistry.
  12. Weber C, Blazquez S, Marion S, Ausseur C, Vats D, Krzeminski M, Rigothier S, Maroun RC, Bhattacharya A, Guillen N. (2008) “Bioinformatics and functional analysis of an Entamoeba histolytica mannosyltransferase necessary for parasite complement resistance and hepatical infection”. PloS Negl. Trop. Dis. 2(2), e165 (Feb 13, 2008). doi/10.1371/journal.pntd.0000165.
  13. Aggarwal SM, Jain R, Bhattacharya A, Azam A. (2008). “Inhibitors of Escherichia coli serine acetyltransferase block proliferation of Entamoeba histolytica Trophozoites”. Int. J. Parasitol. 38, 136-141
  14. A Nandi and  R Ramaswamy (2008). “Synchronization of Coupled Stochastic Oscillators: The effect of topology”. Pramana 70,  1065-74
  15. C Bonhomme, P Renesto, S Nandi, A Lynn, D Raoult (2008). “Serological microarray for a paradoxical diagnostic of Whipple's disease”. Eur J Clin Microbiol Infect Dis. Jul 2.
  16. Sahni, N.S., Piepel, G.F., N;s, T., Product and Process Improvement Using Mixture-Process Variable Methods and Robust Optimization Techniques


Book

        1. Vig L Multiple Robot Teaming: Coalition Formation: From Software Agents to Robots, VDM Verlag, (2008)
        2. Godbole R,  Ramaswamy R, Lilavati's Daughters, “The women scientists of India”,  Indian Academy of Sciences, Bangalore: 2008.  ISBN: 9788186450051


2007

  1. Vig L and Adams JA. (2007). "Coalition Formation: From Software Agents to Robots". Journal of Robotic and Intelligent Systems.
  2. Nandi A, Santosh G, Brojen Singh, R. K. and Ramaswamy R. (2007). “Effective mechanisms for the synchronization of stochastic oscillators”. Physical Review E. 76, 041136.
  3. Banerjee D, Martin N, Nandi S, Shukla S, Dominguez A, Mukhopadhyay G, Prasad R. (Epub 2007 Jun 16), “A genomewide steroid response study of major human fungal pathogen Candida albicans”. Mycopathologia. 2007 Jul;164(1):117.
  4. Azad RK, Lawrence J, Thakur V and Ramaswamy R. “Segmentation of Genomic DNA Sequences, in Advanced Computational Methods in Biocomputing and Bioimaging”, ed. by Tuan D. Pham et.al.,(Nova Science Publishers, NY, 2007).
  5. Thakur V, Azad RK, Ramaswamy R. (2007). “Markov models of Genome segmentation” Physical Review E. 75, 011915.
  6. Srivastava PK, Desai DK, Nandi S, Lynn A (2007). “HMM-ModE -  Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences”. BMC Bioinformatics. 8,104.
  7. Vishnoi A, Roy R, Bhattacharya A (2007). “Comparative analysis of Bacterial genomes: Identification of divergent regions in Mycobacterial strains  using an anchor-based approach”. Nucleic Acid Res. 35, No 11, 3654-3667.
  8. Stephen P, Vijayan R, Bhat A, Subbarao N, Bamezai RN (2007) Molecular “modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors”. J Comput Aided Mol Des. (Accepted)
  9. Vijayan R, Subbarao N and Mallick BN (2007) “In silico Modeling of a1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist”. American Journal of Biochemistry and Biotechnology 3 (4): 216-224, 2007
  10. Sengupta S and Lynn A . Rutenberg (2007) “Modeling partitioning of Min proteins between daughter cells after septation in Escherichia coli”. Phys. Biol. 4:145-153
  11. Sengupta S, X. Yang and Paul G. Higgs (2007) “The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes” J. Mol. Evol. 64:662-688 (2007).


2006

  1. K Gupta, H P Singh, B Biswal, and R Ramaswamy (2006). Adaptive targeting of chaotic response in periodically stimulated neural systems Chaos 16: 023116-17
  2. G Alexe, G S Dalgin, R Ramaswamy, C Delisi and G Bhanot  (2006). Data perturbation independent diagnosis and validation of breast-cancer subtypes using   clustering and patterns Cancer Informatics Online; 2: 243;74
  3. Naes T., Aastveit, A. And Sahni, N.S. (2006) Analysis of split-plot designs: an overview and comparison of methods, Quality and Reliability Engineering International.
  4. Lovekesh Vig and Julie A. Adams (2006).  Multi-Robot Coalition Formation, IEEE Transactions on Robotics, 22 (4)
  5. Lovekesh Vig and Julie A. Adams (2006).  Market Based Multi-Robot Coalition Formation, Distributed Autonomous Robotic Systems ( DARS), Minneapolis, editors   R. Voyles and M. Gini,
  6. Krishnamachari A, Srinivas T, Sanadhya SK and Balasundaram S (2006). Perceptron Decision Tree Model for E.coli Promoters. Proceedings of IncoB 2006, New Delhi
  7. Mandal, P.K., Rawal, K., Ramaswamy, R., Bhattacharya, A., Bhattacharya, S. (2006). Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to Entamoeba histolytica. Nucleic Acids Res. 34,5752-63.
  8. Haimovich, A. D., Byrne B., Ramaswamy R., Welsh, W. J. (2006) Wavelet Analysis   of DNA Walks J Comput Biol.  13, 1289-1298.
  9. Mehra, A., Fredrick, J., Petri, W. A. Jr, Bhattacharya, S., Bhattacharya, A., (2006) Expression and function of a family of transmembrane kinases from the protozoan parasite Entamoeba histolytica. Infect Immun. 74, 5341-51.
  10. Bhattacharya, A., Padhan, N., Jain, R., Bhattacharya, S. (2006) Calcium-binding proteins of Entamoeba histolytica. Arch Med Res. 37,221-5.
  11. Pandey, S. P., Krishnamachari A. (2006) Computational analysis of plant RNA Pol-II promoters. BioSystems. 83, 38-50.
  12. Pareek, A., Singh, A., Kumar, M., Kushwaha, H. R., Lynn, A. M., Singla-Pareek, S. L. (2006) Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis. Plant Physiol. 142, 380-97.
  13. Desai, D. K., Srivastava, P., Lynn, A. M.. Identifying drug targets from metabolic enzymes, Proceedings of the National Seminar and Workshop on Bioinformatics and Computational Biology-2006, held at Mahila Mahavidyalaya, Banaras Hindu University, Varanasi March 22-24, 2006.


2005

  1. R Ramaswamy (2005). The natural effectiveness of mathematics in the biological sciences. Current Science (Bangalore) 2005; 88: 38187
  2. Sahni N.S., Sharma P., Tibshirani R.; Array based detection of cancer based on gene-expression patterns in peripherial blood cells Breast Cancer Research 7, 2005.
  3. Sahni N.S., Aastveit A., & Naes T.;In-line process and product control using spectroscopy and multivariate calibration; Journal of Quality Technology 37(1)
  4. Sahni N.S., Isaksson T., and Naes T.; Comparison of methods for transfer of calibration models in near-infared spectroscopy : A case study based on correcting path length differences using fiber-optic transmittance probes in in-line near-infrared spectroscopy. Applied spectroscopy ISSN 0003-7028 CODEN APSPA4
  5. Lovekesh Vig and Julie A. Adams (2005).  "Issues in Multi-Robot Coalition Formation", Third International Multi-Robot Systems Workshop, From Swarms to Intelligent Automata, Washington D. C., editors Lynne E. Parker, Frank E. Schneider and Allan C. Schultz.
  6. Lovekesh Vig and Julie A. Adams (2005).  "A Framework for Multi-Robot Coalition Formation", In the Proceedings of the second Indian International Conference on   Artificial Intelligence, Pune, India.
  7. Gourinath, S., Padhan, N., Alam N., Bhattacharya, A. (2005) Crystallization and preliminary crystallographic analysis of calcium-binding protein-2 from Entamoeba histolytica and its complexes with strontium and the IQ1 motif of myosin V. Acta Crystallograph 61,417-20.
  8. Loftus, B., Anderson, I., Davies, R., Alsmark, U. C., Samuelson, J., Amedeo, P., Roncaglia, P., Berriman, M., Hirt, R. P., Mann, B. J., Nozaki, T., Suh, B., Pop, M., Duchene, M., Ackers, J., Tannich, E.,  Leippe, M., Hofer, M., Bruchhaus, I., Willhoeft, U., Bhattacharya, A., Chillingworth, T., Churcher, C., Hance, Z., Harris, B., Harris,    D., Jagels, K., Moule, S., Mungall, K., Ormond, D., Squares, R., Whitehead, S., Quail,     M. A., Rabbinowitsch, E., Norbertczak, H., Price, C., Wang, Z., Guillen, N., Gilchrist, C., Stroup, S. E., Bhattacharya, S., Lohia, A., Foster, P. G., Sicheritz-Ponten, T., Weber, C., Singh, U., Mukherjee, C., El-Sayed, N. M., Petri, W. A. Jr., Clark, C. G., Embley, T. M., Barrell, B., Fraser, C. M., Hall, N. (2005) The genome of the protist parasite Entamoeba histolytica. Nature. 433,865-8.
  9. Nandi, S., Mehra, N., Lynn, A. M., Bhattacharya, A. (2005) Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution BMC Genomics. 6, 116.
  10. Vats, D., Vishwakarma, R. A., Bhattacharya, S., Bhattacharya, A. (2005) Reduction of cell surface glycosylphosphatidylinositol conjugates in Entamoeba histolytica by antisense blocking of E. histolytica GlcNAc-phosphatidylinositol deacetylase expression: effect on cell proliferation, endocytosis, and adhesion to target cells. Infect   Immun. 73, 8381-92.
  11. Bakre, A. A., Rawal, K., Ramaswamy, R., Bhattacharya, A., Bhattacharya, S. The LINEs and SINEs of Entamoeba histolytica: comparative analysis and genomic distribution. Exp Parasitol. 110, 207-13.
  12. Bansal-Mutalik, R., Mustafi, S. M., Bhattacharya, A., Chary, K. V. (2005) Sequence specific 1HN, 13C and 15N resonance assignments of a novel calcium-binding protein from Entamoeba histolytica. J Biomol NMR. 31, 379-80.
  13. Deswal, R., Singh, R., Lynn, A. M., Frank, R. (2005) Identification of immunodominant regions of Brassica juncea glyoxalase I as potential antitumor immunomodulation targets. Peptides. 26, 395-404.
  14. Sharma, P., Sahni, N. S., Tibshirani, R., Skaane, P., Urdal, P., Berghagen, H., Jensen, M., Kristiansen, L., Moen, C., Sharma, P., Zaka, A., Arnes, J., Sauer, T., Akslen, L. A., Schlichting, E., Borresen-Dale, A. L., Lonneborg. A. (2005) Early detection of breast cancer based on gene-expression patterns in peripheral blood cells. Breast Cancer Res. 7, R634-44.
  15. Sahni, N. S., Isaksson, T., Naes, T. (2005) Comparison of methods for transfer of calibration models in near-infared spectroscopy: a case study based on correcting path length differences using fiber-optic transmittance probes in in-line near-infrared spectroscopy. Appl Spectrosc. 59, 487-95.
  16. Agarwal, S. M. (2005) Evolutionary rate variation in eukaryotic lineage specific human intronless proteins. Biochem Biophys Res Commun. 337, 1192-7.
  17. Agarwal, S. M., Gupta, J. (2005) Comparative analysis of human intronless proteins. Biochem Biophys Res Commun. 331, 512-9.


2004

  1. Sahni, N.S., Isaksson, T., and Naes, T. (2004).; In-line near infrared spectroscopy in product and process monitoring in the food industry, Journal of NIR spectroscopy.
  2. Krishnamachari, A., moy Mandal, V., Karmeshu. (2004) Study of DNA binding sites using the Renyi parametric entropy measure. J Theor Biol. 227, 429-36.
  3. Karmeshu and Krishnamachari "Sequence variability and long-range dependence in DNA: An Information theoretic perspective" Lecture notes in Computer Science. Vol. 3316, p1354, 2004. Springer Publications.
  4. Mandal, P. K., Bagchi, A., Bhattacharya, A., Bhattacharya, S. (2004) An Entamoeba histolytica LINE/SINE pair inserts at common target sites cleaved by the restriction enzyme-like LINE-encoded endonuclease. Eukaryot Cell. 2004 3, 170-9.
  5. Chakrabarty, P., Sethi, D. K., Padhan, N., Kaur, K. J., Salunke, D. M., Bhattacharya, S., Bhattacharya, A. (2004) Identification and characterization of EhCaBP2. A second member of the calcium-binding protein family of the protozoan parasite Entamoeba histolytica. J Biol Chem. 279, 12898-908
  6. Sharma, D., Issac, B., Raghava, G. P., Ramaswamy, R. (2004) Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics. 20, 1405-12.
  7. Singh, B.K., Subba Rao, J., Ramaswamy, R., Sinha, S. (2004) The role of heterogeneity on the spatiotemporal dynamics of host-parasite metapopulation. Ecolo. Modeling. 180. 435-443.


2003

  1. R Ramaswamy and R K Azad (2003). Analysis of DNA sequences through segmentation: Exploring the mosaic via statistical measures Physica Scripta 2003; T106: 2125
  2. Satish, S., Bakre, A. A., Bhattacharya, S., Bhattacharya, A. (2003) Stress-dependent expression of a polymorphic, charged antigen in the protozoan parasite Entamoeba  histolytica. Infect Immun. 71, 4472-86.
  3. Bhattacharya, A., Bhattacharya, S., Ackers, J. P. (2003) Nontranslated polyadenylated RNAs from Entamoeba histolytica. Trends Parasitol. 19, 286-9.
  4. Ghosh, S, Satish, S., Tyagi, S., Bhattacharya, A., Bhattacharya, S. Differential use of  multiple replication origins in the ribosomal DNA episome of the protozoan parasite Entamoeba histolytica. Nucleic Acids Res. 31, 2035-44.
  5. Jha, S., Karnani, N., Lynn, A. M., Prasad, R. (2003) Covalent modification of cysteine 193 impairs ATPase function of nucleotide-binding domain of a Candida drug efflux pump. Biochem Biophys Res Commun.310, 869-75.


2002

  1. G Aggarwal and R Ramaswamy (2002). Ab-initio gene prediction: Prokaryote Genome annotation with GLIMMER and GeneScan, Journal of Biosciences (Supplement 1); 27: 7 14
  2. Bhattacharya, S., Bakre, A., Bhattacharya, A. (2002) Mobile genetic elements in protozoan parasites. J Genet. 81, 73-86.
  3. Azad, R.K., Subba Rao, J., Li, W., Ramaswamy, R. (2002) Simplifying the mosaic description of DNA sequence. Phys. Rev., E 66 (3), 031913.
  4. Azad, R.K., Pernola-Galvan, P., Ramaswamy, R., Subba Rao, J. (2002) Segmentation of Genomic DNA through entropic divergenceL Power laws and Scaling. Phys. Rev., E 65 (5), 051909.