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PUBLICATIONS DURING 2007


  • Kaur, J.; Singh, K.V.; Boro, R.; Thampi, K.R.; Raje, M.; Varshney, G.C. and Suri, C.R.
    Immunochromatographic dipstick assay format using gold nanoparticles labeled protein-hapten conjugate for the detection of atrazine. Environ. Sci. Technol. 41, 5028-5036, 2007.


  • Vivona, S.; Gardy, J.L.; Ramachandran, S.; Brinkman, F.S.L.; Raghava, G.P.S.; Flower, D.R. and Filippini, F.
    Computer aided biotechnology: from immunoinformatics to reverse vaccinology. Trends Biotechnol., 26, 190-200, 2008.


  • Lata, S. and Raghava, G.P.S.
    CytoPred: a server for prediction and classification of cytokines. Protein Eng. Des. Sel., 21, 279-282, 2008.


  • Pashov, A.; Monzavi-Karbassi, B.; Raghava, G.P.S. and Kieber-Emmons, T.
    Peptide mimotopes as prototypic templates of broad-spectrum surrogates of carbohydrate antigens for cancer vaccination. Crit. Rev. Immunol., 27, 247-270, 2007.


  • Raghava, G. P. S.
    Prediction of subcellular localization of proteins using machine learning techniques and evolutionary information. Amino Acids, 33, X-XI, 2007.


  • Bachhawat, N. and Singh, B.
    Mycobacterial PE_PGRS proteins contain calcium-binding motifs with parallel beta-roll folds. Genomics Proteomics Bioinformatics, 5:236-241, 2007.


  • Saha, S. and Raghava, G. P. S.
    Prediction of allergenic proteins and mapping of IgE epitopes in allergens. Nature Protocols 10.1038/nprot.2007.505, 2007 (Online)


  • Singh, H. and Raghava, G. P. S.
    Prediction and mapping of promiscuous MHC class II binders in an antigen sequence. Nature Protocols 10.1038/nprot.2007.502, 2007 (Online)


  • Lata, S.; Sharma, B.K. and Raghava, G. P. S.
    Analysis and prediction of antibacterial peptides. Nature Protocols 10.1038/nprot.2007.503, 2007 (Online)


  • Kumar, M.; Verma, R. and Raghava, G. P. S.
    Mitpred2: An improved method for predicting mitochondrial proteins using SVM and HMM. Nature Protocols 10.1038/nprot.2007.488, 2007 (Online)


  • Suresh, K.; Mayilraj, S.; Bhattacharya, A. and Chakrabarti, T.
    Planococcus columbae sp. nov., isolated from pigeon faeces. Int. J. Syst. Evol. Microbiol., 57, 1266-1271, 2007.


  • Suresh, K.; Prakash, D.; Rastogi, N. and Jain, R.K.
    Clostridium nitrophenolicum sp. nov., a novel anaerobic p-nitrophenol-degrading bacterium, isolated from a subsurface soil sample. Int. J. Syst. Evol. Microbiol., 57, 1886-1890, 2007.


  • Muthukrishnan, S.; Garg, A. and Raghava, G.P.S.
    Oxypred: prediction and classification of oxygen-binding proteins. Genomics Proteomics Bioinformatics, 5, 250-252, 2007.


  • Kumar, M., Gromiha, M.M. and Raghava, G.P.S.
    Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins: Structure, Function and Bioinformatics, 71, 189-194, 2007.


  • Shahi, P.; Sharma, R.; Sanger, S.; Kumar, I. and Jolly, R.S
    Formation of amyloid fibrils via longitudinal growth of oligomers. Biochemistry. 46, 7365-7373, 2007.


  • Tiwary, B.N.; Prasad, B.; Ghosh, A.; Kumar, S. and Jain, R.K.
    Characterization of two novel biovar of Agrobacterium tumefaciens isolated from root nodules of Vicia faba. Curr. Microbiol., 55, 328-333, 2007.


  • Shukla, A.; Sharma, S. and Guptasarma, P.
    Confocal spectrofluorimetric evidence for the hetero-aggregation of sequence-scrambled forms of two model all-beta sheet proteins. Int. J. Biol. Macromol., 41, 650-654. 2007.


  • Kumar, M.; Gromiha, M.M. and Raghava G.P.S.
    Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics. 8, 463, 2007.


  • Mir, M.A. and Agrewala, J.N.
    Influence of CD80 and CD86 co-stimulation in the modulation of the activation of antigen presenting cells. Curr. Immunol. Rev., 3, 160-169, 2007.


  • Ghosh, A.; Goyal, A. and Jain, R.K.
    Study of methanol-induced phenotypic changes in a novel strain of Acinetobacter lwoffii. Arch. Microbiol.,188, 533-539, 2007.


  • Patnaik, P.R.
    Sensitivity propagations in response to start-up perturbations during batch fermentations with complementary cultures. Chem. Eng. Res. Des., 85, 1079-1085, 2007.


  • Patnaik, P.R.
    "Intelligent" descriptions of microbial kinetics in finitely dispersed bioreactors: neural and cybernetic models for PHB biosynthesis by Ralstonia eutropha. Microb. Cell Fact., 8, 6-23, 2007.


  • Patnaik, P.R.
    Fractal analysis of the attenuation of noise inflow to bioreactors under monotonic, oscillating and chaotic conditions. Intl. J. Chem. Reactor Eng., 5, A23, 2007.


  • Patnaik, P.R.
    Fractal characterization of fermentations with budding yeast under deterministic and chaotic conditions. Fractals, 15, 163-171, 2007.


  • Kaur, J.; Singh, K.V.; Boro, R.; Thampi, K.R.; Raje, M.; Varshney, G.C. and Suri C.R.
    Immunochromatographic dipstick assay format using gold nanoparticles labeled protein-hapten conjugate for the detection of atrazine. Environ. Sci. Technol., 41, 5028-5036, 2007.


  • Shukla, A.; Sharma, S. and Guptasarma, P.
    Confocal spectrofluorimetric evidence for the hetero-aggregation of sequence-scrambled forms of two model all-beta sheet proteins. Int. J. Biol. Macromol., 41, 650-654,2007.


  • Kapoor, D.; Chandrayan, S.K.; Ahmed, S. and Guptasarma, P.
    Using DNA sequencing electrophoresis compression artifacts as reporters of stable mRNA structures affecting gene expression. Electrophoresis, 28, 3862-3867, 2007.


  • Bharadwaj, S.; Shukla, A.; Mukherjee, S.; Sharma, S.; Guptasarma, P.; Chakraborti, A.K. and Chakrabarti, A.
    Putative structure and characteristics of a red water-soluble pigment secreted by Penicillium marneffei. Med. Mycol., 45, 419-427, 2007.


  • Andrianifahanana, M.; Singh, A.P.; Nemos, C.; Ponnusamy, M.P.; Moniaux, N.; Mehta, P.P.; Varshney, G.C. and Batra, S.K.
    IFN-Y-induced expression of MUC4 in pancreatic cancer cells is mediated by STAT-1 upregulation: a novel mechanism for IFN-Y response. Oncogene, 26, 7251-7261, 2007.


  • Rishi, L.; Dhiman, R.; Raje, M. and Majumdar S.
    Nitric oxide induces apoptosis in cutaneous T cell lymphoma (HuT-78) by downregulating constitutive NF-kappaB. Biochim Biophys Acta., 1770; 1230-1239, 2007.


  • Rashid, M.; Saha, S. and Raghava, G.P.S.
    Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. BMC Bioinformatics, 8, 337, 2007.


  • Moniaux, N.; Chaturvedi, P.; Varshney, G.C.; Meza, J.L.; Rodriguez-Sierra, J.F.; Aubert, J.P. and Batra, S.K.
    Human MUC4 mucin induces ultra-structural changes and tumorigenicity in pancreatic cells. Br. J. Cancer, 97, 345-357, 2007.


  • Osman, S.; Moissl, C.; Hosoya, N.; Briegel, A.; Mayilraj, S.; Satomi M. and Venkateswaran, K.
    Tetrasphaera remsis sp. nov., isolated from the Regenerative Enclosed Life Support Module Simulator (REMS) air system. Int. J. Syst. Evol. Microbiol., 57, 2749-2753, 2007.


  • Goyal, D.; Sahoo, D.K. and Sahni, G.
    Hydrophobic interaction expanded bed adsorption chromatography (HI-EBAC) based facile purification of recombinant streptokinase from E. coli inclusion bodies. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci., 850, 384-391, 2007.


  • Radhakishan, K.V.
    Structural Biology, Protein Conformations and Drug Designing. Current Protein and Peptide Science. 8, 376-380, 2007


  • Kaur, H.; Garg, A. and Raghava, G. P. S.
    PEPstr: A de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept Lett., 14, 626-30, 2007.


  • Lata, S.; Sharma, B.K. and Raghava, G. P. S.
    Analysis and prediction of antibacterial peptides. BMC Bioinformatics, 8, 263, 2007.


  • Mishra, N.; Kumar, M. and Raghava, G. P. S.
    Support vector machine based method for predicting Glutathione S-transferases proteins. Protein Pept Lett., 6, 575-80, 2007.


  • Bhasin, M.and Raghava, G. P. S.
    A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes. J. Biosci., 32,
    31-42. 2007.


  • Greenbaum et al. ...... Raghava, G.P.S.
    Towards a consensus on datasets and evaluation metrics for developing B cell epitope prediction tools. J. Mol. Recognit., 20, 75-82, 2007.


  • Ganguli, D.; Kumar, C. and Bachhawat, A.K.
    The alternative pathway of glutathione degradation is mediated by a novel protein complex involving three new genes in Saccharomyces cerevisiae. Genetics , 175, 1137-1151, 2007.


  • Kaur, J. and Bachhawat, A.K.
    Yct1p, a novel, high-affinity, cysteine specific transporter from the yeast Saccharomyces cerevisiae. Genetics, 176, 877-890, 2007.


  • Patnaik. P.R.
    Robustness analysis of the E. coli chemosensory system to perturbations in chemoattractant concentrations. Bioinformatics, 23, 875-881, 2007.


  • Manickam, N.; Mishra, R. and Mayilraj, S.
    A novel pathway for the biodegradation of gamma-hexachlorocyclohexane by a Xanthomonas sp. Strain ICH12. J. Appl. Microbiol., 102, 1468-1478, 2007.


  • Sharma, N.; Pandey, J.; Gupta, N. and Jain, R.K.
    Growth and physiological response of Arthrobacter protophormiae RKJ100 toward higher concentrations of o-nitrobenzoate and p-hydroxybenzoate. FEMS Microb iol. Lett., 271, 65-70, 2007.


  • Patnaik, P.R.
    Hybrid filtering of feed stream noise from oscillating yeast cultures by combined Kalman and neural network configurations. Bioproc. Biosyst. Eng., 30, 181-188, 2007.


  • Patnaik, P.R.
    A reappraisal of the plasmid stability problem in chemostat cultures. Ind. J. Biotechnol., 6, 267-270, 2007.


  • Patnaik, P.R.
    Analysis of the effect of flow interruptions on fed-batch fermentation for PHB production by Ralstonia eutropha in finitely dispersed bioreactors. Chem. Eng. Commun., 194, 603-617, 2007.


  • Bhardwaj, S.; Sutar, R.; Bachhawat, A.K.; Singhi, S. and Chakrabarti, A.
    PCR-based identification and strain typing of Pichia anomala using the ribosomal intergenic spacer region IGS1. J. Med. Microb. 56, 185-189, 2007.


  • Cameotra, S.S.
    Preservation of microorganisms as deposits for patent application. Biochem. Biophys. Res. Comm., 353, 849-850, 2007.


  • Agrewala, J.N.; Brown, D.M.; Lepak, N.M.; Duso, D.; Huston, G. and Swain, S.L.
    Unique Ability of Activated CD4+ T Cells but Not Rested Effectors to Migrate to Non-lymphoid Sites in the Absence of Inflammation. J. Biol. Chem., 282, 6106-6115, 2007.


  • Alam, M.S.; Garg, S.K. and Agrawal, P.
    Molecular function of WhiB4/Rv3681c of Mycobacterium tuberculosis H37Rv: a[4Fe-4S] cluster co-ordinating protein disulphide reductase. Molecular Microbiol., 63, 1414-1431, 2007.


  • Pandey, J.; Ganesan, K. and Jain, R.K.
    Variations in T-RELF profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers. J. Microbiol. Method, 68, 633-638, 2007.


  • Chaudhuri, S.R.; Mallam, J.N.; Barrios, P.C.; Wadhwa, P.N.; Hurwitz, M.Y. and Hurwitz, R.L.
    Modulation of adenoviral transduction in vitro and in vivo by hyaluronan and its receptor CD44. Molecular Therapy, 15, 566-570, 2007.


  • Dhiman, R.; Raje, M. and Majumdar, S.
    Differential expression of NF-kB in mycobacteria infected THP-1 affects apoptosis. Biochim. Biophy. Acta., 1770, 649-659, 2007.


  • Sen, Pradip; Wallet M.A.; Zuoan, Y.; Huang, Y.; Henderson, M.; Mathews, C.E.; Earp, H.S.; Matsushima, G.; Baldwin, A.S. and Tisch, R.
    Apoptotic cells induce MerTK-dependent blockade of NF-kB activation in dendritic cells. Blood, 109,
    653-660, 2007.


  • Raje, C.I.; Kumar, S.; Harle, A; Nanda, J.S. and Raje, M.
    A microphage cell surface localized Glyceraldehyde-3-phosphate dehydrogenase functions as a transferring receptor. J. Biol. Chem., 282, 3252-3261, 2007.


  • Garg, S.K.; Alam, M.S.; Radhakishan, K.V. and Agrawal, P.
    Expression and characterization of .-(1,4)-glucan branching enzyme Rv1326c of Mycobacterium tuberculosis H37Rv. Protein Expr. Purif., 51, 198-208, 2007.


  • Saluja, Puja and Prasad, G.S.
    Debaryomyces singareniensis sp.nov., a novel yeast species isolated from a coal mine soil in India. FEMS Yeast Research, 17, 132-135, 2007.


  • Ghosh, A.; Khurana, M.; Mayilraj, S. and Jain, R.K.
    Bacillus lehensis sp. Nov., an alkalitolerant bacterium isolated from soil of Leh, India. Int. J. Syst. Evol. Microbiol., 57, 238-242, 2007.


  • Saluja, Puja and Prasad, G.S.
    Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India Int. J. Syst. Evol. Microbiol., 57, 414 - 418, 2007.


  • Kaur, J.; Rajamohan, G. and Dikshit, K.L.
    Cloning and characterization of promoter-active DNA sequences from streptococcus equisimilis. Curr. Microbiol., 54, 48-53, 2007.


  • Sharma, S.; Chopra, K.; Kulkarni, S.K. and Agrewala, J.N.
    Resveratrol and curcumin suppress immune response through CD28/CTLA-4 and CD80 costimulatory pathway. Clin. Exp. Immunol., 147, 155-163, 2007.


  • Garg, S.K.; Alam, Md. S.; Soni, V.; Radhakishan, K.V. and Agrawal, P.
    Characterisation of Mycobacterium tuberculosis WhiB1/ Rv3219 as a protein disulfide reductase. Protein Expr.Purif., 52, 422-432, 2007.

 
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