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Home >> Publications of CDFD
Publications of CDFD

2014

Raju SR Adduri, Viswakalyan Kotapalli, Neha A Gupta, Swarnalata Gowrishankar, Mukta Srinivasulu, Mohammed M Ali, Subramanyeshwar Rao, Shantveer G Uppin, Umanath K Nayak, Snehalatha Dhagam, Mohana V Chigurupati and Murali D Bashyam. P53 nuclear stabilization is associated with FHIT loss and younger age of onset in squamous cell carcinoma of oral tongue. BMC Clinical Pathology, 2014, in press.

Anupam Sinha and H.A.Nagarajaram (2014) Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics DOI: 10.1002/pmic.201400249

Borah, S., Raju, S., Srivastava, V.K. and Kaur, R. (2014) A pivotal role for a tail subunit of the RNA polymerase II mediator complex, CgMed2, in azole tolerance and adherence in Candida glabrata. Antimicrobial Agents and Chemotherapy (In press).

Srivastava, V.K., Suneetha, K.J. and Kaur, R. (2014) A systematic analysis reveals an essential role for high-affinity iron uptake system, hemolysin and CFEM domain-containing protein in iron homeostasis and virulence in Candida glabrata. Biochemical Journal (In press).

Shah, A.H., Singh, A., Dhamgaye, S., Chauhan, N., Vandeputte, P., Suneetha, K.J., Kaur R, Mukherjee, P.K., Chandra, J., Ghannoum, M.A., Sanglard, D., Goswami, S.K. and Prasad, R. (2014) Novel role of a family of major facilitator transporters in biofilm development and virulence of Candida albicans. Biochemical Journal 460: 223-235.

Bairwa, G., Rasheed, M., Taigwal, R., Sahoo, R. and Kaur, R. (2014) Glycosylphosphatidylinositol (GPI)-linked aspartyl proteases regulate vacuole homeostasis in Candida glabrata. Biochemical Journal 458: 323-334.

Ratheesh R, Viswakalyan K, Mohana V, Sujit CP, Mukta S and Murali D Bashyam. A positive family history of cancer or lifestyle factors may not explain the high incidence of early-onset CRC in India. Colorectal cancer, 2014; in press.

Shashni, R., Qayyum, M. Z., Vishalini, V., Dey, D. and Sen, R. (2014). Redundancy of primary RNA-binding functions of the bacterial transcription terminator, Rho. Nucleic Acids Research, in press.

Arunkumar KP (2014) Book review of the Annual Review of Genetics 2013, Bonnie Bassler et al., (eds) Current Science 106: 1755-1757.

Gopinathan KP and Arunkumar KP (2013) Javaregowda Nagaraju (1954-2012). Current Science 104:657.

Abdul Mueed Bidchol, Ashwin Dalal, Hitesh Shah, Suryanarayana S, Sheela Nampoothiri, Madhulika Kabra, Neerja Gupta, Sumita Danda, Kalpana Gowrishankar, Shubha R Phadke, Seema Kapoor, Mahesh Kamate, IC Verma, Ratna Dua Puri, VH Sankar, A Radha Rama Devi, SJ Patil, Prajnya Ranganath, S Jamal Md Nurul Jain, Meenal Agarwal, Ankur Singh, Pallavi Mishra, Parag M Tamhankar, Puthiya Mundyat Gopinath, Nagarajaram HA, Kapaettu Satyamoorthy, Katta Mohan Girisha (2014) GALNS Mutations in Indian Patients with Mucopolysaccharidosis IVA Am J Med Genet Part A (Accepted)

Siddaramappa J Patil, Gaurava Kumar Rai, Venkatraman Bhat, Vakkalagadda A Ramesh, H A Nagarajaram, Jyoti Matalia, Shubha R Phadke (2014) Distal Arthrogryposis Type 5D With A Novel ECEL1 Gene Mutation Am J Med Genet Part A DOI: 10.1002/ajmg.a.36702

Pradhan B.B., Chatterjee S. (2014). Reversible non-genetic phenotypic heterogeneity in bacterial quorum sensing. Molecular Microbiology.Vol.92(3),557-569.

Aamir Ali, Sailaja Naga Veeranki and Shweta Tyagi (2014). A SET-domain-independent role of WRAD complex in cell-cycle regulatory function of mixed lineage leukemia. Nucleic Acids Res. May 31 2014 [Epub ahead of print]

Rachita Halehalli and H.A.Nagarajaram (2014) Viral Proteins that Bridge Unconnected Proteins and Components in Human PPI Network. Molecular Biosystems 10, 2448-2458

Murali D. Bashyam, Ajay K. Chaudhary, Manjari Sinha, Hampapathalu A. Nagarajaram, Radha RamaDevi, Prajnya Ranganath, Ashwin Dalal, Leena Bashyam, Neerja Gupta, Madhulika Kabra Mamta Muranjan, Ratna D. Puri, Ishwar C. Verma, Sheela Nampoothiri, Jayarama S. Kadandale. Splice, insertion-deletion and nonsense mutations that perturb the Phenylalanine hydroxylase transcript cause Phenylketonuria in India. J Cell Biochem, 2014, 115:566-574.

Ratheesh Raman, Viswakalyan Kotapalli, Raju Adduri, Swarnalata Gowrishankar, Leena Bashyam, Ajay Chaudhary, Mohana Vamsy, Sujith Patnaik, Mukta Srinivasulu, Regulagadda Sastry, Subramanyeshwar Rao, Anjayneyulu Vasala, NarasimhaRaju Kalidindi, Jonathan Pollack, Sudha Murthy and Murali Bashyam. Evidence for possible non-canonical pathway(s) driven early-onset colorectal cancer in India, Molecular carcinogenesis, 2014; 53:E181.E186.

Anusha Uttarilli, Prajnya Ranganath, S. Jamal Md Nurul Jain1, Krishna Prasad, Anupam Sinha, Ishwar C Verma, Shubha R Phadke, Ratna D Puri, Sumita Danda, Mamta N Muranjan, Ganesh Jevalikar, H A Nagarajaram, Ashwin B Dalal (2014) Novel mutations of the ARSB gene in Indian patients with Mucopolysaccharidosis Type VI Indian J. Med. Res. (Accepted)

Md Khursheed and Murali D Bashyam. Apico-basal polarity complex and cancer. J Biosciences 2014; 39:145-155.

Dutta UR, Vempally S, Ranganath P, Dalal A A novel combined 15q11.2 duplication and a bisatellited supernumerary marker derived from chromosome 22: Molecular characterization of the marker. Gene. 2014 Feb 5. pii: S0378-1119(14)00137-1. doi: 10.1016/j.gene.2014.02.002. [Epub ahead of print]

Mudunuri, S.B., Patnana, S. and Nagarajaram, H.A. (2014) MICdb3.0: A Comprehensive Resource of Microsatellite Repeats from Prokaryotic Genomes Database, doi:10.1093/database/bau005

Ratheesh Raman, Ravikanth Kongara, Viswakalyan Kotapalli, Swarnalata Gowrishankar, Regulagadda A Sastry, Bheerappa Nagari, and Murali D Bashyam. Pathological stage significantly predicts survival in colorectal cancer patients: a study from two tertiary care centres in India. Colorectal cancer, 2014; in press.

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2013

Ghosh S., Shukla D., Suman K., Lakshmi B.J., Manorama R., Kumar S. and Bhandari R. Inositol hexakisphosphate kinase 1 maintains hemostasis in mice by regulating platelet polyphosphate levels. Blood (2013) 122, 1478-1486.

Bairwa, G., Sriram, B., and Kaur, R. (2013) Aspartyl proteases in human pathogenic fungi: roles in physiology and virulence. In: The Fungal Cell Wall, Edited by Héctor M. Mora-Montes, Nova Science Publishers. Pages: 159-198.

Kaur, R. (2013) Review of: Annual Review of Microbiology, 2012. Edited by Susan Gottesman, Caroline S. Harwood and Olaf Schneewind. Current Science 105: 390-391.

Mishra, S., Mohan, S., Godavarthi, S. and Sen, R. (2013). The interaction surface of a bacterial transcription elongation factor required for complex formation with an antiterminator during transcription antitermination. Journal of Biological Chemistry, 288 (39), 28089–28103

Ranjan, A., Banerjee, R., Pani, B., Sen, U. and Sen, R. (2013). The moonlighting function of bacteriophage P4 capsid protein, Psu, as a transcription antiterminator. Bacteriophage 3:2, e25657.

Ranjan, A., Banerjee, R., Sharma, S., Sen, U. and Sen, R. (2013). Structural and mechanistic basis of antitermination of Rho-dependent transcription termination by a bacteriophage capsid protein. Nucleic Acids Research, 41 (14):6839-6856.

Murali D Bashyam and Ratheesh Raman. Molecular origins of colon and rectal cancer: not a Wnt-Wnt situation. Current colorectal cancer reports. 2013; 9:365-371.

Bairwa, G., Rasheed, M., Taigwal, R., Sahoo, R. and Kaur, R. (2013) Glycosylphosphatidylinositol (GPI)-linked aspartyl proteases regulate vacuole homeostasis in Candida glabrata. Biochemical J (In press).

Rai, M.N., Borah, S., Bairwa, G., Balusu, S.,Goritala, N. and Kaur, R. (2013) Establishment of an in vitro system to study intracellular behavior of Candida glabrata in human THP-1 macrophages.. J. Vis. Exp. 82: e50625. Equal contribution.

Murali D. Bashyam, Ajay K. Chaudhary, Manjari Kiran, Venkat Reddy, Hampapathalu A. Nagarajaram, Ashwin Dalal, Leena Bashyam, Deepti Suri, Anju Gupta, Neerja Gupta, Madhulika Kabra, Ratna Puri, RadhaRamaDevi, Seema Kapoor, Sumita Danda. Molecular analyses of novel ASAH1 mutations causing Farber lipogranulomatosis: analyses of exonic splicing enhancer inactivating mutation. Clin Genet, 2013, Nov 8. doi: 10.1111/cge.12316.

Sridhar Kavela, Swapnil R. Shinde, Raman Ratheesh, Kotapalli Viswakalyan, Murali Bashyam, Swarnalata Gowrishankar, Mohana Vamsy, Sujith Pattnaik, Subramanyeshwar Rao, Regulagadda Sastry, Mukta Srinivasulu, Junjie Chen, Maddika S Reddy. PNUTS functions as a proto-oncogene by sequestering PTEN. Cancer research. 2013; 73:205-214.

Manjari Kiran and H.A.Nagarajaram (2013) Global versus local hubs in human protein-protein interaction network J.Proteome Res. 12: 5436.5446

Ramaswamy Pandilla, Viswakalyan Kotapalli, Swarnalata Gowrishankar, MohanaVamsy Chigurupati, Sujith Patnaik, Shantveer Uppin, Subramanyeshwar Rao, NarasimhaRaju Kalidindi, Sastry Regulagadda, Challa Sundaram, Mukta Srinivasulu, Anjayneyulu Vasala, and Murali Dharan Bashyam. Distinct genetic aberrations in esophageal adeno and squamous carcinoma. Eur J Clin Invest; 2013; 43 (12): 1233-1239

Nagasowjanya, T., Kranthi Raj, B., Sreethi Reddy, K., and Kasbekar, D. P. (2013) An apparent increase in meiotic silencing strength in crosses involving inbred Neurospora crassa strains. Fungal Genet. Biol. (in press).

Kasbekar, D. P. (2013) Neurospora Duplications, and Genome Defense by RIP and Meiotic Silencing. In : Neurospora: Genomics and Molecular Biology. Edited by D. P. Kasbekar and K. McCluskey Caister Academic Press, Norfolk, UK. Pages 109-127.

Kiran S, Chatterjee N, Singh S, Kaul SC, Wadhwa R, Ramakrishna G. Intracellular distribution of human SIRT7 and mapping of the nucle(ol)ar localization signal. FEBS J. 2013 May 17. doi: 10.1111/febs.12346. [Epub ahead of print]

Md Khursheed, Jayaprakash N Kolla, Viswakalyan Kotapalli, Neha Gupta, Swarnalata Gowrishankar, Shantveer G Uppin, Regulagadda Sastry, Suman Koganti, Challa Sundaram, Jonathan R Pollack, Murali D Bashyam. ARID1B, a member of the human SWI/SNF chromatin remodeling complex, exhibits tumor suppressor activities in pancreatic cancer cell lines. British journal of cancer, 2013; 108:2056-2062.

Usha R Dutta, Vijaya Kumar Pidugu, Ch Venkateshwar Goud, Christiane Hoefers, Monika Hagemann and Ashwin Dalal (2013). Identification and Molecular Cytogenetic Characterization of a novel complex Y chromosome rearrangement in a boy with disorder of sexual development. GENE 519; 374-380.

Beaulieu ED, Ionescu M, Chatterjee S, Yokota K, Trauner D, Lindow S. (2013). Characterization of a Diffusible Signaling Factor (DSF) from Xylella fastidiosa. Mbio. Vol. 4: e00539-12.

Chatterjee S., PandeyA. (2013). Signaling in plant-microbe interactions. Plant stress Vol. 7: 52-59.

Pradhan BB, Ranjan M, Chatterjee S. (2012). XadM, a novel adhesin of Xanthomonas oryzae pv. oryzae, exhibits similarity to Rhs family proteins and is required for optimum attachment, biofilm formation and virulence. Molecular Plant-Microbe Interactions . Vol. 25: 1157-1170.

Anupam Sinha and H.A.Nagarajaram (2013) Effect of Alternative Splicing on the Degree Centrality of nodes in PPI networks of Homo sapiens J.Proteome Res. 12:1980-1988

Vishal Acharya and H.A.Nagarajaram (2013) Response to: Statistical Analysis of Missense Mutation Classifiers Human Mutat 34 407

Muley VY, Ranjan A (2013) Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways PLOS ONE 10.1371/journal.pone.0054325

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2012

Gowrishankar, J., Krishna Leela, J., and Anupama, K. 2012. R-loops in bacterial transcription: Their causes and consequences. Transcription 4: 153.157.

Krishna Leela, J., Syeda, A.H., Anupama, K., and J. Gowrishankar. 2012. Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli. Proc Natl Acad Sci USA 110: 258-263.

Marbaniang, C.N., and J. Gowrishankar. 2012. Transcriptional Cross-Regulation between Gram-Negative and Gram-Positive Bacteria, Demonstrated Using ArgP-argO of Escherichia coli and LysG-lysE of Corynebacterium glutamicum. J Bacteriol. 194: 5657.5666.

Vijaya kumar Pidugu and Usha R Dutta (2012): Fluorescence in .situ Hybridization: Technology and its application in Molecular Medicine. Journal of Cytology and Genetics, 13, 1-8.

Usha R Dutta, Vijaya kumar P, Ashwin B Dalal. (2012): Molecular and Cytogenetic Characterization of Two Patients with Recurrent miscarriages and X-Autosome Translocation. Journal of Research in Medical Sciences 17; 572-4.

Vineeth VS, Suttur S Malini, Sreenivasa G, Usha R Dutta. (2012): High incidence of sperm dysfunction in a varicocele infertile man: case report. Asia Pacific Journal of Reproduction, vol (1), Number 1, March; 61- 64.

Muley VY, Ranjan A (2012) Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction.PLoS One.7(7):e42057.

Ali J, Thummala SR, Ranjan A (2012) The parasite specific substitution matrices improve the annotation of apicomplexan proteins. BMC Genomics.13 Suppl 7:S19.

Rai, M.N., Balusu, S., Goritala, N., Lakshmi, D., and Kaur, R. (2012) Functional genomic analysis of Candida glabrata-macrophage interaction. Role of chromatin remodeling in virulence. PLoS Pathog. 8: e1002863.

Borah, S., Raju, S. and Kaur, R. (2011) The Rho1 GTPase-activating protein CgBem2 is required for survival of azole stress in Candida glabrata. Journal of Biological Chemistry 286: 34311-34324.

Bairwa, G., Balusu, S., and Kaur, R. (2012) Aspartyl proteases in human pathogenic fungi: roles in physiology and virulence in the book entitled "The Fungal Cell Wall", Ed. Héctor M. Mora-Montes, Nova Science Publishers (In press).

Jadav R.S., Chanduri M.V.L., Sengupta S. and Bhandari R. Inositol Pyrophosphate Synthesis by Inositol Hexakisphosphate Kinase 1 is Required for Homologous Recombination Repair J. Biol. Chem. (2012) doi:10.1074/jbc.M112.396556

Banerjee, R., Nath, S., Ranjan, A., Khamrui, K., Pani, B. Sen, R. and Sen , U. (2012). The first structure of Polarity Suppression protein, Psu from Enterobacteria phage P4, reveals a novel fold and a knotted dimer. Journal of Biological Chemistry. 44667-44675.

Muteeb, G., Dey, D., Mishra, S. and Sen, R. (2012). A multi-pronged strategy by an antiterminator to overcome Rho-dependent termination. Nucleic Acids Research, 40(22), 11213-11228.

Shashni, R., Mishra, S., Kalayani, B. S. and Sen. R. (2012). Suppression of in vivo Rho-dependent transcription termination defects: evidence for kinetically controlled steps. Microbiology, 158:1468 - 1481.

Ramakrishna G, Anwar T, Angara RK, Chatterjee N, Kiran S, Singh S. (2012) Role of cellular senescence in hepatic wound healing and carcinogenesis. European Journal of Cell Biology, 91 (10),739-747.

Y. Akhter, M. T. Ehebauer, S. Mukhopadhyay, and S. E. Hasnain (2012). The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more? Biochimie. 94: 110-116.

Suresh B. Mudunuri, Priyatosh Mishra, and Nagarajaram, H.A. (2012) In Silico Survey of Distribution and Frequency of Imperfect Microsatellite Repeats in Viral Genomes. Proceedings of IEEE International Conference on Data Science & Engineering (ICDSE 2012), Vol. 1, pp. 31-36 (http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6282303)

Patil SJ, Bhat V, Dalal A, Santosh JS. Confirmation of the Zechi-Ceide syndrome. Am J Med Genet A. 2012;158A(6):1467-71

Angalena R, Aggarwal S, Phadke SR, Dalal A. Compound heterozygote condition in beta thalassemia major due to a novel single nucleotide deletion (-T) at codon 69 in association with IVS 1-5 (G>C) mutation. Int J Lab Hematol. 2012 Mar 12 [Epub ahead of print].

Ponnala R, Ranganath P, Dutta UR, Pidugu VK, Dalal AB. Phenotypic and molecular characterization of partial trisomy 2q resulting from insertion-duplication in chromosome 18q: a case report and review of literature. Cytogenet Genome Res. 2012;136(3):229-34.

Muranjan M, Agarwal S, Lahiri K, Bashyam M. Novel biochemical abnormalities and genotype in farber disease. Indian Pediatr. 2012 Apr 8;49(4):320-2.

Pradhan BB, Ranjan M, Chatterjee S. (2012). XadM, a novel adhesin of Xanthomonas oryzae pv. oryzae, exhibits similarity to Rhs family proteins and is required for optimum attachment, biofilm formation and virulence. Molecular Plant-Microbe Interaction .[Pub. ahead of Print. http://dx.doi.org/10.1094/MPMI-02-12-0049-R. posted 05/09/2012]

Murali D Bashyam, Ajay K Chaudhary, Manjari Sinha, H A Nagarajaram, A Radha Rama Devi, Leena Bashyam, E Chandrakanth Reddy, Ashwin Dalal (2012). Molecular genetic analysis of MSUD from India reveals mutations causing altered protein truncation affecting the C-termini of E1α and E1β. Journal of Cellular Biochemistry 113:3122-3132

Bhat KH, Chaytanya CK, Parveen N, Varman R, Ghosh S, Mukhopadhyay S. The PPE protein Rv1168c of Mycobacterium tuberculosis augments transcription from HIV-1 LTR promoter.J Biol Chem. 2012 Mar 15. [Epub ahead of print].

M D Bashyam, A K Chaudhary, E C Reddy, V Reddy, V Acharya, H A Nagarajaram, A R R Devi, L Bashyam, A B Dalal, N Gupta, M Kabra, M Agarwal, S R Phadke, R Tainwala, R Kumar, S V Hariharan. A founder ectodysplasin A receptor (EDAR) founder mutation results in a high frequency of the autosomal recessive form of Hypohidrotic Ectodermal Dysplasia in India. Br J Dermatol.2012; 166:819-829.

Murali Dharan Bashyam, Ajay K Chaudhary, Vijay Bhat. The IVS2+837T>G appears to be a relatively common 'rare' β-GLOBIN gene mutation among β-Thalassemia patients in the South Indian state of Karnataka. Hemoglobin 2012;36(5):497-503.

Ray R, Pradhan BB, Ranjan M, Chatterjee S. (2012). Atypical regulation of virulence associated functions by a Diffusible Signal Factor in Xanthomonas oryzae pv. oryzae. Molecular Plant-Microbe Interaction. Vol.25: 789-801

Pankaj Kumar and H.A.Nagarajaram (2012) A Study on Mutational Dynamics of Simple Sequence Repeats in Relation to Mismatch Repair System in Prokaryotic Genomes J. Mol. Evol. 74 127-139

Suresh B. Mudunuri, Priyatosh Mishra and H.A. Nagarajaram (2012) "Distributional Analysis and Motif Frequencies of Compound Microsatellite Repeats in Viral Genomes.", Proceedings of IEEE International Conference on Computing, Electronics & Electrical Technologies (ICCEET), 2012, vol.1, pp.887-893, 21-22 March 2012.

Vishal Acharya and H.A.Nagarajaram (2012) Hansa: An automated method for discriminating disease and neutral human nsSNPs Hum Mutat 33 332-337

AH Shain, CP Giacomini, K Matsukuma, CA Karikari, MD Bashyam, M Hidalgo, A Maitra, JR Pollack. Convergent structural alterations define SWI/SNF chromatin remodeler as a central tumor suppressive complex in pancreatic cancer. Proc Natl Acad Sci, USA. 2012, 109:E252-E259.

Murali Bashyam, Guroji Purushotham, Ajay K Chaudhary, Madhumohan Rao, Vishal Acharya, Tabrez Mohammad, Hampapatalu Nagarajaram, Vuppaladadhiam Hariram, Calambur Narasimhan. A low prevalence of MYH7/MYBPC3 mutations among Familial Hypertrophic Cardiomyopathy patients in India. Mol Cell Biochem. 2012, 360:373-382.

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2011

Chatterjee N, Kiran S, Ram BM, Islam N, Ramasarma T, Ramakrishna G. Diperoxovanadate can substitute for H(2)O(2) at much lower concentration in inducing features of premature cellular senescence in mouse fibroblasts (NIH3T3). Mech Ageing Dev. 2011 May;132(5):230-9

A Radha Rama Devi, Usha R Dutta. (2012): Ring chromosome 20 associated with refractory epilepsy: case report. Asian Journal of Medical Sciences 2(2011) 141-144.

Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, et al. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania. 2011. American Journal of Human Genetics, Vol. 89(4), Oct 7, 516-528.

Ali J, Paila U, Ranjan A(2011) ApicoAlign: an alignment and sequence search tool for apicomplexan proteins. BMC Genomics 12(Suppl 3):S6.

Almeida RP, Killiny N, Newman KL, Chatterjee S, Ionescu M, Lindow S. (2011) Contribution of rpfB to Cell-cell Signal Synthesis, Virulence, and Vector Transmission of Xylella fastidiosa. Molecular Plant Microbe Interaction. Vol. 25: 453-462.

Anupama, K., Krishna Leela, J., and J. Gowrishankar. 2011. Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol. 82:1330.1348.

Marbaniang, C.N., and J. Gowrishankar. 2011. Role of ArgP (IciA) in lysine-mediated repression in Escherichia coli. J Bacteriol.193: 5985-5996.

Saxena, S., and J. Gowrishankar. 2011a. Modulation of Rho-dependent transcription termination in Escherichia coli by the H-NS family of proteins. J Bacteriol. 193: 3832.3841.

Saxena, S., and J. Gowrishankar. 2011b. Compromised factor-dependent transcription termination in a nusA mutant of Escherichia coli: spectrum of termination efficiencies generated by perturbations of Rho, NusG, NusA, and H-NS family of proteins. J Bacteriol. 193: 3842.3850.

Almeida RP, Killiny N, Newman KL, Chatterjee S, Ionescu M, Lindow S. (2011) Contribution of rpfB to Cell-cell Signal Synthesis, Virulence, and Vector Transmission of Xylella fastidiosa. Molecular Plant Microbe Interaction. 2011 Dec 28. [Epub ahead of print].

Li YR, Zou HS, Che YZ, Cui YP, Guo W, Zou LF, Chatterjee S, Biddle EM, Yang CH, Chen GY. (2011) A novel regulatory role of HrpD6 in regulating hrp-hrc-hpa genes in Xanthomonas oryzae pv. oryzicola. Mol Plant Microbe Interact. 9:1086-101.

Usha R. Dutta , Vijaya Kumar Pidugu, Venkatesh Goud, Ashwin B. Dalal Mosaic Down syndrome with a marker: Molecular cytogenetic characterization of the marker chromosome. Gene. 2011 Dec 28. [Epub ahead of print] PMID:22245181 http://www.ncbi.nlm.nih.gov/pubmed/22245181

Suttur S, Malini, Vijaya Kumar Pidugu, Ashwin B. Dalal, Usha R Dutta. Evaluation of sex chromosomal anomalies in sperms among infertile males by Fluorescence in situ Hybridization. Journal of Cytology & Genetics, vol 12 (NS) 77-84(2011)

Patil SJ, Ponnala R, Shah S, Dalal A. Mosaic Trisomy 9 Presenting with Congenital Heart Disease, Facial Dysmorphism and Pigmentary Skin Lesions: Intricate Issues of Genetic Counseling. Indian J Pediatr. 2011 Oct 6. [Epub ahead of print]

Ponnala R, Dalal A. Partial monosomy 7q. Indian Pediatr. 2011 May 7;48(5):399-401.

Padma Priya T, Dalal AB. Tuberous Sclerosis: Diagnosis and Prenatal Diagnosis by MLPA. Indian J Pediatr. 2011 May 4. [Epub ahead of print]

Kumar R, Panigrahi I, Dalal A, Agarwal S. Sickle Cell Anemia-Molecular Diagnosis and Prenatal Counseling: SGPGI Experience. Indian J Pediatr. 2011 Jun 29. [Epub ahead of print]

Anupam Sinha and H.A.Nagarajaram (2011) Studies on Protein-Protein Interactions: A New Frontier in Computational Biology (key note address) in "Proceedings of 2nd International Conference on Metacomputing 15-16, Dec. 2011, Goa, India" Editor: Dr. P.K.Roy, Allied Publishers Pvt. Ltd., New Delhi.

Md. Tabrez Shamim and H A Nagarajaram (2011) A Hierarchical Approach to Protein Fold Recognition J. Integr. Bioinform. 8:185-, 2011 (online journal http://journal.imbio.de/index.php?paper_id=185)

Md. Tabrez Shamim and Nagarajaram, H.A. (2011) SVM-Based method for protein structural class prediction using secondary structural content and structural information of amino acids J.Bioinform. Comput. Biol 9: 489-502

Pankaj Kumar, P. S. Chitanya and H A Nagarajaram (2011) PSSRdb: A Relational Database of Polymorphic Simple Sequence Repeats Extracted from Prokaryotic Genomes Nucleic Acid Res. 39(suppl 1): D601-D605

Kwei KA, Shain AH, Bair R, Montgomery K, Karikari CA, van de Rijn M, Hidalgo M, Maitra A, Bashyam MD, Pollack JR. SMURF1 Amplification Promotes Invasiveness in Pancreatic Cancer. PLoS One. 2011;6(8):e23924.

Kalyani, B. S., Muteeb, G., Qayyum, M. Z. and Sen, R. (2011). Interaction with the nascent RNA is a pre-requisite for the recruitment of Rho to the transcription elongation complex in vitro. J. Mol. Biol, 413, 548-560.

Swapna, G., Chakraborty A, Kumari, V., Sen, R. and Nagaraja, V. (2011). Mutations in .' subunit of E.coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance. Molecular Microbiology. 80(5):1169-85.

Chalissery, J., Muteeb, G., Nisha C. K., Mohan, S. Jisha, V and Sen, R. (2011). Interaction surface of the transcription terminator Rho required to form a complex with the C-terminal domain of the antiterminator NusG. Journal of Molecular Biology, 405, 49-64.

S. Mukhopadhyay**, S.Nair and S. Ghosh** (2011). Pathogenesis in tuberculosis: transcriptomicapproaches to unraveling virulence mechanisms and finding new drug targets. FEMS Microbiology Reviews (In Press) (**Corresponding Author)

Mahali, S., Raviprakash, N., Manna S.K.* (2011): Advanced glycation end products (AGE) induce apoptosis via a novel pathway: involvement of Ca2+ mediated by interleukin-8. Journal of Biological Chemistry http://www.jbc.org/doi/10.1074/lbc.M111.279190.

Naik, U.S., Gangadharan, C., Abbagani, K., Nagalla, B., Dasari, N., and Manna, S.K.* (2011): A study of nuclear transcription factor kappaB in childhood autism. Plos One 6: e19488.

S. Mukhopadhyay* and K. N. Balaji* (2011). The PE and PPE proteins of Mycobacterium tuberculosis. Tuberculosis (In Press)

A. Das and S. Mukhopadhyay* (2011). The evil axis of obesity, inflammation and type-2 diabetes. Endocrine, Metabolic & Immune Disorders - Drug Targets 11:23-31 (*Corresponding Author)

S. Nair, A. D. Pandey and S. Mukhopadhyay* (2011). The PPE18 protein of Mycobacterium tuberculosis inhibits NF-kB/rel-mediated proinflammatory cytokine production by upregulating and phosphorylating SOCS3 protein. Journal of Immunology 186: 5413-5424 (*Corresponding Author)

Gunnarsdóttir ED, Nandineni MR, et al. Larger mtDNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communications, 2011 Mar; 2:228

Usha R Dutta, Rajitha P, Vijaya kumar P, Ashwin B Dalal. (2011): Cytogenetic abnormalities in 1162 couples with recurrent miscarriages in southern region of India: report and review. Journal of Assisted Reproduction and Genetics (2) 28: 145- 148. (http://www.ncbi.nlm.nih.gov/pubmed/20931274)

Angalena R, Prabitha KN, Chaudhary AK, Bashyam MD, Jain S, Dalal AB. A novel homozygous point mutation at codon 82 (HBB:c.247A > T)) in the beta-globin gene leads to thalassemia major. Int J Lab Hematol. 2010 Oct;32(5):548-549 (http://www.ncbi.nlm.nih.gov/pubmed/20136848)

Usha R Dutta, Rajitha P, Vijaya kumar P, Ashwin B Dalal. (2011): Molecular Cytogenetics Illustrated: SKY and FISH Usha R Dutta, Vijaya Kumar Pidugu, Ashwin B Dalal, Newsletter of Genetics Chapter of Indian Academy of Pediatrics, Vol 4, Issue 1 (Jan-Mar 2011).

Järn Rüssel, Usha Dutta, Dorothea Wand, Dietmar Schlote, Ingo Hansmann. (2009): The 9p24.3 breakpoint of a constitutional t(6;9)(p12;p24) presenting in a patient with chronic lymphocytic leukemia maps close to the putative promoter region of DMRT2 gene. Cytogenetic and Genome Research 125:81-86.

Maddika S@., Kavela S., Rani M., Palicharla VR and Chen J@. WWP2 is an E3 ubiquitin ligase for PTEN. Nature Cell Biol 2011 (In press) [@Equal corresponding author].

Narendra P. Singh, Sri R. Madabhusi, Surabhi Srivastava, R. Senthilkumar, C. Neeraja, Sanjeev Khosla,* and Rakesh K. Mishra,* (2011) Epigenetic profile of the euchromatic region of human Y chromosome. Nucleic Acids Research, doi:10.1093/nar/gkq1342 * corresponding authors

Thiagarajan D, Dev RR, Khosla S (2011) The DNA methyltranferase Dnmt2 participates in RNA processing during cellular stress. Epigenetics 6:103-113.

Bairwa, G. and Kaur, R. (2011) A novel role for a glycosylphosphatidylinositol-anchored aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata. Mol. Microbiol. 79 (4): 900-913.

Yadav, A.K., Desai, P.R., Rai, M.N., Kaur, R., Ganesan, K. and Bachhawat, A.K. (2011) Glutathione biosynthesis in the yeast pathogens Candida glabrata and Candida albicans: Essential in C. glabrata, and essential for virulence in C. albicans. Microbiology 157: 484-495.

Kole, L., Giri, B., Manna S.K., Pal, B., and Ghosh, S. (2011): Biochanin-A, an isoflavon, showed anti-proliferative and anti-inflammatory activities through the inhibition of iNOS expression, p38-MAPK and ATF-2 phosphorylation and blocking NFκB nuclear translocation. European Journal of Pharmacology. 653: 8-15

Majumdar S., Dutta K., Manna S.K. Basu A., and Bishayi B. (2011): Possible protective role of chloramphenicol in TSST-1 and coagulase positive Staphylococcus aureus induced septic arthritis with altered levels of inflammatory mediators. Inflammation 34: 268-281.

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2010

Kaur, R. (2009) Review of: Lilavati’s Daughters: The Women Scientists of India, Edited by Rohini Godbole and Ram Ramaswamy, Indian Academy of Sciences, Bangalore, 2008, 369 pages. Current Science 96: 1137-38.

Subhadeep Chatterjee. 2010. Fatal attraction: bacteria exploit fungal heterokaryon incompatibility to obtain nutrients. Journal of Bioscience. Vol. 35(3): 329-330.

Subhadeep Chatterjee, Killiny S, Almeida RPP and Lindow SE. 2010. Role of Cyclic di-GMP in Xylella fastidiosa Biofilm Formation, Plant Virulence and Insect Transmission. Molecular plant- Microbe Interactions. Vol. 23(10): 1356-1363

Muteeb, G. and Sen, R. (2010). Random mutagenesis using mutator strain. Methods in Molecular Biology, 634, 411-419.

Khamurai, S., Ranjan, A., Pani, B., Sen, R. and Sen, U. (2010) Crystallization and preliminary X-Ray analysis of Psu, an inhibitor of bacterial transcription terminator, Rho. Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 2), 204-6.

Nisha, C. K., Ranjan, A., Kalyani, S., Wal, M. and Sen, R. (2010). A bacterial transcription terminator with inefficient molecular motor action but with a robust transcription termination function. Journal of Molecular Biology, 395, 966-982.

Dalal AB, Sarkar A, Priya TP and Madhusudan R. Nandineni. Giuffrè-Tsukahara syndrome: Evidence for X-linked dominant inheritance and review. American Journal of Medical Genetics, A. 2010 Aug; 152A (8): 2057-60.

Madhusudan R. Nandineni, S.P.R. Prasad, Ch.V. Goud, D.S. Negi, J. Nagaraju and J. Gowrishankar. DNA-based identification of victims of the Mangalore air crash of May 2010. Current Science (2010), 99 (3): 341-342

Manderwad GP, Gokul G, Kannabiran C, Honavar SG, Khosla S, Vemuganti G (2010) Hypomethylation of the DNMT3L Promoter in Ocular Surface Squamous Neoplasia (OSSN). Archives of Pathology & Laboratory Medicine 134:1193-1196.

Suresh B Mudunuri, Pankaj Kumar, Allam Appa Rao, S Pallamsetty and H A Nagarajaram (2010) G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences Bioinformation 5: 221-223

Dalal AB, Sarkar A, Priya TP, Nandineni MR. Giuffr-Tsukahara syndrome: Evidence for X-linked dominant inheritance and review. Am J Med Genet A. 2010;152A(8):2057-60.(http://www.ncbi.nlm.nih.gov/pubmed/20635354)

Priya TP, Philip N, Molho-Pessach V, Busa T, Dalal A, Zlotogorski A. H syndrome: novel and recurrent mutations in SLC29A3. Br J Dermatol. 2010;162(5):1132-4. (http://www.ncbi.nlm.nih.gov/pubmed/20199539)

Agarwal S, Tamhankar PM, Kumar R, Dalal A. Clinical and haematological features in a compound heterozygote (HBB:c.92 + 5G > C/HBB:c.93-2A > C) case of thalassaemia major. Int J Lab Hematol. 2010;32(3):369-72. (http://onlinelibrary.wiley.com/doi/10.1111/j.1751-553X.2009.01157.x/abstract)

Girisha KM, Vahab SA, Dalal AB, Gopinath PM, Satyamoorthy K. Compound heterozygosity for HbD Punjab and polyadenylation signal mutation causes clinically asymptomatic mild hypochromia and microcytosis. Ann Hematol. 2010;89(6):625-6. (http://www.ncbi.nlm.nih.gov/pubmed/19727721)

Padma Priya T, Ashwin Dalal. Triplet Primed PCR (TP-PCR) A Versatile Method For Molecular Diagnosis Of Triplet Repeat Disorders. Newsletter of Genetics Chapter of Indian Academy of Pediatrics, Vol 3, Issue 3 (July-Sept 2010)

Werner J.K. Jr., Speed T. and Bhandari R. Protein pyrophosphorylation by diphosphoinositol pentakisphosphate (InsP7). Methods Mol Biol. (2010) 645, 87-102.

Nirmala Yabaluri* and Murali D Bashyam*. 2010. Hormonal regulation of gluconeogenic gene transcription in the liver. J Biosci 35:473-484 (in press) *shared corresponding authorship.

Bashyam MD, Chaudhary A, Reddy E, RamaDevi A, Savithri G, Ratheesh R, Bashyam L, Mahesh E, Sen D, Puri R, Verma I, Nampoothiri S, Vaidyanathan S, Chandrasekhar M, Kantheti P. 2010. Phenylalanine hydroxylase gene mutations in phenylketonuria patients from India: identification of novel mutations that affect PAH RNA. Mol Genet Metabolism 100:96-99.

Bose S , Sakhuja P, Bezawada L, Agarwal AK, Kazim SN, Khan LA, Sarin SK and Ramakrishna G (2010) Hepatocellular carcinoma with persistent hepatitis B virus infection shows unusual downregulation of Ras expression and differential response to Ras mediated signaling. Journal of Gastroenterologyand Hepatology ( In press)

N. Bashir, F. Kounsar, S. Mukhopadhyay and S. E. Hasnain (2010). Mycobacterium tuberculosis conserved hypothetical protein rRv2626c modulates macrophage effector functions. Immunology 130:34-45.

Manna S.K.*, Bose, J.S., Gangan, V., Raviprakash, N., Navneetha, T., Raghavendra, P.B., Babajan, B., Kumar, C.S., and Jain, S.K. (2010): Novel derivative of benzofuran induces cell death mostly by G2/M cell cycle arrest through p53-dependent pathway but partially by Inhibition of NF-kB. Journal of Biological Chemistry (In press).

Purushotham G, Madhumohan K, Anwaruddin M, Nagarajaram H, Hariram V, Narasimhan C, Bashyam MD. The MYH7 p.R787H mutation causes hypertrophic cardiomyopathy in two unrelated families. Exp Clin Cardiol. 2010 Spring;15(1):e1-4.

K. Alam, S. Ghousunnissa, S, Nair, V. L. Valluri and S. Mukhopadhyay* (2010). Glutathione-redox balance regulates c-rel driven IL-12 production in macrophages: possible implications in anti-tuberculosis immunotherapy. Journal of Immunology, 184:2918-2929.

Manna S.K.*, Babajan, B., Raghavendra, P. B., Raviprakash, N. and Kumar, C. S. (2010): Inhibiting TNF receptor associated factor 2-mediated activation of nuclear factor kappaB facilitates induction of activator protein-1. Journal of Biological Chemistry 285: 11617-11627.

Suresh, B.M, Rao, A.P, Mishra, P. and Nagarajaram, H.A. (2010) . Comparative Analysis of Microsatellite Detecting Software: A Significant Variation in Results and Influence of Parameters, Proceedings of International Symposium on Biocomputing, (ISB 2010), Kerala, February 15-17, 2010. (Link to ACM Digital Library)

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2009

Gokul G, Ramakrishna G, and Khosla S (2009) Reprogramming of HeLa cells upon DNMT3L overexpression mimics carcinogenesis. Epigenetics 4: 322-329.

Kumar R, Tamhankar PM, Panigrahi I, Dalal A , Agarwal S. A novel beta-globin mutation (HBB:c.107A>G; or codon 35 beta (A-->G)) at alpha-beta chain interfaces. Ann Hematol. 2009 ;88(12):1269-71. (http://www.ncbi.nlm.nih.gov/pubmed/19488752)

Ashwin Dalal. Stem cell therapy:Current status. Newsletter of Genetics Chapter of Indian Academy of Pediatrics, Vol 2, Issue 2 (Apr-Jun 2009)

Sowjanya AP, Paul P, Vedantham H, Ramakrishna G, Vidyadhari D, Vijayaraghavan K, Laksmi S, Sudula M, Ronnett BM, Das M, Shah KV, Gravitt PE; Community Access to Cervical Health Study Group. Suitability of self-collected vaginal samples for cervical cancer screening in periurban villages in Andhra Pradesh, India. Cancer Epidemiol Biomarkers Prev. 2009 May;18(5):1373-8

S. Nair, P. A. Ramaswamy, S. Ghosh, D. C. Joshi, N. Pathak, I. Siddiqui, P. Sharma, S. E. Hasnain, S. C. Mande and S. Mukhopadhyay* (2009) The PPE18 of Mycobacterium tuberculosis interacts with TLR2 and activates IL-10 induction in macro-phage. Journal of Immunology, 183:6269-6281.

Raghavendra, P.B., Pathak N., and Manna S. K.* (2009): Novel role of Thiadiazolidine derivatives in inducing cell death through Myc-Max, Akt, FKHR, and FasL pathway. Biochemical Pharmacology 78: 495-503.

Basu D, Khare G, Singh S, Tyagi A, Khosla S, Mande SC (2009) A novel nucleoid-associated protein of Mycobacterium tuberculosis is a sequence homolog of GroEL. Nucleic Acids Res. Jun 15. [Epub ahead of print]

Vinukonda Govindaiah, Shaik Mohammad Naushad, Krishnamurthy Prabhakara Prasad Chintakindi Krishna, Akella Radha Rama Devi. Association of parental hyperhomocysteinemia and C677T Methylenetetrahydrofolate reductase (MTHFR) polymorphism with recurrent pregnancy loss. Clinical Biochemistry 42 (2009) 380.386

Govindaiah Vinukonda , Naushad Shaik Mohammad , Jamal Md Nurul Jain , Krishna Prasad Chintakindi , Radha Rama Devi Akella. Genetic and environmental influences on total plasma homocysteine and coronary artery disease (CAD) risk among South Indians. Clinica Chimica Acta 405 (2009) 127.131

Mohammad, Naushad Shaik; Jain, Jamal Md Nurul; Chintakindi, Krishna Prasad; Singh, Ram Prakash; Naik, Usha; Akella, Radha Rama Devi Aberrations in folate metabolic pathway and altered susceptibility to autism Psychiatric Genetics. 19(4):171-176, August 2009.

Korupolu, R.V., Achary, M.S. , Aneesa, F., Sathish, K., Wasia, R., Sairam, M., Nagarajaram, H.A and Singh, S.S. (2009) Profilin oligomerization and its effect on poly (l-p roline) binding and phosphorylation Int. J.Biol.Macromol. (Accepted)

Suresh B. Mudunuri, Allam Appa Rao, S Pallamsetty, Priyatosh Mishra and H.A.Nagarajaram (2009) VMD: Viral Microsatellite Database - A Comprehensive Resource for All Viral Microsatellites. Journal of Computer Science and Systems Biology. 22: 283-000. doi:10.4172/jcsb.1000043: 001-004

Nonsense -mediated decay: linking a basic cellular process to human disease. Bashyam MD. Expert Rev Mol Diagn. 2009 May;9(4):299-303.

Dalal A, Mehrotra RN (2009). Hypertrichosis, hyperkeratosis and mental retardation syndrome: further delineation of phenotype. Clin Dysmorphol. ;18(2):83-4

Murali D Bashyam, Angalena R, Ajay Chaudhary, Ashwin Dalal. Hemoglobin D (Iran) masquerading as Hemoglobin E: An interesting case report. Newsletter of Genetics Chapter of Indian Academy of Pediatrics, Vol 2, Issue 1 (Jan-Mar 2009)

Murali D Bashyam Senthil Kumar, Aruna Ramachandran and Seyed E Hasnain. (2009). Octamer and heat shock elements regulate transcription from the AcMNPV polyhedrin gene promoter. Arch Virol 154:445-456

Murali D Bashyam. (2009). Studies on nonsense mediated decay reveal novel therapeutic options for genetic diseases. Recent patents on DNA & Gene Sequences 3:7-15

Achary, M.S. and Nagarajaram, H.A. (2009) Effects of Disease Causing Mutations on the Essential Motions in proteins. J. Biomol.Struct.Dyn. 26:609-624

Johny S, Chakraborty S, Gadagkar R and Nagaraju J (2009) Polymorphic microsatellite loci for primitively eusocial wasp Ropalidia marginata. Molecular Ecology Resources 9: 2203-2205.

Arunkumar KP, Mita K and Nagaraju J (2009) Silkworm Z chromosome is enriched in testis-specific genes. Genetics On line March 30: as 10.1534/genetics.108.099994

Pandey RC, Datta D, Mukerjee R, Srinivasan A, Mahalingam S, Sawaya BE. (2009). HIV-1 Vpr: a closer look at the multifunctional protein from the structural perspective. Curr . HIV Res. 7(2) :114-128.

Manna SK and Gangadharan C (2009) Decrease in RelA phosphorylation by inhibiting protein kinase A induces cell death in NF-kappaB-expressing and drug-resistant tumor cells. Molecular Immunology 46: 1340-1350.

Bose JS, Gangan V, Jain SK and Manna SK (2009) Novel caffeic acid ester derivative induces apoptosis by expressing FasL and downregulating NF-kappaB: Potentiation of cell death mediated by chemotherapeutic agents. Journal of Cellular Physiology 218: 653-662.

Bose JS, Gangan V, Jain SK and Manna SK (2009) Downregulation of inflammatory responses by novel caffeine acid ester derivative by inhibiting NF-kappaB. Journal of Clinical Immunology 29: 90-98.

Arunkumar KP, Mita K and Nagaraju J (2009) Silkworm Z chromosome is enriched in testis-specific genes. Genetics On line March 30: as 10.1534/genetics.108.099994

Johny S, Chakraborty S, Gadagkar R and Nagaraju J (2009) Polymorphic microsatellite loci for primitively eusocial wasp Ropalidia marginata. Molecular Ecology Resources 9: 2203-2205.

Pani, B., Ranjan, A. and Sen, R. (2009). Interaction surface of bacteriophage P4 protein Psu required for the complex formation with the transcription terminator Rho. Journal of Molecular Biology. 389. 647-660.

Kumar, S., Balakrishna, K., Agarwal, G. S., Merwyn, S., Rai, G. P., Batra, H. V., Sardesai, A. A., and J. Gowrishankar. 2009. Th1-type immune response to infection by pYV-cured phoP-phoQ null mutant of Yersinia pseudotuberculosis is defective in mouse model. Antonie Van Leeuwenhoek. 95 :91-100

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2008

Subhadeep Chatterjee, Rodrigo P. P. Almeida, and Steven Lindow. 2008. Living in two Worlds:The Plant and Insect Lifestyles of Xylella Fastidiosa. Annu. Rev. Phytopathol. Vol. 46:243-71.

Paila U, Kondam R, Ranjan A(2008) Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome. Nucleic Acids Res. 36 :6664-6675.

Khan N, Alam K, Mande SC, Valluri VL, Hasnain SE and Mukhopadhyay S (2008). Mycobacterium tuberculosis heat shock protein 60 modulates immune response to PPD by manipulating the surface expression of TLR2 on macrophages. Cellular Microbiology. 10: 1711-1722.

Akif Mohd, Khare G, Tyagi AK, Mande SC and Sardesai AA (2008)Functional studies on multiple thioredoxins from Mycobacterium tuberculosis. J. Bacteriol. 190: 7087- 7095.

Kumar P, Issac B, Dodson EJ, Turkenburg JP and Mande SC (2008) Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein. J. Mol. Biol. 383: 482- 493.

Hegde S, Manimaran P and Mande SC (2008) Dynamic changes in protein functional linkage networks revealed by integration with gene expression data. PLoS Comput. Biol. 4: e1000237.

Naushad SM, Jain Jamal MN, Prasad CK, Rama Devi AR (2008). Relationship between methionine synthase, methionine synthase reductase genetic polymorphisms and deep vein thrombosis among South Indians. Clin Chem Lab Med 46(1):73-79.

K Prabhakara, Damien L Bruno, Priya Padman, Suma Prasad, R Sudheer Kumar, Howard R Slater, A Radha Ramadevi (2008). Prenatal detection of deletion-duplication of chromosome 3 arising from meiotic recombination of familial pericentric inversion. Prenat Diag 28(5):466-8

Kevin A. Kwei*, Murali D. Bashyam*#, Jessica Kao, Raman Ratheesh, Edumakanti C. Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon-La Choi, Sreejata Chatterjee, Collins A. Karikari, Keyan Salari, Pei Wang, Tina Hernandez-Boussard, Gowrishankar Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack. (2008) Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer. PLOS Genet 4:e100081 (*shared first authorship and senior authorship).

Achary, M.S. and Nagarajaram, H.A. (2008) Comparative docking studies of CYP1b1 and its PCG associated mutant forms. Journal of Biosciences. 33:699-713

Srinivasan A, Ayyavoo V, Mahalingam S, Kannan A, Boyd A, Datta D, Kalyanaraman VS, Cristillo A, Collman RG, Morellet N, Sawaya BE, Murali R. (2008) A comprehensive analysis of the naturally occurring polymorphisms in HIV-1 Vpr: potential impact on CTL epitopes. Virol J. 5:1-17

Arunkumar KP, Kifayathullah L, Nagaraju J (2008) Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera). Molecular Ecology Resources 9: 268-270.

Mrinal N and Nagaraju J (2008) Intron loss is associated with gain of function in the evolution of the gloverin family of antibacterial genes in Bombyx mori. Journal of Biological Chemistry 283: 23376-23387.

Kanginakudru S, Metta M, Jakati RD, Nagaraju J (2008) Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evolutionary Biology 8:174.

Arunkumar KP, Tomar A, Daimon T, Shimada T, Nagaraju J (2008) WildSilkbase: An EST database of wild silkmoths. BMC Genomics 9: 338.

Singh J and Nagaraju J (2008) In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum). Insect Molecular Biology 17: 427-436.

Komissarova, N., Velikodvorskaya, T., Sen, R. King, R. A., Banik-Maiti, S. and Weisberg, R. A. (2008). Inhibition of a Transcriptional Pause by RNA Anchoring to RNA polymerase. Molecular Cell, 31, 683-694****.

Dutta, D., Chalissery, J. and Sen, R. (2008). Transcription termination factor Rho prefers catalytically active elongation complex for releasing RNA. Journal of Biological Chemistry, 283(29), 20243-20251.

Bhandari R***, Juluri KR, Resnick AC and Snyder SH (2008) Gene deletion of inositol hexakisphosphate kinase 1 reveals inositol pyrophosphate regulation of insulin secretion, growth, and spermiogenesis. Proceedings of the National Academy of Sciences of the USA 105: 2349-2353

Draskovic P, Saiardi A, Bhandari R***, Burton A, Ilc G, Kovacevic M, Snyder SH and Podobnik M (2008) Inositol hexakisphosphate kinase products contain diphosphate and triphosphate groups. Chemistry and Biology 15: 274-286

Ponnusamy S, Alderson NL, Hama H, Bielawski J, Jiang JC, Bhandari R***, Snyder SH, Jazwinski SM and Ogretmen B (2008) Regulation of telomere length by fatty acid elongase 3 in yeast: Involvement of inositol phosphate metabolism and ku70/80 function. Journal of Biological Chemistry 283: 27514-27524
(***Work done elsewhere)

Khan N, Alam K, Nair S, Valluri VL, Murthy KJR and Mukhopadhyay S. (2008). Strong immune responses to the PPE protein Rv1168c are associated with active tuberculosis disease. Clinical and Vaccine Immunology 15:974-980

Hussain MA, Naveed SA, Sechi LA, Ranjan, Alvi A, Ahmed I, Ranjan A, Mukhopadhyay S, and Ahmed N. (2008). Isocitrate dehydrogenase of Helicobacter pylori potentially induces humoral immune response in subjects with peptic ulcer disease and gastritis. PLoS ONE. 3:e1481.

Tundup, N. Pathak, M. Ramanadham, S. Mukhopadhyay, K. J. Murthy, N. Z. Ehtesham, and S. E. Hasnain (2008). The co-operonic PE25/PPE41 protein complex of Mycobacterium tuberculosis elicits increased humoral and cell mediated immune response. PLoS ONE. 3:e3586.

Sowpati DT, Thiagarajan D, Sharma S, Sultana H, John R, Surani A, Mishra RK, Khosla S. (2008). An intronic DNA sequence within the mouse Neuronatin gene exhibits biochemical characteristics of an ICR and acts as a transcriptional activator in Drosophila.Mech Dev. 125:963-973.

Paila U, Kondam R and Ranjan A (2008) Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome. Nucleic Acids Res., 36: 6664 - 6675.

Rajesh V, Singamsetti VK, Vidya S, Gowrishankar M, Elamaran M, Tripathi J, Radhika NB, Kochar D, Ranjan A, Roy SK, and Das A.(2008) Plasmodium falciparum: genetic polymorphism in apical membrane antigen-1 gene from Indian isolates. Exp. Parasitol. 119:144-151.

Vindal V, Ashwantha Kumar E, and Ranjan A (2008) Identification of operator sites within the upstream region of the putative mce2R gene from mycobacteria. FEBS Lett. 582:1117-1122.

( Subhadeep Work done elsewhere)

Subhadeep Chatterjee ***, Karyn L. Newman, and Steven E. Lindow. 2008. Cell-cell signaling in Xylella fastidiosa suppresses movement and xylem vessel colonization in grape Molecular Plant-Microbe Interactions.Vol. 21(10): 1309-1315.

Subhadeep Chatterjee***, Rodrigo P. P. Almeida, and Steven Lindow. 2008. Living in two Worlds:The Plant and Insect Lifestyles of Xylella Fastidiosa. Annu. Rev. Phytopathol. Vol. 46:24371

Subhadeep Chatterjee***, Christina Wistrom, and Steven E. Lindow. 2008. A cell-cell signaling sensor is required for virulence and insect transmission of Xylella fastidiosa. Proc Natl Acad Sci USA. Vol.105(7), pp2670-2675.

*** (This article was highlighted in the perspective in Science Magazine - Signaling [Science Signaling 1 (21), pe23. [DOI: 10.1126/stke.121pe23])

Karyn L. Newman#, Subhadeep Chatterjee # Kimberly A. Ho, and Steven E. Lindow. 2008. Virulence of Plant Pathogenic Bacteria Attenuated by Degradation of Fatty Acid Cell-to-Cell Signaling Factors Molecular Plant-Microbe Interactions. Vol. 21(3): pp. 326-334.

(# Equal contribution first author)

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2007

Akhtar Y, Ahmed I, Devi SM and Ahmed N (2007). The co-evolved Helicobacter pylori and gastric cancer: Trinity of bacterial virulence, host susceptibility and lifestyle. Infectious Agents and Cancer 2:2.

Archak S, Meduri E, Kumar PS and Nagaraju J (2007) InSatDb: a microsatellite database of fully sequenced insect genomes. Nucleic Acids Research 35:D36-D39.

Khan N, Ghousunnissa S, Jegadeeswaran SM, Thiagarajan D, Hasnain SE and Mukhopadhyay S (2007) Anti-B7-1/B7-2 antibody elicits innate-effector responses in macrophages through NF-kB-dependent pathway. International Immunology 19:477-486.

Meglecz E, Anderson SJ, Bourguet D, Butcher R, Caldas A, Cassel-Lundhagen A, d'Acier AC, Dawson DA, Faure N, Fauvelot C, Franck P, Harper G, Keyghobadi N, Kluetsch C, Muthulakshmi M, Nagaraju J, Patt A, Petenian F, Silvain JF and Wilcock HR (2007) Microsatellite flanking region similarities among different loci within insect species. Insect Molecular Biology 16:175-185.

Naushad SM, Jamal NJ, Angalena R, Prasad CK, and Devi AR (2007) Hyperhomocysteinemia and the compound heterozygous state for methylene tetrahydrofolate reductase are independent risk factors for deep vein thrombosis among South Indians. Blood Coagulation & Fibrinolysis 18:113-117.

Raghavendra PB, Sreenivasan Y, and Manna S, K. (2007): Oleandrin induces apoptosis in human, but not in murine cells: dephosphorylation of Akt, expre ssion of FasL, and alteration of membrane fluidity. Mol Immunol. 44:2292-2302

Sreenu VB, Kumar P, Nagaraju J and Nagarajaram HA (2007) Simple sequence repeats in mycobacterial genomes Journal of Biosciences 32:1-15.

Vidyasagar M, Hasnain SE, Mande SC, Nagarajaram HA, Ranjan A, Acharya MS, Anwaruddin, Arun SK, Gyanrajkumar, Kumar D, Priya S, Ranjan S, Reddi BR, Seshadri J, Sravan Kumar P, Swaminathan S, Umadevi P and Vindal V (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry- academia collaboration) Current Science 92:29-38.

Ahmed N, Majeed AA, Ahmed I, Hussain MA, Alvi A, Devi SM, Rizwan M, Ranjan A, Sechi LA, and Megraud F (2007) genoBASE pylori: A genotype search tool and database of human gastric pathogen Helicobacter pylori. Infection Genetics and Evolution. 7(4):463-8.

Archak S, Reddy VLN and Nagaraju J (2007) High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis: 28, 2396-2405

Banerjee S, Nandyala AK, Raviprasad P, Ahmed N and Hasnain SE (2007) Iron dependent Iron binding activity of Mycobacterium tuberculosis aconitase. Journal of Bacteriology. 189(11):4046-52.

M D Bashyam A RadhaRama Devi, C K Reddy and S Ranjan. 2007. Molecular genetic analysis of Hypohidrotic Ectodermal Dysplasia patients from India reveals novel mutations in the EDA and EDAR genes. Br J Dermatol 158:163-167.

Bashyam M. D. and S. E. Hasnain.; Array-based Comparative Genomic Hybdidization: applications in cancer and tuberculosis; in Bioarrays, Ed K Appasani, Humana Press, 2007,pp 107-121.

M D Bashyam, G R Savithri, M Gopikrishna, C Narasimhan. 2007. A p.R870H mutation in the beta cardiac myosin heavy chain 7 gene causes Familial Hypertrophic Cardiomyopathy in several members of an Indian family. Canad J Cardiol. 23:788-790.

Boddupalli CS, Ghosh S, Rahim SS, Nair S, Ehtesham NZ, Hasnain SE and Mukhopadhyay S (2007) Nitric oxide inhibits interleukin-12 p40 through p38 MAPK-mediated regulation of calmodulin and c-rel. Free Radical Biology and Medicine. 42: 686-697

Chalissery J, Banerjee, S, Bandey I and Ranjan Sen (2007) Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex. Journal of Molecular Biology.

Gandhe AS, Gude J and Nagaraju J (2007) Immune upregulation of novel anti-bacterial proteins from silkmoths (Lepidoptera) that resemble lysozymes but lack muramidase activity. Insect Biochemistry and Molecular Biology. 37: 655-66.

Gokul G, Gautami B, Malathi S, Sowjanya A, Poli U, Jain M, Ramakrishna G and Khosla S (2007) DNA methylation profile at the DNMT3L promoter: a potential biomarker for cervical cancer. Epigenetics.

Goyal K, Mohanty D and Mande SC (2007) PAR-3D: A server to predict protein active site residues. Nucleic Acids Research. 35: W503-505.

** Kaur R, Ma B and Cormack BP (2007) A family of aspartyl proteases is required for virulence of Candida glabrata. Proceedings of the National Academy of Sciences, USA. 104:7628-33 (*** work done from elsewhere)

Kumari G, Singhal PK, Rao MR, Mahalingam S (2007) Nuclear transport of Ras-associated tumor suppressor proteins: Different transport receptor binding specificities for arginine-rich nuclear targeting signals. Journal of Molecular Biology

Laishram RS and Gowrishankar J (2007) Environmental regulation operating at the promoter clearance step of bacterial transcription. Genes & Development.

Manna SK, Aggarwal RA, Sethi G, Aggarwal BB and Ramesh GT (2007) Morin (3,5,7,2',4'-pentahydroxyflavone) abolishes NF-kB activation induced by various carcinogens and inflammatory stimuli, leading to suppression of NF-kB-regulated gene expression and upregulation of apoptosis. Clinical Cancer Research.

Mukhopadhyay S, Nair S and Hasnain SE (2007) Nitric oxide: Friendly rivalry in tuberculosis. Current Signal Transduction Therapy : 2: 121-28

Rasheedi S, Aruna R, Nasreen ZE and Hasnain SE (2007) Biochemical characterization of Sf9 Sp family-like protein factors reveals interesting features. Archives of Virology.

Rasheedi S, Ghosh S, Suragani M, Tuteja N, Sopory SK, Hasnain, S E, Nasreen, Z E (2007) Pisum sativum Contains A Factor With Strong Homology to CIF5B. Gene.

Sailu Y, Goyal K and Mande SC (2007) Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data. Genome Research. 17: 527- 535.

Salih B, Abasiyanik F, Ahmed N (2007). A preliminary study on the genetic profile of cag pathogenicity island and other virulent gene loci of Helicobacter pylori strains from Turkey. Infection Genetics and Evolution.

Savitri S, Aparna D, Prashanth K, Justine KP, Ahmed N, Prashan K, Das T and Hasnain S E (2007) High-resolution genome profiling differentiated Staphylococcus epidermidis strains from patients with ocular infections and normal individuals: A Pilot study. Journal of Clinical Microbiology.

Sechi LA, Ruhel A, Ahmed N, Usai D, Paccagnini D, Felis G and Zannetti S (2007) Mycobacterium avium subspecies paratuberculosis is able to infect and persist in enteric glial cells. World Journal of Gastroenterology. 13 (43):5731-5.

DGC Terrance, Thangamani A., and Varsha srivasatava. (2007) Study of DNA variation in three breeds of European rabbit. DNA and Cell Biology 26(7): 505-515.

Suresh BM and Nagarajaram HA (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics.23: 1181-1187.

Vindal V, Ranjan S and Ranjan A (2007) In silico analysis and characterization of GntR family of regulators from Mycobacterium tuberculosis. Tuberculosis.87:242-247

Yusuf A, Smanla T and Hasnain SE (2007) Novel Biochemical Properties of a CRP/FNR Family Transcription Factor from Mycobacterium tuberculosis. International Journal of Medical Microbiology.

Cheeran, A., Kolli, N. and Sen, R. (2007). The Site of Action of the Antiterminator Protein N from the Lambdoid Phage H-19B. Journal of Biological Chemistry, 282(42), 30997-31007.

Md Tabrez A S, Moahmmad Anwaruddin and Nagarajaram H A (2007) Support vector machine based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs. Bioinformatics. 23: 3320-3327.

K. Goyal and S. C. Mande. (2007) Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins Struct Funct Bioinform. In press.

Sechi LA, Felis GE, Ahmed N, Paccagnini D, Usai D, Ortu S, Molicotti P, Zanetti S. (2007) Genome and transcriptome scale portrait of sigma factors in Mycobacterium avium subsp. paratuberculosis. Infect Genet Evol. 2007 Jul; 7(4):424-32.

Devi SM, Ahmed I, Francalacci P, Hussain MA, Akhter Y, Alvi A, Sechi LA, Megraud F, Ahmed N. (2007) Ancestral European roots of Helicobacter pylori in India. BMC Genomics. 20;8:184.

Duggirala A, enchappa P, Sharma S, Peeters JK, Ahmed N, Garg P, Das T, Hasnain SE (2007) High-resolution genome profiling differentiated Staphylococcus epidermidis isolated from patients with ocular infections and normal individuals. Invest Ophthalmol Vis Sci. 48(7):3239-45.

Talwar GP, Ahmed N, Saini V. (2007) The use of the name Mycobacterium w for the leprosy immunotherapeutic bacillus creates confusion with M. tuberculosis-W Beijing strain): A suggestion. Infect Genet Evol. 26; [Epub ahead of print] In Press

Ahmed N, Saini V, Raghuvanshi S, Khurana JP, Tyagi AK, Tyagi AK, Hasnain SE. Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into mycobacterium evolution. PLoS ONE. 2(10):e968

Gandhe, A S., John, S H and Nagaraju, J. Noduler, A novel immune upregulated protein mediates nodulation response in insects. Journal of Immunology 2007 (In press)

Biju, S D., Bocxlaer, I V., Giri, V B., Roelants, K., Nagaraju, J and Bossuyt, F. (2007) A new nightfrog, Nyctibatrachus minimus sp. nov. (Anura: Nyctibatrachidae): The smallest frog from India. Current Science. 93: 854-858

Reddy, V L N., Archak, S and Nagaraju, J. (2007) Capillary Electrophoresis is essential for microsatellite marker based detection and quantification of adulteration of basmati rice (Oryza sativa). Journal of Agricultural and Food Chemistry. 55: 8112-8117.

Kanginakudru, S., Royer, C., Edupalli S V., Jalabert, A., Mauchamp, B., Chandrashekaraiah, Prasad, S V., Chavancy, G., Couble, P and Nagaraju, J. (2007) Targeting ie-1 gene by RNAi induces baculoviral resistance in lepidopteran cell lines and in the transgenic silkworms. Insect Molecular Biology. 16: 635-44

Archak S and Nagaruju J (2007) Computational prediction of rice (Oryza sativa) miRNA targets. Genomics Proteomics and Bioinformatics (In press)

Ravi Kumar A, Satish V, Balakrish Nair G, Nagaraju J (2007) Genetic charecterization of Virbio chlerae strains by inter simple sequence repeat-PCR. FEMS microbiology letters 272: 251 - 258

Book Chapter
Bashyam MD and Hasnain SE (2007) Array-based comparitive Genomic Hybridization: applications in cancer and tuberculosis. Bioarrays, Ed. K Appasani, Humana press.

Sen R, Chalissery J and Muteeb G (2007). Nus factors of Escherichia coli. Invited chapter of the book Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM press.

Top

2006
Sander Granneman, ChieYu Lin, Erica A. Champion, Madhusudan R. Nandineni, Cornelia Zorca and Susan J. Baserga. The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis. Nucleic Acids Research (2006), 34: 3189-3199.

Manna S. K., Manna P., and Sarkar A. (2006): Inhibition of RelA phosp horylation sensitizes chemotherapeutic agents-mediated apoptosis in constitutive NF-kappaB-expressing and chemoresistant cells. Cell Death & Differentiation 2006 Apr 28; [Epub ahead of print] PMID: 16645640 [PubMed - as supplied by publisher]

Manna S. K., Rangasamy T., Wise K., Sarkar S., Shishodia S., Biswal S., and Ramesh G. T. (2006): Environmental Tobacco Smoke Activates Nuclear Transcription Factor kappa B, Activator Protein-1, and Stress Responsive Kinases in Mouse Brain. Biochemical Pharmacology 71(11):1602-1609.

Sarkar S., Wise K. C., Manna S. K., Ramesh V., Yamauchi K., Thomas R. L., Wilson B. L., Kulkarni A. D., Pellis N. R., and Ramesh G. T. (2006): Activation of activator protein-1 in mouse brain regions exposed to stimulated microgravity. In Vitro Cellular & Developmental Biology – Animal 42(3): 96-99. <>

Manna S. K., Sarkar, A., and Sreenivasan, Y. (2006): alpha-Melanocyte Stimulating Hormone downregulates CXC receptors through activation of neutrophil elastase. European Journal of Immunolog36(3): 754-769.

Archana S Gandhe, Arunkumar KP, Serene H John, Nagaraju J (2006) Analysis of bacteria-challenged wild silkmoth, Antheraea mylitta (Lepidoptera) transcriptome reveals potential immune genes. BMC Genomics 7:184

Gutierrez MC, Ahmed N (joint first authors), Willery E, Narayanan S, Hasnain SE, Chauhan DS, Katoch VM, Vincent V, Locht C and Supply P (2006) Predominance of ancestral lineages of Mycobacterium tuberculosis in India suggests an ancient focus of tuberculosis in South Asia. Emerging Infectious Dis (Accepted).

MD Bashyam, A RadhaRama Devi, M Gopikrishna, R Ratheesh, G Savithri and G Swarnalata. (2006). Farber lipogranulomatosis-clinical and molecular genetic analysis reveals a novel mutation In an Indian family. J Hum Genet. (In press).

Banerjee S, Chalissery J, Bandey I and Sen R(2006) Rho-dependent transcription termination. More questions than answers. Journal of Microbiology 44:11-22.

Du X, Subba Rao, MRK, Xue Qin Chen, Wei Wu, Mahalingam S and Balasundaram D (2006) The homologous putative GTPases Grn1p from fission yeast and the human GNL3L are required for growth and play a role in processing of nucleolar pre-rRNA. Molecular Biology of the Cell 17; 460-474.

Kazim SN, Sarin SK, Sharma BC, Khan LA, Hasnain SE (2006) Characterization of naturally occurring and Lamivudine-induced surface gene mutants of hepatitis B virus in patients with chronic hepatitis B in India. Intervirology 49:152-160.

Khan N, Rahim SS, Boddupalli CS, Ghousunnissa S, Padma S, Pathak N, Thiagarajan D, Hasnain SE, Mukhopadhyay S (2006) Hydrogen peroxide inhibits IL-12 p40 induction in macrophages by inhibiting c-rel translocation to the nucleus through activation of calmodulin protein. Blood 107:1513-1520.

Kenchappa P, Duggirala A, Ahmed N, Pathengay A, Das T and Hasnain SE (2006) Fluorescent amplified fragment length polymorphism (FAFLP) genotyping demonstrates the role of biofilm-producing methicillin-resistant periocular Staphylococcus epidermidis strains in postoperative endophthalmitis. BMC Ophthalmology 6: 1.

Manna SK, Sarkar A and Sreenivasan Y (2006) α-Melanocyte Stimulating Hormone downregulates CXC receptors through activation of neutrophil elastase. European Journal of Immunology 36: 754-769.

Manna SK, Sreenivasan Y and Sarkar A (2006) Cardiac glycoside inhibits IL-8-induced biological responses by downregulating IL-8 receptors through altering membrane fluidity. Journal of Cell Physiology 207:195-207.

Manna SK, Rangasamy T, Wise K, Sarkar S, Shishodia S, Biswal S and Ramesh GT (2006) Environmental tobacco smoke activates nuclear transcription factor kappa B, activator protein-1, and stress responsive kinases in mouse brain. Biochemical Pharmacology 71: 1602-1609.

Radha Rama Devi A, Naushad S M and Krishna Prasad C (2006) Evaluation of total plasma homocysteine in Indian newborns using heel-prick samples. Indian Journal of Pediatrics 73: 21-26.

Ramasarma T and Rao AV (2006) Decavanadate interacts with microsomal NADH oxidation system and enhances cytochrome C reduction. Molecular and Cellular Biochemistry 281: 139-144.

Rao KR, Ahmed N, Sriramula S, Sechi LA and Hasnain SE (2006) Rapid identification of Mycobacterium tuberculosis Beijing genotypes on the basis of the mycobacterial interspersed repetitive unit locus 26 signature. Journal of Clinical Microbiology 44:274-277.

Rao KR, Kauser F, Sriramula S, Sechi LA, Ahmed N and Hasnain SE (2006) Analysis of genomic downsizing on the basis of region-of-difference polymorphism profiling of Mycobacterium tuberculosis patient isolates reveals geographic partitioning. Journal of Clinical Microbiology 43:5978-5982.

Sechi LA, Ahmed N, Felis GE, Dupre I, Cannas S, Fadda G, Bua A and Zanetti S (2006) Immunogenicity and cytoadherence of recombinant heparin binding haemagglutinin (HBHA) of Mycobacterium avium subsp. paratuberculosis: Functional promiscuity or a role in virulence? Vaccine 24:236-243.

Sechi LA, Mara L, Cappai P, Frothingam R, Ortu S, Leoni A, Ahmed N and Zanetti S (2006) Immunization with DNA vaccines encoding different mycobacterial antigens elicits a Th1 type immune response in lambs and protects against Mycobacterium avium subspecies paratuberculosis infection. Vaccine 24:229-235.

Singhal PK, Rajendra Kumar P, Subba Rao MRK, Mahesh Kyasani and Mahalingam S. (2006) Simian Immunodeficiency Virus Vpx is imported into the nucleus via importin alpha dependent and independent pathways. Journal of Virology 80: 526-536.

Sreenu VB, Kumar P, Nagaraju J and Nagarajaram H A (2006) Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity. BMC Genomics 7:78.

Tundup S, Akhter Y, Thiagarajan D and Hasnain SE (2006) Clusters of PE and PPE genes of Mycobacterium tuberculosis are organized in operons: evidence that PE Rv2431c is co-transcribed with PPE Rv2430c and their gene products interact with each other. FEBS Letters 580:1285-1293.

Varsha (2006) DNA fingerprinting in criminal justice system: An overview. DNA and Cell Biology 25: 181-188.

Vijaykrishnan S, Qamra R, Verma C, Sen R and Mande SC (2006) Cation-mediated interplay of loops in Mycobacterium tuberculosis Chaperonin-10. Journal of Biomolecular and Structural Dynamics 23: 365-37.

Arunkumar KP, Metta M and Nagaraju J (2006) Molecular phylogeny of silkmoths reveals the origin of domesticated silkmoth, Bombyx mori from Chinese B. mandarina and paternal inheritance of Antheraea proylei mitochondrial DNA. Molecular Phylogenetics and Evolution.

Khurad AM, Kanginakudru S, Qureshi SO, Rathod MK, Rai MM and Nagaraju J (2006) A new Bombyx mori larval ovarian cell line highly susceptible to nucleopolyhedrovirus. Journal of Invertebrate Pathology.

Johny S, Kanginakudru S, Muralirangan MC and Nagaraju J (2006) Morphological and molecular characterization of a new microsporidian (Protozoa: Microsporidia) isolated from Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae). Parasitology.

Manna SK, Manna P and Sarkar A (2006) Inhibition of RelA phosphorylation sensitizes chemotherapeutic agents-mediated apoptosis in constitutive NF-kappaB-expressing and chemoresistant cells. Cell Death & Differentiation

Negi DS, Alam M, Bhavani SA and Nagaraju J (2006) Multi-step microsatellite mutation in the maternally transmitted locus D13S317: A case of maternal allele mismatch in the child. International Journal of Legal Medicine.

Pani, B., Banerjee, S., Chalissery,J., Abhishek, M., Ramya, M. L., Suganthan, R. and Sen, R. (2006). Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein Psu. Journal of Biological Chemistry.

Qamra R, Prakash P, Aruna B, H asnain SE and Mande SC (2006) A crystal structure of Mycobacterium tuberculosis chorismate mutase reveals an unexpected gene duplication, and suggest a role in host-pathogen interactions. Biochemistry

Ranjan S, Seshadri J, Vindal V. Yellaboina S and Ranjan A (2006) iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species. Nucleic Acids Research

Ranjan S, Yellaboina S and Ranjan A (2006) IdeR: From target recognition to physiological functions. Critical Reveiws in Microbiology
Sarkar S, Wise KC, Manna SK, Ramesh V, Yamauchi K, Thomas RL, Wilson BL, Kulkarni AD, Pellis NR and Ramesh GT (2006) Activation of activator protein-1 in mouse brain regions exposed to stimulated microgravity. In Vitro Cell Developmental Biology – Animal

Yellaboina S, Ranjan S, Vindal V and Ranjan A (2006) Comparative analysis of iron regulated genes in mycobacteria. FEBS Letters

Bashyam MD and Hasnain SE (2006) Array-based comparitive genomic hybridization: applications in cancer and tuberculosis. Bioarrays, Ed. K Appasani, Humana press.

Devi SM, Ahmed I, Khan AA, Rahman SA, Alvi A, Sechi LA and Ahmed N (2006). Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island. BMC Genomics 7(1):191.

M.S. Achary, A. B.M. Reddy, S. Chakrabarti , S.G. Panicker, A.K. Mandal, N.Ahmed, D. Balasubramanian, S.E. Hasnain, and Nagarajaram HA (2006) Disease Causing Mutations in Proteins: Structural Analysis of the CYP1b1 Mutations Causing Primary Congenital Glaucoma in Humans. Biophysical Journal. (In Press).

Book Chapter
Madhusudan R. Nandineni. Annual Review of Genomics and Human Genetics (2005). Current Science (2006), 91: 1413-1415.

Top

2005

Kaur, R., Domergue, R., Zupancic, M. and Cormack, B.P. (2005) A yeast by any other name: Candida glabrata and its interaction with the host. Current Opinion in Microbiology 8: 378-384

Sander Granneman, Madhusudan R. Nandineni and Susan J. Baserga. The putative ATPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14. Molecular and Cellular Biology (2005), 25: 10352-10364.

Subhadeep Chatterjee* and Ramesh V. Sonti. 2005. Virulence deficiency caused by a transposon insertion in the purH gene of Xanthomonas oryzae pv. oryzae. Canadian Journal of Microbiol. Vol. 51, 575-581.

* (Corrosponding author).

H.A.Nagarajaram ,Prathima Iengar and Indira Ghosh (2005) In silico approach to antimalarial drug discovery: Design of selective inhibitor to Plasmodium falciparum aspartic proteases Frontiers in Biophysics 168-181.

Ahmed N (2005) 23 years of the discovery of Helicobacter pylori: Is the debate over? Annals Clinical Microbiology and Antimicrobials 4:17. (Editorial)

Ali SM, Khan AA, Tiwari SK, Ahmed N, Rao LV and Habibullah CM (2005) Association between Cag-pathogenicity island in Helicobacter pylori isolates from peptic ulcer, gastric carcinoma and non-ulcer dyspepsia subjects with histological changes. World Journal of Gastroenterolgy 11: 6815-6822

Ali SM, Khan AA, Ahmed I, Musaddiq M, Ahmed KS, Polasa H, Rao LV, Habibullah CM, Sechi LA and Ahmed N (2005) Antimicrobial activities of eugenol and cinnamaldehyde against the human gastric pathogen Helicobacter pylori. Annals of Clinical Microbiology and Antimicrobials 4: 20

Akif M, Suhre K, Verma C and Mande SC (2005) Conformational flexibility of M. tuberculosis thioredoxin reductase: crystal structure and normal mode analysis. Acta Crystallogaphica D61:1603 -1611

Banerjee S, Nandyala A, Podili R, Katoch VM and Hasnain SE (2005) Comparison of Mycobacterium tuberculosis isocitrate dehydrogenases (ICD-1 and ICD-2) reveals differences in coenzyme affinity, oligomeric state, pH tolerance and phylogenetic affiliation. BMC Biochemistry 6: 20

Cheeran A, Suganthan R, Swapna G, Bandey I, Acharya S, Nagarajaram HA and Sen R (2005) E.coli RNA polymerase mutations impaired for H 19B N specific transcription antitermination are located close to the upstream edge of 7RNA:DNA hybrid and beginning of RNA exit channel of elongation complex. Journal of Molecular Biology 352: 28-43

Deshpande A, Nimsadkar S and Mande SC (2005) Effect of alcohols on protein hydration: Crystallographic analysis of hen egg white lysozyme in presence of alcohols. Acta Crystallogaphica D61:1005-1008

Habibullah CM, Habeeb MA and Ahmed N. (2005) Helicobacter pylori: Eradicate or not? Indian Journal of Medical Research (Editorial) 122:93-95

Kauser F, Hussain MA, Ahmed I, Srinivas S, Devi M, Majeed AA, Rao KR, Khan AA, Sechi LA and Ahmed N (2005) Comparing genomes of Helicobacter pylori isolates recovered from ulcer disease patients in England. BMC Microbiology 5:32

Kenchappa P, Sangwan VS, Ahmed N, Rao KR, Pathengay A, Mathai A, Mansoori T, Das T, Hasnain SE and Sharma S (2005) High-resolution genotyping of Pseudomonas aeruginosa strains linked to acute post cataract surgery endophthalmitis outbreaks in India. BMC Annals of Clinical Microbiology and Antimicrobials. 4; 19

Manna SK, Sarkar S, Barr J, Wise K, Barrera EV, Jejelowo O, Rice-Ficht AC and Ramesh GT (2005) Single walled carbon nanotube induces oxidative stress and activates nuclear transcription factor-kB in human keratinocytes. Nano Letters 5: 1676-84

Manna SK, Felix K, Wise K, Barr J and Ramesh GT (2005) Low levels of arsenite activates nuclear factor-kappa B and activator protein-1 in immortalized mesencephalic cells. Journal of Biochemical and Molecular Toxicology 19: 67-77

Marec F, Neven L G, Robinson A S, Vreysen M,. Goldsmith M R, Nagaraju J and Franz G (2005) Development of genetic sexing strains in Lepidoptera: From traditional to transgenic approaches. Journal of Economic Entomology 98: 248-259

Miao XX, Xu SJ, Li MH, Li MW, Huang JH, Dai FY, Marino SW, Mills DR, Zeng P, Mita K, Jia SH, Zhang Y, Liu WB, Xiang H, Guo QH, Xu AY, Kong XY, Lin HX, Shi15YZ, Lu G, Zhang X, Huang W, Yasukochi Y, Sugasaki T, Shimada T,

Nagaraju J, Xiang ZH, Wang SY, Goldsmith MR, Lu C, Zhao GP and Huang YP (2005) Simple sequence repeat-based consensus linkage map of Bombyx mori. Proceedings of the National Academy of Sciences USA 102:16303-16308

Nagaraja GM, Mahesh G, Satish V, Madhu M, Muthulakshmi M and Nagaraju J (2005) Genetic mapping of Z-chromosome and identification of W-chromosome specific markers in the silkworm, Bombyx mori. Heredity 95:148-157

Padma S, Sowjanya AP, Poli UR, Jain M, Rao BN and Ramakrishna G (2005) Downregulation of calcineurin activity in cervical carcinoma. Cancer Cell International 5:7

Prakash P, Pathak N and Hasnain SE (2005) PheA (Rv3838c) of Mycobacterium tuberculosis encodes an allosterically regulated monofunctional prephenate dehydratase that requires both catalytic and regulatory domains for optimum activity. Journal of Biological Chemistry 280:20666-20671

Prakash P, Yellaboina S, Ranjan A and Hasnain SE (2005) Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis ORFs. Bioinformatics 21: 2161-2166

Prakash P, Aruna B, Sardesai AA and Hasnain SE (2005) Purified recombinant hypothetical protein coded by open reading frame Rv1885c of Mycobacterium tuberculosis exhibits a monofunctional AroQ class of periplasmic chorismate mutase activity. Journal of Biological Chemistry 280:19641-19648

Prouzet-Mauleon V, Hussain MA, Lamouliatte H, Kauser F, Megraud F and Ahmed N (2005) Pathogen evolution in vivo: genome dynamics of two isolates obtained nine years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. Journal of Clinical Microbiology 43:4237-4241

Qamra R, Mande SC, Coates, ARM and Henderson B (2005) The unusual chaperonins of Mycobacterium tuberculosis. Tuberculosis 85, 385-394

Qamra R, Prakash P, Aruna B, Hasnain SE and Mande SC (2005) Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis chorismate mutase. Acta Crystallographica F61:473-475

Sah NK, Singh SN, Sahdev S, Banerji S, Jha V, Khan Z and Hasnain SE (2005) Indian herb 'Sanjeevani' (Selaginella bryopteris) can promote growth and protect against heat shock and apoptotic activities of ultra-violet and oxidative stress. Journal of Biosciences 30: 499-505

Sechi LA, Gazouli M, Ikonomopoulos J, Lukas JC, Scanu AM, Ahmed N, Fadda G and Zanetti S (2005) Mycobacterium avium subsp. paratuberculosis, genetic susceptibility to Crohn?s disease and the Sardinians: Way ahead. Journal of Clinical Microbiology 43:5275-5277

N. Silswal, A. K. Singh, B. Aruna, S. Mukhupadhyay, S. Ghosh, and Z. Ehtesham (2005). Human resistin stimulates the pro-inammatory cytokines TNF-. and IL-12 in macrophages by NF-.B-dependent pathway. Biochemical and Biophysical Research Communications 334:1092-1101

Singh A, Sowjanya P and Ramakrishna G (2005) The Wild type Ras: Road ahead. FASEB Journal 19 : 161-169.

Sowjanya AP, Jain M, Poli UR, Padma S, Das M, Shah KV, Rao BN, Devi AR, Gravitt PE and Ramakrishna G (2005) Prevalence and distribution of high-risk Human papilloma virus (HPV) types in invasive squamous cell carcinoma of the cervix and in normal women in Andhra Pradesh, India. BMC Infectious Diseases 5(1):116

Vijay Kumar S, Ranjan S, Saxena V, Rajesh V, Roy SK, Kochar D, Ranjan A and Das A (2005) Plasmodium falciparum: genetic diversity of C-terminal region of MSP-1 in isolates from Indian sub-continent. Experimental Parasitolgy 110: 384-388

Varadarajan P, Mahalingam S, Gandotra S, Dorairajoo DS, D’souza VM and Balasundaram D (2005) The functionally conserved nucleoporins Nup124p from fission yeast and the human Nup153 mediate nuclear import and activity of the Tf1 retrotransposon and HIV-1 Vpr. Molecular Biology of the Cell 16: 1823-1838

Varsha (2005) DNA fingerprinting : An overview. Proceedings of A.P. Akademi of Sciences 9: 317-323

Wise KC, Manna SK, Yamauchi K, Ramesh V, Wilson BL, Thomas RL, Sarkar S, Kulkarni AD, Pellis NR and Ramesh GT (2005) Activation of nuclear transcription factor kappa B in mouse brain induced by a stimulated microgravity. In Vitro Cell Developmental Biology – Animal 41: 118-123

Ahmed K S, Khan AA, Tiwari SK, Ali SM, Ahmed I, Kauser F, Hussain MA, Abid Z, Habeeb A, Ahmed N and Habibullah CM (2005). Prevalence study of Helicobacter pylori at Oral and Gastroduodenal Sites of South Indian Population to Elucidate Transmission pathways. Singapore Med. J (I n press).

Ahmed N and Sechi LA (2005) Helicobacter pylori and gastroduodenal pathology: New threats of the old friend. Annals Clin. Microbiol. Antimicrobials (In press).

Alvi A, Khan AA, Tiwari SK, Abid Z, Ahmed KS, Habeeb A, Ishaq M, Ahmed N and Habibullah C M (2005). Frequency of Intestinal Metaplasia and Dysplasia among subjects infected with cagE, cagT and vacA positive Helicobacter pylori. World J Gastroenterol (In press).

Arvind Singh, Pavani Sowjanya and Ramakrishna G. (2005). The Wild type Ras: Road ahead. FASEB J. 19(2): 161-169.

Bashyam, M.D, Ryan Bair, Young H Kim, Pei Wang, Tina Hernandez-Boussard, Trobert Tibshirani, Anirban Maitra, Jonathan R. Pollack. Array-based comparaative genomic hybridization identifies localized DNA ampilfications and homozygous deletions in pancreatic cancer. Neoplasia, 7:556-56 2.

F. Marec, L. G. Neven, A. S. Robinson, M. Vreysen, M. R. Goldsmith, J. Nagaraju, G. Franz (2005) Development of genetic sexing strains in Lepidoptera: From traditional to transgenic approaches. Journal of Economic Entomology 98(2): 248-259

Felix, K., Manna, S.K., Wise, K., Barr, J., and Ramesh, G.T. (2005) Low Levels of Arsenite Activates Nuclear Factor kappa B and Activator Protein-1 in Immortalized Mesencephalic Cells. Journal of Biochemical and Molecular Toxicology 19(2), 67-77.

Kauser F, Hussain M A, Ahmed I, Ahmad N, Habeeb A, Khan A A and Ahmed N (2005) Comparing genomes of Helicobacter pylori strains from the high altitude desert of Ladakh, India J. Clin. Microbiol. (In press).

M. Dharma Prasad, M. Muthulakshmi, M. Madhu, Sunil Archak, K. Mita and J. Nagaraju (2005) Survey and analysis of microsatellites in the silkworm, Bombyx mori: Frequency, Distribution, Mutations, Marker potential and their Conservation in heterologous species Genetics 169:197-214.

Manna, P., Narang, K. K., and Manna, S. K. (2005) 1,2,4-thiadiazolidine derivative inhibits Nuclear Transcription Factor-kappaB and its dependent genes activation but induces apoptosis. International Journal of Cancer 113, 549-560.

Nagaraja GM, Mahesh G, Satish V, Madhu M, Muthulakshmi M and Nagaraju J (2005) Genetic mapping of Z-chromosome and identification of W-chromosome specific markers in the silkworm, Bombyx mori. Heredity (In press).

Padma S, Sowjanya AP, Poli UR, Jain M, Rao B, Ramakrishna G. (2005) Downregulation of calcineurin activity in cervical carcinoma. Cancer Cell Int. Apr 1;5(1):7.

Prakash P., Yellaboina S., Ranjan A. and Hasnain S.E.(2005) Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis ORFs Bioinformatics 00,000-000 (In press).

Prasad,M.D., Muthulakshmi,M., Arunkumar,K.P., Madhu,M., Sreenu,V.B., Pavithra,V., Bose,B., Nagarajaram, H.A., Mita,K., Shimada, T. and Nagaraju, J. (2005) SilkSatDb: A microsatellite database of the silkworm, Bombyx mori. Nucleic Acids Research. 33: D403-D406.

R.K.Gundu, B.Bose, S.Swamynathan, V.B.Sreenu, N.Pavan, S.Acharya and Nagarajaram HA Frontiers in Bioinformatics Research: The Biodiversity Issues (2005) In: "Biodiversity : Status and Prospects" Editors: Pramod Tandon, Manju Sharma and Renu Swarup, Narosa Publishing House, New Delhi.*

Tiwari SK, Khan AA, Ahmed KS, Ahmed I, Kauser F, Hussain MA, Ali SM, Alvi A, Abid Z, Habeeb A, Ahmed N and Habibullah CM. (2005) Rapid diagnosis of Helicobacter pylori infection in dyspeptic patients using salivary secretion: A non-invasive approach. Singapore Med. J (In press).

Tiwari SK, Khan AA, Khan SA, Ali SM, Habeeb A, Kauser F, Hussain MA, Ahmed N and Habibullah CM. (2005). PCR based analysis of the cag-PAI of Helicobacter pylori from saliva: An approach for rapid molecular genotyping in correlation with disease status. J. Gasteroenterol. Hepatol. (In press).

Wise, K.C., Manna, S.K., Yamauchi, K., Ramesh, V., Wilson, B.L., Thomas, R.L., Sarkar, S., Kulkarni, A.D., Pellis, N.R., Ramesh, G.T. (2005) Activation of nuclear transcription factor kappa B in mouse brain induced by a stimulated microgravity. In Vitro Cellular & Developmental Biology - Animal (In press).

Vucenik I, Ramakrishna G, Tantivejkul K, Anderson LM, Ramljak D. (2005) Inositol hexaphosphate (IP6) blocks proliferation of human breast cancer cells through a PKCdelta-dependent increase in p27Kip1 and decrease in retinoblastoma protein (pRb) phosphorylation. Breast Cancer Res Treat. May;91(1):35-45.

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2004

Kaur, R., Castano, I. and Cormack, B.P. (2004) Functional genomic analysis of fluconazole susceptibility in the pathogenic yeast Candida glabrata: Roles of calcium signaling and mitochondria. Antimicrobial Agents and Chemotherapy 48: 1600-1613.

Madhusudan R. Nandineni R.S. Laishram and Gowrishankar, J. Osmosensitivity associated with insertions in argP (iciA) or glnE in glutamate synthase (GOGAT)-deficient mutants of Escherichia coli. Journal of Bacteriology (2004), 186: 6391-6399.

Madhusudan R. Nandineni and Gowrishankar, J. Evidence for an arginine exporter encoded by yggA (argO) that is regulated by the LysR-type transcriptional regulator ArgP in Escherichia coli. Journal of Bacteriology (2004), 186:3539-3546.

A. M. Khurad, A. Mahulikar, M. K. Rathod, M. M. Rai, S. Kanginakudru, and J. Nagaraju. (2004). Vertical Transmission of Nucleopolyhedrovirus in the Silkworm, Bombyx mori L. Journal of Invertebrate Pathology 87: 8-15.

A. Radha Rama Devi and S.M. Naushad. "Newborn screening in India". The Indian Journal of Pediatrics 71(2). 157-160.

A.Radha Rama Devi, V. Govindiah, G. Ramakrishna and S.M. Naushad. "Prevalence of Methylene tetrahydrofolate reductase polymorphism in South Indian population." Current Science 86(3) 44 0-443.

Abid Hussain M, Kauser F, Khan A A, Tiwari S, Habibullah CM and Ahmed N (2004). Molecular genotyping of Helicobacter pylori isolates from different human populations using genomic fingerprinting of ERIC regions: Implications in strain identification and geographic evolution. J. Clin. Microbiol. 42:2372-2378 (June 2004).

Ahmed N and Hasnain S E (2004) Genomics of Mycobacterium tuberculosis:Old threats and new trends. Indian J Med Res (In press).

Ahmed Kamal, G. Ramesh, O. Srinivas, P. Ramulu, N. Laxman ,Tasneem Rehana, M.Deepak, M.S. Achary and Nagarajaram HA (2004). Design, Synthesis, and Evaluation of Mixed Imine-Amine Pyrrolobenzodiazepine Dimers with Efficient DNA-Binding Affinity and Potent Cytotoxicity. Bio-organic & Medicinal Chemistry 12:5427-5436.

Ahmed N, Alam M, Rajender Rao K, Kauser F, Ashok Kumar N, Qazi N N, Sangal V, Sharma VD, Das R, Katoch VM, Murthy KJR, Suneetha S, Sharma S K, Sechi LA, Gilman RH and Hasnain SE (2004). Molecular genotyping of a large, multi-centric collection of tubercle bacilli indicates geographical partitioning of strain variation: Implications in global epidemiology of M. tuberculosis. J. Clin. Microbiol. (In press).

Awasthi AK, Nagaraja G, Naik G, Kanginakudru S, Thangavelu K, Nagaraju J. (2004) Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays. BMC Genet. Jan 10; 5(1): 1 online version.

NBSdb: New Born Screening Database (2004) Buddhaditta Bose, Gyan Rajkumar, M. Narendar Pavan, A RadhaRama Devi, Nagarajaram, HA Indian Journal of Medical Informatics online.

Carroll I M, Ahmed N, Beesley S M, Khan A A, Ghousunnissa S, O Moráin C A and Smyth C J (2004) Microevolution between paired antral and paired antral and corpus Helicobacter pylori isolates recovered from individual patients. J Med Microbiol (In press).

Carroll I M, Khan AA and Ahmed N (2004). Revisiting the pestilence of Helicobacter pylori: insights into geographical genomics and pathogen evolution. Infection Genet Evol. (In press).

Felix, K., Wise, K., Manna, S., Yamauchi, K., Wilson, B. L., T homas, R., Kulkarni, A., Pellis, N. R., and Ramesh, G. T. (2004): Altered Cytoki ne Expression in Tissues of Mice Subjected to Simulated Microgravity. Mole cular and Cellular Biochemistry 266, 79-85.

Hasnain SE and Ahmed N (2004). Leptospirosis: An epidemiologic, genomic and evolutionary perspective. Lancet Infectious Diseases 00:0000-0000 (In press).

King, R.A., Markov, D., Sen, R., Severinov, K. and Weisberg, R. A. (2004) A conserved Zinc binding site in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex. J. Mol. Biol., 342(4): 1143-54.

Kauser F, Khan AA, Hussain MA, Carroll IM, Ahmad N, Tiwari S, Shouche Y, Das B, Jyohtirmayee CS, Alam M, Ali SM, Habibullah CM, Sierra R, Megraud F, Sechi LA and Ahmed N (2004). The cag pathogenicity island (cag-PAI) of Helicobacter pylori is disrupted in majority of patient isolates from different human populations. J. Clin. Microbiol. 42: 0000-0000 (September 2004) (In press).

R. Qamra and S. C. Mande. (2004) Crystal structure of the 65kDa heat shock protein, Chaperonin 60.2 of Mycobacterium tuberculosis. J. Bacteriol.(2004) v. 186, 8105-8113.

R. Qamra, V. Srinivas and S. C. Mande (2004) Mycobacterium tuberculosis GroEL homologues unusually exist as lower oligomers and retain the ability to suppress aggregation of substrate proteins. J. Mol. Biol. (2004) v.342, 605-617.

S. S. Rahim, N. Khan, C. S. Boddupalli, S. E. Hasnain and S. Mukhopadhyay* (2004). IL-10 mediated suppression of IL-12 production in RAW 264.7 cells also involves c-rel transcription factor. Immunology 114:313-321 (*Corresponding Author)

S. Mukhopadhyay*, V. M. L. Srivastava, P. K. Murthy and S. E. Hasnain (2004). Poorer NF-.B signaling by microfilariae in macrophages from BALB/c mice affects their ability to produce cytotoxic levels of nitric oxide to kill microfilariae. FEBS Letters 567:275-280 (*Corresponding Author)

S. Ghosh, S. Rasheedi, S. S. Rahim, S. Banerjee, R. K. Choudhary, P. Chakhaiyar, N. Z. Ehtesham, S. Mukhopadhyay and S. E. Hasnain (2004). Method for enhancing solubility of the expressed recombinant proteins in Escherichia coli. Biotechniques 37:418-423

M D Bashyam and S E Hasnain. (2004) The extracytoplasmic function sigma factors: role in bacterial pathogenesis. Infection, Genetics and Evolution 49:408-413.

Majeed, A.A., Ahmed, N., Rao, K.R., Ghousunnissa, S., Kausar, F., Bose, B., Nagarajaram, H.A., Katoch, V.M., Cousins, D.V., Sechi, L.A., Gilman, R.H. and Hasnain, S.E. (2004) AmpliBASE MTTM: A Mycobacterium tuberculosis diversity knowledgebase. Bioinformatics Published online ahead of print edition (In press).

Manna, P, Singh, R., Narang, K. K., and Manna, S. K. (2004): Synthesis, anti-fungal, antitumor and anti-inflammatory activities of some new 5-substitutedarylimino-2-N-p-tolylsulphonyl-3-oxo-1,2,4-thiadiazolidines. Indian Journal of Heterocyclic Chemistry 13: 249-252.

Metta M, Kanginakudru S, Gudiseva N, Nagaraju J. (2004) Genetic characterization of the Indian cattle breeds, Ongole and Deoni (Bos indicus), using microsatellite markers - a preliminary study. BMC Genet. 5:16. online version

Murali Dharan Bashyam, Leena Bashyam, Gorinabele R Savithri, Munimanda Gopikrishna, Vartul Sangal, Akela Radha Rama Devi. (2004) Molecular genetic analyses of b-thalassemia in South India reveals rare mutations in the b-globin gene. Journal of Human Genetics, 49:408-413.

Nagaraja, J. Nagaraju and H. A. Ranganath (2004) Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms Genes and Genetic systems 79: 293-299.

Nagaraju. J (2004) Spider silks: A possible key to evolution of spiders Heredity 93: 520-521.

Prabhakara K, Angelena M, Ramadevi AR (2004) Familial (9;11)(p22;p15.3)pat translocation and XX sex reversal in a phenotypic boy with cryptorchidism and delayed development. Genetic Counseling 51(4), 355-357.

Prabhakara K, Ramadevi AR (2004) Premature centromere division versus C-anaphases in cultures: Need for consensus and guidelines. American Journal of Medical Genetics 124(3):331.

Prabhakara K, Wyandt HE, Huang XL, Prasad KS, Ramadevi AR (2004) Recurrent proximal 18p monosomy and 18q trisomy in a family with a maternal pericentric inversion of chromosome 18. # Ann Genet 47: 297-303.

S. N. Rao, M. Muthulakshmi, S. Kanginakudru, and J. Nagaraju (2004) Phylogenetic relationships of three new microsporidian isolates from the silkworm, Bombyx mori. Journal of Invertebrate Pathology 86:87-95.

Sarkar, A., Sreenivasan, Y., Ramesh, G. T., and Manna, S. K. (2004) Beta-D-glucoside suppresses TNF-induced activation of nuclear transcription factor kappaB but potentiates apoptosis. Journal of Biological Chemistry 279(32), 33768-33781 May 25 [Epub ahead of print].

Siddiqi N, Das R, Pathak N, Banerjee S, Ahmed N, Katoch V M, and Hasnain SE (2004) Mycobacterium tuberculosis isolate with a distinct genomic identity overexpresses a TAP like efflux pump. Infection 32:109-11.

Sreenu, V.B., Ranjitkumar, G., Swaminathan, S., Priya, S., Bose, B., Narendra Pavan, M., Nagaraju, J., Nagarajaram, H.A. (2004) MICdb - Database of Prokaryotic Microsatellites. Nucleic Acids Research Published in online database issue.

T. Ramasarma and H. N. Ravishankar (2004) Formation of an oxo-radical of peroxovanadate during reduction of diperoxovanadate with vanadyl sulfate or ferrous sulfate Biochemica Biophysica Acta (In press).

Tiwari SK, Khan AA, Khan SA, Ali SM, Habeeb A, Kauser F, Hussain MA, Ahmed N and Habibullah CM. (2004). PCR based analysis of the cag-PAI of Helicobacter pylori from saliva: An approach for rapid molecular genotyping in correlation with disease status. Gasteroenterol. Hepatol. (In press)

Vardhini D, Suneetha S, Joshi DSM, Karuna S, Magee X, Vijayalakshmi DSR, Sridhar V, Karunakar KV, Ahmed N, Archelos JJ, Suneetha LM (2004). Comparative proteomics of the M. leprae binding protein myelin P0: its implication in leprosy and other neurodegenerative diseases. Infection Genet Evol 4: 21-28.

Wise K., Manna S., Barr J., Gunasekar P., and Ramesh G. (2004) Activation of activator protein-1 DNA binding activity due to low level of manganese exposure in pheochromocytoma cells. Toxicology Letters 147(3): 237-244.
Yashodha R, Kathirvel M, Sumathi R, Gurumurthi K, Archak S, Nagaraju J. Genetic analysis of Casuarinas using ISSR and FISSR markers (2004). Genetica 122: 161-172.

Yellaboina S., Ranjan S., Chakhaiyar P., Hasnain SE, and Ranjan A. (2004) Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae. BMC Microbiology 4:38.

Yellaboina S., Seshadri J., Senthil Kumar M. and Ranjan A. (2004) Predictregulon: A webserver for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Nucleic Acids Research32: W318-320.

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2003

Sharma K.G., Kaur, R. and Bachhawat, A.K. (2003) The glutathione-mediated detoxification pathway in yeast: an analysis using the red pigment that accumulated in certain adenine biosynthetic mutants of yeast reveals the involvement of novel genes. Archives of Microbiology 180: 108-117.

Castano, I., Kaur, R., Pan, S., Cregg, R., De Las Penas, A., Guo, N., Biery, M.C, Craig, N.L. and Cormack B.P. (2003) Tn7-based genome-wide random insertional mutagenesis of Candida glabrata. Genome Research 13: 905-915.

Subhadeep Chatterjee Rajan Sakaranarayan and Ramesh V Sonti. 2003. PhyA, a secreted protein of Xanthomonas oryzae pv. oryzae, is required for optimum virulence and growth under phytic acid as a sole phosphate source. Molecular Plant-Microbe Interactions. Vol.16(11), 973-982.

Ahmad, R, Kamra, A. and Hasnain, S.E. (2003) Fibroin silk proteins from the non-mulberry silkworm Philosamia ricini are biochemically and immunochemically distinct from those of the mulberry silkworm Bombyx mori. DNA and Cell Biology 00: 000-000 (In press).

Ahmed N, Alam M, Majeed A A, Rahman S A, Cataldi A, Cousins D and Hasnain, S. E. (2003). Genome sequence based, comparative analysis of the fluorescent amplified fragment length polymorphisms (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex. Infection Genet. Evol. 2: 193-199.

Ahmed N, Caviedes L, Alam M, Rao K R, Sangal V, Sheen P, Gilaman RH and Hasnain SE (2003). Distinctiveness of Mycobacterium tuberculosis genotypes from Human Immunodeficiency Virus Type 1-Seropositive and -Seronegative patients in Lima, Peru. J. Clinical Microbiol. 41: 1712-1716.

Ahmed N, Khan AA, Alvi A, Tiwari S, Jyothirmayee CS, Kauser F, Ali A and Habibullah CM (2003). Genomic analysis of Helicobacter pylori from Andhra Pradesh, South India: Molecular evidence for three major genetic clusters Current Science 85:1579-1586.

Ali, S. and Hasnain, S.E. (2003) Genomics of the Human Y Chromosome: 1- Association with male infertility. Gene 321: 25-37.

Aparna, G., Bhuyan, A.K., Sahdev, S., Hasnain, S.E., Kaufman, R.J. and Ramaiah, K.V.A. (2003) Stress-induced apoptosis in Spodoptera frugiperda (Sf9) cells: Baculovirus p35 mitigates eIF2 phosphorylation. Biochemistry 00: 000-000 (In press).

Bashyam, M. D. (2003). Prokaryotic Genom (Michel Blot ed.). Book Review, Current Science, 84:1366-1367. *

Bashyam, M.D. and Hasnain, S.E. (2003) The Human Genome Sequence: impact on health care. Indian Journal of Medical Research 117:43-65.

Bashyam, M. D. and S. Mukhopadhyay (2003). Status of Tuberculosis in India-2003 (R. Nayak, M. S. Shaila and G. R. Rao eds.) and Trends in Malaria and Vaccine Research: The current Indian Scenario (D. Raghunath and R.Nayak eds.). Book Review, Infection, Genetics and Evolution 3:75-77. *

Bashyam, M. D., Gorinabele R Savithri, Murugapiran S Kumar, Calambur Narasimhan and Pratibha Nallari (2003). Molecular genetics of familial hypertrophic cardiomyopathy (FHC). J. Hum. Genet. 48:55-64.

Carroll I M, Ahmed N, Beesley S M, Khan A A, O Mor?in C A and Smyth C J (2003) Fine Structure Molecular Typing of Irish Helicobacter pylori Isolates and their Genetic Relatedness to Strains from Four Different Continents. J. Clin. Microbiol. 41:5755-5759.

Chari VB, K Khaleel-ur-Rehman, N Ahmed, CM Habibullah and SS Singh (2003) UV-B induced stimulation of phosphatidyl inositol 3 kinase in human foetal hepatocytes. Hepatology Research 000:000-000 (In press).

Choudhary, R.K., Mukhopadhyay, S., Chakhaiyar, P., Sharma, N., Murthy K.J.R., Katoch, V.M. and Hasnain S.E. (2003) PPE antigen Rv2430c of Mycobacterium tuberculosis induces a strong B-cell response. Infection Immunity 71: 6338-6343.

Ghosh, S., Singh, A. K., Aruna, B., S. Mukhopadhyay, and Ehtesham, N. Z. (2003) The genomic organization of mouse resistin reveals major difference from the human resistin. Gene 305: 27=34.

Cousins D V, Bernardelli A, Bastida R, Cataldi A, Quse V, Dow S, Redrobe S, Duignan P, Murray A, Dupont C, Ahmed N, Collins DM, Ray Butler W, Dawson D, Rodriguez D, Louriero J, Romano MI, Alito A and Zumarraga M (2003). Tuberculosis in seals is caused by a novel member of the Mycobcterium tuberculosis complex: Mycobacterium tuberculosis subsp. pinnipedae subsp. nov. International J. Systematic Evolutionary Microbiol. 53: 1305-1314 http://dx.doi.org/10.1099/ijs.0.02401-0.

G Ranjit Kumar, M Narendar Pavan, B. Bose, S Swaminathan, Geetha Thanu, P Prashanthi, B Phani Prasad, V B Sreenu, M Sridhar Achary and Nagarajaram HA (2003) EMBnet India Node (EIN) at the Centre for DNA Fingerprinting and Diagnostics: Serving the Indian sub-continent in Bioinformatics. Bioinformatics India 1 2:67-77 (An Invited Article). **

Nagarajaram HA and S.E.Hasnain (2003) Current Status of Post-Genomics Computational Biology "Computing and Information Sciences : Recent Trends" Editor: J.C.Misra, Narosa Publishing House, New Delhi.*

Hasnain, S.E. (2003) Molecular epidemiology of infectious diseases: a case for increased surveillance. Bulletin of the World Health Organization 81:474 (An Invited editorial).**

Hasnain, S.E., Begum, R., Ramaiah, K.V.A., Sahdev S., Shajil, E.M., Taneja, T.K., Manjari, M., Athar, M., Sah,N.K. and Krishnaveni, M., Journal of Biosciences - Review (2003) Host-Pathogen interactions during Apoptosis. Journal of Biosciences 28: 349-358.

Khaleel-ur-Rehman K Ayesha Q, Ahmed N. and Habibullah C M (2003). Tyrosine aminotransferase and gamma-glutamyl transferase activity in human foetal hepatocyte primary cultures under proliferative conditions. Cell Biochem. Func. Published online ahead of print edition. July (2003) (In press)

King, R.A., Sen, R., and Weisberg, R.A. (2003) Using a Lac Repressor Roadblock to Analyze the E.coli Transcription Elongation Complex. Methods in Enzymology, 370:207-18.

Kumar KS, Govindaiah V, Naushad SE, Devi RR, Jyothy A. (2003) Plasma homocysteine levels correlated to interactions between folate states and methylene tretrahydrofolate reductase gene mutation in women with unexplained pregnancy loss. Journal of Obstetrics and Gynaecology. 23: 55-58.

Mandal AK, Prabhakara K, Raddy ABM, Ramadevi AR, Panicker SG (2003) Congenital glaucoma associated with 22p+ variant in a dysmorphic child. Indian Journal of Ophthalomology 51(4), 355-357.

Mohan, M., Taneja, T.K., Sahdev, S., Begum, R., Athar, M. and Hasnain, S.E. (2003) Antioxidants Prevent UV-Induced Apoptosis by Inhibiting Mitochondrial Cytochrome C Release and Caspase Activation in Spodoptera frugiperda (Sf9) Cells. Cell Biology International 27: 483-490.

Panicker, S.G., Mandal, A.K., Reddy, A.B.M., Gothwal, V. and Hasnain, S.E. (2003) Correlations of genotypes with phenotypes in Indian patients with primary congenital glaucoma. Investigative Ophthalmology and Visual Sciences 44:000-000 (In press).

Prasad MD, Han S-J, Nagaraju J, Lee W-J and Brey PT (2003) Cloning and characterization of an eukaryotic initiation factor-2 alpha kinase from the silkworm, Bombyx mori. Biochemica et Biophysica Acta 1628 56-63.

Prasad MD and J.Nagaraju (2003) A comparative phylogenetic analysis of full-length mariner elements isolated from Indian tasar silkmoth, Antheraea mylitta (Lepidoptera: saturniidae) J. Bioscience 28 443-453.

Priscilla Priyadarshini, Bulusu S. Murthy, J. Nagaraju, L. Singh (2003) A GATA-binding protein expressed predominantly in the pupal ovary of the silkworm, Bombyx mori. Insect Biochemistry and Molecular Biology 33 185-195.

Reddy, A.B.M., Panicker, S.G., Mandal, A.K., Hasnain, S.E. and Balasubramanian, D. (2003) Identification of R368H as a predominant CYPB1 allele causing primary congenital glaucoma in Indian patients.Investigative Ophthalmology and Visual Sciences00: 000-000 (In press).

Rekha T, Khan, A A, Ayesha A, Ahmed N and Habibullah CM (2003). Differentiation of Helicobacter pylori isolates before and after treatment by Fluorescent amplified fragment length polymorphism. Indian J. Medical Microbiol. 21:166-171 .

Sahdev, S., Taneja, T.K., Mohan, M., Sah, N.K.,Khar A.K., Hasnain, S.E. and Athar, M. (2003) Baculovirus p35 inhibits oxidant-induced activation of mitochondrial apoptotic pathway. Biochemical and Biophysical Research Communications 307: 483-490.

Sarkar, A., Sreenivasan, Y., and Manna, S. K. (2003): alpha-Melanocyte Stimulating Hormone induces cell death in mast cells: Involvement of NF-kB. FEBS Letter 549(1-3), 87-93.

Sarkar, A., Sreenivasan, Y., and Manna, S. K. (2003): Alpha-Melanocyte Stimulating Hormone inhibits lipopolysaccharide-induced biological responses by downregulating CD14 from macrophages. FEBS Letter 553(3): 286-94.

Sen, R. and Dasgupta, D. (2003) Simple fluorescence assays to probe the conformational changes of E.coli RNA polymerase during transcription initiation. Methods in Enzymology, 370:598-605.

Shiras A, Bhosale A, Shepal V, Shukla R, Baburao VS, Prabhakara K, Shastry P (2003) A Unique model system for tumor progression in GBM comprising two developed human neuro-epithelial cell lines with differential transforming potential and coexpressing neuronal and glial markers. Neoplasia, 5(6), 520-53.

1. Sreenivasan, Y., Sarkar, A., and Manna, S. K. (2003): Mechanism of Cytosine arab inoside mediated apoptosis: Role of Rel A (p65) dephosphorylation.Oncogene 22(28), 4356-4369.

Sreenivasan, Y., Sarkar, A., and Manna, S. K. (2003): Oleandrin suppresses activation of nuclear transcription factor-kappaB and activator protein-1 and potentiates apoptosis induced by ceramide. Biochem. Pharmacol. 66(11): 2223-39.

Sriramana Kanginakudru, Edupalli Venkata Subbaiah, Pierre Couble and Javaregowda Nagaraju LepidopteraAbstracts. (2003) Towards development of baculoviral resistant strains of the silkworm, Bombyx mori. Sixth International Workshop on the Molecular Biology and Genetics of the Lepidoptera.16pp. Journal of Insect Science, 3:36, Available online: http://insectscience.org/3.36

T. C. Terwilliger, M. S. Park, G. S. Waldo, J. Berendzen, L.-W. Hung, C.-Y. Kim, C. V. Smith, J. C. Sacchettini, M. Bellinzoni, R. Bossi, E. De Rossi, A. Mattevi, A. Milano, G. Riccardi, M. Rizzi, M. M. Roberts, A. R. Coker, P. Tormay, G. Fossati, P. Mascagni, A. R.M. Coates, S. P. Wood, C. W. Goulding, M. Apostol, D. H. Anderson, H. S. Gill, D. S. Eisenberg, B. Taneja, S. Mande, E. Pohl, V,. Lamzin, P. Tucker, M. Wilmanns, C. Colovos, W. Meyer-Klaucke, A. W. Munro, K. J. McLean, K. R. Marshall, D. Leys, J. K. Yang, H.-J. Yoon, B. I. Lee, M. G. Lee, J. E. Kwak, B. W. Han, J. Y. Lee, S.-H. Baek, S. W. Suh, M. M. Komen, V. ML. Arcus, E. N. Baker, J. S. Lott, W. JacobsU Jr.,UT. Alber,U B. Rupp (2003) The TB Structural Genomics Consortium: A Resource for TB Biology Tuberculosis 83, 223- 249.

V.B.Sreenu, G.Ranjitkumar, S.Swaminathan, S.Priya, B.Bose, M.N.Pavan, Geetha Thanu, J.Nagaraju and Nagarajaram HA (2003) MICAS: A fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Applied Bioinformatics 2(3) 165-168.

V.B.Sreenu, Vishwanath Alevoor, J.Nagaraju and Nagarajaram HA (2003) MICdb: Database of Prokaryotic Microsatellites Nucleic Acids Research 31: 106-108

Bashyam, M.D, Viswanathan, P., Venkaiah, B., Kumar, S., Rasheedi, S. and Vrati, S. and Hasnain, S.E. (2003) The homologous region sequence (hr1) of Autographa californica multinucleocapsid polyhedrosis virus can enhance transcription from non-baculoviral promoters in mammalian cells. Journal of Biological Chemistry 278: 52564 - 52571.

Yellaboina S., Chakhaiyar P., Hasnain SE., and Ranjan A. (2003) Computational prediction of DtxR regulon-A Dissection of physiological process controlled by DtxR in Corynebacterium species. Proceedings of IEEE Computational System Bioinformatics Conference 442-443.**

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2002

Subhadeep Chatterjee and Ramesh V. Sonti. 2002. rpfF mutants of Xanthomonas oryzae pv. oryzae are deficient in virulence and growth under low iron conditions. Molecular Plant-Microbe Interactions. Vol.15(5), 463-471

Ali S and SE Hasnain (2002) Molecular dissection of the human Y-chromosome. Gene 283: 1-10.

Ahmed N, A Bal, AA Khan, M Alam, A Kagal, V Arjunwadkar, A Rajput, AA Majeed, SA Rahman, S Banerjee, S Joshi and R Bharadwaj (2002) Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India. Infection Genetics and Evolution 1: 237-242.

Ata-ur-Rasheed M, GK Vemuganti, SG Honavar, N Ahmed, SE Hasnain, and C Kannabiran (2002) Mutational analysis of the RB1 gene in Indian patients with Retinoblastoma. Ophthalmic Genetics 23: 121-128.

Bashyam, M. D. (2002). Microarrays for the Neurosciences : An essential guide. Daniel H. Geschwind and Jeffery P. Gregg (eds.). Book Review, Current Science 83:649-650. *

Bashyam, M. D. (2002) Understanding cancer metastasis: an urgent need for using differential gene expression analysis. Cancer 94: 1821-1829.

Brian L, SP Singh, D Lai, M Cartas, S Mahalingam and A Srinivasan (2002) Signature LXXLL motif is required for the transformation function of the unique human herpesvirus-8 protein, Kaposin. Journal of Virology 000: 000-000 (In press).

Bhupesh T and SC Mande (2002) Crystal structure of Mycobacterium tuberculosis chaperonin-10 at 3.5 A resolution. Acta Crystallogr v.277, 13257-13267.

C. W. Goulding, M. Apostol, D. H. Anderson, H. S. Gill, C. V. Smith, M. R. Kuo,J. K. Yang, G. S. Waldo, S. W. Suh, R. Chauhan, A. Kale, N. Bachhawat, S. C. Mande, J. M. Johnston, J. S. Lott, E. N. Baker, V. L. Arcus, D. Leys, K. J. McLean, A. W. Munro, J. Berendzen, V. Sharma, M. S. Park, D. Eisenberg, J. Sacchettini, T. Alber, B. Rupp, W. Jacobs, Jr. and T. C. Terwilliger (2002) The TB Structural genomics consortium: providing a structural foundation for drug discovery. Curr. Drug Targets- Infect. Dis. (2002) v.2, 121- 141.

G. Rajamohan, M. Dahiya, S. C. Mande, K. L. Dikshit (2002) Function of 90-loop (Thr90-Glu100) region of staphylokinase in plasminogen activation probed through site-directed mutagenesis and loop deletion. Biochem J. v.365, 379-389.

Hasnain SE (2002) Conference report MEEGID-V: Fifth international meeting on molecular epidemiology and evolutionary genetics in infectious diseases. Infection Genetics and Evolution 000: 000-000 (In press).

J. Dhar, A. H. Pande, V. Sundram, J. S. Nanda, S. C. Mande and G. Sahni. (2002) Involvement of a nine-residue loop in the generation of the macromolecular substrate-specificity by the activator complex through interaction with substrate kringle domains. J. Biol. Chem. v.277, 13257- 13267.

Kamal A, N Laxman, G Ramesh, P Ramulu, O Srinivas, K Neelima, AK Kondapi, VB Sreenu and Nagarajaram HA (2002) Design, synthesis, and evaluation of new non-cross linking pyrrolobenzodiazepine dimers with efficient DNA-binding ability and potent antitumour activity  J. Med. Chem 45 4679-4688.

Kazim SN, SM Wakil, LA Khan, S Raiesuddin, MK Pervez, V Thakur, RC Guptan, SE Hasnain and SK Sarin (2002) Prevalence and profile of lamivudine induced mutations in the surface and polymerase genes of HBV among Indian population. Journal of Medical Virology 000: 000-000 (In press).

Kazim SN, SM Wakil, LA Khan, SE Hasnain and SK Sarin (2002) Vertical transmission of hepatitis B virus despite maternal lamivudine therapy.The Lancet 359: 1488-1493.

Nagaraju, J (2002)Application of genetic principles for improving silk production. Current Science 83, 409-414.

Nagaraju, J and Goldsmith, M. R (2002) Silkworm genomics - progress and prospects.Current Science 83, 415-425.

Nagaraju J, M Kathirvel, R Ramesh Kumar, EA Siddiq and SE Hasnain (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence -based ISSR-PCR and SSR markers. Proc. Natl. Acad. Sci. USA, 99: 5836-5841.

Nagaraju J, M Kathirvel, EV Subbiah, M Muthulakshmi and LD Kumar (2002) FISSR-PCR : a simple and sensitive assay for highthroughput genotyping and genetic mapping. Molecular and Cellular Probes 16: 67-72.

Narayanan E, Nagarajaram HA , C Ramakrishnan and N Srinivasan (2002) Effect of solvent molecules on the stereochemical code of glycine residue PROTEINS 49 326-334.

Panicker SG, ABM Reddy, AK Mandal, N Ahmed, Nagarajaram HA, SE Hasnain and D Balasubramanian (2002) Identification of novel mutations causing familial primary congenital glaucomas in Indian pedigrees. Investigative Ophthalmology and Visual Science 43: 1358-1366.

Panicker S G, Srirangan S, Mandal A K, Reddy ABM, Ahmed N and Hasnain S. E. (2002) Novel Mutations in FOXC1 wing region causing Axenfeld-Rieger anomaly. Investigative Ophthalmol. Visual Sci. 43: 3613-3616

Prabhakara K, U Dutta and Ramadevi AR (2002) A partial 15q22 trisomy arising due to segregation of maternal 10;15 reciprocal translocation. Indian Pediatrics 39: 1050-1054.

Prabhakara K, P Padman, U Dutta, M Angeleena, K Sekher and A Radha Ramadevi (2002) Meiotic impairment in an oligozoospheric male with translocation t(5;13). In the Proceedings of National Conference of Expanding Horizons of Human Genetics, Eds: Bhasin MK, Kalla AK, pp55-60.**

Prasad, M.D., Nurminsky, D.L., Nagaraju, J (2002) Characterization and molecular phylogenetic analysis of mariner elements from wild and domesticated species of silkmoths. Mol. Phylogenet. Evol. 25: 210-217.

R. Chauhan and S. C. Mande (2002) Site directed mutagenesis reveals a novel catalytic mechanism of Mycobacterium tuberculosis Alkylhydroperoxidase C. Biochem J. 367, 255- 261.

R. Kaur, R. Pathania, V. Sharma, S. C. Mande and K. L. Dikshit (2002) Chimeric Vitreoscilla Hemoglobin (VHb) Carrying a Flavoreductase Domain Relieves Nitrosative Stress in Escherichia coli: New Insight into the Functional Role of VHb. Appl. Environ. Microbiol. v.68, 152-160.

R. Qamra, B. Taneja and S. C. Mande (2002) Conserved sequence features in small b- barrels. Prot. Eng., 15, 967- 77..

Ramadevi AR, K Prabhakara and U Dutta (2002) Familial (11;21) (p13;q22) pat balanced reciprocal translocation in a female child with regression of milestones. Annals de Genetique 45: 13-15.

Ramadevi AR, U Naik, U Dutta, Srikanth and K Prabhakara (2002) De novo pericentric inversion of chromosome 4, inv (4p16q12), in boy with piebaldism and mental retardation. American Journal of Medical Genetics 113: 190-192.

Rajkumari K and J Gowrishankar (2002) An N-terminally truncated RpoS (S) protein in Escherichia coli is active in vivo and exhibits normal environmental regulation even in the absence of rpoS transcriptional and translational control signals. Journal of Bacteriology 000: 000-000 (In press).

S. Bhatia, S. Mukhopadhyay, E. Jarman, G. Hall, A. George, S. Rath, J. R. Lamb, and V. Bal, (2002). Scavenger receptor-specific allergen delivery elicits IFN-g-dominated immunity and directs established Th2-dominated responses to a non-allergic phenotype. Journal of allergy and clinical immunology 109: 321-328.

S. Mukhopadhyay, M. Mohanty, A. Mangla, A. George, V. Bal, S. Rath, and B. Ravindran (2002). Macrophage effector functions controlled by Bruton's tyrosine kinase are more crucial for microfilarial clearance than the cytokine balance of T cell responses. Journal of Immunology 168, 2914-21.

S Paneerselvam, N Vanaja, Ch V Goud, A Sheeba, G V Rao and C Damodaran (2002) Allele frequency distribution for nine fluorescent based STR loci in Tamil Population (South India). Journal of Forensic Sciences 47: 226-227.

Siddiqi NA, S Mohammed, S Hussain, RK Choudhary, N Ahmed, Prachee, S Banerjee, GR Savithri, M Alam, N Pathak, A Amin, M Hanief, VM Katoch, SK Sharma and SE Hasnain (2002) Molecular characterization of multi-drug resistant isolates of Mycobacterium tuberculosis from patients in North-India. Antimicrobial Agents and Chemotherapy 46: 443-450.

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2001

Kaur, R.*, Kostrub, C.F. and Enoch, T. (2001) Structure-function analysis of fission yeast Hus1-Rad1-Rad9 checkpoint complex. Molecular Biology of Cell 12: 3744-3758. *Corresponding author

Jain D, DT Nair, JG Swaminathan, EG Abraham, J Nagaraju and DM Salunke (2001) Structure of the induced antibacterial protein from tasar silkworm, Antheraea mylitta : Implications to molecular evolution. Journal of Biological Chemistry 276 : 41377-41382.

Kholi A, V Gupta, S Krishnamurthy, SE Hasnain and R Prasad (2001) Specificity of drug transport mediated by CaMDRI: a major facilitator of Candida albicans.Journal of Biosciences26: 333-339.

Kumar LD, M Kathirvel, GV Rao and J Nagaraju (2001) DNA profiling of disputed chilli samples (Capsicum annum) using ISSR-PCR and FISSR-PCR marker assays. Forensic Science International 116: 63-68.

Nagaraju J, V Klimenko and P Couble (2001) The silkworm Bombyx mori, a model genetic system. In: Encyclopedia of Genetics (Ed Reeves, E) Fitzroy Dearborn, London, UK p:219-239 .

Nagaraju J, KD Reddy, GM Nagaraja and BN Sethuraman (2001) Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori. Heredity (UK) 86: 588-597.

Nagaraju J (2001) Identification of a gene associated with Bt resistance in the lepidopteran host, Heliothis virescens and its implications in Bt transgenic based pest control.Current Science 81:746-747.

Parvez MK, V Thakur, SN Kazim, RC Guptan, SE Hasnain and SK Sarin (2001) Base-pair Alterations in the Epsilon-lower Stem due to a Novel Double Substitution in the Precore Gene of HBV -e Negative Variant were Recovered by Secondary Mutations. Virus Genes 23: 315-320

Prabhakara K, Ramadevi AR (2001) Cytogenetics of Male Infertility. In: The Infertility Manual (Eds. Rao KA, P Brinsden), Federation of Indian Societies of Obstetrics & Gynecologists (FOGSI) p 134-143. *

Rajkumari K and J Gowrishankar (2001) In vivo expression from the RpoS-dependent P1 promoter of the osmotically regulated proU operon in Escherichia coli and Salmonella enterica serovar Typhimurium: activation by rho and hns mutations and by cold stress. Journal of Bacteriolology 183: 6543-6550.

MD Bashyam, Ramachandran A, P Viswanathan, S Ghosh, MS Kumar and SE Hasnain (2001) The bountiful and baffling baculovirus: The story of polyhedrin transcription. Current Science 81: 998-1010.

SaiSree L, M Reddy and J Gowrishankar (2001) IS186 insertion at a hot spot in the lon promoter as a basis for Lon protease deficiency of Escherichia coli B: identification of a consensus target sequence for IS186 transposition. Journal of Bacteriology 183: 6943-6946.

Sardesai AA and J Gowrishankar (2001) trans-Acting mutations in loci other than kdpDE that affect kdp operon regulation in Escherichia coli: effects of cytoplasmic thiol oxidation status and nucleoid protein H-NS on kdp expression. Journal of Bacteriology 183: 86-93.

Sardesai AA and J Gowrishankar (2001) Improvement in K+-limited growth rate associated with expression of the N-terminal fragment of one subunit (KdpA) of the multi-subunit Kdp transporter in Escherichia coli. Journal of Bacteriology 183: 3515-3520.

Siddiqi NA, MD Shamim, A Amol Amin, DS Chauhan, Ram Das, Kiran Srivastava, D Singh, VD Sharma, VM Katoch, SK Sharma, M Hanief and SE Hasnain (2001) Typing of drug resistant isolates of Mycobacterium tuberculosis from India using the IS6110 element reveals substantive polymorphism. Infection Genetics and Evolution 1: 109-116.

Srinivas VR, K Bachhawat-Sikder, S Habib, SE Hasnain and A Surolia (2001) Expression of winged bean agglutinin in Spodoptera frugiperda insect cell expression system. Bioscience Reports21: 361

Suvas S, V Singh, S Sahdev, H Vohra and JN Agrewala (2001) Distinct role of CD80 and CD86 in the regulation of the activation of B cell and B cell lymphomas. Journal of Biological Chemistry 277(10): 7766

Vanitharani R, S Mahalingam, Y Rafaeli, SP Singh, A Srinivasan, DB Weiner and V Ayyavoo (2001) HIV-1 Vpr transactivates LTR-directed expression through sequences present within -278 to -176 and increases virus replication in vitro. Virology 289: 334-342.

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2000

Bashyam MD, S Ghosh, A Ramachandran, P Viswanathan and SE Hasnain (2000) Multiple regulatory circuits for transcription from the polyhedrin gene promoter of the Autographa californica multiple nucleocapsid nuclear polyhedrosis virus. Proceedings of the Indian Natlonal Science Academy (PINSA) B66 : 83-96.

Habib S and SE Hasnain (2000) Differential activity of two non-hr origins during replication of the baculovirus AcMNPV genome. Journal of Virology 74: 5182-5189.

Kapoor D, RC Guptan, SM Wakil, SN Kazim, SN Kaul, R Agarwal, SR Raisuddin, SE Hasnain and SK Sarin (2000) Beneficial effects of lamivudine in hepatitis B virus-related decompensated cirrhosis. Journal of Hepatology 33: 308-311.

Nagaraju J (2000) Recent advances in the silkworm, Bombyx mori. Current Science 78: 151-161.

Raman LA, N Siddiqi, M Shamim, M Deb, G Mehta and SE Hasnain (2000) Molecular characterization of Mycobacteriumabscessus strains isolated from a hospital outbreak. Emerging Infectious Diseases 6: 561-562.

Rao GV and SE Hasnain (2000) CDFD - A synthesis of quality service and globally competitive science. Asia Pacific Journal of Biotechnology 6: 114-117. **

Shah NK, TK Taneja and SE Hasnain (2000) Mitochondria can power cells to life and death. Resonance 5: 74-84.

Shi YP, P Das, B Holloway, V Udhayakumar, JE Tongren, F Candal, S Biswas, R Ahmad, SE Hasnain and AA Lal (2000) Development, expression, and murine testing of a multistage Plasmodium falciparum malaria candidate vaccine. Vaccine 18: 2902-2914.

Sudhakar A, A Ramachandran, S Ghosh, SE Hasnain, RJ Kaufman and KVA Ramaiah (2000) Phosphorylation of serine 51 in initiation factor2 alpha (elF2a ) promotes complex formation between elFa (P) and elF2B and causes inhibition in the guanine nucleotide exchange activity of elF2B. Biochemistry 39: 12929-12938.

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1999

Prabhjeet Singh, Subhadeep Chatterjee, Ranjana Pathania and Sukhdev S. Bhullar. 1999. Enhanced wheat germ agglutinin accumulation in the germinating embryos of wheat (Triticum aestivum L.) appears to be a general stress response. Current Science. Vol.76(8), 1140-1142.

B. Ravindran, P. K. Sahoo, M. Mohanty, S. Mukhopadhyay and A. P. Dash (1999). Increased susceptibility of mice with XID mutation to Brugia malayi infection. Medical Science Research, 27:135-137

S. Mukhopadhyay**, P. K. Sahoo, A. George, V. Bal, S. Rath and B. Ravindran (1999) Delayed clearance of filarial infection and enhanced Th1 immunity due to modulation of macrophage APC functions in xid mice. Journal of Immunology 163:875-883

S. Mukhopadhyay**, A. George, V. Bal, B. Ravindran and S. Rath (1999). Bruton's tyrosine kinase deficiency in macrophages inhibits nitric oxide generation leading to enhancement of interleukin-12 induction. Journal of Immunology 163:1786-1792

Ahmed N (1999) Evaluation of PCR technique in rapid diagnosis of tuberculosis in dairy cattle. Livestock International 3: 9-13.

Ahmed N, RJ Khan and NA Ganai (1999) DNA amplification assay for rapid detection of bovine tubercle bacilli in semen. Animal Reproduction Science 57: 15-21.

Ali S and SE Hasnain (1999) Conservation, management and documentation of livestock genetic resources and biodiversity: A biotechnology perspective. Current Science 77: 1154-1158.

Rao GV (1999) Interaction between Science and Law: A better Judicial System. The Criminal Law Journal 191-192.

Reddy KD, EG Abraham and J Nagaraju (1999) Microsatellites of the silkworm, Bombyx mori: abundance, polymorphism and strain characterization. Genome 42: 1057-1065.

Reddy KD, EG Abraham and J Nagaraju (1999) Genetic characterization of the silkworm, Bombyx mori by inter-simple sequence repeat (ISSR) - anchored PCR. Heredity (UK) 83: 681-687.

Sudhakar A, T Krishnamoorthy, A Jain, U Chatterjee, SE Hasnain, RJ Kaufman and KVA Ramaiah (1999) Serine 48 in initiation factor 2a (eIF2a ) is required for high-affinity interaction between eIF2a (P) and eIF2B. Biochemistry 38: 15398-15403.

Sah NK, TK Kaur, N Pathak, R Begum, M Athar and SE Hasnain (1999) The baculovirus anti-apoptotic p35 gene also functions via an oxidant dependent pathway. Proceedings of the National Academy of Sciences, USA96: 4838-4843. Sharma A, MP Niphadkar, M Kathirvelu, J Nagaraju and L Singh (1999) DNA fingerprinting variability within and among the silkworm Bombyx mori genotypes and estimation of their genetic relatedness using Bkm-derived probe. Journal of Heredity (USA) 90: 315-319.

Kaur, R. and Bachhawat, A.K. (1998) The yeast multidrug resistance pump, Pdr5p, confers reduced drug resistance in the erg mutants of Saccaharomyces cerevisiae. Microbiology 145: 809-818.

Ingavale, S.S.¶, Kaur, R.¶, Aggarwal, P. and Bachhawat, A.K. (1998) A minisatellite sequence within the propeptide region of the vacuolar carboxypeptidase Y gene of Schizosaccharomyces pombe. Journal of Bacteriology 180: 3727-3729. ¶Equal contribution.

Kaur, R., Ingavale, S.S. and Bachhawat, A.K. (1997) PCR-mediated direct gene disruption in Schizosaccharomyces pombe. Nucleic Acids Research 25: 1080-1081.

Kaur, R., Kumar, R. and Bachhawat, A.K. (1995) Selective recovery of DNA fragments from silica particles: effect of A-T content and elution conditions. Nucleic Acids Research 23: 4932-4933.

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# This article is rated as one of the top 25 articles in this journal from 2000 to 2004, ranking 18th in the list.
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