Publications



2014
    36.   Alka Jadaun, Raja Sudhakar.D, N. Subbarao and Aparna Dixit “In silico screening for novel inhibitors of DNA polymerase III Alpha Subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)", Accepted in PLOSOne

    35.   Kumar M, Gantasala NP, Roychowdhury T, Thakur PK, Banakar P, Shukla RN, Jones MG, Rao U "De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae", PLoS One. 2014 May 6;9(5):e96311. doi: 10.1371/journal.pone.0096311. eCollection 2014. PMID: 24802510

    34.   Ponnusamy Kalaiarasan, Bhupender Kumar, Rupali Chopra, Vibhor Gupta, Naidu Subbarao, Rameshwar NK Bamezai, "silico Screening, Genotyping, Molecular Dynamics Simulation and Activity studies of SNPs in Pyruvate Kinase M2", Accepted in PloseOne(2014)

    33.   Palash Nath,Anirban Chakraborti and D. Sanyal “Ab initio calculation of magnetic properties of p-block element doped ZnO”, Royal Society of Chemistry Adv.,2014,4, 45598

    32.   R. Chicheportiche and A. Chakraborti, “Copulas and time series with long-ranged dependences”, Phys. Rev. E (2014)89, 042117

    31.   A. Chakraborti, D. Challet, A. Chatterjee, M. Marsili, Y.-C. Zhang, B.K. Chakrabarti“Statistical mechanics of competitive resource allocation using agent-based models”,, Physics Reports, doi:10.1016/j.physrep. (2015)2014.09.006.

    30.   R.K. Brojen Singh, Numerical Detection of Stochastic to Deterministic Transition. J. Compt. Nonlinear Dyn. (2014) Doi:10.1115/1.4027441.

    29.   Kh. Kabita, J. Maibam, B. I. Sharma, R.K.Thapa and R.K. Brojen Singh, "Density Functional Theory Study of Electronic Structure, Elastic Properties and Phase Transition of Gallium Phosphide (GaP)", Adv. Sc. Eng. Med. (2014) 6, 354.

    28.   BA Ahanger, R. K. Brojen Singh and Z. A. Ansari, "Thermal Perturbation in Dye-SensitizedSolar Cell", Mat. Focus (2014), 3,1–5.

    27.   Shefeeq. T, N Ahmad, Ravins, R. K. Brojen Singh, "Diffusional Drug Release from Cylindrical Matrices Into a Finite Medium with Boundary Layer Effect", Adv. Sc. Eng. Med. 6, 948 (2014)

    26.   Shahnawaz Ali, Md. Z. Malik, Md. J. Alam, R Ishrat and R. K. Brojen Singh,. "Evolutionary trace analysis of p53 protein: A statistical analysis of conserved aminoacids in p53 protein", Accepted in J. Bioinformatics and Int. Control(2014).

    25.   Gurumayum Reenaroy Devi , Md. Jahoor Alam, and R.K. Brojen Singh, "Synchronization in stress p53 network. Mathematical Medicine and Biology(2014)", (Accepted)

    24.   Kh. Kabita, Jameson Maibam, B. Indrajit Sharma, R. K. Brojen Singh and R. K. Thapa, "Density functional theory study on pressure induced structural transformation, elastic properties and electronic structure of gallium arsenide (GaAs)", Int. J. of Innov. and Appl. Sts. (2014) 8, 382-393

    23.   Nafis, S., Kalaiarasan, P., Singh, R. B., Husain, M., & Bamezai, R. N, "Apoptosis regulatory protein–protein interaction demonstrates hierarchical scale-free fractal network. Briefings in bioinformatics", (2014)doi: 10.1093/bib/bbu036

    22.   Agarwal, M., Kumar, N., & Vig, L., "Non-additive multi-objective robot coalition formation. Expert Systems with Applications", (2014) 41(8), 3736-3747.

    21.   Amit Srivastava, Rupali Chopra, Shafat Ali, Shweta Agarwal, Lovekesh Vig, and Ramesh Bamezai, "Inferring population structure and relationships using minimal independent markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering", Nucleic Acids Research, 2014, 42 (15),

    20.   Khan, Taushif; Ghosh, Indira, "Modularity in protein structures: A study on all alpha proteins",  Journal of Biomolecular Structure & Dynamics(2014) (Accepted for publication).

    19.   Harsh Parikh, Apoorvi Singh, Annangarachari Krishnamachari and Kushal Shah, "Computational prediction of origin of replication in bacterial genomes using correlated entropy measure (CEM)", BioSystems(2014) (accepted)

    18.   Mohd Danishuddin, Arbab Khan, Mohammad Faheem, Ponnusamy Kalaiarasan, Mohd Hassan Baig, Naidu Subbarao and Asad U. Khan, "Structure-based screening of inhibitors against KPC-2: designing potential drug candidates against multidrug-resistant bacteria", Journal of Biomolecular Structure and Dynamics, (2014), Vol 32, 5, 741-750

    17.   Kamaldeep Gill, Lokesh Nigam, Ratnakar Singh,Suresh Kumar, Naidu Subbarao,Dhyam Singh Chauhan, Sharmistha Dey, "The Rational Design of Specific Peptide Inhibitor against p38α MAPK at Allosteric-Site: A Therapeutic Modality for HNSCC(2014)", PlosOne (2014) 9 (7), e101525

    16.   Yachana Jha, Gaurav Sablok, Naidu Subbarao, Raja Sudhakar, M. H. U. Turabe Fazil, R. B. Subramanian, Andrea Squartini and Sunil Kumar, "Bacterial-induced expression of RAB18 protein in Orzya sativa salinity stress and insights into molecular interaction with GTP ligand. Journal of Molecular Recognition" (2014) 27 (9), 521-527

    15.   Mohd H Baig, D Raja Sudhakar, Ponnusamy Kalaiarasan, Gulshan Wadhawa, Naidu Subbarao Mohtashim Lohani, Asad U Khan "Effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase", PLOSOne(2014),9(12), e112456

    14.   Ponnusamy Kalaiarasan, Subarao Naidu, Rameshwar NK Bamezai, "Molecular simulation of Tyr105 phosphorylated Pyruvate kinase M2 to understand its Structure and Dynamics", in Journal of Molecular Modeling(2014),20,9,1-12

    13.   Amit Kumar, Nidhi Agarwal, Lalit Pant, Jay Prakash Singh, Indira Ghosh, Naidu Subbarao, "PfalDB: An Integrated Drug Targets and Chemical Database for Plasmodium falciparum", Current Drug Targets(2014),15,12,1089-1093

    12.   Vijayan Ramachandran, Naidu Subbarao, "Manoharan Natesan Homology modeling of LAMMER kinase of Plasmodium falciparum and to identify the interaction of crtical resdiues involved in binding of ATP by Molecular docking simulation study", International Journal of Advanced Life Sciences(2014),7,2,311-320.

    11.   Sinha, S., & Lynn, A. M, "HMM-ModE: implementation, benchmarking and validation with HMMER3". BMC research notes, (2014)7(1), 483.

    10.   Qayum, A., Lynn, A. M., & Arya, R. "Traditional Knowledge System Based GIS Mapping of Antimalarial Plants: Spatial Distribution Analysis. Journal of Geographic Information System", (2014),6(05), 478.

    9.   P Narang, S Khan, AJ Hemrom, AM Lynn, "MetaNET-a web-accessible interactive platform for biological metabolic network analysis". BMC Systems Biology(2014) 8 (1), 130.

    8.   S Singh, U Bajpai, AM Lynn, "Structure based virtual screening to identify inhibitors against MurE Enzyme of Mycobacterium tuberculosis using AutoDock Vina", Bioinformation(2014) 10 (11), 697

    7.   Kumari, R., Kumar, R., Consortium, O. S. D. D., & Lynn, A.M, "g_mmpbsa-A GROMACS tool for high-throughput MM-PBSA calculations. Journal of chemical information and modeling" (2014)54 (7), pp 1951–1962.

    6.   Meher, B. R., Kumar, M. V. S., & Bandyopadhyay, P. "Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from Molecular Dynamics. Journal of Biomolecular Structure and Dynamics", (2014)32(6), 899-915.

    5.   Hasnain, S., McClendon, C. L., Hsu, M. T., Jacobson, M. P., & Bandyopadhyay, P. "A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion. PloS one", (2014)9(9), e106466.

    4.   Sahu, N., Gadre, S. R., Rakshit, A., Bandyopadhyay, P., "Miliordos, E., & Xantheas, S. S.. Low energy isomers of (H2O) 25 from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations. The Journal of chemical physics", (2014),141(16), 164304.

    3.  Singh, P., Sarkar, S. K., & Bandyopadhyay, P, "Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b). The Journal of chemical physics", (2014)141(1), 015103.

    2.   Hasnain, S., Jacobson, M. P., & Bandyopadhyay, P., "A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA. Chemical Physics Letters", (2014), 591, 253-258.

    1.  Jean-Numa Gillet, "Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles," in Journal of Biomolecular Structure and Dynamics, Published online: April, 15, 2014, DOI: 10.1080/07391102.2014.907544

    Book Chapters/Proceedings

    1.   MJ Alam, V Singh, RK Brojen Singh, "Switching Mechanism in the p53 Regulatory Network Systems and Synthetic Biology" (Book Chapter) (2014)

    2.   Anirban Chakraborti, Yoshi Fujiwara, Asim Ghosh, Jun-ichi Inoue and Sitabhra Sinha, in Eds. F. Abergel, H. Aoyama, B. K. Chakrabarti, A. Chakraborti and A. Ghosh, “Physicists’ Approaches to a Few Economic Problems”, Econophysics and Data Driven Modelling of Market Dynamics (Springer, Milan, 2015)

    3.   “Maximizing a Psychological Uplift in Love Dynamics”, M. Banerjee, A. Chakraborti and J. Inoue, in Eds. R. Lopez-Ruiz, D. Fournier-Prunaret, Y. Nishio, C. Gracio, Nonlinear Maps and their Applications, Springer Proceedings in Mathematics & Statistics (Springer International Publishing, Switzerland, 2015).

    4.   “Kinetic Exchange Models in Economics and Sociology”, S. Goswami and A. Chakraborti, in Eds. R. Lopez- Ruiz, D. Fournier-Prunaret, Y. Nishio, C. Gracio, Nonlinear Maps and their Applications, Springer Proceedings in Mathematics & Statistics (Springer International Publishing, Switzerland, 2015).


  • 2013     Publications (15) & Book Chapter: (3)
      1. Ashutosh Vishwa Bandhu, Neha Aggarwal and Supratim Sengupta, "Revisiting the Physico-Chemical Hypothesis of Code Origin: An Analysis Based on Code-Sequence Coevolution in a Finite Population", Origins of Life and Evolution of Biospheres 43(6):465-489 (2013) DOI: 10.1007/s11084-014-9353-x

      2. Manoj Agarwal, Naveen Kumar, Lovekesh Vig, "Non-additive multi-objective robot coalition formation Expert Systems and Applications", Volume 41, Issue 8, 2014 Pages 3736-3747


      3. Kh. Kavita Devi, J. Maibam, BI Sharma, R.K. Thapa and R.K. Brojen Singh, "DFT study of electronic structure, elastic properties and phase transition of GaP" Adv. Sc. Eng. Med. 6, 354 (2014).


      4. Jameson Maibam, Kh. Kabita, B. Indrajit Sharma, R. K. Thapa and R. K. Brojen Singh. DFT study on electronic structures and elastic properties of AgX (X=C, N) in rock salt structure (2013) In. J. of Sc. Techn. (Accepted).


      5. Kh. Kavita Devi, J. Maibam, BI Sharma, R.K. Brojen Singh and R.K. Thapa. First principle calculation of pressure induced phase transition and band structure of GaP.I. J. Appl. Phys. (2013) (Accepted)


      6. R.K. brojen Singh. Numerical detection of stochastic to deterministic transition J. Comp. Non-Linear Dyn. (2013) (Accepted)


      7. Aiman Ahmad, Anis Ahmad, Himani Varshney, Abdul Rauf, Mohd Rehan, Naidu Subbarao ,Asad U. Khan, " Designing and synthesis of novel antimicrobial heterocyclic analogs of fatty acids", Accepted 21 October 2013,http://dx.doi.org/10.1016/j.ejmech.2013.10.051.


      8. Ashutosh Shandilya, Sajeev Chacko, B. Jayaram & Indira Ghosh, "A plausible mechanism for the antimalarial activity of artemisinin: A computational approach" Nature, SCIENTIFIC REPORTS vol 3 : 2513 , 2013, DOI:10.1038/srep02513


      9. Vivek Kumar Singh, Indira Ghosh, "Methylerythritol phosphate pathway to isoprenoids: Kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum" in FEBS Letters , Accepted 17 June 2013. http://dx.doi.org/10.1016/j.febslet.2013.06.024


      10. Rentala Madhubala, V S Gowri, Indira Ghosh, Amit Sharma, "Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major", in BMC Genomics ( 2013).


      11. Jean-Numa Gillet and Indira Ghosh, "Concepts on the protein folding problem , in Journal of Biomolecular Structure and Dynamics", online 2013, http://dx.doi.org/10.1080/07391102.2012.748546


      12. Hosseini Ashraf, Indira Ghosh, Pramod Khandekar, Mohammad Hiresh Ayoubian, "Simple sequence repeats in specific gene groups of shigella genome", IOABJ; Vol. 4: Issue 1;17–24(2013).


      13. Mohd Danishuddin, Arbab Khan, Mohammad Faheem, Ponnusamy Kalaiarasan, Mohd Hassan Baig, Naidu Subbarao and Asad U. Khan, "Structure-based screening of inhibitors against KPC-2: designing potential drug candidates against multidrug-resistant bacteria", Accepted in Joural of Biomolecular Structure and Dynamics, (2013) DOI:10.1080/07391102.2013.789988


      14. Nida Zaidi, Ejaz Ahmad, Mohd Rehan, Gulam Rabbani, Mohammad R. Ajmal, Yusra Zaidi, Naidu Subbarao and Rizwan H. Khan, "Biophysical Insight into Furosemide Binding to Human Serum Albumin: A Study To Unveil Its Impaired Albumin Binding in Uremia", Accepted in publication the journal of PHYSICAL CHEMISTRY B , (2013) DOI: 10.1021/jp3069877


      15. Jean-Numa Gillet. "Ultralow Thermal Conductivity Minimum in Silicon Supercrystals with Weakly and Strongly Bonded Germanium Nanodots for Thermoelectrics", ACS Sustainable Chemistry and Engineering., 1 (6), pp. 611-618, DOI: 10.1021/sc400020c (2013).


  • 2012       Publications (24) & Book Chapter: (3)
    • Kamaldeep Gill, Abhay K. Singh , Vaishali Kapoor, Lokesh Nigam , Rahul Kumar, Prasida Holla, Satya N. Das, Savita Yadav, Naidu Subbarao, Bidhu Kalyan Mohanti, Sharmistha Dey, "Development of peptide inhibitor as a therapeutic agent against head and neck squamous cell carcinoma (HNSCC) targeting p38α MAP kinase", Accepted for Publication in Biochimica et Biophysica Acta(2012).


    • Ashish Gupta, Lovekesh Vig and David C. Noelle, "A Cognitive Model for Automaticity in Motor Skill Learning", Journal of Robotic and Intelligent Systems, 2012 (In Press)


    • Shikha Pal, Madhur Mishra, D. Raja Sudhakar, Mohammed Haris Siddiqui, "In‐silico designing of a potent analogue against HIV‐1 Nef protein and protease by predicting its interaction network with host cell proteins, Journal of Pharmacy and Bioallied Sciences", January-March 2013 Vol 5 Issue 1

    • Sanjiv K Dwivedi and S. Sengupta, " Classification of HIV-1 sequences using profile Hidden Markov Models", PLoS One 7(5):e36566 (2012).

    • S. Sengupta, J. Derr, A. Sain and A.D. Rutenberg, "Stuttering Min oscillations within E. coli bacteria: a stochastic polymerization model", Physical Biology, 9, 056003 (2012).

    • Singh P and Sengupta S, "Phylogenetic analysis and comparative genomics of purine riboswitch distribution in prokaryotes", Evolutionary Bioinformatics 8, 589-609 .

    • Sarbashis Das, Priyanka Duggal, Rahul Roy, Vithal P. Myneedu, Digamber Behera, Hanumanthappa K. Prasad & Alok Bhattacharya , "Identification of Hot and Cold spots in genome of Mycobacterium tuberculosis using Shewhart Control Charts", Nature Scientific Reports- http://dx.doi.org/10.1038/srep00297

    • Chung-Chau Hon, Christian Weber,Odile Sismeiro, Caroline Proux,Mikael Koutero,Marc Deloger,Sarbashis Das, Mridula Agrahari, Marie-Agnes Dillies, Bernd Jagla, Jean-Yves Coppee3, Alok Bhattacharya and Nancy Guillen, "Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytic, Nucleic Acid Research", (2012) 1-17, doi: 10.1093/nar/gks1271

    • Jonathan P. Furado, Anuja P Rahalkar, Sudhanshu Sjankar, Pradipa Bandhyopadhyay and Sridhar R Godre, "Facilitating minima search for large water clusters at MP2 level via Molecular tailoring", J.Phy.Chem. Letters(2012)

    • Biswaranjan Meher, Mattaparthi Venkata Satish Kumar, Smriti Sharma and Pradipta Bandhyopadhyay, "Conformational Dynamics of HIV-1 protease: a comparative dynamic simulation study with multiple amber force fields", Journal of Bioinformatics and computational biology(2012)
    • Sudhanshu Shankar and Pradipta Bandhyopadhyay, "Determination of low energy structures of a small RNA hairpin using Monte Carlo based techniques", J.Biosciences 37(3) 533-538

    • Uddipan Sarma, Archana Sareen, Moitrayee Maiti, Vanita Kamat, Raki Sudan, Sushmita Pahari,Neetu Srivastava, Somenath Roy, Sitabhra Sinha, Indira Ghosh, Ajit G. Chande, Robin Mukhopadhyaya, Bhaskar Saha, "Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases" PLoS ONE (2012),7: July 2012 e39898 doi:10.1371/journal.pone.0039898

    • Uddipan Sarma & Indira Ghosh, "Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops" BMC Research Notes. (2012) 5:287 DOI:10.1186/1756-0500-5-2872012.


    • Uddipan Sarma & Indira Ghosh , "Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade" BMC Systems Biology. (2012 ) 6:82 DOI:10.1186/1752-0509-6-82.


    • Rithvik Vinekar, Chandra Verma, Indira Ghosh , "Functional relevance of dynamic properties of dimeric NADP-dependent isocitrate dehydrogenases" BMC Bioinformatics (2012) Volume 13 Supplement 17, S 2.

    • Mobashar Hussain Urf Turabe Fazil, Sunil Kumar, Naidu Subba Rao , Chandrabose Selvaraj, Sanjeev Kumar Singh, Haushila Prasad Pandey & Durg Vijai Singh, "Comparative structural analysis of two proteins belonging to quorum sensing system in Vibrio cholerae , Journal of Biomolecular Structure and Dynamics", DOI:10.1080/07391102.2012.687523

    • Smriti Sharma and Pradipta Bandyopadhyay, "Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, molecular dynamics simulation and quantum mechanical calculation", Journal of molecular modeling(2012), v18, 481-492

    • Rupesh Kumar, Amitabha Bose, Birendra Nath Mallick, "A Mathematical Model towards Understanding the Mechanism of Neuronal Regulation of Wake-NREMS-REMS States", PLOSOne, 7(8), : e42059. doi:10.1371/journal.pone.0042059

    • Kushal Shah and A. Krishnamachari. "Nucleotide correlation based measure for identifying origin of replication in genomic sequences", BioSystems vol. 107 (1), 52-55,2012

    • Kushal Shah and A. Krishnamachari. "On the origin of three base periodicity in genomes", BioSystems, vol.103(3) 142-144,2012.

    • Rentala Madhubala, V S Gowri, Indira Ghosh, Amit Sharma. “Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major” in BMC Genomics ( 2013).

    • Jean-Numa Gillet and Indira Ghosh. “Concepts on the protein folding problem” in Journal of Biomolecular Structure and Dynamics, in press (2013).

    • Ajeet Mandal, Antresh Kumar, Ashutosh Singh , AndrewM.Lynn , Khyati Kapoor and Rajendra Prasad, "A key structural domain of the Candida albicans Mdr1 protein", Biochem. J. (2012) 445 (313–322)

    • DA Gideon, R Kumari, AM Lynn, KM Manoj, "What is the Functional Role of N-terminal Transmembrane Helices in the Metabolism Mediated by Liver Microsomal Cytochrome P450 and its Reductase?", Cell Biochemistry and Biophysics, 1-11

    • Priya Singh and Pradipta Bandyopadhyay, "Accurate Calculation of the Density of States near the Ground-State Energy of the Peptides Met-Enkephalin and (Alanine)5 with the Wang-Landau Method: Lessons Learned", Journal of Atomic, Molecular, and Optical Physics, Volume 2012 (2012), doi:10.1155/2012/782806


    • A Book Chapter:
      1. Kushwaha Hemant Ritturaj and Ghosh Indira , “Bioinformatics Approach for Finding Target Protein in Infectious Disease” In Bioinformatics of Human Proteomics, Translational Bioinformatics 3, DOI 10.1007/978-94-007-5811-7_10, X. Wang (ed.), © Springer Science+Business Media Dordrecht 2013.


      2. Kushwaha Hemant Ritturaj and Ghosh Indira. ”Target Identification using Systems Approach in Infectious Diseases” . In TRANSLATIONAL RESEARCH IN NEW DRUG DEVELOPMENT. Ed. Ray Arunabha & Gulati Kavita ( V.P, India ), 2012.


      3. Kushwaha HR, Ghosh I, Pareek A. "General overview of bioinformatics tools in agricultural sciences. In: Biotechnology in agricluture and medicine" : Principles & Practice. ed. Gupta AK, Pareek A, Gupta SM.(I. K. International, INDIA),2011



  • 2011       Publications (36)
    • Fractal symmetry of protein interior: what have we learned? Anirban Banerji & Indira Ghosh in Cellular and Molecular Life Sciences , (2011) Aug;68(16):2711-3726.

      Plant Stress Gene Database: A Collection of Plant Genes Responding to Stress Condition by Ratna Prabha, Indira Ghosh , Dhananjaya P. Singh in ARPN Journal of Science and Technology, VOL. 1, NO. 1, November 2011.

      Rout AK, Padhan N, Barnwal RP, Bhattacharya A, Chary KVR.1. “Calmodulin-like protein of Entamoeba histolytica: Solution structure and calcium binding properties of partially folded protein”. Biochem. 50, 181-193 (2011)

      Somlata, Bhattacharya S., Bhattacharya A. "A C2 domain protein kinase initiates phagocytosis in the protozoan parasite Entamoeba histolytica." Nat. Commun. 2, 230 (2011)

      Kumari V, Sharma R, Yadav VP, Gupta AK, Bhattacharya A , Bhattacharya S. "Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: role of the LINE-encoded endonuclease”. BMC Genomics 12, 267 (2011)

    • Bharti R, Das, R, Sharma, P, Katoch, K. and Bhattacharya, A. (2011) MTCID: A database of genetic polymorphisms in clinical isolates of Mycobacterium tuberculosis. Tuberculosis (2012), doi:10.1016/j.tube.2011.12.001


    • Candida Vaz, Arvind Singh Mer, Alok Bhattacharya, Ramakrishna Ramaswamy (2011) "MicroRNAs Modulate the Dynamics of the NF-κB Signaling Pathway". PLoS ONE 6(11): e27774. doi:10.1371/journal.pone.0027774


    • Dhwani K. Desai, Soumyadeep Nandi, Prashant K. Srivastava, and Andrew M. Lynn, “ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities,” Advances in Bioinformatics, vol. 2011, Article ID 743782, 12 pages, 2011. doi:10.1155/2011/743782


    • Amit Rahi, Mohd Rehan, Rajni Garg, Deeksha Tripathi, Andrew M. Lynn, Rakesh Bhatnagar, Enzymatic characterization of Catalase from Bacillus anthracis and prediction of critical residues using information theoretic measure of Relative Entropy, Biochemical and Biophysical Research Communications, Volume 411, Issue 1, 22 July 2011, Pages 88-95, ISSN 0006-291X, 10.1016/j.bbrc.2011.06.099.


    • Ejaz Ahmad, Gulam Rabbani, Nida Zaidi, Saurabh Singh, Mohd Rehan, Mohd Moin Khan,Shah Kamranur Rahman, Zainuddin Qadri, Mohd. Shadab, Mohd. Tashfeen Ashraf, Naidu Subbarao, Rajiv Bhat and Rizwan Hasan Khan, "selectivity of Human Serum Albumin to Enantiomeric and Isoelectronic Pollutants Dissected by Spectroscopy, Calorimetry and Bioinformatics", Accepted PloS ONE(2011)


    • Isha Nagpal, N.Subbarao, S.Gourinath, Virtual Screening of potential inhibitors against O-acetylserine sulfhydrylase of Entamoeba histolytica of Cysteine Biosynthetic pathway, Accepted for publication in PLOS One journal,2011.


    • Vishvanath, Isha Nagpal, N.Subbarao and M.Rajeswari, In-silico modeling of a novel OXA-51 from β-lactam-resistant Acinetobacter baumannii and its interaction with various antibiotics Accepted for publication in Journal of Molecular Modeling.


    • Dhar, Suman; Nitharwal, Ram Gopal; Verma, Vijay; Subbarao, Naidu; Dasgupta, Santanu; Choudhury, Nirupam "DNA binding activity of Helicobacter pylori DnaB helicase:the role of N-terminal domain in modulating DNA binding activities",Accepted FEBS Journal (2011)


    • Kushal Shah and A. Krishnamachari. "On the origin of three base periodicity in genomes", BioSystems (accepted)


    • Ashish Gupta and Lovekesh Vig , "A dual association model for Acquisition and Extinction", Man Machine and Beyond, Italian Association of Artificial Intelligence, Palermo, 2011.


    • Ashish Gupta, Lovekesh Vig and David C. Noelle, "A Cognitive Model for generalization during Sequential Learning", Journal of Robotics, Special Issue on Cognitive and Neural Aspects, 2011


    • Kushal Shah and A. Krishnamachari. "Nucleotide correlation based measure for identifying origin of replication in genomic sequences", BioSystems (accepted)


    • Lovekesh Vig, Ashish Gupta and Abhinandan Basu. "On the Relation between Hunger, Dopamine and Action Rate",In Proceedings of the Fourth Indian International Conference on Artificial Intelligence, 2011.


    • Lovekesh Vig, Ashish Gupta and Abhinandan Basu, “A Neurocomputational model for the role of hunger in Dopamine mediated actions”, Journal of Intelligent Systems (Accepted, in Press)


    • Manoj Aggarwal,Lovekesh Vig, and Naveen Kumar, “A Multiple Objective approach to robot Coalition Formation”, Internationaal Conference of Intelligent Robotic Application , Aachen, 2011.


    • Ashish Gupta, Lovekesh Vig and David C. Noelle, “A Dual Association Model for the Extinction of Animal Conditioning”, Neurocomputing 74 (2011), pp. 3531-3542


    • Sudhanshu Shanker and Pradipta Bandyopadhyay . "Monte Carlo Temperature Basin Paving with Effective Fragment Potential: An Efficient and Fast Method for Finding Low Energy Structures of Water Clusters (H2O)20 and (H2O)25", J. Phys. Chem. A, 115 (42), 11866–11875 (2011)


    • Priya Singh, Subir K. Sarkar and Pradipta Bandyopadhyay . "Understanding the applicability and limitations of Wang–Landau method for biomolecules: Met-enkephalin and Trp-cage", Chem. Phys. Lett. 514, 357–361 (2011).


    • Smriti Sharma and Pradipta Bandyopadhyay. "Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, Molecular Dynamics simulation and quantum mechanical calculation", J. Mol. Modeling (In Press)


    • K.Shah, V.Gelfreic, V.Rom-Kedar, D.Turaev. "Robust exponential acceleration in time-dependent billiards", Physical Review Letters 106, 074101 (2011).


    • K.Shah. "Energy growth rate in smoothly oscillating billiards", Physical Review E 83, 046215 (2011).


    • Hemant R. Kushwaha, Gautam Kumar, Praveen Verma, Sneh L. Singla-Pareek, Ashwani Pareek. "Analysis of a salinity induced BjSOS3 protein from Brassica indicate it to be structurally and functionally related to its ortholog from Arabidopsis" Plant Physiology and Biochemistry, 2011 (Accepted)


    • Varshney A, Rehan M, Rabbani G, Khan RH, Subbarao N "Elimination of Endogenous Toxin, Creatinine from Blood Plasma Depends on Albumin Conformation: Site Specific Uremic Toxicity & Impaired Drug Binding". PLoS ONE | February 2011 | Volume 6 | Issue 2 | e17230


    • Kumar S, Raj I, Nagpal I, Subbarao N and Gourinath S. "Structural and biochemical studies of Serine Acetyltransferase reveal why the parasite Entamoeba histolytica cannot form Cysteine Synthase complex". JBC, February, 2011. in Press.


    • Bandyopadhyay P,Hungyo Kharerin , "Monte Carlo Energy Landscape Paving and Basin Paving simulation of RNA T-loop hairpin". Chem. Phys.Lett., 502, 130 (2011).


    • Indira Ghosh, Proteins will Fold Anyway!!, Journal of Biomolecular Structure & Dynamics, Volume 28, Issue Number 4, February 2011


    • Anirban Banerji & Indira Ghosh, "Mathematical criteria to observe mesoscopic emergence of protein biochemical properties", in J Math Chem (2011) 49:643–665


    • Biyani N, Mandal S, Seth C, Saint M, Natarajan K, Indira Ghosh, Madhubala R;. Characterization of Leishmania donovani aquaporins shows presence of subcellular aquaporins similar to tonoplast intrinsic proteins of plants. PLoS One. (2011);6(9):e24820.


    • Vikram Singh and Rama Ramaswamy, Spectral analysis of long noncoding RNAs, International Conference on BioInformatics and Computational Biology, BICB 2011, B31–B38. (ISBN: 978-981-08-8119-1)


    • Kumar G, Kushwaha HR , Purty RS, Kumari S, Singla-Pareek SL, Pareek A. Cloning, Structural and Expression Analysis of OsSOS2 in Contrasting Cultivars of Rice under Salinity Stress. Genes, Genomes and Genomics, 2011, Vol. 5.


    • Kushwaha HR, Singla-Pareek SL, Sopory SK, Pareek A. Understanding the "Commoneome" operative in plants in response to various abiotic Stresses. In: Improving Crop Resistance to Abiotic Stress. ed. Tuteja et. al.(Wiley-Blackwell, Wiley-VCH Verlag GmbH & Co., Germany),2011



  • 2010       Publications (23)
    • K.Shah. "Asymptotic solution of Fokker-Planck equation for plasma in Paul traps", Physics of Plasmas 17,054501 (2010).

      K.Shah. "Plasma response to nonlinear time-periodic electric fields in one dimension", Phys. Plasmas 17, 112301 (2010).

      K.Shah, D. Turaev and V. Rom-Kedar. "Fermi AccelerationExponential energy growth in a Fermi accelerator", Physical Review E 81, 056205 (2010).

      Manish Agarwal, Hemant R. Kushwaha,Charusita Chakravarty. “Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides”. Journal of Physical Chemistry B, 114, 651 (2010)

      Khan SN, Yennamalli R, Subbarao N, Khan AU, “ Mitoxantrone Induced Impediment of Histone Acetylation and Structural Flexibility of the Protein.”, Cell Biochem Biophys. 2010 Dec 8. doi : 10.1007/s12013-010-9141-9

      Srinivasan A and Ramakrishnan G., “Parameter screening and selection for ILP using Designed Experiments. 19th International Conference on Inductive Logic Programming”. Lecture Notes in Computer Science LNCS 5989, Springer (to appear), 2010.

      Bandyopadhyay P. “Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H2O)20 and (H2O)50”. Chem. Phys. Lett. 487, 133, 2010.

      Singh TU, Jafri HH and Ramaswamy R. “Transition to weak generalized synchrony in chaotically driven flows”. Physical Review, E 81, 016208-1—7, 2010.

      Agrawal M, Prasad A and Ramaswamy R. ”Quasiperiodic forcing of coupled chaotic systems”. Physical Review, E 81, 026202-1—6, 2010.

      Prasad A, Dhamala M, Adhikari BM, and Ramaswamy R. “Amplitude death in nonlinear oscillators with nonlinear coupling”. Physical Review, E 81, 027201-1—4, 2010. Cruz JM, Escalona J, Parmananda P, Karnatak R, Prasad A, and Ramaswamy R. “The phase--flip transition in coupled electrochemical cells”. Physical Review E 81, 046213-1—4, 2010.

      Gupta R, Greco D, Auvinen P and Arjas E. “Bayesian integrated modeling of expression data: A case study on RhoG”. Accepted BMC Bioinformatics, 2010.

      RajKumar Brojen Singh, Vikram Singh and Ram Ramaswamy “Stochastic Synchronization of Circadian Rythms, Journal of Systems Sciences and Complexity” (2010) 23: 978–988

      Banerji A & Indira Ghosh Revisiting the Myths of Protein Interior: "Studying Proteins with Mass-Fractal Hydrophobicity-Fractal and Polarizability-Fractal Dimensions" in PLoS ONE 4(10): e7361. oi:10.1371/journal.pone.0007361 (2010)

      Aditi Borkar, Indira Ghosh, Dhananjay Bhattacharyya,"Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace:" A Molecular Mechanics Approach, in Journal of Biomolecular Structure &Dynamics, Volume 27, Issue Number 5, (2010).

      Nidhi Puri, Om Prakash, Raman Manoharlal, Monika Sharma, Indira Ghosh and Rajendra Prasad "Analysis of physico-chemical properties of substrates of ABC and MFS multidrug transporters of pathogenic Candida albicans", in European Journal of Medicinal Chemistry , Vol. 45, Issue 11, November 2010, 4813-4826)

    • Anirban Banerji and Indira Ghosh, "Mathematical criteria to observe mesoscopic emergence of protein biochemical properties", in J Math Chem Nov (2010) :DOI 10.1007/s10910-010-9760-9

      Kapoor K, Rehan M and A.M.Lynn Prasad R, Employing information theoretic measures and mutagenesis to identify residues critical for drug-proton antiport function in Mdr1p of Candida albicans., PLoS ONE 5(6): e11041. doi:10.1371/journal.pone.0011041

      Dhaneswar Prusty, Ashraf Dar, Rashmi Priya, Atul Sharma, Srikanta Dana, Nirupam Roy Choudhury, N. Subba Rao and Suman Kumar Dhar, “Single-stranded DNA binding protein from human malarial parasite Plasmodium falciparum is encoded in the nucleus and targeted to the apicoplast” , Nucleic Acids Research, 2010, 1-17 doi:10.1093/nar/gkq565

      Shashank Hambarde, Ragothaman M. Yennamalli , Naidu Subbarao , Sudhir Chandna; "Predictive inference on cytoplasmic and mitochondrial thioredoxin peroxidases in the highly radioresistant Lepidopteran insect Spodoptera frugiperda", Bioinformation 4: 399-404, 2010

      Mobashar Hussain Urf Turabe Fazil, Sunil Kumar, Naidu Subbarao , Haushila Prasad Pandey, Durg Vijai Singh, "Homology modelling of a sensor histidine kinase from Aeromonas hydrophila", Journal of Molecular Modeling 16:1003–1009, 2010

      Ankita Varshney, Priyankar Sen, Ejaz Ahmad, Mohd. Rehan, Naidu Subbarao , Rizwan Hasan Khan, "Ligand binding strategies of human serum albumin: How can the cargo be utilized?", Chirality 22:77-87, 2010

      Vaz C, Ahmad H M, Sharma P, Gupta R, Kumar L, Kulshreshtha R, Bhattacharya A.Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood.BMC Genomics 2010, 11:288.

      Agarwal S, Vaz C, Bhattacharya A, Srinivasan A.Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM).BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S29.


  • 2009       Publications (17)
    • Das S, Vishnoi A, and Bhattacharya A ; ABWGAT: Anchor Based Whole Genome Analysis Tool . Bioinformatics Advance Access published on October 14, 2009. doi:10.1093/bioinformatics/btp587


    • Singh P, Bandyopadhyay P, Bhattacharya S, Krishnamachari A and Sengupta S “ Riboswitch detection using profile Hidden Markov Models ” . BMC Bioinformatics 2009, 10:325


    • Vinekar R and Ghosh I “Determination of Phosphorylation Sites for NADP-specific Isocitratedehydrogenase from Mycobacterium tuberculosis”. Journal of Biomolecular Structure & Dynamics, Volume 26, Issue Number 6, p 663-895 (June 2009)


    • Kampmann T, Yennamalli R , Campbell P, Stoermer MJ,Fairlie DP, Kobe B and Young PR. “ In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses” , Antiviral Res. (2009).


    • Das S*, Yennamalli RM*, Vishnoi A*,Gupta P and Bhattacharya A. “Single nucleotide variations associated with Mycobacterium tuberculosis KZN strains” , Journal of Biosciences, 2009 (Accepted for publication) (* Equal contribution)


    • Banerji A, Ghosh I. “A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in Proteins”, European Biophysics Journal, 2009(Feb.)


    • Vishnoi A, Srivastava A, Roy R,  Bhattacharya A. “MGDD: Mycobacterium tuberculosis genome diversity database”, BMC Genomics  9:373, (2009) doi:10.1186/1471-2164-9-373


    • Prasad A, Agrawal M and Ramaswamy R. “ Strange nonchaotic attractors in driven delay–dynamics in Nonlinear Dynamics”, ( Chapters in Book) Eds. M. Daniel and S. Rajasekar (Narosa, New Delhi 2009) pp 299–304.


    • Bandyopadhyay P, Kuntz ID. “Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction ”Biopolymers, 91, 68, (2009)


    • Meher BR, Kumar MVS, Bandyopadhyay P. “Molecular Dynamics simulation of HIV-protease with polarizable and non-polarizable force fields” . Indian Journal of Physics, 2009,83, 81(invited article).


    • Vashist J,Vishvanath, Kapoor R, Kapil A, Yennamalli R, Subbarao N , Rajeswari MR.“Interaction of nalidixic acid and ciprofloxacin with wild type and mutated quinolone-resistance-determining region of DNA gyrase A” . Indian J Biochem. Biophys., 2009,46(2):147-53.


    • Nandi A, Vaz C, Bhattacharya A and Ramaswamy R . “ miRNA regulated dynamics in circadian oscillator models” . BMC Systems Biology 2009, 3:45


    • Kushwaha HR, Singh AK, Sopory SK, Singla-Pareek SL and Pareek A. “Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa  L.  reveals their developmental and stress regulation” .BMC Genomics 2009, 28;10:200.


    • Sabharwal KS VP, Kushwaha HR, Sopory SK, Singla-Pareek SL, Pareek A. “Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. ” . Funct Integr Genomics. 2009 Feb;9(1):109-23. Epub 2008 Jul 2.


    • Yennamalli R, Subbarao N, Kampmann T, McGeary RP, Young PR, Kobe B.“Identification of novel target sites and an inhibitor of the dengue virus E protein” . J Comput. Aided Mol. Des., 2009, (pub ahead of print)..


    • Sahni NS,Piepel GF, and Naes T. “Product and Process Improvement Using Mixture-Process Variable Methods and Robust Optimization Techniques ”.Journal of Quality Technology. 2009,41(2).


    • Kelkar A, Vivek T, Ramaswamy R, Deobagkar D. “Characterisation of inactivation domains and evolutionary strata in Human X chromosome through Markov segmentation”.PloS One,2009.



  • 2008       Publications (16) & Book Chapter: (2)
    • Lyakhov IG., Krishnamachari A , and Thomas D. Schneider (2008). “Discovery of novel tumor suppressor p53 response elements using information theory Nucleic Acids Research 36(11):3828-33


    • Hosseini A., Ranade SH., Ghosh I., Khandekar P. “Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes”, DNA Seq. 2008, 19(3):167-76.


    • Khan SN, Islam B, Yennamalli R, Zia Q, Subbarao N, Khan AU."Characterization of doxorubicin binding site and drug induced alteration in the functionally important structural state of oxyhemoglobin", J Pharm Biomed Anal. 2008, 48(4):1096-104(Dec).


    • Khan SN, Islam B, Yennamalli R, Sultan A, Subbarao N, Khan AU, "Interaction of mitoxantrone with human serum albumin: spectroscopic and molecular modeling studies", European Journal of Pharmaceutical Sciences, 2008, 35(5):371-82 (Dec).


    • Oswal N, Sahni NS, Bhattacharya A, Komath SS. and Muthuswami R “Unique motifs identification of A proteins from glycosyltransferases of the GT4 family” , BMC Evolutionary Biology.


    • Tyagi S, Vaz C,Gupta V, Bhatia R, Maheswari S, Srinivasan A and Bhattacharya A “CID-miRNA: A web server for prediction of novel miRNA precursors in human genome.” Biochemical and Biophysical Research Communications (2008).


    • Singh A, Hemant R. Kushwaha and Sharma P. “Molecular modelling and comparative structural account of aspartyl beta-semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv)” . J Mol Model. 2008 Apr;14(4):249-63.


    • Mueller DS, kampmann T, Yennamalli R, Young PR and Kobe B and Mark AE (2008).“Histidine protonation and the activation of viral fusion proteins”. Biochemical Society Transactions 36, 43-45


    • Bandyopadhyay P. “Assessment of Two Surface Monte Carlo (TSMC) method to find stationary points of (H2O)15 and (H2O)20 clusters” . Theoretical Chemistry Accounts 120(1), 307-312. (2008)


    • Bandyopadhyay P. (2008). “Two-surface Monte Carlo with basin hopping: Quantum mechanical trajectory and multiple stationary points of water cluster”. The journal of chemical physics 128, 134103.


    • Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy K R , Kuntz ID, and Gibson BW(2008) “Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking”. Analytical Chemistry.


    • Weber C, Blazquez S, Marion S, Ausseur C, Vats D, Krzeminski M, Rigothier S, Maroun RC, Bhattacharya A, Guillen N. (2008) “Bioinformatics and functional analysis of an Entamoeba histolytica mannosyltransferase necessary for parasite complement resistance and hepatical infection”. PloS Negl. Trop. Dis. 2(2), e165 (Feb 13, 2008). doi/10.1371/journal.pntd.0000165.


    • Aggarwal SM, Jain R, Bhattacharya A, Azam A. (2008). “Inhibitors of Escherichia coli serine acetyltransferase block proliferation of Entamoeba histolytica Trophozoites”. Int. J. Parasitol. 38, 136-141


    • A Nandi and  R Ramaswamy (2008). “Synchronization of Coupled Stochastic Oscillators: The effect of topology”. Pramana 70,  1065-74


    • C Bonhomme, P Renesto, S Nandi, A Lynn, D Raoult (2008). “Serological microarray for a paradoxical diagnostic of Whipple's disease”. Eur J Clin Microbiol Infect Dis. Jul 2.


    • Sahni, N.S., Piepel, G.F., N;s, T., Product and Process Improvement Using Mixture-Process Variable Methods and Robust Optimization Techniques



    • Book

            1. Vig L Multiple Robot Teaming: Coalition Formation: From Software Agents to Robots, VDM Verlag, (2008)


            2. Godbole R,  Ramaswamy R, Lilavati's Daughters, “The women scientists of India”,  Indian Academy of Sciences, Bangalore: 2008.  ISBN: 9788186450051

  • 2007       Publications (11)
    • Vig L and Adams JA. (2007). "Coalition Formation: From Software Agents to Robots". Journal of Robotic and Intelligent Systems.


    • Nandi A, Santosh G, Brojen Singh, R. K. and Ramaswamy R. (2007). “Effective mechanisms for the synchronization of stochastic oscillators”. Physical Review E. 76, 041136.


    • Banerjee D, Martin N, Nandi S, Shukla S, Dominguez A, Mukhopadhyay G, Prasad R. (Epub 2007 Jun 16), “A genomewide steroid response study of major human fungal pathogen Candida albicans”. Mycopathologia. 2007 Jul;164(1):117.


    • Azad RK, Lawrence J, Thakur V and Ramaswamy R. “Segmentation of Genomic DNA Sequences, in Advanced Computational Methods in Biocomputing and Bioimaging”, ed. by Tuan D. Pham et.al.,(Nova Science Publishers, NY, 2007).


    • Thakur V, Azad RK, Ramaswamy R. (2007). “Markov models of Genome segmentation” Physical Review E. 75, 011915.


    • Srivastava PK, Desai DK, Nandi S, Lynn A (2007). “HMM-ModE -  Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences”. BMC Bioinformatics. 8,104.


    • Vishnoi A, Roy R, Bhattacharya A (2007). “Comparative analysis of Bacterial genomes: Identification of divergent regions in Mycobacterial strains  using an anchor-based approach”. Nucleic Acid Res. 35, No 11, 3654-3667.
    • Stephen P, Vijayan R, Bhat A, Subbarao N, Bamezai RN (2007) Molecular “modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors”. J Comput Aided Mol Des. (Accepted)


    • Vijayan R, Subbarao N and Mallick BN (2007) “In silico Modeling of a1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist”. American Journal of Biochemistry and Biotechnology 3 (4): 216-224, 2007


    • Sengupta S and A Rutenberg. (2007) “Modeling partitioning of Min proteins between daughter cells after septation in Escherichia coli”. Phys. Biol. 4:145-153


    • Sengupta S, X. Yang and Paul G. Higgs (2007) “The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes” J. Mol. Evol. 64:662-688 (2007).

  • 2006       Publications (13)
    • K Gupta, H P Singh, B Biswal, and R Ramaswamy (2006). Adaptive targeting of chaotic response in periodically stimulated neural systems Chaos 16: 023116-17


    • G Alexe, G S Dalgin, R Ramaswamy, C Delisi and G Bhanot  (2006). Data perturbation independent diagnosis and validation of breast-cancer subtypes using   clustering and patterns Cancer Informatics Online; 2: 243;74


    • Naes T., Aastveit, A. And Sahni, N.S. (2006) Analysis of split-plot designs: an overview and comparison of methods, Quality and Reliability Engineering International.


    • Lovekesh Vig and Julie A. Adams (2006).  Multi-Robot Coalition Formation, IEEE Transactions on Robotics, 22 (4)


    • Lovekesh Vig and Julie A. Adams (2006).  Market Based Multi-Robot Coalition Formation, Distributed Autonomous Robotic Systems ( DARS), Minneapolis, editors   R. Voyles and M. Gini,


    • Krishnamachari A, Srinivas T, Sanadhya SK and Balasundaram S (2006). Perceptron Decision Tree Model for E.coli Promoters. Proceedings of IncoB 2006, New Delhi


    • Mandal, P.K., Rawal, K., Ramaswamy, R., Bhattacharya, A., Bhattacharya, S. (2006). Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to Entamoeba histolytica. Nucleic Acids Res. 34,5752-63.


    • Haimovich, A. D., Byrne B., Ramaswamy R., Welsh, W. J. (2006) Wavelet Analysis   of DNA Walks J Comput Biol.  13, 1289-1298.
    • Mehra, A., Fredrick, J., Petri, W. A. Jr, Bhattacharya, S., Bhattacharya, A., (2006) Expression and function of a family of transmembrane kinases from the protozoan parasite Entamoeba histolytica. Infect Immun. 74, 5341-51.


    • Bhattacharya, A., Padhan, N., Jain, R., Bhattacharya, S. (2006) Calcium-binding proteins of Entamoeba histolytica. Arch Med Res. 37,221-5.


    • Pandey, S. P., Krishnamachari A. (2006) Computational analysis of plant RNA Pol-II promoters. BioSystems. 83, 38-50.


    • Pareek, A., Singh, A., Kumar, M., Kushwaha, H. R., Lynn, A. M., Singla-Pareek, S. L. (2006) Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis. Plant Physiol. 142, 380-97.


    • Desai, D. K., Srivastava, P., Lynn, A. M.. Identifying drug targets from metabolic enzymes, Proceedings of the National Seminar and Workshop on Bioinformatics and Computational Biology-2006, held at Mahila Mahavidyalaya, Banaras Hindu University, Varanasi March 22-24, 2006.

  • 2005       Publications (17)
    • R Ramaswamy (2005). The natural effectiveness of mathematics in the biological sciences. Current Science (Bangalore) 2005; 88: 38187

    • Sahni N.S., Sharma P., Tibshirani R.; Array based detection of cancer based on gene-expression patterns in peripherial blood cells Breast Cancer Research 7, 2005.


    • Sahni N.S., Aastveit A., & Naes T.;In-line process and product control using spectroscopy and multivariate calibration; Journal of Quality Technology 37(1)


    • Sahni N.S., Isaksson T., and Naes T.; Comparison of methods for transfer of calibration models in near-infared spectroscopy : A case study based on correcting path length differences using fiber-optic transmittance probes in in-line near-infrared spectroscopy. Applied spectroscopy ISSN 0003-7028 CODEN APSPA4


    • Lovekesh Vig and Julie A. Adams (2005).  "Issues in Multi-Robot Coalition Formation", Third International Multi-Robot Systems Workshop, From Swarms to Intelligent Automata, Washington D. C., editors Lynne E. Parker, Frank E. Schneider and Allan C. Schultz.


    • Lovekesh Vig and Julie A. Adams (2005).  "A Framework for Multi-Robot Coalition Formation", In the Proceedings of the second Indian International Conference on   Artificial Intelligence, Pune, India.


    • Gourinath, S., Padhan, N., Alam N., Bhattacharya, A. (2005) Crystallization and preliminary crystallographic analysis of calcium-binding protein-2 from Entamoeba histolytica and its complexes with strontium and the IQ1 motif of myosin V. Acta Crystallograph 61,417-20.


    • Loftus, B., Anderson, I., Davies, R., Alsmark, U. C., Samuelson, J., Amedeo, P., Roncaglia, P., Berriman, M., Hirt, R. P., Mann, B. J., Nozaki, T., Suh, B., Pop, M., Duchene, M., Ackers, J., Tannich, E.,  Leippe, M., Hofer, M., Bruchhaus, I., Willhoeft, U., Bhattacharya, A., Chillingworth, T., Churcher, C., Hance, Z., Harris, B., Harris,    D., Jagels, K., Moule, S., Mungall, K., Ormond, D., Squares, R., Whitehead, S., Quail,     M. A., Rabbinowitsch, E., Norbertczak, H., Price, C., Wang, Z., Guillen, N., Gilchrist, C., Stroup, S. E., Bhattacharya, S., Lohia, A., Foster, P. G., Sicheritz-Ponten, T., Weber, C., Singh, U., Mukherjee, C., El-Sayed, N. M., Petri, W. A. Jr., Clark, C. G., Embley, T. M., Barrell, B., Fraser, C. M., Hall, N. (2005) The genome of the protist parasite Entamoeba histolytica. Nature. 433,865-8.


    • Nandi, S., Mehra, N., Lynn, A. M., Bhattacharya, A. (2005) Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution BMC Genomics. 6, 116.


    • Vats, D., Vishwakarma, R. A., Bhattacharya, S., Bhattacharya, A. (2005) Reduction of cell surface glycosylphosphatidylinositol conjugates in Entamoeba histolytica by antisense blocking of E. histolytica GlcNAc-phosphatidylinositol deacetylase expression: effect on cell proliferation, endocytosis, and adhesion to target cells. Infect   Immun. 73, 8381-92.


    • Bakre, A. A., Rawal, K., Ramaswamy, R., Bhattacharya, A., Bhattacharya, S. The LINEs and SINEs of Entamoeba histolytica: comparative analysis and genomic distribution. Exp Parasitol. 110, 207-13.


    • Bansal-Mutalik, R., Mustafi, S. M., Bhattacharya, A., Chary, K. V. (2005) Sequence specific 1HN, 13C and 15N resonance assignments of a novel calcium-binding protein from Entamoeba histolytica. J Biomol NMR. 31, 379-80.


    • Deswal, R., Singh, R., Lynn, A. M., Frank, R. (2005) Identification of immunodominant regions of Brassica juncea glyoxalase I as potential antitumor immunomodulation targets. Peptides. 26, 395-404.
    • Sharma, P., Sahni, N. S., Tibshirani, R., Skaane, P., Urdal, P., Berghagen, H., Jensen, M., Kristiansen, L., Moen, C., Sharma, P., Zaka, A., Arnes, J., Sauer, T., Akslen, L. A., Schlichting, E., Borresen-Dale, A. L., Lonneborg. A. (2005) Early detection of breast cancer based on gene-expression patterns in peripheral blood cells. Breast Cancer Res. 7, R634-44.


    • Sahni, N. S., Isaksson, T., Naes, T. (2005) Comparison of methods for transfer of calibration models in near-infared spectroscopy: a case study based on correcting path length differences using fiber-optic transmittance probes in in-line near-infrared spectroscopy. Appl Spectrosc. 59, 487-95.


    • Agarwal, S. M. (2005) Evolutionary rate variation in eukaryotic lineage specific human intronless proteins. Biochem Biophys Res Commun. 337, 1192-7.


    • Agarwal, S. M., Gupta, J. (2005) Comparative analysis of human intronless proteins. Biochem Biophys Res Commun. 331, 512-9.

  • 2004       Publications (7)
    • Sahni, N.S., Isaksson, T., and Naes, T. (2004).; In-line near infrared spectroscopy in product and process monitoring in the food industry, Journal of NIR spectroscopy.

      Krishnamachari, A., moy Mandal, V., Karmeshu. (2004) Study of DNA binding sites using the Renyi parametric entropy measure. J Theor Biol. 227, 429-36.

      Karmeshu and
      Krishnamachari "Sequence variability and long-range dependence in DNA: An Information theoretic perspective" Lecture notes in Computer Science. Vol. 3316, p1354, 2004. Springer Publications.

      Mandal, P. K.,Bagchi, A.,
      Bhattacharya, A., Bhattacharya, S. (2004) An Entamoeba histolytica LINE/SINE pair inserts at common target sites cleaved by the restriction enzyme-like LINE-encoded endonuclease. Eukaryot Cell. 2004 3, 170-9.

      Chakrabarty, P., Sethi, D. K., Padhan, N., Kaur, K. J., Salunke, D. M., Bhattacharya, S., Bhattacharya, A. (2004) Identification and characterization of EhCaBP2. A second member of the calcium-binding protein family of the protozoan parasite Entamoeba histolytica. J Biol Chem. 279, 12898-908

      Sharma, D., Issac, B., Raghava, G. P., Ramaswamy, R. (2004) Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics. 20, 1405-12.

      Singh, B.K.,Subba Rao, J., Ramaswamy, R., Sinha, S. (2004) The role of heterogeneity on the spatiotemporal dynamics of host-parasite metapopulation. Ecolo. Modeling. 180. 435-443.

  • 2003       Publications (5)
    • R Ramaswamy and R K Azad (2003). Analysis of DNA sequences through segmentation: Exploring the mosaic via statistical measures Physica Scripta 2003; T106: 2125

      Satish, S., Bakre, A. A., Bhattacharya, S., Bhattacharya, A. (2003) Stress-dependent expression of a polymorphic, charged antigen in the protozoan parasite Entamoeba  histolytica. Infect Immun. 71, 4472-86.

      Bhattacharya, A., Bhattacharya, S., Ackers, J. P. (2003) Nontranslated polyadenylated RNAs from Entamoeba histolytica. Trends Parasitol. 19, 286-9.

      Ghosh, S, Satish, S., Tyagi, S., Bhattacharya, A., Bhattacharya, S. Differential use of  multiple replication origins in the ribosomal DNA episome of the protozoan parasite Entamoeba histolytica. Nucleic Acids Res. 31, 2035-44.

      Jha, S., Karnani, N., Lynn, A. M., Prasad, R. (2003) Covalent modification of cysteine 193 impairs ATPase function of nucleotide-binding domain of a Candida drug efflux pump. Biochem Biophys Res Commun.310, 869-75.

  • 2002       Publications (4)
    • G Aggarwal and R Ramaswamy (2002). Ab-initio gene prediction: Prokaryote Genome annotation with GLIMMER and GeneScan, Journal of Biosciences (Supplement 1); 27: 7 14

      Bhattacharya,S., Bakre, A.,
      Bhattacharya, A. (2002) Mobile genetic elements in protozoan parasites. J Genet. 81, 73-86.

      Azad, R.K., Subba Rao, J., Li, W., Ramaswamy, R. (2002) Simplifying the mosaic description of DNA sequence. Phys. Rev., E 66 (3), 031913.

      Azad, R.K., Pernola-Galvan, P., Ramaswamy, R., Subba Rao, J. (2002) Segmentation of Genomic DNA through entropic divergenceL Power laws and Scaling. Phys. Rev., E 65 (5), 051909.