SC&IS : Publications
- Y Gigani, S Gupta, A Lynn, K Asotra, BKCa CHANNEL BASED CHEMICAL ENTITY RECOGNITION USING PATENT DATA CURATION AND MOLECULAR FIELD ALIGNMENT TECHNIQUE, Pharmacophore An International Research Journal 7 (4)
- A Qayum, R Arya, AM Lynn , Ethnobotanical perspective of antimalarial plants: traditional knowledge based study, BMC research notes 9 (1), 67
- M Kamran, S Sinha, P Dubey, AM Lynn, SK Dhar, Identification of putative Z‐ring‐associated proteins, involved in cell division in human pathogenic bacteria Helicobacter pylori, FEBS letters 590 (14), 2158-2171
- D Singh, S Rawat, M Waseem, S Gupta, A Lynn, M Nitin, N Ramchiary, ... Molecular modeling and simulation studies of recombinant laccase from Yersinia enterocolitica suggests significant role in the biotransformation of non-steroidal anti-inflammatory drugs, Biochemical and biophysical research communications 469 (2), 306-312
- Co-movements in financial fluctuations are anchored to economic fundamentals: A mesoscopic mapping, K Sharma, B Gopalakrishnan, AS Chakrabarti, A Chakraborti, arXiv preprint arXiv:1612.05952.
- Resonance Raman scattering and ab initio calculation of electron energy loss spectra of MoS 2 nanosheets, A Chakraborti, AS Patel, PK Kanaujia, P Nath, GV Prakash, D Sanyal, Physics Letters A 380 (48), 4057-4061.
- Can an interdisciplinary field contribute to one of the parent disciplines from which it emerged? A Chakraborti, D Raina, K Sharma, The European Physical Journal Special Topics 225 (17-18), 3127-3135.
- Investigating resonance energy transfer from protein molecules to van der Waals nanosheets, AS Patel, P Mishra, PK Kanaujia, SS Husain, GV Prakash, A Chakraborti, arXiv preprint arXiv:1611.07182.
- Thermal Equilibrium in D-dimensions: From Fluids and Polymers to Kinetic Wealth Exchange Models, M Patriarca, E Heinsalu, A Singh, A Chakraborti, arXiv preprint arXiv:1610.03367.
- Sectoral co-movements in the Indian stock market: A mesoscopic network analysis, K Sharma, S Shah, AS Chakrabarti, A Chakraborti, arXiv preprint arXiv:1607.05514.
- Physicists' approach to studying socio-economic inequalities: Can humans be modelled as atoms? K Sharma, A Chakraborti, arXiv preprint arXiv:1606.06051.
- Gold nanoflowers as efficient hot-spots for surface enhanced Raman scattering. AS Patel, S Juneja, PK Kanaujia, GV Prakash, A Chakraborti, arXiv preprint arXiv:1604.02793.
- Quantifying invariant features of within-group inequality in consumption across groups. Anindya S Chakrabarti, Arnab Chatterjee, Tushar K Nandi, Asim Ghosh, Anirban Chakraborti.
- Invariant features of spatial inequality in consumption: The case of India. A Chatterjee, AS Chakrabarti, A Ghosh, A Chakraborti, TK Nandi, Physica A: Statistical Mechanics and its Applications 442, 169-181.
- Performance Evaluation of Empirical Mode Decomposition Algorithms for Mental Task Classification. A Gupta, D Kumar, A Chakraborti, K Sharma. bioRxiv, 076646.
- P Prathipati, C Nagao, S Ahmad, K Mizuguchi, Improved pose and affinity predictions using different protocols tailored on the basis of data availability, Journal of computer-aided molecular design 30 (9), 817-828.
- M Fernandez, S Ahmad, JI Abreu, A Sarai, Large-scale recognition of high-affinity protease–inhibitor complexes using topological autocorrelation and support vector machines, Molecular Simulation 42 (5), 420-433.
- VK Singh,A Krishnamachari,Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome: Genomics Data 9, 130-136 (2016)
- Madhulata Kumari, Subhash Chandra, Neeraj Tiwari and Naidu Subbarao, High throuput virtual screening to identify Novel inhibitors for Mehionyl-tRNA synthetase of Brucella mellitensis, Bioinformation 2016
- Ramachandran Vijayan, Naidu Subbarao, Natesan Manoharan Computational Study Enlightens the Structural Role and Molecular Mechanism of Marine Algal Compound Fucoidan against Hepatocellular Carcinoma Markers, International Journal of Bioscience, Biochemistry and Bioinformatics(2016) ,321-328
- A Jadaun, N Subbarao, A Dixit Allosteric inhibition of topoisomerase I by pinostrobin: Molecular docking, spectroscopic and topoisomerase I activity studies Accepted for publication Journal of Photochemistry and Photobiology B: Biology 2016
- Hit To Lead Optimization, And 3D QSAR Modeling of Imidazolopiperazines Derivatives against Malaria Based On PLSR Machine Learning Technique, M Kumari, N Tiwari, N Subbarao, S Chandra, Imperial Journal of Interdisciplinary Research 2 (12), 2016
- in vivo anti-inflammatoryactivity and dockin study of newly synthesized benzamidazole derivatives bearing oxadiazole and morpholine rings M shahar Yar Ankita Rathore, Raja Sudhakar, Mohamed Jawed Ahsan, Abuzer Ali, Naidu Subbarao, Suender Singh Yadav, Sadiq Umer ... Bioorganic Chemistry, 2016
- Design, synthesis of allosteric peptide activator for human SIRT1 and its biological evaluation in cellular model of Alzheimer's disease, SD Rahul Kumar, Lokesh Nigam, Amrendra Pratap Singh, Kusum Singh, Naidu Subbarao, European Journal of Medicinal Chemistry, 2016
- 3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum, Neeraj Tiwari and Naidu Subbarao, Madhulata Kumari, Subhash Chandra, BMC Structural Biology, 2016
- Interaction of the recently approved anticancer drug nintedanib with human acute phase reactant α 1-acid glycoprotein, AS Abdelhameed, MR Ajmal, K Ponnusamy, N Subbarao, RH Khan, Journal of Molecular Structure 1115, 171-179, 2016
- Docking and Molecular Dynamics simulation study of EGFR1 with EGF like peptides to understand molecular interactions, Naidu Subbarao D.Rajasudhakar, Kalaisaran Ponnusamy, Molecular Biosystems, 2016
- 3D QSAR basedhit to lead optimization of Imidazolopiperazines derivatives against P.falciparum, Neeraj Tiwari and Naidu Subbarao and Subhash Chandra Madhulata Kumari,, Imperial Journal of Interdisciplinary Research 2 (12), 2016
- Designing, synthesis and antimicrobial action of oxazoline and thiazoline derivatives of fatty acid esters, Naidu Subbarao and Asad U Khan Anis Ahmad, D.Raja Sudhakar, journal of Biomolecular Structure and dynamics, 2016
- Pharmacophore based virtual screening for identification of marine bioactive compounds as inhibitors against macrophage infectivity potentiator (Mip) protein of Chlamydia trachomatis, Subbarao Naidu and Manoharan Natesan Vijayan Ramachandran , Elavarasi Padmanaban, Kalaiarasan Ponnusamy, RSC Advances, 2016
- Transcription regulation of nuclear receptor PXR: role of SUMO-1 modification and NDSM in receptor function RT Priyanka, Naidu Subbarao, Niti Puri, Molecular and Cellular Endocrinology 420, 194-207, 2016
- Arnab Bhattacherjee, Dana Krepel and Yaakov Levy, Coarse-grained models for studying protein diffusion along DNA: WIREs Computational Molecular Science 2016. doi: 10.1002/wcms.1262 (2016)
- Rajan Shrivastava, Avijit Rakshit, Sudhanshu Shanker, Lovekesh Vig, Pradipta Bandyopadhyay, A combination of Monte Carlo Temperature Basin Paving and graph theory: water cluster low energy structures and completeness of search. J.Chem.Sci (2016), 128, 1507.
- Priya Singh, P. Bandyopadhyay, S. K. Sarkar,Folding-unfolding transition in the mini-protein villin headpiece (HP35): An equilibrium study using the Wang-Landau algorithm. Chem. Phys., 468, 1-8 (201
- Sudhanshu Shanker and Pradipta Bandyopadhyay, J.Bio.Str.Dyn. (in press, 2016), How Mg2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E coli Loop E of 5S rRNA: A Molecular Dynamics and Reference Interaction Site Model (RISM) study.
- T.Asada, K.Ando, P.Bandyopadhyay, S.Koseki, Free Energy Contribution Analysis using Response Kernel Approximation: Insights into the Acylation Reaction for beta–lactamase, J.Phys.Chem.B( in press), 2016
- R. Kaalia, I. Ghosh, Semantics based approach for analyzing disease-target associations, Journal of Biomedical Informatics 62 June (2016) 125–135
- Rama Kaalia, Ashwin Srinivasan,Amit Kumar and Indira Ghosh; ILP-assisted de novo drug design. Machine Learning, June 2016, Volume 103, Issue 3, pp 309–341,published online , DOI 10.1007/s10994-016-5556-x. March 2016.
- Sandeep Kumar, Binod K. Kanaujia, Shantanu Dwari, Ganga Prasad Pandey, and Dinesh Kumar Singh, “11–17 GHz Reconfigurable Stacked Power Amplifier Using Matched Slant Microstrip Line for Ku Band Application,” Wireless Personal Communication Springer vol. , pp., 2016. (Accepted)
- Sachin Kumar, Binod Kr Kanujia, Mukesh k. khandelwal and A. K. Gautam, “Single-Feed Superstrate Loaded Circularly Polarized Microstrip Antenna for Wireless Applications,” Wireless Personal Communication Springer vol. , pp.1-11, 2016. (Accepted)
- Naveen Jaglan, Binod K. Kanaujia, samir D Gupta and Sweta Srivastava “Triple Band Notched UWB Antenna Design Using Electromagnetic Band Gap Structures,”Progress In Electromagnetics Research C (USA) vol. 66, pp.139-147, 2016.
- Naveen Jaglan, samir D Gupta, Binod K. Kanaujia and Sweta Srivastava “Band Notched UWB Circular Monopole Antenna with Inductance Enhanced modified mushroom EBG structures,” Wireless Networks Springer vol. , pp. , 2016. (Accepted)
- S. Yadav, A.K.Gautam, Anil k Sinh, Binod Kr Kanaujia and K Rambabu, “Design of Band-Rejected UWB Planar Antenna with Integrated Bluetooth Band” IET Microwaves, Antenna & Propagation, (UK) vol. , no. , pp. , 2016. (Accepted).
- Binod Kr Kanujia, Mukesh k. khandelwal, Santanu Dwari, Sachin Kumar and A. K. Gautam, “Analysis and Design of Compact High Gain Microstrip Patch Antenna with Defected Ground Structure for Wireless Applications,” Wireless Personal Communication, Springer vol. , pp. , 2016. (Accepted)
- Sandeep Kumar, Mitul Handa, Himanshu Bhasin and Binod K. Kanaujia, Shantanu Dwari, “Optimized Threshold Voltage Variation for Tunable Body Biasing CMOS Power Amplifier",” Wireless Personal Communication, Springer vol. , pp. , 2016. (Accepted)
- Kunal Srivastava, Ashwani Kumar, A.K Verma,Q. Zhang, Binod Kr Kanujia, and S Dwari, “Integrated GSM and UWB Fractal Monopole Antenna with Triple Notches,” Microwave and Optical Technology Letters, (USA) vol.58, no.10, pp.2364-2366, 2016.
- Anil kumar Singh, Ravi kumar Gangwar, and Binod Kr Kanujia, “Circularly Polarized Annular Ring Microstrip Antenna for High Gain Application,”Electromagnetic, Taylor and Francis vol.36, no.6, pp.379-391, 2016
- Pallavi Bartwal, A.K.Gautam, Anil k Sinh, Binod Kr Kanaujia and K Rambabu, “Design of Compact Multi-Band Meander-Line Antenna for GPS/WLAN/WiMAX band Applications in Laptops/Tablets” IET Microwaves, Antenna & Propagation, (UK) vol. , no. , pp. , 2016. (Accepted).
- Jugal Kishor, Binod Kr Kanujia, Shantanu Dwari, and Ashwani Kumar, “Bandpass Filter Using Dielectric Resonator with Transmission Zeros,” Microwave and Optical Technology Letters, (USA) vol.58, no.7, pp.1583-1586, 2016.
- Kunal Srivastava, Ashwani Kumar, and Binod Kr Kanujia, “Design of Compact Penta-Band and Hexa-Band Microstrip Antennas” Frequenz (Germany) vol. 70, no. 3-4, pp.101-111, Jan. 2016.
- J. P. Keshari, Binod Kr Kanujia, Mukesh k. khandelwal, Pritam Singh Bakariya and R. M. Mehra, “Single-Feed Circularly Polarized Stacked Patch Antenna with Small Frequency Ratio for Dual-Band Wireless Applications” International Journal of Microwave and Wireless Technologies Cambridge University Press, (UK) vol. , pp. , 2016. (Accepted)
- A.K.Gautam, Lalit Kumar, Binod Kr Kanaujia and K Rambabu, “Design of Compact F-shaped slot Triple Band Antenna for WLAN/WiMAX Applications” IEEE Trans. Antennas Propagat., (USA) vol. 64, no. 03, pp. 1101-1105, March 2016.
- Akanksha Farswan, A.K.Gautam, Binod Kr Kanaujia and K Rambabu, “Design of Koch Fractal Circularly Polarized Antenna for Handheld UHF RFID Reader Applications” IEEE Trans. Antennas Propagat., (USA) vol. 64, no. 2, pp. 771-775, 2016.
- S. Yadav, A. K. Gautam, and Binod Kr Kanujia, “Design of miniaturized single band notch micro strip antenna with enhanced UWB performance,” Microwave and Optical Technology Letters, (USA) vol. 58, no. 6, pp. 1494-1499, 2016.
- Kunal Srivastava, Ashwani Kumar, and Binod Kr Kanujia, “Design of Compact Penta-Band Microstrip Antennas,” Microwave and Optical Technology Letters,(USA) vol. 58, no. 4, pp. 836-838, 2016.
- A. K. Gautam, A. Bisht and Binod Kr Kanujia, “A Wideband Antenna With Defected Ground Plane for WLAN/WiMAX Applications” International Journal of Electronics and Communication AEU Elsevier, (Germany) vol. 70, no. 3, pp. 354-358, 2016.
- Anil kumar Singh, Ravi kumar Gangwar, and Binod Kr Kanujia, “Sectored Annular Ring Microstrip Antenna with DGS for Circular Polarization,” Microwave and Optical Technology Letters, (USA) vol.58, no.3, pp.569-573, 2016.
- Deepak Gangwar, Sushrut Das, R. L. Yadav and B. K. Kanaujia, “Circularly Polarized Inverted Stacked High Gain Antenna with Frequency Selective Surface,” Microwave and Optical Technology Letters, (USA) vol.58, no.3, pp.732-740, 2016.
- Sharma M.K*., Sharma R., Cao P., Harkenrider M., Jenkins J., Grimwood J., Zhang J., Udvardi M.K., Schmutz J. and Ronald P.C. (2015) Targeted switchgrass BAC library screening and sequence analysis identifies predicted biomass-related and stress response-related genes. BioEnergy Research, 9 (1): 109-122.
- Sharma R., Wungrampha W., Singh V., Pareek A. and Sharma, M.K. (2016) Halophytes as Bioenergy Crops. Frontiers in Plant Science doi: 10.3389/fpls.2016.01372.
- Kundu S., Sharma R. (2016) In silico Identification and taxonomic distribution of plant class C GH9 endoglucanases. Frontiers in Plant Science http://dx.doi.org/10.3389/fpls.2016.01185.
- Chandran A.K.N., Yoo Y.H., Cao P., Sharma R., Sharma M.K., Dardick C., Ronald P.C. and Jung K.H. (2016) Updated rice kinase database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. Rice 9:40
- Harkenrider M., Sharma R., Vleesschauwer D.D., Tsao, L., Zhang X., Chern M., Canlas P., Zuo S. and Ronald P.C. (2016) Overexpression of rice Wall-Associated Kinase 25 (WAK25) alters resistance to bacterial and fungal pathogens. Plos One 11 (1):e0147310.
- Gupta P., Sharma R., Sharma M.K., Sharma M.P., Stapute G.K., Garg S., Singla-Pareek, S.L., Pareek A. (2016) Signaling cross talk between biotic and abiotic stress responses in soybean. Abiotic and Biotic Stresses in Soybean Production: Soybean Production, Volume 1, 27-52.
- Khemka N, Singh VK, Garg R, Jain M. (2016) Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development. Scientific Reports 6, 33297. doi:10.1038/srep33297
- Shankar R, Bhattacharjee A, Jain M. (2016) Transcriptome analysis in different rice cultivars provides novel insights into drought and salinity stress responses. Scientific Reports 6, 23719. DOI: 10.1038/srep23719.
- Bhattacharjee A, Khurana JP, Jain M. (2016) Characterization of rice homeobox genes, OsHOX22 and OsHOX24, and over-expression of OsHOX24 in transgenic Arabidopsis suggest their role in abiotic stress response. Frontiers in Plant Science 7, 627. doi: 10.3389/fpls.2016.00627.
- Jain M, Srivastava PL, Verma M, Ghangal R, Garg R. (2016) De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis. Scientific Reports 6, 22456. doi: 10.1038/srep22456.
- Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M. (2016) Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea. Scientific Reports 6, 19228. doi: 10.1038/srep19228
- Kotwal S, Kaul S, Sharma P, Shankar R, Jain M, Dhar M. (2016) De novo transcriptome analysis of medicinally important Plantago ovata using RNA-Seq. PLoS ONE 11,e0150273. doi:10.1371/journal.pone.0150273.
- Dixit AB, Banerjee J, Srivastava A, Tripathi M, Sarkar C, Kakkar A, Jain M, Chandra S. (2016) RNA-Seq analysis of hippocampal tissues reveals novel candidate genes for drug refractory epilepsy in patients with MTLE-HS. Genomics 107, 178-188.
- Singh, G.P., Sangita Kansal, Basic Results on Crisp Boolean Petri Nets, In:Modern Mathematical Methods and High Performance Computing in Science and Technology, 83-88, Chapter 6, Springer proceedings in Mathematics & Statistics, Series 171 (Edition No.1), ISBN 978-981-10-1454-6, Springer Singapore, 2016
- Singh, G.P., Applications of Petri nets in electrical, electronics and optimizations, Procedings of International Conference on Electrical, Electronics, and Optimization Techniques IEEE XCplore, catalog 978-1-4673-9939-5/16, 2016.
- Sarbashis Das , B.M. Fredrik Pettersson , Phani Rama Krishna Behra , Malavika Ramesh , Santanu Dasgupta , Alok Bhattacharya , and Leif A. Kirsebom, Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics Genome Biol. Evol. 7(7):1871–1886
- Tanmoy Roychowdhury , Saurav Mandal & Alok Bhattacharya, Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis(2015) Scientific Reports | 5:12567 | DOI: 10.1038/srep12567
- Avni Sinha, Kandasamy Eniyan, Swati Sinha, Andrew Michael Lynn, Urmi Bajpai Functional analysis of TPM domain containing Rv2345 of Mycobacterium tuberculosis identifies its phosphatase activity, Elsevier, doi:10.1016/j.pep.2015.03.003
- Abdul Qayum, Rakesh Arya, Pawan Kumar, Andrew M Lynn, Socio-economic, epidemiological and geographic features based on GIS-integrated mapping to identify malarial hotspots, Malaria Journal (Impact Factor: 3.11). 05/2015; 14(1):192. DOI: 10.1186/s12936-015-0685-4 Source: PubMed
- Deepti Singh, Surender Rawat, Mohd Waseem,Sunita Gupta, Andrew M Lynn, Molecular modeling and simulation studies of recombinant laccase from Yersinia enterocolitica suggests significant role in the biotransformation of non-steroidal anti-inflammatory drugs Biochemical and Biophysical Research Communications (Impact Factor: 2.3). 12/2015; 469(2). DOI: 10.1016/j.bbrc.2015.11.096
- “Statistical mechanics of competitive resource allocation using agent-based models”, A. Chakraborti, D. Challet, A. Chatterjee, M. Marsili, Y.-C. Zhang, B.K. Chakrabarti, Physics Reports 552, 1-25 (2015).
- “Invariant features of spatial inequality in consumption: the case of India”, Arnab Chatterjee, Anindya S. Chakrabarti, Asim Ghosh, Anirban Chakraborti, Tushar K. Nandi, Physica A 442, 169-181 (2016).
- Singh, G.P. and Kansal, K., Basic Results on Crisp Boolean Petri Nets, accepted for the publication in LNCS, Springer.
- Kansal, S., Singh, G.P. and Acharya, M., On the problem of characterizing Boolean Petri nets, Int. Jr. of Comp. Appli., Found. of Comp. Sci., New York, USA, 128(2), October 2015, 1-4, ISBN 973-93-80889-69-7.
- Singh, G.P., Basic properties of Petri nets, SRMS Journal of Mathematical Sciences, pub- lished by Department of Mathematics, Shri Ram Murti Smarak College of Engg. & Tech., Bareilly-243202, U.P., India, 1(1), 2015, 54-71, ISBN: 2394-725X.
- Singh, G.P., Kansal, S. and Acharya, M., Characterization of Boolean Petri net containing strong chain cycle, submitted to Elsevier.
- Khan ,Taushif & Ghosh Indira; Modularity in protein structures: A study on all alpha proteins. Journal of Biomolecular Structure & Dynamics, 2015 Feb 11:1-15.
- Rama Kaalia,Amit Kumar,Ashwin Srinivasan, and Indira Ghosh;, An Ab Initio Method for Designing Multi-Target Specific Pharmacophores using Complementary Interaction Field of Aspartic Proteases. Mol. Inf. 2015, 34, 2 –16
- Topological variance in protein structure: an insight from kinetics and functional study T Khan, I Ghosh , Journal of Biomolecular Structure and Dynamics 33 (sup1), 113-114
- Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M. (2015) Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.Scientific Reports (accepted). (IF = 5.578)
- Mohd Shariq; Navin Kumar; Rajesh Kumari; Amarjeet Kumar; Naidu Subbarao; Gauranga Mukhopadhyay, Biochemical Analysis of CagE: a VirB4 Homologue of Helicobacter pylori Cag-T4SS PlosOne(2015)
- Priyanka, Naidu Subbarao, Niti Puri, Rakesh Tyagi Transcription regulation of nuclear receptor PXR: role of SUMO-1 modification and NDSM in receptor function, Molecular and Cellular Endocrinology,2015
- Sumit K Chaturvedi; Parvez Alam; Javed M Khan; Mohammad K Siddiqui; Zeeshan Ahmad; Ponnusamy Kalaiarasan; Naidu Subbarao; Biophysical insight into the anti-amyloidogenic behavior of taurine, International Journal of Biological Macromolecules, 80, 375-384(2015)
- Mohd Ishtikhar, Mohd. Sajid Ali, Ayman M. Atta, H. A. Al-Lohedan, Lokesh Nigam, Naidu Subbarao, Rizwa H Khan, Interaction of biocompatible natural rosin-based surfactants with human serum albumin: A biophysical study Journal of luminiscence,167, 399-407(2015)
- Functional dissection of Proliferating Cell Nuclear Antigens (1&2) in human malarial parasite Plasmodium falciparum : possible involvement in DNA replication and DNA damage response, Biochemical Journal, 470 (1), 115-129(2015)
- Mohammad Hassan Baig, Khurshid Ahmad, Qambar Hasan, Mohd Kalim Ahmad Khan, Naidu Subbarao, Mohammad Amjad Kamal and Inho Choi Interaction of glucagon G-protein coupled receptor with known natural anti-diabetic compounds: Multi-scoring in silico approach. Evidence-Based Complementary and Alternative Medicine Special issue on "Herbal Medicines and Natural Products Targeting G Protein-Coupled Receptors in Management of Diseases", Article ID 497253, 6 pages, . doi:10.1155/2015/497253 (2015)
- Vijayan Ramachandran, Subbarao Naidu and Manoharan Natesan Discovery of Marine Sponge Compound as Promising Inhibitor for Macrophage Infectivity Potentiator (Mip) Protein against Chlamydia pneumoniae.International journal of Bioscience, Biochemisty and Bioinformatics,6,5(3),202-210, 2015
- 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), 13,3, e0119760 PLOSOne(2015)
- 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, 10 (3), 1-21 PloseOne(2015)
- Ramachandran Vijayan, N.Subbarao, Natesan Manoharan In silico Analysis of Conformational Changes Induced by Normal and Mutation of Macrophage Infectivity Potentiator catalytic residues and its Interactions with Rapamycin, Interdisciplinary Sciences: Computational Life Science(2015), 7,1-8
- Sharma, S., Kumar, A., Kundu, S. and Bandyopadhyay, P. (2015), Molecular dynamics simulations indicate that tyrosineB10 limits motions of distal histidine to regulate CO binding in soybean leghemoglobin. Proteins, 83: 1836–1848. doi:10.1002/prot.24867
- An analytical correlated random walk model and its application to understand subdiffusion in crowded environment, J. Chem. Phys. 143, 114104 (2015); http://dx.doi.org/10.1063/1.4930275
- Jasleen Gundh, Awaneesh Singh, R. K. Brojen Singh. Ordering Dynamics in Neuron Activity Pattern Model: An Insight to Brain Functionality. PloS One (2015) DOI: 10.1371/journal.pone.0141463.
- G.R. Devi, Md.J. Alam and R.K. Brojen Singh. Synchronization in stress p53 network. Math. Med. Biol. (2015) doi: 10.1093/imammb/dqv002.
- Md. Z. Malik, S. Ali, Md.J. Alam, R. Ishrat and R.K. Brojen Singh. Dynamics of p53 and Wnt cross talk. Comp. Biol. Chem. (Accepted) doi:10.1016/j.compbiolchem.2015.07.014 (2015).
- Md.J. Alam, S. Kumar, V. Singh and R.K. Brojen Singh. Bifurcation in cell cycle dynamics regulated by p53. PloS One (2015) DOI: 10.1371/journal.pone.0129620.
- Md.J. Alam, V. Singh and R.K. Brojen Singh. Switching Mechanism in the p53 Regulatory Network. Chapter, Syst. And Synthetic Biol. 195-216 (2015).
- Kh. Kabita, B. I. Sharma, J. Maibam, R. K. Brojen Singh and R.K. Thapa. Structural Phase Transition of Indium Arsenide under induced pressure: A Density functional theory study. J. Appl. Fund. Sc. 1, 2395-5562 (2015). 34. M Jameson, Kh. Kabita, B.I. Sharma, B. Ramendu, RK Thapa, R.K. Brojen Singh. Density Functional Theory: Band Structure. Inv. J. Renew. Energy 5, 2231-3419 (2015).
- Kh. Kabita, M Jameson, B.I. Sharma, RK Thapa, R.K. Brojen Singh. First principle study on pressure-induced electronic structure and elastic properties of indium phosphide (InP). DOI:10.1007/s12648-015-0701-0 (2015).
- Kh. Kabita, B. Indrajit Sharma, Jameson Maibam, R. K. Brojen Singh and R.K. Thapa. STRUCTURAL PHASE TRANSITION OF INDIUM ARSENIDE UNDER INDUCED PRESSURE: A DENSITY FUNCTIONAL THEORY STUDY. J. Appl. Fund. Sc. 1, 2395 (2015).
- K Kabita, J Maibam, B I Sharma, R K Thapa and R K Brojen Singh. First principle study on pressure-induced electronic structure and elastic properties of indium phosphide (InP). Ind. J. Phys. 89, 1265 (2015).
- Kh Kabita, Jameson Maibam, B Indrajit Sharma, R K Brojen Singh and R K Thapa. First principles phase transition, elastic properties and electronic structure calculations for cadmium telluride under induced pressure: density functional theory, LDA, GGA and modified Becke–Johnson potential. Mat. Res. Exp. 3, 015901 (2016).
- Kh. Kabita, M. Jameson, B.I. Sharma, R.K. Brojen Singh, R.K. Thapa. A detailed first principle study on the structural, elastic, and electronic properties of indium arsenide (InAs) under induced pressure. Can. J. Phys. (doi: 10.1139/cjp-2015-0275) (2015).
- Kh. Kabita, Jameson Maibam, Indrajit Sharma, R. K. Brojen Singh, R.K. Thapa. Adv. Sc. Lett. 21, 2906 (2015).
- Maibam Jameson,Kh. Kabita, B I. Sharma, Bhattacharjee Ramendu,Thapa R.K., R. K. Brojen Singh. Density Functional Theory: Band Structure. Inv. J. Ren. En. 5, 2231 (2015).
- Sharma M.K*., Sharma R*., Cao P., Harkenrider M., Jenkins J., Grimwood J., Zhang J., Udvardi M.K., Schmutz J. and Ronald P.C. (2015) Targeted switchgrass BAC library screening and sequence analysis identifies predicted biomass-related and stress response-related genes. BioEnergy Research, DOI 10.1007/s12155-015-9667-1.
- Jung K.H., Cao P., Sharma R., Jain R., and Ronald, P.C. (2015) Phylogenomics databases for facilitating functional genomics in rice. Rice, 8: 26.
- Sharma R., Mishra M., Gupta B., Parsania C., Pareek S.L.S., and Pareek A. (2015) De Novo assembly and characterization of stress transcriptome in a salinity-tolerant variety CS52 of Brassica juncea. Plos One. 10(5):e0126783.
- Lao J., Sharma M.K., Sharma R., Fernandez-Nino S.M G., Schmutz J., Ronald P.C., Haezlewood J.L., and Schwessinger. (2015) Proteome profile of the endomembrance of developing coleoptiles from switchgrass (Panicum virgatum).Proteomics. DOI: 10.1002/pmic.201400487
- Manoj Agarwal, Naveen Kumar, and Lovekesh Vig, "Parallel Multi Objective Coalition Formation", Expert Systems and Applications, 42 (21), 7797-7811, 2015
- Pankaj Malhotra, Lovekesh Vig, Gautam Shroff and Puneet Agarwal, "Long Short Term Memory Networks for Anomaly Detection in Time Series", European Symposium on Artificial Neural Networks, Belgium, 2015
- Sucheta Chouhan and Lovekesh Vig, "Anomaly Detection in ECG Time Signals through Deep Long Short-Term Memory based Recurrent Neural Network Architecture" , DSAA, Paris, 2015
- Urminder Singh, Sucheta Chouhan, A. Krishnamachari and Lovekesh Vig, "Ensemble of Deep Long Short Term Memory Networks for Labelling Origin of Replication Sequences", DSAA, Paris, 2015
Book Chapters/Conference Proceedings
- “Econophysics and Data Driven Modelling of Market Dynamics”, Eds. F. Abergel, H. Aoyama, B. K. Chakrabarti, A. Chakraborti and A. Ghosh, (Springer, Milan, 2015).
- “Physicists’ Approaches to a Few Economic Problems”, 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, Econophysics and Data Driven Modelling of Market Dynamics (Springer, Milan, 2015).
- “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).
- Eds. A Chakraborti, S Chatterjee and P Pradhan, “Proceedings of the STATPHYS-KOLKATA VIII”, Journal of Physics: Conference Series 638 (2015).
- “Preface: STATPHYS-KOLKATA VIII”, A Chakraborti, S Chatterjee and P Pradhan, Journal of Physics: Conference Series 638, 011001 (2015).
- “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).
- “Essentials of Econophysics Modelling”, Physics Today 68, 1, 44 (2015), A. Chakraborti; Book written by František Slanina, Oxford U. Press, 2014. (411 pp.).
- “Spatiotemporal pattern formation in a prey-predator model under environmental driving forces”, Anuj Kumar Sirohi; Banerjee, Malay; Chakraborti, Anirban, Journal of Physics: Conference Series 638, pp. 12004-12014 (2015).
- Ankit Verma, Ramya Hebbalaguppe, Lovekesh Vig, Swagat Kumar and Ehtesham Hassan, "Pedestrian Detection via Mixture of CNN Experts and Thresholded Aggregate Channel Features", IEEE International Conference on Computer Vision (ICCV) Workshop on Assistive Technologies, 2015
- Gaurangi Anand, Ah Kazmi, Pankaj Malhotra, Lovekesh Vig, Gautam Shroff, Puneet Agarwal,"Deep Temporal Features to Predict Repeat Buyers", NIPS Workshop on Learning for E-Commerce, Montreal, 2015
- Mohit Yadav, Pankaj Malhotra, S. Sriram, Gautam Shroff, Lovekesh Vig, "Augmenting Time series data with ODE models for Anomaly Detection", NIPS Workshop on Time Series Analysis, Montreal, 2015
- 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
- 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
- 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) 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
- R. Chicheportiche and A. Chakraborti, “Copulas and time series with long-ranged dependences”, Phys. Rev. E (2014)89, 042117
- 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.
- R.K. Brojen Singh, Numerical Detection of Stochastic to Deterministic Transition. J. Compt. Nonlinear Dyn. (2014) Doi:10.1115/1.4027441.
- 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.
- BA Ahanger, R. K. Brojen Singh and Z. A. Ansari, "Thermal Perturbation in Dye-SensitizedSolar Cell", Mat. Focus (2014), 3,1–5.
- 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)
- 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).
- Gurumayum Reenaroy Devi , Md. Jahoor Alam, and R.K. Brojen Singh, "Synchronization in stress p53 network. Mathematical Medicine and Biology(2014)", (Accepted)
- 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
- 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
- Agarwal, M., Kumar, N., & Vig, L., "Non-additive multi-objective robot coalition formation. Expert Systems with Applications", (2014) 41(8), 3736-3747.
- 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),
- Khan, Taushif; Ghosh, Indira, "Modularity in protein structures: A study on all alpha proteins", Journal of Biomolecular Structure & Dynamics(2014) (Accepted for publication).
- 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)
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- Sinha, S., & Lynn, A. M, "HMM-ModE: implementation, benchmarking and validation with HMMER3". BMC research notes, (2014)7(1), 483.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
MJ Alam, V Singh, RK Brojen Singh, "Switching Mechanism in the p53 Regulatory Network Systems and Synthetic Biology" (Book Chapter) (2014)
- 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
- 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
- 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).
- 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).
- 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.
- 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
- Suehiro Iwata ,Pradipta Bandyopadhyay , and Sotiris S. Xantheas, "Cooperative Roles of Charge Transfer and Dispersion Terms in Hydrogen-Bonded Networks of (H2O)n, n = 6, 11, and 16", J.Phys.Chem. A, 2013, 117 (30), pp 6641–6651. http://pubs.acs.org/doi/abs/10.1021/jp403837z
- Avijit Rakshit, Pradipta Bandyopadhyay, "Finding low energy minima of (H2O)25 and (H2O)30 with temperature basin paving Monte Carlo method with effective fragment potential: New 'global minimum' and graph theoretical characterization of low energy structures", Theoretical and Computational Chemistry, 2013 (In press)
- Biswa Ranjan Meher , Mattaparthi Venkata Satish Kumar, Pradipta Bandyopadhyay, "Inter-chain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: New insights from Molecular Dynamics",Journal of Biomolecular Structure & Dynamics (In Press, 2013)
- Pradipta Bandyopadhyay, "Increasing the efficiency of Monte Carlo simulation with sampling from an approximate potential.",Chem. Phys. Lett. 556, 341 (2013)
- Ravi Datta Sharma, Rajnee Kanwal, Andrew M. Lynn, Prerna Singh, Syed Tazeen Pasha, Tasneem Fatma, Safdar Jawaid, "High temperature unfolding of a truncated hemoglobin by molecular dynamics simulation",Journal of molecular modeling 19 (9), 3993-4002 http://link.springer.com/article/10.1007/s00894-013-1919-4
- Manpreet Kaur Rawal, Mohammad Firoz Khan, Khyati Kapoor, Neha Goyal, Sobhan Sen, Ajay Kumar Saxena, Andrew M Lynn, Joel DA Tyndall, Brian C Monk, Richard D Cannon, Sneha Sudha Komath, Rajendra Prasad, "Insight into Pleiotropic Drug Resistance ATP-binding Cassette Pump Drug Transport through Mutagenesis of Cdr1p Transmembrane Domains",Journal of Biological Chemistry 288 (34), 24480-24493 http://www.jbc.org/content/288/34/24480.short
- Indresh Kumar Maurya, Chaitanya Kumar Thota, Sachin Dev Verma, Jyotsna Sharma, Manpreet Kaur Rawal, Balaguru Ravikumar, Sobhan Sen, Neeraj Chauhan, Andrew M Lynn, Virander Singh Chauhan, Rajendra Prasad, "Rationally designed transmembrane peptide mimics of the multidrug transporter protein Cdr1 act as antagonists to selectively block drug efflux and chemosensitize azole-resistant clinical isolates of Candida albicans",Journal of Biological Chemistry 288 (23), 16775-16787 http://www.jbc.org/content/288/23/16775.short
- 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
- 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
- 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", online 2013, http://dx.doi.org/10.1080/07391102.2012.748546
- 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).
- 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
- 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
- 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).
- 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:
- 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.
- 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.
- 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
- 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
- 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.
- 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.
computational model to study mass
inhomogeneity and hydrophobicity inhomogeneity in Proteins”,
European Biophysics Journal, 2009(Feb.)
Vishnoi A, Srivastava A, Roy R, Bhattacharya A.
Mycobacterium tuberculosis genome
diversity database”, BMC Genomics 9:373, (2009)
- 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.
- 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
- Vig L Multiple Robot Teaming: Coalition Formation: From Software Agents to Robots, VDM Verlag, (2008)
- Godbole R,
Ramaswamy R, Lilavati's Daughters, “The women
scientists of India”, Indian Academy of Sciences,
Bangalore: 2008. ISBN: 9788186450051
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.