Research Publications

Following is list of research publications published by team under GENESIS publications. You may get list of publications with citation information from Google Scholar page of GENESIS.






Papers of Year-2016

    Papers of Year-2015

    1. Singh S, Chaudhary K, Dhanda SK, Bhalla S, Usmani S.S, Gautam A, Tuknait A, Agrawal P, Mathur D and Raghava GPS (2015). SATPdb: a database of structurally annotated therapeutic peptides. Nucleic Acid Research doi: 10.1093/nar/gkv1114
    2. Bhutani I, Gupta P, Madathil R, Parkesh R.(2015). Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies. PLoS One10(3):e0119771. doi: 10.1371/journal.pone.0119771.
    3. Loharch S, Bhutani I, Jain K, Gupta P, Sahoo DK, Madathil R, Parkesh R. . (2015). EpiDBase: A Curated database for small molecule modulators of Epigenetic Landscape. Database (Oxford). 2015. pii: bav013. doi: 10.1093/database/bav013.
    4. Qureshi A, Tandon H, Kumar M.(2015). AVP-IC50 Pred: Multiple machine learning techniques based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50 ). Biopolymer doi: 10.1002/bip.22703.
    5. Kumar Gupta A, Kumar M. (2015). HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep.5:12522. doi: 10.1038/srep12522.
    6. Karthikeyan M, Pandit Y, Pandit D, Vyas R.(2015). MegaMiner: A Tool for Lead Identification Through Text Mining Using Chemoinformatics Tools and Cloud Computing Environment. Comb Chem High Throughput Screen. 2015;18(6):591-603.
    7. Karthikeyan M, Pandit D, Bhavasar A, Vyas R.(2015). Design and Development of ChemInfoCloud: An Integrated Cloud Enabled Platform for Virtual Screening. Comb Chem High Throughput Screen. 2015;18(6):604-19.
    8. Karthikeyan M, Pandit D, Vyas R.(2015).Protein Ligand Complex Guided Approach for Virtual Screening. Comb Chem High Throughput Screen. 2015;18(6):577-90.
    9. Karthikeyan M, Rajamohanan PR, Vyas R.(2015). Prediction of Bioactive Compounds Using Computed NMR Chemical Shifts. Comb Chem High Throughput Screen. 2015;18(6):562-76.
    10. Karthikeyan M, Pandit D, Vyas R.(2015).ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening. Comb Chem High Throughput Screen. 2015;18(6):544-61.
    11. Karthikeyan M, Vyas R.(2015).Role of Open Source Tools and Resources in Virtual Screening for Drug Discovery. Comb Chem High Throughput Screen. 2015;18(6):528-43.
    12. Karthikeyan M, Vyas R.(2015). Editorial: Design and Development of New Chemoinformatics Tools for Virtual Screening. Comb Chem High Throughput Screen. 2015;18(6):526-7.
    13. Das A, Panda A, Singh D, Chandrababunaidu MM, Mishra GP, Bhan S, Adhikary SP, Tripathy S(2015). Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278. Genome Announc. 2015 Apr 2;3(2). pii:e00228-15. doi: 10.1128/genomeA.00228-15.
    14. Das S, Singh D, Madduluri M, Chandrababunaidu MM, Gupta A, Adhikary SP,Tripathy S(2015). Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix campylonemoides Strain VB511288. Genome Announc. 2015 3(2). pii: e00226-15. doi: 10.1128/genomeA.00226-15.
    15. Chandrababunaidu MM, Sen D, Tripathy S.(2015). Draft Genome Sequence of Filamentous Marine Cyanobacterium Lyngbya confervoides Strain BDU141951. Genome Announc.3(2). pii: e00066-15. doi: 10.1128/genomeA.00066-15.
    16. Singh D, Chandrababunaidu MM, Panda A, Sen D, Bhattacharyya S, Adhikary SP,Tripathy S.(2015) Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India. Genome Announc. 3(2). pii: e00064-15. doi: 10.1128/genomeA.00064-15.
    17. Bhattacharyya S, Chandrababunaidu MM, Sen D, Panda A, Ghorai A, Bhan S, Sanghi N, Tripathy S. (2015). Draft Genome Sequence of Exopolysaccharide-Producing Cyanobacterium Aphanocapsa montana BDHKU 210001. Genome Announc.3(2). pii: e00057-15. doi: 10.1128/genomeA.00057-15.
    18. Sen D, Chandrababunaidu MM, Singh D, Sanghi N, Ghorai A, Mishra GP, Madduluri M, Adhikary SP, Tripathy S. (2015).Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India. Genome Announc. 3(2). pii: e00009-15. doi: 10.1128/genomeA.00009-15.
    19. Ettayapuram Ramaprasad AS, Singh S, Gajendra P. S R, Venkatesan S (2015) AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides. PLoS ONE 10(9): e0136990. doi:10.1371/journal.pone.0136990
    20. Jha A, Panzade G, Pandey R, Shankar R (2015). A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. Nucl. Acids Res.43(18): 8713–8724. doi: 10.1093/nar/gkv871
    21. Bhatia R, Gautam A, Gautam SK, Mehta D, Kumar V, Raghava GP, Varshney GC (2015). Assessment of SYBR Green I Dye-Based fluorescence Assay for Screening Antimalarial Activity of Cationic Peptides and DNA Intercalating Agents. Antimicrob Agents Chemother59(5):2886-9. doi: 10.1128/AAC.03266-14.
    22. Sarkar, S. C., and Rup, R. (2015). Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges. Database(oxford) pii: bau126. doi: 10.1093/database/bau126.
    23. Aggarwal RK, Dawar C, Das S, Sharma S (2015). Draft genome sequences of two drug-resistant isolates of Pseudomonas aeruginosa obtained from keratitis patients in India. Genome Announc 3(1). pii: e01404-14. doi: 10.1128/genomeA.01404-14.
    24. Loharch S, Bhutani I, Jain K, Gupta P, Sahoo DK, Madathil R, Parkesh R. (2015). EpiDBase: A Curated database for small molecule modulators of Epigenetic Landscape. Database(oxford)pii: bav013. doi: 10.1093/database/bav013.
    25. Shafi A, Chauhan R, Gill T, Swarnkar MK, Sreenivasulu Y, Kumar S, Kumar N, Shankar R, Ahuja PS, Singh AK. (2015). Expression of SOD and APX genes positively regulates secondary cell wall biosynthesis and promotes plant growth and yield in Arabidopsis under salt stress. Plant Mol Biol. 87(6):615-31. doi: 10.1007/s11103-015-0301-6
    26. Abinaya E, Narang P, Bhardwaj A (2015). FROG Fingerprinting Genomic Variation Ontology. PLoSOne.10(8):e0134693. doi: 10.1371/journal.pone.0134693.
    27. Gautam A, Sharma M, Vir P, Chaudhary K, Kapoor P, Kumar R, Nath SK, Raghava GP. (2015). Identification and characterization of novel protein-derived arginine-rich cell-penetrating peptides. Eur J Pharm Biopharm.89:93-106. doi: 10.1016/j.ejpb.2014.11.020.
    28. Khanam T, Shukla A, Rai N, Ramachandran R. (2015). Identification of Critical Determinants for Substrate Recognition and Catalysis in the M. tuberculosis Class II AP-endonuclease/3’-5' Exonuclease III. Biochim. Biophys. Acta.1854(5):505-16. doi: 10.1016/j.bbapap.2015.02.019.
    29. Panwar B, Raghava GP (2015). Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides. Genomics 105(4):197-203. doi: 10.1016/j.ygeno.2015.01.005.
    30. Singh H, Singh S, Raghava GP. (2015). In silico platform for predicting and initiating β-turns in a protein at desired locations. Proteins.83(5):910-21. doi: 10.1002/prot.24783.
    31. Shukla H, Kumar V, Singh AK, Singh N, Kashif M, Siddiqi MI, Yasoda Krishnan M, Sohail Akhtar M. (2015). Insight into the structural flexibility and function of Mycobacterium tuberculosis isocitrate lyase. Biochimie.110:73-80. doi: 10.1016/j.biochi.2014.12.016.
    32. Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC. (2015). Insights into the origin of Clostridium botulinum strains: Evolution of distinct restriction endonuclease sites in rrs (16S rRNA gene). Indian J Microbiol.55(2):140-50. doi: 10.1007/s12088-015-0514-z.
    33. Mishra AK, Agnihotri P, Srivastava VK1, Pratap JV. (2015). Novel protein-protein interaction between spermidine synthase and S-adenosylmethionine decarboxylase from Leishmania donovani. Biochem Biophys Res Commun.456(2):637-42. doi: 10.1016/j.bbrc.2014.12.008.
    34. Shah P, Tiwari S, Siddiqi MI. (2015). Recent Progress in the Identification and Development of Anti-Malarial Agents using Virtual Screening based Approaches. Comb Chem High Throughput Screen.18(3):257-68.
    35. Rajput NK, Singh V, Bhardwaj A (2015). Resources, challenges and way forward in rare mitochondrial diseases research. Version 2. F1000Res[revised 2015 Aug 13];4:70. doi: 10.12688/f1000research.6208.2. eCollection 2015.
    36. Renu Vyas Purva Goel, M. K. S. S. T. B. D. K. (2015). Role of chemoinformatics methods in knowledge based virtual screening of kinase inhibitors. Combinatorial Chemistry and High Throughput Screening.
    37. Kachhap S, Singh B. (2015). Role of DNA conformation and energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes. J Biomol Struct Dyn.33(10):2069-82. doi: 10.1080/07391102.2014.995709.
    38. B. Sharma H. K. Srivastava, G. G., and Sastry, G. N. (2015). Sastry Energy Decomposition Analysis of Cation-p, Metal Ion-Lone Pair, Hydrogen Bonded, Charge Assisted Hydrogen Bonded and p-p Interactions. J. Comp. Chem. 36(8):529-38. doi: 10.1002/jcc.23827.
    39. Bhutani I, Loharch S, Gupta P, Madathil R, Parkesh R. (2015). Structure, dynamics, and interaction of Mtb (Mycobacterium tuberculosis) DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies. PloS One 10(3):e0119771. doi: 10.1371/journal.pone.0119771.
    40. Neela.Y.I., S. G. N. (2015). Theoretical investigation of anion (F-, Cl-) and cation (Na+) interactions with substituted benzene [C6H6-nYn (Y = -F, -CN, -NO2; n = 1-6)],. Mol. Phys.
    41. Kumar V Krishna S, S. M. I. (2015). Virtual screening strategies: recent advances in the identification and design of anti-cancer agents. Methods.71:64-70. doi: 10.1016/j.ymeth.2014.08.010.
    42. Dhar J, Chakrabarti P, Saini H, Raghava GP, Kishore R. (2015). ω-turn: A novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C-H⋅⋅⋅O interaction. PROTEINS: Structure, Function and Bioinformatics.83(2):203-14. doi: 10.1002/prot.24720.
    43. Shah P, Saquib M, Sharma S, Husain I, Sharma SK, Singh V, Srivastava R, Shaw AK, Siddiqi MI. (2015). 3D-QSAR and molecular modeling studies on 2,3-dideoxy hexenopyranosid-4-uloses as anti-tubercular agents targeting alpha-mannosidase. Bioorg Chem.59:91-6. doi: 10.1016/j.bioorg.2015.02.001.
    44. Rajput NK, Singh V, Bhardwaj A (2015). Resources, challenges and way forward in rare mitochondrial diseases research. F1000Research(version2)4:70. doi: 10.12688/f1000research.6208.2.
    45. Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC (2015). Insights into the origin of Clostridium botulinum strains: Evolution of distinct restriction endonuclease sites in rrs (16S rRNA gene). Indian J Microbiol 55: doi:10.1007/s12088-015-0514-z
    46. Goswami A, Roy Chowdhury A, Sarkar M, Saha SK, Paul S and Dutta C (2015).   Strand-biased gene distribution, purine asymmetry and environmental factors influence protein evolution in Bacillus. FEBS Lett. 589: 629-638. doi: 10.1016/j.febslet.2015.01.028.
    47. Mandloi S and Chakrabarti S (2015). PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool. Scientific Reports. 5:10021. doi: 10.1038/srep10021.
    48. Theeya N, Ta A, Das S, Mandal RS, Chakrabarti O, Chakrabarti S, Ghosh AN, Das S. (2015). An inducible and secreted eukaryote-like serine/threonine kinase of Salmonella enteric serovar Typhi promotes intracellular survival and pathogenesis. Infect Immun. 83(2):522-33.doi: 10.1128/IAI.02521-14.
    49. Anshu A, Mannan MA, Chakraborty A, Chakrabarti S, Dey M. (2015). A novel role for protein kinase Kin2 in regulating HAC1 mRNA translocation, splicing, andtranslation. Mol Cell Biol. 35(1):199-210. doi: 10.1128/MCB.00981-14
    50. Bhattacharyya M and Chakrabarti S (2015).   Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies. Malaria Journal, 14:70. doi: 10.1186/s12936-015-0562-1.
    51. Chandrababunaidu MM, Singh D, Sen D, Bhan S, Das S, Gupta A, Adhikary SP, Tripathy S. (2015). Draft Genome Sequence of Tolypothrix boutellei Strain VB521301. Genome Announc. 3(1). pii: e00001-15. doi: 10.1128/genomeA.00001-15.
    52. SP Shinde, AK Banerjee, N Arora, US Murty, VR Sripathi, M Pal-Bhadra.(2015). Computational approach for elucidating interactions of cross-species miRNAs and their targets in Flaviviruses. J Vector Borne Dis. 52(1):11-22.
    53. Shinde S, Arora N, Bhadra U. (2015). A Complex Network of MicroRNAs Expressed in Brain and Genes Associated with Amyotrophic Lateral Sclerosis. Int J Genomics.2013:383024. doi: 10.1155/2013/383024.
    54. Aggarwal RK, Dawar C, Das S, Sharma S. 2015. Draft genome sequences of two drug-resistant isolates of Pseudomonas aeruginosa obtained from keratitis patients in India. Genome Announc 3(1):e01404-14. doi:10.1128/genomeA.01404-14.
    55. Abinaya E, Narang P, Bhardwaj A.(2015).FROG - Fingerprinting Genomic Variation Ontology. PLoS One.10(8):e0134693. doi: 10.1371/journal.pone.0134693.
    56. Neela.Y.I., Sastry G.N. (2015). Theoretical investigation of anion (F-, Cl-) and cation (Na+) interactions with substituted benzene [C6H6-nYn (Y = -F, -CN, -NO2; n = 1-6)].  Mol. Phys. 113(2) 137-148. doi 10.1080/00268976.2014.948940 
    57. Kumar R, Chaudhary K, Sharma M, Nagpal G, Chauhan JS, Singh S, Gautam A, Raghava GP. AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides. Nucleic Acids Res.43(Database issue):D956-62. doi: 10.1093/nar/gku1141.

    Papers of Year-2014

    1. Dwivedi GR, Upadhyay HC, Yadav DK, Singh V, Srivastava SK, Khan F, Darmwal NS, Darokar MP (2014). 4-Hydroxy-alpha Tetralone and its Derivative as Drug Resistance Reversal Agents in Multi Drug Resistant Escherichia coli. Chemical biology & drug design. 83(4):482-92. doi: 10.1111/cbdd.12263.
    2. Srivastava S, Sowpati DT, Garapati HS, Puri D, Dhawan J, et al. (2014). A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes. Genomics Data 2: 78-81. doi: 10.1016/j.gdata.2014.05.001.
    3. Masood N, Fatima K, Luqman S (2014). A Modified Method for Studying Behavioral Paradox of Antioxidants and Their Disproportionate Competitive Kinetic Effect to Scavenge the Peroxyl Radical Formation. The Scientific World Journal. doi: 10.1155/2014/931581.
    4. Mujahid M, Kunte S, Muthukrishnan M (2014). A new enantioselective synthesis of (S)-2-ethoxy-3-(4-hydroxyphenyl) propanoic acid esters (EEHP and IEHP), useful pharmaceutical intermediates of PPAR agonists. Tetrahedron Letters 55(21): 3223-3226.
    5. R. Anjaneyulu M. Mujahid, M. S. M. M. (2014). A new enantioselective synthesis of the antiparkinson agent safinamide. Synthesis.46(13): 1751-1756. DOI: 10.1055/s-0033-1341104
    6. Chakraborty A, Chakrabarti S (2014). A survey on prediction of specificity-determining sites in proteins. Briefings in bioinformatics.16(1):71-88. doi: 10.1093/bib/bbt092
    7. Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., et. al.,(2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, 513(7518), 409–413.
    8. Saha SK, Goswami A, Dutta C (2014). Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal. BMC genomics.15:430. doi: 10.1186/1471-2164-15-430.
    9. Meier C, Spitschak A, Abshagen K, Gupta S, Mor JM, Wolkenhauer O, Haier J, Vollmar B, Alla V, Pützer BM. (2014). Association of RHAMM with E2F1 promotes tumour cell extravasation by transcriptional up-regulation of fibronectin. J Pathol.234(3):351-64. doi: 10.1002/path.4400.
    10. Qureshi A, Thakur N, Tandon H, Kumar M (2014). AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic acids research 42: D1147-D1153.doi: 10.1093/nar/gkt1191.
    11. Sharma A, Dutta P, Sharma M, Rajput NK, Dodiya B, Georrge JJ, Kholia T; OSDD Consortium, Bhardwaj A. (2014). BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts. J Cheminform. 6(1):46. eCollection 2014.
    12. Premkumar JR, Sastry GN.(2014). Cation-Alkane Interaction. J. Phys. Chem. 118(48):11388-98. doi: 10.1021/jp5076862.
    13. Yadav GP, Shree S, Maurya R, Rai N, Singh DK, Srivastava KK, Ramachandran R. (2014). Characterization of M. tuberculosis SerB2, an essential HAD-family phosphatase, reveals novel properties. PLOS One.9(12):e115409. doi: 10.1371/journal.pone.0115409
    14. Pal U, Sen S, Maiti NC (2014). C-alpha-H Carries Information of Hydrogen Bond Involving Geminal Hydroxyl Group: A Case Study With Hydrogen Bonded Complex of HFIP and Tertiary Amines. J Phys Chem A 118(6):1024-30. doi: 10.1021/jp411488a.
    15. Chakraborty A, Mukherjee S, Chattopadhyay R, Roy S, Chakrabarti S (2014). Conformational Adaptation in the E. coli Sigma 32 Protein in Response to Heat Shock. The Journal of Physical Chemistry B.118(18):4793-802. doi: 10.1021/jp501272n.
    16. Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, et al. (2014). Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic acids research. 42(12):7539-52. doi: 10.1093/nar/gku465.
    17. Maity M, Pramanik SK, Pal U, Banerji B, Maiti NC (2014). Copper (I) oxide nanoparticle and tryptophan as its biological conjugate: a modulation of cytotoxic effects. Journal of nanoparticle research 16: 1-13.
    18. Mushtaq K, Chodisetti SB, Rai PK, Maurya SK, Amir M, Sheikh JA, Agrewala JN (2014). Decision-making critical amino acids: role in designing peptide vaccines for eliciting Th1 and Th2 immune response. Amino Acids 46(5):1265-74. doi: 10.1007/s00726-014-1692-4.
    19. dav D, Kalani K, K Singh A, Khan F, K Srivastava S, et al. (2014). Design, synthesis and in vitro evaluation of 18β-glycyrrhetinic acid derivatives for anticancer activity against human breast cancer cell line MCF-7. Curr med chem 21(9): 1160-1170.
    20. Sharma A, Singla D, Rashid M, Raghava GP. (2014). Designing of peptides with desired half-life in intestine-like environment. BMC Bioinformatics.15:282. doi: 10.1186/1471-2105-15-282.
    21. Kumar R, Chaudhary K, Singla D, Gautam A, Raghava GP (2014). Designing of promiscuous inhibitors against pancreatic cancer cell lines. Scientific reports 4:4668. doi: 10.1038/srep04668.
    22. Janardhan S, Narahari Sastry G (2014). Dipeptidyl Peptidase IV Inhibitors: A New Paradigm in Type 2 Diabetes Treatment. Current drug targets 15(6): 600-621.
    23. Dkhar HK, Gopalsamy A, Loharch S, Kaur A, Bhutani I, Saminathan K, Bhagyaraj E, Chandra V, Swaminathan K, Agrawal P, Parkesh R*, Gupta P (2014). Discovery of Mycobacterium tuberculosis α-1,4-glucan branching enzyme (GlgB) inhibitors by structure and ligand based virtual screening. J Biol Chem. 2014 Nov 10. pii: jbc.M114.589200. [Epub ahead of print] PubMed PMID: 25384979
    24. Kumar D, Mondal AK, Yadav AK, Dash D. (2014). Discovery of rare protein coding genes in model methylotroph Methylobacterium extorquens AM1. Proteomics.14(23-24):2790-4. doi: 10.1002/pmic.201400153.
    25. Sreenivas A Sathyanarayana Reddy G, S. S. (2014). Draft Genome Sequence of a Psychrophilic Bacterium, Sphingomonas antarcticum, Isolated from the Soils of Schirmacher Oasis, Antarctica. Genome Announcement.2(5). pii: e00696-14. doi: 10.1128/genomeA.00696-14.
    26. Reddy G. S. N. Sreenivas A, S. S. (2014). Draft Genome Sequence of Cryobacterium roopkundensis Strain RuGl7, Isolated from a Soil Sample in the Vicinity of Roopkund Lake, Himalayas, India. Genome Announc. 2(6). pii: e01206-14. doi: 10.1128/genomeA.01206-14.
    27. Singh A, Sreenivas A, Reddy GS, Pinnaka AK, Shivaji S (2014). Draft genome sequence of Lutibaculum baratangense strain AMV1T, isolated from a mud volcano in Andamans, India. Genome announc. 2(4). pii: e00735-14. doi: 10.1128/genomeA.00735-14.
    28. Sarkar AS, Rup R (2014). Dynamics of GLI regulation in hedgehog signaling pathway and strategy to control cancerous situation.
    29. Yadav I, Singh H, Imran KM, Chaudhury A, Raghava G, et al. (2014). EGFRIndb: Epidermal Growth Factor Receptor Inhibitor Database. Anticancer Agents Med Chem. 2014;14(7):928-35.
    30. Singh H Singh S, Raghava GP. (2014). Evaluation of protein dihedral angle prediction methods. PLoS One.9(8):e105667. doi: 10.1371/journal.pone.0105667.
    31. Ranjan R Ahamad N, A. S. (2014). Fission Yeast Drp1 is an essential protein required for recovery from DNA damage and chromosome segregation. DNA Repair. 24:98-106. doi: 10.1016/j.dnarep.2014.09.006.
    32. Ishaq M, Khan MA, Sharma K, Sharma G, Dutta RK, Majumdar S2 (2014). Gambogic acid induced oxidative stress dependent caspase activation regulates both apoptosis and autophagy by targeting various key molecules (NF-κB, Beclin-1, p62 and NBR1) in human bladder cancer cells. Biochim Biophys Acta. 1840(12):3374-84. doi: 10.1016/j.bbagen.2014.08.019.
    33. Paul, A., Samaddar, S., Bhattacharya, A., Banerjee, A., Das, A., Chakrabarti, S., & DasGupta, M. (2014). Gatekeeper tyrosine phosphorylation is autoinhibitory for Symbiosis Receptor Kinase. FEBS Letters, 588(17), 2881–2889. doi: 10.1016/j.febslet.2014.06.056.
    34. Aditya S, Bhumika V, Khatri I, Srinivas T, Subramanian S, et al. (2014). Grimontia indica AK16(T), sp. nov., isolated from a seawater sample reports the presence of pathogenic genes similar to Vibrio genus. PLOS One. 9(1):e85590. doi: 10.1371/journal.pone.0085590
    35. Ahmad S, Gupta S, Kumar R, Varshney GC, Raghava GP (2014). Herceptin Resistance Database for Understanding Mechanism of Resistance in Breast Cancer Patients. Scientific reports 4:4483. doi: 10.1038/srep04483.
    36. Nizamuddin S. TK (2014). Human Origin, health and diseases in India. Gain of Genomic Research in Biology and Medicine.
    37. Kumar V, Khan S, Gupta P, Rastogi N, Mishra DP, Ahmed S, Siddiqi MI. (2014). Identification of novel inhibitors of human Chk1 using pharmacophore-based virtual screening and their evaluation as potential anti-cancer agents. J Comput Aided Mol Des.28(12):1247-56. doi: 10.1007/s10822-014-9800-9.
    38. Prakash O, Ahmad A, Tripathi VK, Tandon S, Pant AB, Khan F. (2014). In Silico Assay Development for Screening of Tetracyclic Triterpenoids as Anticancer Agents against Human Breast Cancer Cell Line MCF7. PLOS One.9(11):e111049. doi: 10.1371/journal.pone.0111049.
    39. Kalani K, Kushwaha V, Sharma P, Verma R, Srivastava M, Khan F, Murthy PK, Srivastava SK. (2014). In Vitro, In Silico and In Vivo Studies of Ursolic Acid as an Anti-Filarial Agent. PLOS One. 9(11):e111244. doi: 10.1371/journal.pone.0111244.
    40. Badrinarayan P, Sastry GN (2014). Informatics and modelling approaches in drug discovery.
    41. Shah, P., Tiwari, S., & Siddiqi, M. I. (2014). Integrating molecular docking, CoMFA analysis, and machine-learning classification with virtual screening toward identification of novel scaffolds as Plasmodium falciparum enoyl acyl carrier protein reductase inhibitor. Medicinal Chemistry Research, 23(7), 3308–3326.
    42. Bhardwaj A (2014). Investigating the role of site specific synonymous variation in disease association studies. Mitochondrion 16: 83-88. doi: 10.1016/j.mito.2013.12.005.
    43. Tiwari S, Singh S, Pandey P, Saikia SK, Negi AS, Gupta SK, Pandey R, Banerjee S. (2014). Isolation, structure determination, and antiaging effects of 2, 3-pentanediol from endophytic fungus of Curcuma amada and docking studies. Protoplasma. 251(5):1089-98. doi: 10.1007/s00709-014-0617-0.
    44. Ramamoorthy S, Garapati HS, Mishra RK. (2014). Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation. Gene. 551(2):167-75. doi: 10.1016/j.gene.2014.08.052.
    45. Jha AN, Sundaravadivel P, Singh VK, Pati SS, Patra PK, Kremsner PG, Velavan TP, Singh L, Thangaraj K. (2014). MBL2 variations and malaria susceptibility in Indian populations. Infect Immun.82(1):52-61. doi: 10.1128/IAI.01041-13.
    46. Shinde S, Bhadra U (2014). microRNA gene interaction in Amyotrophic Lateral Sclerosis dataset. Dataset Papers in Science 2014: 24.
    47. Sharma R., S. S. B. P. S. G. N. (2014). Modeling Chemical and Biological (Re)activity. Current Research \& Information on Pharmaceutical Sciences.
    48. Choudhury C, Deva Priyakumar U, Sastry GN.(2014). Molecular dynamics investigation of the active site dynamics of mycobacterial cyclopropane synthase during various stages of the cyclopropanation process. Journal of Structural Biology, 187(1), 38–48. doi: 10.1016/j.jsb.2014.04.007.
    49. Azhagiya Singam ER1, Rajapandian V, Subramanian V. (2014). Molecular dynamics simulation study on the interaction of collagen-like peptides with gelatinase-A (MMP-2). Biopolymers. 101(7): 779–794. doi: 10.1002/bip.22457.
    50. Badrinarayan P, Choudhary C, Sastry GN (2014). Multiscale approaches in modeling biological systems. (S2B2). Springer.
    51. Singh SS, Thakur TS (2014). New crystalline salt forms of levofloxacin: conformational analysis and attempts towards the crystal structure prediction of the anhydrous form. CrystEngComm 16, 4215-4230. DOI: 10.1039/C4CE00263F.
    52. Francis A, Sunitha B, Vinodh K, Polavarapu K, Katkam SK, Modi S, Bharath MM, Gayathri N, Nalini A, Thangaraj K. (2014). Novel TCAP Mutation c.32C>A Causing Limb Girdle Muscular Dystrophy 2G. PLOS One 9(7):e102763. doi: 10.1371/journal.pone.0102763.
    53. Khurana R, Verma VK, Rawoof A, Tiwari S, Nair RA, Mahidhara G, Idris MM, Clarke AR, Kumar LD. (2014). OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer. BMC bioinformatics. 15:15. doi: 10.1186/1471-2105-15-15.
    54. Mehta D, Anand P, Kumar V, Joshi A, Mathur D, Singh S, Tuknait A, Chaudhary K, Gautam SK, Gautam A, Varshney GC, Raghava GP.(2014). ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. Database(oxford). 2014. pii: bau051. doi: 10.1093/database/bau051.
    55. Nagpal G, Sharma M, Kumar S, Chaudhary K, Gupta S, Gautam A, Raghava GP. (2014). PCMdb: Pancreatic Cancer Methylation Database. Sci Rep. 4:4197. doi: 10.1038/srep04197.
    56. Krishna S, Singh DK, Meena S, Datta D, Siddiqi MI, Banerjee D. (2014). Pharmacophore-based screening and identification of novel human ligase I inhibitors with potential anti-cancer activity. J Chem Inf Model. 54(3):781-92. doi: 10.1021/ci5000032.
    57. Sachdeva R, Singh B (2014). Phosphorylation of Ser-180 of rat aquaporin-4 shows marginal affect on regulation of water permeability: molecular dynamics study. Journal of Biomolecular Structure and Dynamics 32(4): 555-566. doi: 10.1080/07391102.2013.780981
    58. Panwar B, Arora A, Raghava GP. (2014). Prediction and classification of ncRNAs using structural information. BMC genomics 15:127. doi: 10.1186/1471-2164-15-127.
    59. Panwar B, Raghava GP. (2014). Prediction of uridine modifications in tRNA sequences. BMC Bioinformatics. 15:326. doi: 10.1186/1471-2105-15-326.
    60. Bawankule DU, Trivedi P, Pal A, Shanker K, Singh M, Sharma P, Khan F, Maurya AK, Verma RK, Gupta MM. (2014). Protective Mechanism of Lignans from Phyllanthus amarus Against Galactosamine/Lipopolysaccharide-Induced Hepatitis: An In-Vivo and In-Silico Studies. Current topics in medicinal chemistry 14(8): 1045-1055.
    61. Yadav DK, Kalani K, Khan F, Srivastava SK. (2014). QSAR and docking studies on chalcone derivatives for antitubercular activity against M. tuberculosis H37Rv. J. Chemometrics. 28(6):499-507. DOI: 10.1002/cem.2606
    62. Kalani K, Yadav DK, Singh A, Khan F, Godbole MM, Srivastava SK. (2014). QSAR Guided Semi-synthesis and In-Vitro Validation of Anticancer Activity in Ursolic Acid Derivatives. Current topics in medicinal chemistry 14(8): 1005-1013.
    63. Chauhan JS, Dhanda SK, Singla D, Open Source Drug Discovery Consortium, Agarwal SM, Raghava GP.(2014). QSAR-based models for designing quinazoline/ imidazothiazoles/pyrazolopyrimidines based inhibitors against wild and mutant EGFR. PLoS One. 9(7):e101079. doi: 10.1371/journal.pone.0101079.
    64. Nidhi, Siddiqi MI. (2014). Recent advances in QSAR-based identification and design of anti-tubercular agents. Current Pharmaceutical Design, 20(27), 4418–4426.
    65. Kumar V, Chandra S, Siddiqi MI (2014). Recent advances in the development of antiviral agents using computer-aided structure based approaches. Curr Pharm Des 20(21): 3488-3499.
    66. Rai N, Taher N, Singh M, Chaubey G, Jha AN, Singh L, Thangaraj K. (2014). Relic excavated in western India is probably of Georgian Queen Ketevan. Mitochondrion 14(1): 1-6. doi: 10.1016/j.mito.2013.12.002
    67. Paul A, Jha A, Bhardwaj S, Singh S, Shankar R, Kumar S. (2014). RNA-seq-mediated transcriptome analysis of actively growing and winter dormant shoots identifies non-deciduous habit of evergreen tree tea during winters. Sci Rep 4: 5932. doi: 10.1038/srep05932.
    68. Das Roy R, Dash D. (2014). Selection of relevant features from amino acids enables development of robust classifiers. Amino Acids. 46(5):1343-51. doi: 10.1007/s00726-014-1697-z.
    69. J Richard Premkumar Umadevi D., G. N. S. (2014). Quantifying dispersion interaction: A study of alkane and alkene dimers. Indian Journal of Chemistry.
    70. Kaur R, Ramesh M, Bharatam PV, Kishore R (2014). Self-Association Behaviour of a Novel Non-Proteinogenic β-Strand-Mimic in an Organic Solvent. The Journal of Physical Chemistry B. 118(31):9199-208. doi: 10.1021/jp5042074.
    71. Das S, Pal U, Das S, Bagga K, Roy A, Mrigwani A, Maiti NC. (2014). Sequence Complexity of Amyloidogenic Regions in Intrinsically Disordered Human Proteins. PLOS One ;9(3):e89781. doi: 10.1371/journal.pone.0089781
    72. Badrinarayan P, Sastry GN (2014). Specificity rendering 'hot-spots' for aurora kinase inhibitor design: The role of non-covalent interactions and conformational transitions. PLOS One. 9(12):e113773. doi: 10.1371/journal.pone.0113773.
    73. Muvva C, Singam ER, Raman SS, Subramanian V. (2014). Structure-based virtual screening of novel, high-affinity BRD4 inhibitors. Mol Biosyst. 10(9):2384-97. doi: 10.1039/c4mb00243a.
    74. Singh M, Hamid AA, Maurya AK, Prakash O, Khan F, Kumar A, Aiyelaagbe OO, Negi AS, Bawankule DU. (2014). Synthesis of diosgenin analogues as potential anti-inflammatory agents. The Journal of steroid biochemistry and molecular biology. 143:323-33. doi: 10.1016/j.jsbmb.2014.04.006.
    75. Singh NS, Kachhap S, Singh R, Mishra RC, Singh B, Raychaudhuri S. (2014). The length of glycine-rich linker in DNA-binding domain is critical for optimal functioning of quorum-sensing master regulatory protein HapR. Mol Genet Genomics. 289(6):1171-82. doi: 10.1007/s00438-014-0878-5
    76. Mishra NK, Singla D, Agarwal S, Raghava GP (2014). ToxiPred: A server for prediction of aqueous toxicity of small chemical molecules in T. Pyriformis. Journal of Translational Toxicology 1: 21-27.
    77. Gautam A, Kapoor P, Chaudhary K, Kumar R; Open Source Drug Discovery Consortium, Raghava GP. (2014). Tumor Homing Peptides as Molecular Probes for Cancer Therapeutics, Diagnostics and Theranostics. Current medicinal chemistry 21(21): 2367-2391.
    78. Akhoon BA, Singh KP, Varshney M, Gupta SK, Shukla Y, Gupta SK (2014). Understanding the mechanism of Atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods. Plos One. 9(10):e110041. doi: 10.1371/journal.pone.0110041.
    79. Chaubey, G., Singh, M., Crivellaro, F., Tamang, R., Nandan, A., Singh, K., et. al., (2014). Unravelling the distinct strains of Tharu ancestry. European Journal of Human Genetics, 22(12), 1404–1412. doi: 10.1038/ejhg.2014.36.
    80. Qureshi A Thakur N, M. I. T. A. K. M. (2014). VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. Database(Oxford)2014. pii: bau103. doi: 10.1093/database/bau103.
    81. Verma SK, Ranjan R, Kumar V, Siddiqi MI, Ahmed S (2014). Wat1/pop3, a conserved WD repeat containing protein acts synergistically with checkpoint kinase Chk1 to maintain genome ploidy in fission yeast S. pombe. PLOS One 9: e89587. doi: 10.1371/journal.pone.0089587.
    82. Agrawal P, Gupta P, Swaminathan K, Parkesh R (2014). Alpha-Glucan Pathway as a Novel Mtb Drug Target: Structural Insights and Cues for Polypharmcological Targeting of GlgB and GlgE. Curr Med Chem. 21(35):4074-84.
    83. Umadevi D, Panigrahi S, Sastry GN. (2014). Noncovalent Interaction of Carbon Nanostructures. Accounts of Chemical Research. 47(8):2574-81. doi: 10.1021/ar500168b.
    84. Francis A, Sunitha B, Vinodh K, Polavarapu K, Katkam SK, Modi S, Bharath MM, Gayathri N, Nalini A, Thangaraj K (2014). Novel TCAP mutation c.32C>A causing limb girdle muscular dystrophy 2G. PLoS One. 9(7):e102763.doi: 10.1371/journal.pone.0102763.
    85. Lazaridis et al. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513(7518): 409-413. doi: 10.1038/nature13673.
    86. Ramamoorthy, S., Garapati, H.S. and Mishra, R.K.(2014). Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation. Gene. 551(2):167-75. doi: 10.1016/j.gene.2014.08.052.
    87. Muvva C, Singam ER, Raman SS, Subramanian V. (2014). Structure-based virtual screening of novel, high-affinity BRD4 inhibitors. Mol Biosyst. 10(9): 2384-97. doi: 10.1039/c4mb00243a.
    88. harma A, Dutta P, Sharma M, Rajput NK, Dodiya B, Georrge JJ, Kholia T. (2014). OSDD Consortium, Bhardwaj A. BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts. Journal of cheminformatics 6(1):46.
    89. Das Roy R, Bhardwaj M, Bhatnagar V, Chakraborty K, Dash D (2014). How do eubacterial organisms manage aggregation-prone proteome. F1000Res. 3:137. doi:10.12688/f1000research.4307.1. eCollection.
    90. Banerjee A, Dey S, Chakraborty A, Datta A, Basu A, Chakrabarti S, Datta S. (2014). Binding mode analysis of a major T3SS translocator protein PopB with itschaperone PcrH from Pseudomonas aeruginosa. Proteins. 82(12):3273-85. doi: 10.1002/prot.24666.
    91. Nayak MK, Agrawal AS, Bose S, Naskar S, Bhowmick R, Chakrabarti S, Sarkar S,Chawla-Sarkar M. (2014).   Antiviral activity of baicalin against influenza virusH1N1-pdm09 is due to modulation of NS1-mediated cellular innate immune responses. J Antimicrob Chemother. 69(5):1298-310. doi: 10.1093/jac/dkt534.
    92. Bhowmick S, Malar M, Das A, Kumar Thakur B, Saha P, Das S, Rashmi HM, Batish VK, Grover S, Tripathy S. (2014).  Draft Genome Sequence of Lactobacillus casei Lbs2. Genome Announc.2(6). pii: e01326-14. doi: 10.1128/genomeA.01326-14.
    93. Bhowmick S and Tripathy S (2014). A Tale of Effectors; Their Secretory Mechanisms and Computational Discovery in Pathogenic, Non-Pathogenic and Commensal Microbes. Mol Biol. 3 (118), 2 .
    94. Badrinarayan, P.; Sastry, G. N. (2014).    Specificity rendering ′hot-spots′ for Aurora kinase inhibitor design: The role of non-covalent interactions and conformational transitions.  PLOS One 2014. 9(12): e113773. doi: 10.1371/journal.pone.0113773.
    95. J Richard Premkumar, Umadevi D., G Narahari.Sastry. (2014. Quantifying dispersion interaction: A study of alkane and alkene dimers. Indian Journal of Chemistry. 53A: 985-991.
    96. Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK (2014). Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Res. 2014 May 29; 42(12):7539-52. doi: 10.1093/nar/gku465.
    97. Meier C, Spitschak A, Abshagen K, Gupta S, Mor JM, Wolkenhauer O, Haier J, Vollmar B, Alla V, Pützer BM. (2014). Association of RHAMM with E2F1 promotes tumour cell extravasation by transcriptional up-regulation of fibronectin. J Pathol 2014 Jul 7; 234:351-64. doi: 10.1002/path.4400
    98. Sreenivas A, Sathyanarayana Reddy G, Shivaji S. (2014). Draft Genome Sequence of a Psychrophilic Bacterium, Sphingomonas antarcticum, Isolated from the Soils of Schirmacher Oasis, Antarctica. Genome Announc. 2014 Oct 2;2(5). pii: e00696-14. doi: 10.1128/genomeA.00696-14.

    Papers of Year-2013

    1. Latha RS, Vijayaraj R, Padmanabhan J, Singam EA, Chitra K, et al. (2013). 3D-QSAR studies on the biological activity of juvenile hormone mimetic compounds for Culex pipiens Larvae. Medicinal Chemistry Research 22: 5948-5960.
    2. Roy SK, Kumari N, Gupta S, Pahwa S, Nandanwar H, Jachak SM (2013). 7-Hydroxy-(E)-3-phenylmethylene-chroman-4-one analogues as efflux pump inhibitors against Mycobacterium smegmatis mc2 155. European Journal of Medicinal Chemistry 66 :499-507. doi: 10.1016/j.ejmech.2013.06.024.
    3. Shinde S, Arora N, Bhadra U (2013). A complex network of microRNAs expressed in brain and genes associated with amyotrophic lateral sclerosis. International journal of genomics 2013:383024. doi: 10.1155/2013/383024.
    4. Jha AN, Singh VK, Singh R, Pati SS, Patra PK, et al. (2013). A rare non-synonymous c. 102C> G SNP in the IFNB1 gene might be a risk factor for cerebral malaria in Indian populations. Infection, Genetics and Evolution 14: 369-374. doi: 10.1016/j.meegid.2012.12.029.
    5. Mazumder A, Bose M, Chakraborty A, Chakrabarti S, Bhattacharyya SN (2013). A transient reversal of miRNA-mediated repression controls macrophage activation. EMBO reports 14(11): 1008-1016. doi: 10.1038/embor.2013.149. doi: 10.1038/embor.2013.149.
    6. Pathak RU, Mamillapalli A, Rangaraj N, Kumar RP, Vasanthi D, Mishra K, Mishra RK. (2013). AAGAG repeat RNA is an essential component of nuclear matrix in Drosophila. RNA Biol. 10(4):564-71. doi: 10.4161/rna.24326.
    7. Sridhar S, Bhat G, Guruprasad K (2013). Analysis of bortezomib inhibitor docked within the catalytic subunits of the Plasmodium falciparum 20S proteasome. SpringerPlus 2: 566. doi: 10.1186/2193-1801-2-566.
    8. Dhanda SK, Gupta S, Vir P, Raghava G (2013). Prediction of IL4 Inducing Peptides. Journal of Immunology Research 2013:263952. doi: 10.1155/2013/263952.
    9. Bhaskar L, Thangaraj K, Kumar KP, Pardhasaradhi G, Singh L, Rao VR. (2013). Association between Neuropeptide Y Gene Polymorphisms and Alcohol Dependence: A Case-Control Study in Two Independent Populations. European addiction research 19(6): 307-313. doi: 10.1159/000346679.
    10. Smita S, Singh KP, Akhoon BA, Gupta SK, Gupta SK (2013). Bioinformatics Tools for Interpretation of Data Used in Molecular Identification. Analyzing Microbes: Springer. pp. 209-243.
    11. Smita S, Singh KP, Akhoon BA, Gupta SK (2013). Biological Sequence Analysis: Algorithms and Statistical Methods. Analyzing Microbes: Springer. pp. 303-333.
    12. Kumar R, Chaudhary K, Gupta S, Singh H, Kumar S, et al. (2013). CancerDR: cancer drug resistance database. Scientific reports 3:1445. doi: 10.1038/srep01445.
    13. Singh SP, Agnihotri P, Pratap JV (2013). Characterization of a Novel Putative S-Adenosylmethionine Decarboxylase-Like Protein from Leishmania donovani. PLOS One 8(6): e65912.
    14. Roy K, Ghosh M, Pal TK, Chakrabarti S, Roy S (2013). Cholesterol lowering drug may influence cellular immune response by altering MHC II function. Journal of lipid research 54(11): 3106-3115. doi: 10.1194/jlr.M041954.
    15. Dey A, Ramachandran R (2013). Cloning, overexpression, purification and preliminary X-ray analysis of a feast/famine regulatory protein (Rv2779c) from Mycobacterium tuberculosis H37Rv. Acta Crystallographica Section F: Structural Biology Communications 70(pt1): 97-100. doi: 10.1107/S2053230X13033128.
    16. Prakash O, Khan F (2013). Cluster Based SVR-QSAR Modelling for HTS Records: An Implementation for Anticancer Leads Against Human Breast Cancer. Combinatorial chemistry & high throughput screening 16(7): 511-521.
    17. Bhardwaj J, Chauhan R, Swarnkar MK, Chahota RK, Singh AK, et al. (2013). Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC genomics 14: 647. doi: 10.1186/1471-2164-14-647.
    18. Sharma A, Kapoor P, Gautam A, Chaudhary K, Kumar R, et al. (2013). Computational approach for designing tumor homing peptides. Scientific reports 3:1607. doi: 10.1038/srep01607..
    19. Ahanger SH, Srinivasan A, Vasanthi D, Shouche YS, Mishra RK (2013). Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae. Nucleic acids research 41(2): 804-816. doi: 10.1093/nar/gks1178.
    20. Kumar, R., & Raghava, G. P. S. (2013). Hybrid Approach for Predicting Coreceptor Used by HIV-1 from Its V3 Loop Amino Acid Sequence. PloS One, 8(4):e61437. doi: 10.1371/journal.pone.0061437.
    21. Tiwari SK, Agarwal S, Seth B, Yadav A, Nair S, et al. (2013). Curcumin-loaded nanoparticles potently induce adult neurogenesis and reverse cognitive deficits in Alzheimer disease model via canonical Wnt/β-catenin pathway. ACS nano 8(1): 76-103. doi: 10.1021/nn405077y
    22. Singla D, Tewari R, Kumar A, Raghava GP (2013). Designing of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv). Chemistry Central Journal 7(1): 49. doi: 10.1186/1752-153X-7-49.
    23. Dhanda SK, Vir P, Raghava GP (2013). Designing of interferon-gamma inducing MHC class-II binders. Biology direct 8: 30. doi: 10.1186/1745-6150-8-30.
    24. Bhushan A, Joshi J, Shankar P, Kushwah J, Raju SC, et al. (2013). Development of genomic tools for the identification of certain Pseudomonas up to species level. Indian journal of microbiology 53(3): 253-263. doi: 10.1007/s12088-013-0412-1.
    25. Prakash O, Khan F (2013). Development of Method for Three-Point Data Estimation and SVR-QSAR Model to Screen Anti Cancer Leads. Combinatorial chemistry & high throughput screening 16 (6): 425-434.
    26. Upadhyay RD, Yadav AK, Sonawane S, Goankar R, Dash D (2013). Differential Proteomic and Phospho-proteomic Analysis of Normal versus Failed Spermiation in Adult Rats by Label-Free LC-MS/MS. J Anal Bioanal Tech 4:172. doi: 10.4172/2155-9872.1000172
    27. Devi, U., Khatri, I., Kumar, N., Kumar, L., Sharma, D., Subramanian, S., & Saini, A. K. (2013). Draft genome sequence of a plant growth-promoting rhizobacterium, Serratia fonticola strain AU-P3 (3). Genome Announcements, 1(6), e00946–13. doi: 10.1128/genomeA.00946-13.
    28. Singh NK, Kumar S, Raghava GPS, Mayilraj S (2013). Draft genome sequence of Acinetobacter baumannii strain MSP4-16. Genome announcements 1(2): e00137-00113. doi: 10.1128/genomeA.00137-13.
    29. Kaur N, Kumar S, Bala M, Raghava GPS, Mayilraj S (2013). Draft genome sequence of Amycolatopsis decaplanina strain DSM 44594T. Genome announcements 1(2): e00138-00113.doi: 10.1128/genomeA.00138-13.
    30. Shivaji S, Ara S, Bandi S, Singh A, Pinnaka AK (2013). Draft Genome Sequence of Arthrobacter gangotriensis Strain Lz1yT, Isolated from a Penguin Rookery Soil Sample Collected in Antarctica, near the Indian Station Dakshin Gangotri. Genome Announc 1(13): e00347-00313. doi: 10.1128/genomeA.00347-13.
    31. Shivaji S, Ara S, Begum Z, Ruth M, Singh A, et al. (2013). Draft genome sequence of Bhargavaea cecembensis strain DSE10T, isolated from a deep-sea sediment sample collected at a depth of 5,904 m from the Chagos-Laccadive ridge system in the Indian Ocean. Genome announcements 1(3): e00346-00313. doi: 10.1128/genomeA.00346-13.
    32. Shivaji S, Ara S, Begum Z, Srinivas T, Singh A, et al. (2013). Draft genome sequence of Cesiribacter andamanensis strain AMV16T, isolated from a soil sample from a mud volcano in the Andaman Islands, India. Genome announcements 1(3). pii: e00240-13. doi: 10.1128/genomeA.00240-13.
    33. Khatri I, Kaur S, Devi U, Kumar N, Sharma D, Subramanian S, Saini AK. (2013). Draft genome sequence of plant growth-promoting rhizobacterium Pantoea sp. strain AS-PWVM4. Genome announcements 1(6): e00947-00913. doi: 10.1128/genomeA.00947-13.
    34. Devi U, Khatri I, Kumar N, Sharma D, Subramanian S, et al. (2013). Draft genome sequence of plant-growth-promoting rhizobacterium Serratia fonticola strain AU-AP2C, isolated from the pea rhizosphere. Genome announcements 1(6): e01022-01013. doi: 10.1128/genomeA.01022-13.
    35. Reddy GS, Ara S, Singh A, Pinnaka AK, Shivaji S (2013). Draft genome sequence of Psychrobacter aquaticus strain CMS 56T, isolated from a cyanobacterial mat sample collected from water bodies in the McMurdo dry valley region of Antarctica. Genome announcements 1(6): pii: e00918-00913. doi: 10.1128/genomeA.00918-13.
    36. Bala M, Kumar S, Raghava GPS, Mayilraj S (2013). Draft genome sequence of Rhodococcus qingshengii strain BKS 20-40. Genome announcements 1(2): e00128-00113. doi: 10.1128/genomeA.00128-13.
    37. Bala M, Kumar S, Raghava GPS, Mayilraj S (2013). Draft genome sequence of Rhodococcus ruber strain BKS 20-38. Genome announcements 1(2): e00139-00113. doi: 10.1128/genomeA.00139-13.
    38. Kumar S, Bala M, Raghava GPS, Mayilraj S (2013). Draft genome sequence of Rhodococcus triatomae strain BKS 15-14. Genome announcements 1(2): e00129-00113. doi: 10.1128/genomeA.00129-13.
    39. Kumar S, Kaur N, Singh NK, Raghava GPS, Mayilraj S (2013). Draft genome sequence of Streptomyces gancidicus strain BKS 13-15. Genome announcements 1(2): e00150-00113. doi: 10.1128/genomeA.00150-13.
    40. Vikram S, Kumar S, Vaidya B, Pinnaka AK, Raghava GPS (2013). Draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon. Genome announcements 1(2): e00058-00013. doi: 10.1128/genomeA.00058-13.
    41. Pandiyan A, Ray MK (2013). Draft genome sequence of the Antarctic psychrophilic bacterium Pseudomonas syringae strain Lz4W. Genome announcements 1(3): e00377-00313. doi: 10.1128/genomeA.00377-13.
    42. Kumar S, Kaur C, Kimura K, Takeo M, Raghava GPS, et al. (2013). Draft genome sequence of the type species of the genus Citrobacter, Citrobacter freundii MTCC 1658. Genome announcements 1(1): e00120-00112. doi: 10.1128/genomeA.00120-12.
    43. Chowdhury S, Sarkar RR (2013). Drug Targets and Biomarker Identification from Computational Study of Human Notch Signaling Pathway. Clin Exp Pharmacol 3: 2161-1459.1000137. doi:10.4172/2161-1459.1000137
    44. Dhanda SK, Singla D, Mondal AK, Raghava GP (2013). DrugMint: a webserver for predicting and designing of drug-like molecules. Biology direct 8:28. doi: 10.1186/1745-6150-8-28.
    45. Srivastava HK, Sastry GN (2013). Efficient estimation of MMGBSA-based BEs for DNA and aromatic furan amidino derivatives. Journal of Biomolecular Structure and Dynamics 31(5): 522-537. doi: 10.1080/07391102.2012.703071.
    46. Hellen EH, Dana SK, Zhurov B, Volkov E (2013). Electronic implementation of a repressilator with quorum sensing feedback. PLOS One 8(5): e62997. doi: 10.1371/journal.pone.0062997.
    47. Singh GP, Dash D (2013). Electrostatic mis-interactions cause overexpression toxicity of proteins in E. coli. PLOS One 8(5): e64893. doi: 10.1371/journal.pone.0064893.
    48. Sudershan Kumar US, Leena Wahi, Abhilasha Agnihotri, Bajrang Singh, Goel AK (2013). Establishing India's botanic gardens network as a clearing house mechanism in times of rapid global change. Scientific Publishers (India): 77-109.
    49. Singh SB, Biswas D, Rawat J, Sindhwani G, Patras A, et al. (2013). Ethnicity-tailored novel set of ESAT-6 peptides for differentiating active and latent tuberculosis. Tuberculosis 93(6): 618-624. doi: 10.1016/
    50. Ahanger SH, Shouche YS, Mishra RK (2013). Functional sub-division of the Drosophila genome via chromatin looping: The emerging importance of CP190. Nucleus 4(2): 115-122. doi: 10.4161/nucl.23389.
    51. Vikram S, Pandey J, Kumar S, Raghava GPS (2013). Genes Involved in Degradation of para-Nitrophenol Are Differentially Arranged in Form of Non-Contiguous Gene Clusters in Burkholderia sp. strain SJ98. PLOS One 8(12): e84766. doi: 10.1371/journal.pone.0084766.
    52. Moorjani P, Thangaraj K, Patterson N, Lipson M, Loh P-R, et al. (2013). Genetic evidence for recent population mixture in India. The American Journal of Human Genetics 93(3): 422-438. doi: 10.1016/j.ajhg.2013.07.006.
    53. Shinde V, Marcinek P, Rani DS, Sunder SR, Arun S, et al. (2013). Genetic evidence of TAP1 gene variant as a susceptibility factor in Indian leprosy patients. Human immunology 74(6): 803-807.doi: 10.1016/j.humimm.2013.01.001.
    54. Gazi NN, Tamang R, Singh VK, Ferdous A, Pathak AK, et al. (2013). Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal. PLOS One 8(10): e75064. doi: 10.1371/journal.pone.0075064.
    55. Singh, S. V., Kumar, N., Singh, S. N., Bhattacharya, T., Sohal, J. S., Singh, P. K., Raghava, G. P. S. (2013). Genome Sequence of the “Indian Bison Type” Biotype of Mycobacterium avium subsp. paratuberculosis Strain S5. Genome Announcements, 1(1).
    56. Vikram S, Kumar S, Vaidya B, Pinnaka AK, Raghava GPS (2013).Draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon. Genome announcements 1(2): e00058-00013. doi: 10.1128/genomeA.00058-13.
    57. Khatri I, Akhtar A, Kaur K, Tomar R, Prasad GS, et al. (2013). Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. Gut pathogens 5(1): 30. doi: 10.1186/1757-4749-5-30.
    58. Gautam A, Chaudhary K, Singh S, Joshi A, Anand P, et al. (2013). Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. Nucleic acids research:42(Database issue):D444-9. doi: 10.1093/nar/ gkt1008.
    59. Qureshi A, Thakur N, Kumar M (2013). HIPdb: a database of experimentally validated HIV inhibiting peptides. PLOS One 8(1): e54908. doi: 10.1371/journal.pone.0054908.
    60. Chandra V, Mahajan S, Saini A, Dkhar HK, Nanduri R, et al. (2013). Human IL10 gene repression by Rev-erbα ameliorates Mycobacterium tuberculosis clearance. Journal of Biological Chemistry 288(15): 10692-10702. doi: 10.1074/jbc.M113.455915.
    61. Kumar R, Raghava GP (2013). Hybrid Approach for Predicting Coreceptor Used by HIV-1 from Its V3 Loop Amino Acid Sequence. PLOS One 8(4): e61437. doi: 10.1371/journal.pone.0061437.
    62. Gupta S, Ansari HR, Gautam A, Raghava GP (2013). Identification of B-cell epitopes in an antigen for inducing specific class of antibodies. Biology direct 8: 27. doi: 10.1186/1745-6150-8-27.
    63. Anand N, Ramakrishna K, Gupt MP, Chaturvedi V, Singh S, et al. (2013). Identification of 1-[4-Benzyloxyphenyl)-but-3-enyl]-1 H-azoles as New Class of Antitubercular and Antimicrobial Agents. ACS Medicinal Chemistry Letters 4(10): 958-963. doi: 10.1021/ml4002248.
    64. Singh H, Ansari HR, Raghava GP (2013). Improved method for linear B-cell epitope prediction using Antigen’s primary sequence. PLOS One 8(5): e62216. doi: 10.1371/journal.pone.0062216.
    65. Kalani K, Agarwal J, Alam S, Khan F, Pal A, Srivastava SK. (2013). In Silico and In Vivo Anti-Malarial Studies of 18β Glycyrrhetinic Acid from Glycyrrhiza glabra. PLOS One 8(9): e74761.
    66. Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R; Open Source Drug Discovery Consortium, Raghava GP. (2013). In Silico Approach for Predicting Toxicity of Peptides and Proteins. PLOS One 8(9): e73957. doi 10.1371/journal.pone.0073957
    67. Gautam A, Chaudhary K, Kumar R, Sharma A, Kapoor P, et al. (2013). In silico approaches for designing highly effective cell penetrating peptides. J Transl Med 11: 1-12. doi: 10.1186/1479-5876-11-74.
    68. Tyagi A, Kapoor P, Kumar R, Chaudhary K, Gautam A, Raghava GP. (2013). In Silico Models for Designing and Discovering Novel Anticancer Peptides. Scientific reports 3:2984. doi: 10.1038/srep02984.
    69. Chauhan JS, Rao A, Raghava GP.(2013). In silico platform for prediction of N-, O-and C-glycosites in eukaryotic protein sequences. PLOS One 8(6): e67008. doi: 10.1371/journal.pone.0067008.
    70. Rajalakshmi S, Kiran MS, Vaidyanathan VG, Azhagiya Singam ER, Subramaniam V, Nair BU. (2013). Investigation of nuclease, proteolytic and antiproliferative effects of copper (II) complexes of thiophenylmethanamine derivatives. European Journal of Medicinal Chemistry 70: 280-293. doi: 10.1016/j.ejmech.2013.
    71. Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, Jain S, Sati S, Sengupta S, Sachidanandan C, Raghava GP, Sivasubbu S, Scaria V. (2013). lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database 2013: bat034. doi: 10.1093/database/bat034.
    72. Patrick Marcinek, Aditya Nath Jha,Vidyagouri Shinde, Arun Sundaramoorthy, Raja Rajkumar, Naveen Chandra Suryadevara, Sanjeev Kumar Neela, Hoang van Tong, Vellingiri Balachander,Vijaya Lakshmi Valluri, Kumarasamy Thangaraj, and Thirumalaisamy P Velavan. (2013). LRRK2 and RIPK2 variants in the NOD 2-mediated signaling pathway are associated with susceptibility to Mycobacterium leprae in Indian populations. PLOS One 8(8): e73103. doi: 10.1371/journal.pone.0073103.
    73. Kumar CG, Mongolla P, Sujitha P, Joseph J, Babu KS, Suresh G, Ramakrishna KV, Purushotham U, Sastry GN, Kamal A. (2013). Metabolite profiling and biological activities of bioactive compounds produced by Chrysosporium lobatum. Springer Plus strain BK-3 isolated from Kaziranga National Park, Assam, India. SpringerPlus 2(1): 122. doi: 10.1186/2193-1801-2-122.
    74. Jha A, Shankar R (2013). miReader: Discovering Novel miRNAs in Species without Sequenced Genome. PLOS One 8(6): e66857.
    75. K S, Jalali S, Scaria V, Bhardwaj A. (2013). MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variations. PLOS One 8(4): e60066. doi: 10.1371/journal.pone.0060066.
    76. Roy SK, Kumari N, Pahwa S, Agrahari UC, Bhutani KK, Jachak SM, Nandanwar H. (2013). NorA efflux pump inhibitory activity of coumarins from< i> Mesua ferrea. Fitoterapia 90: 140-150. doi: 10.1016/j.fitote.2013.07.015.
    77. Mangal M, Sagar P, Singh H, Raghava GP, Agarwal SM.(2013). NPACT: naturally occurring plant-based anti-cancer compound-activity-target database. Nucleic acids research 41: D1124-D1129. doi: 10.1093/nar/gks1047.
    78. Ahmed F, Kaundal R, Raghava GP.(2013). PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. BMC bioinformatics 14: S9. doi: 10.1186/1471-2105-14-S14-S9
    79. Dhanda SK GS, Vir P, Raghava GP. (2013). Prediction of IL4 inducing peptides. Clin Dev Immunol:2013: 263952. doi: 10.1155/2013/263952
    80. Panwar B, Gupta S, Raghava GP. (2013). Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information. BMC bioinformatics 14: 44. doi: 10.1186/1471-2105-14-44.
    81. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, et al. (2013). Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Molecular & Cellular Proteomics 12(11): 3388-3397.
    82. Yadav AK, Kadimi PK, Kumar D, Dash D. (2013). ProteoStats—a library for estimating false discovery rates in proteomics pipelines. Bioinformatics, 29(21): 2799–2800. doi: 10.1093/bioinformatics/btt490
    83. Kumar Yadav D, Kalani K, Khan F, Kumar Srivastava S (2013). QSAR and Docking Based Semi-synthesis and in vitro Evaluation of 18 β-glycyrrhetinic Acid Derivatives Against Human Lung Cancer Cell Line A-549. Medicinal Chemistry 9(8): 1073-1084.
    84. Yadav DK, K. F. (2013). QSAR, docking and ADMET studies of camptothecin derivatives as inhibitors of DNA topoisomerase-I. J. Chemometrics. 27(1-2): 21-33.
    85. Badrinarayan P, Sastry GN (2013). Rational approaches towards lead optimization of kinase inhibitors: the issue of specificity. Current pharmaceutical design 19(26): 4714-4738.
    86. Sheokand N, Kumar S, Malhotra H, Tillu V, Raje CI, et al. (2013). Secreted glyceraldehye-3-phosphate dehydrogenase is a multifunctional autocrine transferrin receptor for cellular iron acquisition. Biochimica et Biophysica Acta (BBA) 1830(6): 3816-3827. doi: 10.1016/j.bbagen.2013.03.019.
    87. Maity M, Maiti NC (2013). Sequence composition of Binding sites in natively unfolded Human proteins. Journal of Proteins & Proteomics 3(2).
    88. Chowdhury S, Pradhan RN, Sarkar RR. (2013). Structural and logical analysis of a comprehensive hedgehog signaling pathway to identify alternative drug targets for glioma, colon and pancreatic cancer. PLOS One 8(7): e69132. doi: 10.1371/journal.pone.0069132.
    89. Mujahid, M., Gonnade, R. G., Yogeeswari, P., Sriram, D., & Muthukrishnan, M.(2013). Synthesis and antitubercular activity of amino alcohol fused spirochromone conjugates. Bioorganic & medicinal chemistry letters 23: 1416-1419. doi: 10.1016/j.bmcl.2012.12.073
    90. Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, Chaubey G, Goto R, Ho SY, Gallego Romero I, Crivellaro F, Hudjashov G, Rai N, Metspalu M, Mascie-Taylor CG, Pitchappan R, Singh L, Mirazon-Lahr M, Thangaraj K, Villems R, Kivisild T. (2013). The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS genetics 9(11): e1003912. doi: 10.1371/journal.pgen.1003912.
    91. Witt H, Beer S, Rosendahl J, Chen J-M, Chandak GR, et al. (2013). Variants in CPA1 are strongly associated with early onset chronic pancreatitis. Nature genetics 45: 1216-1220. doi: 10.1038/ng.2730.
    92. Jha AN, Sundaravadivel P, Pati SS, Patra PK, Thangaraj K (2013). Variations in ncRNA gene LOC284889 and MIF-794CATT repeats are associated with malaria susceptibility in Indian populations. Malaria journal 12: 345. doi: 10.1186/1475-2875-12-345.
    93. Srivastava S, Puri D, Garapati HS, Dhawan J, Mishra RK (2013). Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters. Epigenetics & chromatin 6: 8. doi: 10.1186/1756-8935-6-8.

    Papers of Year-2012

    1. Srivastava HK, Bohari MH, Sastry GN. (2012). Modeling anti-HIV compounds: the role of analogue-based approaches. Current computer-aided drug design 8(3): 224-248.
    2. Vijayan RS, Trivedi N, Roy SN, Bera I, Manoharan P, Payghan PV, Bhattacharyya D, Ghoshal N. (2012). Modeling the Closed and Open State Conformations of the GABAA Ion Channel-Plausible Structural Insights for Channel Gating. Journal of chemical information and modeling 52(11): 2958-2969.doi: 10.1021/ci300189a.
    3. Srivastava HK, Sastry GN (2012). Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches. Journal of chemical information and modeling 52(11): 3088-3098. doi: 10.1021/ci300385h.
    4. Khan MA, Gahlot S, Majumdar S. (2012). Oxidative stress induced by curcumin promotes the death of cutaneous T-cell lymphoma (HuT-78) by disrupting the function of several molecular targets. Molecular cancer therapeutics 11: 1873-1883.
    5. Roy SK, Pahwa S, Nandanwar H, Jachak SM. (2012). Phenylpropanoids of< i> Alpinia galanga as efflux pump inhibitors in< i> Mycobacterium smegmatis mc< sup> 2 155. Fitoterapia 83(7): 1248-1255.doi: 10.1016/j.fitote.2012.06.008.
    6. Aithal A, Sharma A, Joshi S, Raghava GP, Varshney GC. (2012). PolysacDB: A database of microbial polysaccharide antigens and their antibodies. PLOS One 7(4): e34613.doi: 10.1371/journal.pone.0034613.
    7. Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S. (2012). SPEER-SERVER: a web server for prediction of protein specificity determining sites. Nucleic acids research. 40(Web Server issue):W242-8. doi: 10.1093/nar/gks559.
    8. Chourasia M, Sastry GN. (2012). The Nucleotide, Inhibitor, and Cation Binding Sites of P-type II ATPases. Chemical biology & drug design 79(5): 617-627. doi: 10.1111/j.1747-0285.2012.01334.x.
    9. Rai N, Chaubey G, Tamang R, Pathak AK, Singh VK, Karmin M, Singh M, Rani DS, Anugula S, Yadav BK, Singh A, Srinivasagan R, Yadav A, Kashyap M, Narvariya S, Reddy AG, van Driem G, Underhill PA, Villems R, Kivisild T, Singh L, Thangaraj K. (2012). The phylogeography of Y-chromosome haplogroup h1a1a-m82 reveals the likely Indian origin of the European Romani populations. PLOS One 7(11): e48477. doi: 10.1371/journal.pone.0048477.
    10. Kapoor P, Singh H, Gautam A, Chaudhary K, Kumar R, et al. (2012). TumorHoPe: a database of tumor homing peptides. PLOS One 7(4): e35187.doi: 10.1371/journal.pone.0035187.
    11. Badrinarayan P, Sastry GN (2012). Virtual screening filters for the design of type II p38 MAP kinase inhibitors: a fragment based library generation approach. Journal of Molecular Graphics and Modelling 34: 89-100. doi: 10.1016/j.jmgm.2011.12.009.
    12. Jha AN, Singh VK, Kumari N, Singh A, Antony J, van Tong H, Singh S, Pati SS, Patra PK, Singh R, Toan NL, Song le H, Assaf A, Messias-Reason IJ, Velavan TP, Singh L, Thangaraj K. (2012). IL-4 haplotype-590T,-34T and intron-3 VNTR R2 is associated with reduced malaria risk among ancestral indian tribal populations. PLOS One 7(10): e48136.doi: 10.1371/journal.pone.0048136
    13. Kumar S, Kushwaha H, Bachhawat AK, Raghava GPS, Ganesan K (2012). Genome sequence of the oleaginous red yeast Rhodosporidium toruloides MTCC 457. Eukaryotic cell 11(8): 1083-1084. doi: 10.1128/EC.00156-12.
    14. Kumar S, Vikram S, Raghava GPS (2012). Genome sequence of the nitroaromatic compound-degrading bacterium Burkholderia sp. strain SJ98. Journal of bacteriology 194(12): 3286-3286. v
    15. Kumar S, Subramanian S, Raghava GPS, Pinnaka AK (2012). Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T. Journal of bacteriology 194(14): 3746-3746. doi: 10.1128/JB.00649-12.
    16. Kumar S, Vikram S, Subramanian S, Raghava GPS, Pinnaka AK (2012). Genome Sequence of the Halotolerant Bacterium Imtechella halotolerans K1T. Journal of bacteriology 194(14): 3731-3731. doi: 10.1128/JB.00506-12.
    17. Purushotham U, Sastry GN (2012). Exploration of conformations and quantum chemical investigation of l-tyrosine dimers, anions, cations and zwitterions: a DFT study. Theoretical Chemistry Accounts 131:1093. pp 1-14.
    18. Choudhury C Priyakumar UD, Sastry GN (2015). Dynamics Based Pharmacophore Models for Screening Potential Inhibitors of Mycobacterial Cyclopropane Synthase. J. Chem. Inf. Model.55(4):848-60. doi: 10.1021/ci500737b.
    19. Vikram S, Kumar S, Subramanian S, Raghava GPS (2012). Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300. Journal of bacteriology 194(13): 3543-3543. doi: 10.1128/JB.00532-12.
    20. Kumar S, Randhawa A, Ganesan K, Raghava GPS, Mondal AK (2012). Draft genome sequence of salt-tolerant yeast Debaryomyces hansenii var. hansenii MTCC 234. Eukaryotic cell 11(7): 961-962. doi: 10.1128/EC.00137-12.
    21. Gautam A, Singh H, Tyagi A, Chaudhary K, Kumar R, et al. (2012). CPPsite: a curated database of cell penetrating peptides. Database 2012: bas015. doi: 10.1093/database/bas015.
    22. Srinivasan A, Mishra RK (2012). Chromatin domain boundary element search tool for Drosophila. Nucleic acids research. 40(10):4385-95. doi: 10.1093/nar/gks045.
    23. Vikram S, Pandey J, Bhalla N, Pandey G, Ghosh A, et al. (2012). Branching of the p-nitrophenol (PNP) degradation pathway in burkholderia sp. Strain SJ98: Evidences from genetic characterization of PNP gene cluster. AMB Express 2(1):30. doi: 10.1186/2191-0855-2-30.
    24. Chowdhury AR, Dutta C (2012). A pursuit of lineage-specific and niche-specific proteome features in the world of archaea. BMC genomics 13: 236. doi: 10.1186/1471-2164-13-236.
    25. Purushotham U, Vijay D, Narahari Sastry G (2012). A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions of L-phenylalanine. Journal of computational chemistry 33(1): 44-59. doi: 10.1002/jcc.21942.
    26. Vijayaraj R, Lakshmi Vasavi Devi M, Subramanian V, Chattaraj PK (2012). 3D-QSAR Studies on the Inhibitory Activity of Trimethoprim Analogues against Escherichia coli Dihydrofolate Reductase. Chemical biology & drug design 79(6): 935-942.doi: 10.1111/j.1747-0285.2012.01351.x.