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.

2016

2015

2014

2013

2012

Papers of Year-2016

  1. Subramanian SR, Singam ER, Berinski M, Subramanian V, Wade RC. (2016) Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen. J Phys Chem B. 2016, doi: 10.1021/acs.jpcb.6b02573.
  2. Muvva C, Patra S, Venkatesan S (2016) MMpI: a wide-range of available compounds of Matrix metalloproteinase Inhibitors. PONE-D-15-40973 doi: 10.1371/journal.pone.0159321.
  3. Nidhi Singh, Mohammad Imran Siddiqi. (2016) Molecular Modelling, Substrate Binding Analysis and Molecular Dynamics Simulation Studies. Med Chem. Res. (2016), (Accepted Manuscript).
  4. Vikash Kumar and Mohammad Imran Siddiqi (2016) Structural insight into inhibition of human Class II PI3K isoforms: homology modeling, binding site characterization, docking and molecular dynamics studies. RSC Adv., 2016, 6, 112455-112467 DOI: 10.1039/C6RA15417D.
  5. Gupta AK, Kaur K, Rajput A, Dhanda SK, Sehgal M, Khan MS, Monga I, Dar SA, Singh S, Nagpal G, Usmani SS, Thakur A, Kaur G, Sharma S, Bhardwaj A, Qureshi A, Raghava GP, Kumar M (2016) ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis. Scientific Reports 6, 32713.
  6. Ghosh M, Niyogi S, Bhattacharyya M, Adak M, Nayak DK, Chakrabarti S, Chakrabarti P. (2016) Ubiquitin Ligase COP1 Controls Hepatic Fat Metabolism by Targeting ATGL for Degradation. Diabetes.. pii: db160506.
  7. Bhattacharyya D, Hazra S, Banerjee A, Datta R, Kumar D, Chakrabarti S, Chattopadhyay S. (2016) Transcriptome-wide identification and characterization of CAD isoforms specific for podophyllotoxin biosynthesis from Podophyllumhexandrum. Plant Mol Biol. 92(1-2):1-23.
  8. Jayaswall K, Mahajan P, Singh G, Parmar R, Seth R, Raina A, Swarnkar MK, Singh AK, Shankar R, Sharma RK (2016) Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze). Sci Rep. 2016 Jul 28;6:30412.
  9. Masood N, Khan S, Luqman S, Ahmed S (2016) Thymoquinone disrupts the microtubule dynamics in fission yeast Schizosaccharomyces pombe. AIMS Genetics 3(4): 239-251.
  10. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de (2016) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 538: 201-206.
  11. Bharati AP, Singh N, Kumar V, Kashif M, Singh AK, Singh P,Singh SK, Siddiqi MI, Tripathi T, Akhtar MS. (2016) The mRNA capping enzyme of Saccharomyces cerevisiae has dual specificity to interact with CTD of RNA Polymerase II. Sci Rep. 2016 Aug 9;6:31294. Doi:10.1038/srep31294.
  12. Sarkar RR (2016) The Big Data Deluge in Biology: Challenges and Solutions. Journal of Informatics and Data Mining., 1(2), 14 (2016)
  13. Singh S, Ahmad A, Raghuvanshi DS, Hasanain M, Agarwal K, Dubey V, Fatima K, Alam S, Sarkar J, Luqman S, Khan F, Tandon S, Gupta A (2016) Synthesis of 3,5-dihydroxy-7,8-dimethoxy-2-(4-methoxyphenyl)benzopyran-4-one derivatives as anticancer agents. Bioorg Med Chem Lett. 2016 Nov 1;26(21):5322-5327.
  14. Buduma K, Chinde S, Dommati AK, Sharma P, Shukla A, Srinivas KV, Arigari NK, Khan F, Tiwari AK, Grover P, Jonnala KK. (2016) Synthesis and evaluation of anticancer and antiobesity activity of 1-ethoxy carbonyl-3,5-bis (3'-indolyl methylene)-4-pyperidone analogs. Bioorg Med Chem Lett. 2016 Mar 15;26(6):1633-8.
  15. Sharma P, Prakash O, Shukla A, Rajpurohit CS, Vasudev PG, Luqman S, Srivastava SK, Pant AB, Khan F (2016) Comb Chem High Throughput Screen. 2016;19(8):656-666.
  16. Nayak, A.R., Karade, S.S., Srivastava, V.K., Rana, A.K., Gupta, C.M., Sahasrabuddhe, A.A. And Pratap, J.V. (2016) Structure of Leishmania donovani coronin coiled coil domain reveals an antiparallel 4 helix bundle with inherent asymmetry J. Str. Biol. 195 (1), 129-138.
  17. Dar SA, Gupta AK, Thakur A, Kumar M (2016) SMEpred workbench: a web server for predicting efficacy of chemically modified siRNAs. RNA Biology. 2016.
  18. Dar SA, Thakur A, Qureshi A, Kumar M (2016) Sci Rep. 2016 Jan 28;6:20031. doi: 10.1038/srep20031.
  19. Kumar R, Koul S, Kumar P, Kalia VC (2016) Searching biomarkers in the sequenced genomes of Staphylococcus for their rapid identification. Indian J Microbiol 56:64-71.doi:10.1007/s12088-016-0565-9
  20. Utpal Bhadra, Paromita Das and Manika Pal-Bhadra (2016) RNA Interference (RNAi) as a Metronome of the Circadian Cadence  Mol. Biol. 5:3 http://dx.doi.org/10.4172/2168-9547.1000166
  21. Mathur D, Prakash S, Anand P, Kaur H, Agrawal P, Mehta A, Kumar R, Singh S, Raghava GP (2016) PEPlife: A Repository of the Half-life of Peptides. Scientific Reports 6, 36617
  22. Pal, U., Roy, A., Das, S., Das, S., Kundu, M., Bagga, K., Maiti, N. C. (2016) Origin of Protein Aggregation: Identification of Some Characteristic Traits in Structured and Intrinsically Disordered Proteins. J. Proteins and Proteomics.
  23. S Das, S Das, A Roy, U Pal and Maiti, N. C.(2016) Orientation of tyrosine side chain in neurotoxic Aβ differs in two different secondary structures of the peptide. R. Soc. Open Sci. 3: 160112.
  24. Sharat Chandra, Jyotsana Pandey, Akhilesh Kumar Tamrakar, Mohammad Imran Siddiqi (2016) Multiple Machine Learning Based Descriptive and Predictive Workflow for the Identification of Potential PTP1B Inhibitors. J. Mol. Graph. and Model., http://dx.doi.org/10.1016/j.jmgm.2016.10.020.
  25. Thakur A, Rajput A, Kumar M*. (2016) MSLVP: prediction of multiple subcellular localization of viral proteins using a support vector machine. Mol Biosyst. 2016;12(8):2572-86. doi: 10.1039/c6mb00241b.
  26. Shinde, R. N., Subramanian, K and Singh B (2016) Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS. Sci. Rep. 6, 40452. doi: 10.1038/srep40452 (2016).
  27. Sadeghi M, Ranjbar B, Ganjalikhany MR, Khan F, Schmitz U, Wolkenhauer O, Gupta SK. (2016) MicroRNA and transcription factor gene regulatory network analysis reveals key regulatory elements associated with prostate cancer progression. PLOS ONE 2016.
  28. Agnihotri, P., Singh, S.P., Shakya, A.K. And Pratap, J.V. (2016) Leishmania donovani γ-glutamylcysteine Synthetase is a substrate independent, magnesium dependent ATPase. BB Rep 8, 127-138.
  29. Binod Kumar, Vijayendar Bhalla , C. Raman Suri and Grish C. Varshney (2016) Label-free electrochemical detection of malaria-infected red blood cells. RSC Advances. 6, 75862-75869. DOI: 10.1039/C6RA07665C
  30. Nidhi Singh, Priyanka Shah, Hemlata Dwivedi, Shikha Mishra, Amogh A Sahasrabuddhe, Renu Tripathi and M. I. Siddiqi (2016) Integrated Machine Learning, Molecular Docking, 3D-QSAR Based Approach for Identification of Potential Inhibitors of Trypanosomal N-Myristoyltransferas. Mol. BioSyst., 2016, Accepted Manuscript DOI: 10.1039/C6MB00574H1.
  31. Priyanka Shrivastava, Vikas Navratna, Yumnam Silla, Rikeshwer P. Dewangan, Atreyi Pramanik, Sarika Chaudhary, GeethaVani Rayasam, Anuradha Kumar, Balasubramanian Gopal and Srinivasan Ramachandran (2016) Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues. Sci Rep. 2016 Aug 9;6:30827 doi: 10.1038/srep30827.
  32. Mohanty S, Gautam Y, Maurya AK, Negi AS, Prakash O, Khan F, Bawankule DU. (2016) Indenes and tetralenes analogues attenuates lipopolysaccharide-induced inflammation: An in-vitro and in-vivo study. Chem Biol Interact. 2016 Feb 5;245:12-9.
  33. Chawla V, Kumar R, Shankar R (2016) Identifying wrong assemblies in de novo short read primary sequence assembly contigs . J Biosci. 2016 Sep;41(3):455-74.
  34. Deependra Kumar Singh, Mohd. Kamil Hussain, Shagun Krishna, Amit Laxmikant Deshmukh, Mohammad Shameem, Pooja Maurya, Kanchan Hajela, M. I. Siddiqi and Dibyendu Banerjee (2016) Identification of a Novel Human DNA Ligase I Inhibitor that Promotes Cellular Apoptosis in DLD-1 cells: An in silico and in vitro Mechanistic Study. RSC Adv.,2016, DOI: 10.1039/C6RA22364H.
  35. Bhardwaj J, Gangwar I, Panzade G, Shankar R, Yadav SK (2016) Global de novo protein-protein interactome elucidates interactions of drought responsive proteins in horsegram (Macrotyloma uniflorum). J Proteome Res. 2016 Jun 3;15(6):1794-809.
  36. Mishra A, Nizammuddin S, Basu Mallick C, Singh S, Prakash S, Siddiqui NA, Rai N, Carlus SJ, Sudhakar DV, Tripathi VP, Möls M, Kim-Howard X, Dewangan H, Mishra A, Reddy AG, Roy B, Pandey K, Chaubey G, Das P, Nath SK, Singh L, Thangaraj K (2016) Genotype-phenotype study of Middle Gangetic Plain in India reveals association of rs2470102 with skin pigmentation.  J Invest Dermatol. 2016 Nov 17. doi: 10.1016/j.jid.2016.10.043.
  37. Bhartiya D, Chawla V, Ghosh S, Shankar R, Kumar N (2016) Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics. 2016 Dec;108(5-6):224-231.
  38. ur K, Gupta AK, Rajput A, Kumar M. (2016) ge-CRISPR - An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system. Sci Rep. 2016; 6:30870. doi: 10.1038/srep30870.
  39. Banerjee A, Chakraborty S, Chakraborty A, Chakrabarti S , and Ray K. (2016) Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases. PLoS One. 11(5):e0156252.
  40. Jalili M, Salehzadeh-Yazdi A, Gupta S, Wolkenhauer O, Yaghmaie M, Resendis-Antonio O and Alimoghaddam K. (2016) Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks. Front. Physiol. 2016; 7:375. doi: 10.3389/fphys.2016.00375.
  41. Das, S., Pal, U., Chatterjee, M., Pramanik, S. K., Banerji, B., Maiti, N. C. (2016) Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and DFT Analyses, J. Phys. Chem. A, DOI: 10.1021/acs.jpca.6b10017.
  42. Kumar A, Chawla V, Sharma E, Mahajan P, Shankar R, Yadav SK (2016) Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology. Sci Rep. 2016 Nov 17;6:37244. doi: 10.1038/srep37244.
  43. Singh GK, Karade SS, Ranjan R Ahamad N Ahmed S (2016) C-terminal region of Mad2 plays an important role during mitotic spindle checkpoint in fission yeast Schizosaccharomyces pombe. Mol. Biol. Rep. DOI 10.1007/s11033-016-4083.
  44. Renu Vyasa, Sanket Bapat, Esha Jain, Muthukumarasamy Karthikeyan, Sanjeev Tambe, Bhaskar D. Kulkarni, 2016 Building and analysis of protein-protein interactions related to diabetes mellitus using support vector machine, biomedical text mining and network analysis. Computational Biology and Chemistry, Volume 65, December 2016, Pages 37–44.
  45. Qureshi A, Kaur G, Kumar M (2016) AVCpred: An integrated web server for prediction and design of antiviral compounds. Chem Biol Drug Des. 2016. doi: 10.1111/cbdd.12834.
  46. Das ,S., Pal, U. and Maiti, N. C. (2016) Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach – Identification of pathogen–specific and habitat-specific genes. Sci. Rep.
  47. Renu Vyasa, Sanket Bapat, Purva Goel, Muthukumarasamy Karthikeyan, Sanjeev Tambe, Bhaskar D. Kulkarni, (2016) Application of Genetic Programming (GP) formalism for building disease predictive models from protein-protein interactions (PPI) data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume: PP, Issue: 99 DOI: 10.1109/TCBB.2016.2621042.
  48. N. Viswanadh, P. Mujumdar, M. Sasikumar, S. S. Kunte, M. Muthukrishnan (2016) An alternate synthesis of appetite suppressant (R)-2-benzylmorpholine employing Sharpless asymmetric epoxidation strategy. Tetrahedron Lett., 2016, 57, 861.
  49. Arya A. Das, Darsana T.A. and Elizabeth Jacob (2016) Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology. Bioinformatics.
  50. Priyanka Singh, Tiash Saha, Pankaj Mishra, Maloy Kumar Parai, Sailaja Ireddy, Srinivas Lavanya Kumar M, Shagun Krishna ,Shashi Kant Kumar, Vinita Chaturvedi, Sudhir Sinha, Mohammad Imran Siddiqi, Gautam Panda. (2016) Additional synthesis on thiophene containing trisubstitutedmethanes (TRSMs) as inhibitors of M. tuberculosis and 3D-QSAR studies SAR QSAR Environ Res. 2016 Nov;27(11):911-937.
  51. Ahamad N, Verma SK, Ahmed S (2016) Activation of checkpoint kinase Chk1 by reactive oxygen species resulting from disruption of wat1/pop3 in S. pombe. Genetics 204: 1397-1406 DOI:10.1534/genetics.116.193896.
  52. Gupta S, Chaudhary K, Dhanda SK, Kumar R, Kumar S, Sehgal M, Nagpal G, Raghava GP (2016). A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer. PLOS ONE 11 (11), e0166372.
  53. Kalia VC, Kumar R, Kumar P, Koul S (2016). A genome-wide profiling strategy as an aid for searching unique identification biomarkers for Streptococcus. Indian J Microbiol 56:46-58. doi:10.1007/s12088-015-0561-5.
  54. Chaudhary K, Kumar R, Singh S, Tuknait A, Gautam A, Mathur D, Anand P, Varshney GC, Raghava GP (2016).A Web Server and Mobile App for Computing Hemolytic Potency of Peptides. Sci Rep. 2016 Mar 8;6:22843.
  55. Singh H, Srivastava HK, Raghava GP. (2016).A web server for analysis, comparison and prediction of protein ligand binding sites. Biol Direct. 2016 Mar 25;11(1):14.
  56. Dhanda SK, Vir P, Singla D, Gupta S, Kumar S, Raghava GP (2016).A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PLoS One. 2016 Apr 20;11(4):e0153771
  57. Singh J, Dwivedi A, Mujtaba SF, Singh KP, Pal MK, Chopra D, Goyal S, Srivastav AK, Dubey D, Gupta SK, Haldar C, Ray RS. (2016).Ambient UV-B exposure reduces the binding of ofloxacin with bacterial DNA gyrase and induces DNA damage mediat.ed apoptosis. Int J Biochem Cell Biol. 2016. pii: S1357-2725(16)30001-2. doi:10.1016/j.biocel.2016.01.001.
  58. Dhanda SK, Chaudhary K, Gupta S, Brahmachari SK, Raghava GP (2016).A web-based resource for designing therapeutics against Ebola Virus.Sci Rep. 2016 Apr 26;6:24782.
  59. Kumar R, Raghava GP (2016).ApoCanD: Database of human apoptotic proteins in the context of cancer.Sci Rep. 2016 Feb 10;6:20797.
  60. Tanmoy Mondal, Dhananjaya Pal, Manika Pal-Bhadra and Utpal Bhadra (2016).Argonate machinery silent cancer noises. Cancer surgery 1: 102. doi:10.4172/cns.1000102
  61. Paliwal S, Bhaskar S, Reddy DN, Rao GV, Thomas V, Singh SP, Chandak GR.(2016).Association analysis of PRSS1-PRSS2 and CLDN2-MORC4 variants in non-alcoholic chronic pancreatitis using tropical calcific pancreatitis as model. Pancreas. 2016 Jan 18.
  62. Singh H, Raghava GP (2016).BLAST-based structural annotation of protein residues using Protein Data Bank.Biology Direct 11 (1), 1-13 (2016)
  63. Chaudari NM, Gupta VK and Dutta C. (2016).BPGA- an ultra-fast pan-genome analysis pipeline.Sci Rep 6, 24373, doi:10.1038/srep24373
  64. Harmandeep Kaur Randhawa, Ankur Gautam, Minakshi Sharma, Rakesh Bhatia, Grish C. Varshney, Gajendra Pal Singh Raghava, and Hemraj Nandanwar (2016).Cell-Penetrating Peptide and Antibiotic Combination Therapy: A Potential Alternative to Combat Drug Resistance in Methicillin Resistant Staphylococcus aureusAppl Microbiol Biotechnol 100 (9), 4073-4083; 10.1007/s00253-016-7329-7
  65. Sonkar A, Yadav S, Ahmed S. (2016).Cleavage and polyadenylation factor, Rna14 is an essential protein required for the maintenance of genomic integrity in fission yeast Schizosaccharomyces pombe.BBA Mol Cell Res. 1863(2):189-197
  66. Settu Sridhar, Pallabini Dash, Kunchur Guruprasad (2016).Comparative analyses of the proteins from Mycobacterium tuberculosis and human genomes: Identification of potential tuberculosis drug targets. GENE
  67. A. Subha Mahadevi and G. N. Sastry, (2016).Cooperativity in Noncovalent Interactions.Chem. Rev., 2016, 116, 2775-2825.
  68. Agrawal P, Bhalla S, Usmani SS, Singh S, Chaudhary K, Raghava GP*, Gautam A*. (2016).CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides.Nucleic Acids Res. 2016 Jan 4;44(D1):D1098-103
  69. Singh Nanda J, Kumar R, Raghava GP (2016).dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes.Sci Rep. 2016 Jan 18;6:19340
  70. Singh S, Singh A, Rajkumar R, Katakam SK, Samy SK, Nizamuddin S, Singh A, Shahnawaz S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K (2016).Dissecting the influence of Neolithic demic diffusion on Indian Y-ˇchromosome pool through J2-ˇM172 haplogroup.Sci. Rep. 6: 19157.
  71. SK Alam , VK Yadav , S Bajaj , A Datta, SK Dutta , M Bhattacharyya , S Bhattacharya , S Debnath, S Roy , LA Boardman , TC Smyrk , JR Molina , S Chakrabarti , S Chowdhury, D Mukhopadhyay, and S Roychoudhury. (2016).DNA damage-induced ephrin-B2 reverse signaling promotes chemoresistance and drives EMT in colorectal carcinoma harboring mutant p53.Cell Death and Differentiation 23, 707–722; doi:10.1038/cdd.2015.133;
  72. C. Choudhury, U. D. Priyakumar and G. N. Sastry, (2016).Dynamic ligand-based pharmacophore modeling and virtual screening to identify mycobacterial cyclopropane synthase inhibitors.J. Chem. Sci., 2016, DOI: 10.1007/s12039-016-1069-1
  73. Himanshu Malhotra, Navdeep Sheokand, Santosh Kumar, Anoop S. Chauhan, Manoj Kumar, Priyanka Jakhar,  Vishant M. Boradia, Chaaya I. Raje and Manoj Raje(2016).Exosomes: tunable nano vehicles for macromolecular delivery of transferrin and lactoferrin to specific intracellular compartment. Journal of Biomedical Nanotechnology; 2016
  74. Dwivedi GR, Tiwari N, Singh A, Kumar A, Roy S, Negi AS, Pal A, Chanda D, Sharma A, Darokar MP. (2016).Gallic acid-based indanone derivative interacts synergistically with tetracycline by inhibiting efflux pump in multidrug resistant E. coli. Appl Microbiol Biotechnol. 2016, 100(5):2311-25.
  75. Chaubey G, Singh M, Rai N, Kariappa M, Singh K, Singh A, Singh DP, Tamang R, Rani DS, Reddy AG, Singh VK, Singh L, Thangaraj K (2016).Genetic affinities of the Jewish populations of India.Sci. Rep. 6: 19166.
  76. Kumar, Dhirendra; Yadav, Amit Kumar; Jia, Xinying; Mulvenna, Jason; Dash, Debasis; (2016).Integrated transcriptomic-proteomic analysis using a proteogenomic workflow refines rat genome annotation.Molecular & Cellular Proteomics 15:1 329-339
  77. Puniya BL, Kulshreshtha D, Mittal I, Mobeen A, Ramachandran S.(2016).Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis.Sci Rep. 2016 Mar 22;6:23440. doi: 10.1038/srep23440.
  78. Sriyans Jain, Nirav Thakkar, Jagamohan Chhatai, Manika Pal Bhadra and Utpal Bhadra. (2016).Long non-coding RNA: functional agent for disease traits.RNA Biology
  79. Kachhap S, Priyadarshini P, Singh B. (2016).Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. J Biomol Struct Dyn. 2016 May 4:1-15.
  80. Zou WB, Boulling A, Masamune A, Issarapu P, Masson E, Wu H, Sun XT, Hu LH, Zhou DZ, He L, Fichou Y, Nakano E, Hamada S, Kakuta Y, Kume K, Isayama H, Paliwal S, Mani KR, Bhaskar S, Cooper DN, Férec C, Shimosegawa T, Chandak GR, Chen JM, Li ZS, Liao Z. (2016).No association between CEL-HYB Hybrid allele and chronic pancreatitis in Asian populations. Gastroenterology. 2016 Mar 2. pii: S0016-5085(16)00292-4. doi: 10.1053/j.gastro.2016.02.071.
  81. Dhanda SK, Usmani SS, Agrawal P, Nagpal G, Gautam A, Raghava GP (2016).Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeuticsBrief Bioinform. 2016 Mar 25. pii: bbw025
  82. Chopra D, Ray L, Dwivedi A, Tiwari SK, Singh J, Singh KP, Kushwaha HN, Jahan S, Pandey A, Gupta SK, Chaturvedi RK, Pant AB, Ray RS, Gupta KC. (2016).Photoprotective efficiency of PLGA-curcumin nanoparticles versus curcumin through the involvement of ERK/AKT pathway under ambient UV-R exposure in HaCaT cell line.Biomaterials. 2016; 84:25-41. doi: 10.1016/j.biomaterials.2016.01.018.
  83. Singh H, Kumar R, Singh S, Chaudhary K, Gautam A, Raghava GP (2016).Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell linesBMC Cancer. 2016 Feb 9;16:77.
  84. Chaudhary K, Nagpal G, Dhanda SK, Raghava GP. (2016).Prediction of Immunomodulatory potential of an RNA sequence for designing non-toxic siRNAs and RNA-based vaccine adjuvants.Sci Rep. 2016 Feb 10;6:20678
  85. Gupta S, Chaudhary K, Kumar R, Gautam A, Nanda JS, Dhanda SK, Brahmachari SK, Raghava GP (2016).Prioritization of anticancer drugs against a cancer using genomic features of cancer cells: A step towards personalized medicine. Sci Rep. 2016 Mar 31;6:23857
  86. Nupur LN, Vats A, Dhanda SK, Raghava GP, Pinnaka AK, Kumar A. (2016).ProCarDB: a database of bacterial carotenoids. BMC Microbiol. 2016 May 26;16(1):96. doi: 10.1186/s12866-016-0715-6.
  87. Kumar, Dhirendra; Mondal, Anupam Kumar; Kutum, Rintu; Dash, Debasis; (2016).Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes Proteomics 16:2 226-240
  88. Fatima, K., Masood, N., & Luqman, S. (2016).Quenching of singlet oxygen by natural and synthetic antioxidants and assessment of electronic UV/Visible absorption spectra for alleviating or enhancing the efficacy of photodynamic therapy. Biomedical Research and Therapy, 3(2): 514-527.
  89. Sathish Kumar, B., Raghuvanshi, D.S., Hasanain, M., Alam, S., Sarkar, J., Mitra, K., Khan, F., Negi, A.S., (2016).Recent Advances in chemistry and pharmacology of 2-methoxyestradiol: An anticancer investigational drug. Steroids (2016), doi: http://dx.doi.org/10.1016/j.steroids.2016.03.017
  90. Krishna S, Kumar V, Siddiqi MI. (2016).Recent Advances in Computer-Assisted Structure-Based Identification and Design of Histone Deacetylases Inhibitors.Curr Top Med Chem. 2016;16(9):934-47
  91. Singh S, Chaudhary K, Dhanda SK, Bhalla S, Usmani SS, Gautam A, Tuknait A, Agrawal P, Mathur D, Raghava GP. (2016).SATPdb: a database of structurally annotated therapeutic peptides.Nucleic Acids Res. 2016 Jan 4;44(D1):D1119-26. doi: 10.1093/nar/gkv1114. Epub 2015 Nov 2
  92. Singh KP, Verma N, Akhoon BA, Bhatt V, Gupta SK, Gupta SK, Smita S.(2016).Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains.3 Biotech. 2016. doi:10.1007/s13205-015-0352-z.
  93. Rajput A, Kaur K, Kumar M (2016).SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. Nucleic Acids Res. 2016 Jan 4;44(D1):D634-9. doi: 10.1093/nar/gkv1076. Epub 2015 Oct 20.
  94. Kumar R, Kaur R, Bhondekar AP, Raghava GP (2016).Smell and language : Datacentric approach to predicting smell of a molecule. Journal of Digital Olfaction Volume 4 (2016) DOI: http://dx.doi.org/10.18143/JDOS_v4i1.979
  95. Pal, U, Maity, M.; Khot, N.; Das, S.; Das, S.; Dolui, S. and Maiti, N. C. (2016).Statistical insight of binding regions in disordered human proteome J. Proteins and Proteomics 2016, 7 47-60
  96. C. Choudhury, U. D. Priyakumar and G. N. Sastry, (2016).Structural and Functional Diversities of the Hexadecahydro-1H-Cyclopenta[a] Phenanthrene Framework, a Ubiquitous Scaffold in Steroidal Hormones. Mol. Inform., 2016, 35, 145-157
  97. Noopur Sinha, Saikat Chowdhury And Ram Rup Sarkar* (2016).Structural Insight of NICD-MAML Interactions: Virtual screening, Docking and Molecular Dynamics Study for Identification of Potential Inhibitor. Letters in Drug Design & Discovery, 13(4), 301 - 313 (2016), DOI:10.2174/1570180812666150819003634.
  98. B. Sharma, Y. I. Neela and G. N. Sastry, J (2016). Structures and Energetics of Complexation of Metal Ions with Ammonia, Water, and Benzene: A Computational Study,. Comp. Chem., 2016, 37, 992-1004
  99. Ramakrishna Kuppala, Rushikesh Tambat, Mugunthan G, Neeraj Patel, Hemraj Nandanwar*, Kamlesh K. Bhutani, K. P. Ravindranathan Kartha* (2016).Synthesis and antibacterial activity of ricinoleic acid glycosides.RSC Adv., 2016,6, 3700-3713
  100. Gautam A, Nanda JS, Samuel JS, Kumari M, Priyanka P, Bedi G, Nath SK, Mittal G, Khatri N, Raghava GP. (2106).Topical Delivery of Protein and Peptide Using Novel Cell Penetrating PeptideIMT-P8. Sci Rep. 2016 May 18;6:26278. doi: 10.1038/srep26278.
  101. Manjunath BL, Singh HR, Ravikanth G, Karaba NN, Shankar R, Kumar S, Uma Shankeer R. (2016).Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule.JBSc, March 2016.
  102. Khan MS, Gupta AK, Kumar M (2016).ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases. Epigenomics. 2016 Jan;8(1):67-75. Epub 2015 Dec 18

    103. Papers of Year-2015

    1. Kalia VC, Kumar P, Kumar R, Mishra A, Koul S (2015) Genome wide analysis for rapid identification of Vibrio species. Indian J Microbiol 55:375-383. doi:10.1007/s12088-015-0553-5
    2. Abhishek Subramanian And Ram Rup Sarkar (2015) Dynamics of GLI Regulation and Strategy to Control Cancerous Situation: Hedgehog Signaling Pathway Revisited. Journal of Biological Systems, 23(4), 681 - 719 (2015).
    3. Kalia VC, Kumar P (2015) Genome wide search for biomarkers to diagnose Yersinia infections. Indian J Microbiol 55:366-374. doi:10.1007/s12088-015-0552-6
    4. Vyas R, Bapat S, Jain E, Tambe SS, Karthikeyan M, Kulkarni BD. (2015) A Study of Applications of Machine Learning Based Classification Methods for Virtual Screening of Lead Molecules. Comb Chem High Throughput Screen. 2015;18(7):658-72
    5. Karthikeyan M, Nimje D, Pahujani R, Tyagi K, Bapat S, Vyas R, Pillai Padmakumar K (2015) Chemoinformatics Approach for Building Molecular Networks from Marine Organisms. Comb Chem High Throughput Screen. 2015;18(7):673-84
    6. Vyas R, Karthikeyan M, Nainaru G, Muthukrishnan M. (2015) Pharmacophore and Docking Based Virtual Screening of Validated Mycobacterium tuberculosis Targets. Comb Chem High Throughput Screen. 2015;18(7):624-37.
    7. Karthikeyan M, Vyas R, Tambe SS, Radhamohan D, Kulkarni BD. (2015) Role of Chemical Reactivity and Transition State Modeling for Virtual Screening. Comb Chem High Throughput Screen. 2015;18(7):638-57.
    8. S. Saha and G. N. Sastry (2015) Quantifying cooperativity in water clusters: an attempt towards obtaining a generalised equation. Mol. Phys., 2015, 113, 3031-3041
    9. Mishra A, Antony JS, Gai P, Sundaravadivel P, Hoang van T, Jha AN, Singh L, Velavan TP, Thangaraj K (2015) Mannose-binding Lectin (MBL) as a susceptible host factor influencing Indian Visceral Leishmaniasis. Parasitol Int. 64: 591-ˇ596
    10. Sharma P, Shukla A, Kalani K, Dubey V, Srivastava SK, Luqman S, Khan F (2015) Water Molecules Increases Binding Affinity of Natural PI3Kγ Inhibitors against Cancer. Curr Comput Aided Drug Des. 2015, 11: 279-290
    11. S Bhowmick, S Tripathy* (2015) A Tale of Effectors; Their Secretory Mechanisms and Computational Discovery in Pathogenic, Non-Pathogenic and Commensal Microbes. #
    12. Mohit Tyagi, Nikhil Taxak, Prasad V. Bharatam, Hemraj Nandanwar, K. P. Ravindranathan Kartha (2015) Mechanochemical click reaction as a tool for making carbohydrate-based triazole-linked self-assembling materials (CTSAMs). Carbohydrate research 407, 137–147; doi:10.1016/j.carres.2015.01.022.
    13. N. Viswanadh, R. Velayudham, S. Jambu, S. Sasikumar, M. Muthukrishnan,* (2015) Chiral aziridine ring opening: Facile synthesis of (R)-mexiletine and (R)-phenoxy benzamine hydrochloride Tetrahedron Lett., 2015, 56, 5269.
    14. Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K (2015) The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet. 61:162-172.
    15. Shameem M, Kumar R, Krishna S, Kumar C, Siddiqi MI, Kundu B, Banerjee D. (2015) Synthetic modified pyrrolo[1,4] benzodiazepine molecules demonstrate selective anticancer activity by targeting the human ligase 1 enzyme: An in silico and in vitro mechanistic study. Chem Biol Interact. 2015.
    16. Samuel JS,  Kumar D, Chodisetti SB, Agrewala JN, Singh B, Guptasarma P, Sarkar D (2015) Probing protease sensitivity of recombinant human erythropoietin reveals α3-α4 inter-helical loop as a stability determinant. Proteins. 83:1813-1822.
    17. Shukla H, Kumar V, Singh AK, Rastogi S, Khan SR, Siddiqi MI, Krishnan MY, Akhtar MS (2015) Isocitratelyase of Mycobacterium tuberculosis is inhibited by quercetin through binding at N-terminus Int J Biol Macromol. 2015;78:137-41.
    18. 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.
    19. 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 isocitratelyase. Biochimie. 2015 Mar;110:73-80. doi: 10.1016/j.biochi.2014.12.016. Epub 2015 Jan 7.
    20. 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
    21. Mishra A, Antony JS, Sundaravadivel P, Tong HV, Meyer CG, Jalli RD, Velavan TP, Thangaraj K (2015) Association of Ficolin-ˇ2 Serum Levels and FCN2 Genetic Variants with Indian Visceral Leishmaniasis. PLoS One. 10:e0125940.
    22. R. Sharma and G. N. Sastry, (2015) Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate. Plos One
    23. Verma D, Das L, Gambhir V, Dikshit KL, Varshney GC* (2015) Heterogeneity among Homologs of Cutinase-Like CADBtein Cut5 in Mycobacteria. PLoS ONE 10(7): e0133186. doi:10.1371/journal.pone.0133186.
    24. Bankapalli LK, Mishra RC, Singh Band Raychaudhuri S (2015) Identification of Critical Amino Acids Conferring Lethality in VopK, a Type III Effector Protein of Vibrio cholerae: Lessons from Yeast Model System. Plos One, 10(10)
    25. Mishra A, Nizamuddin S, Arekatla G, Prakash S, Dewangan H, Dominic A, Mishra A, Sudhakar DV, Parine NR, Tupperwar NC, Thangaraj K (2015) IL10 Variant g.5311A Is Associated with Visceral Leishmaniasis in Indian Population. PLoS One. 10:e0124559.
    26. Khan S, Ahmed S. (2015) Role of swi7H4 Mutant Allele of DNA Polymerase α in the DNA Damage Checkpoint Response. PLoS ONE 10(3):e0124063.
    27. S. Saha and G. N. Sastry (2015) J. Phys. Chem. B, 2015, 119, 11121-11135
    28. Nanduri, R., Bhutani, I., Somavarapu, A.K., Mahajan, S., Parkesh, R.*, Gupta, P*. (2015) ONRLDB-manually curated database of experimentally validated ligands for orphan nuclear receptors. Database (Oxford) Oct 30, doi:10.1093/database/bav112.
    29. Kalani K, Chaturvedi V, Alam S, Khan F, Srivastava SK (2015) Anti-tubercular agents from Glycyrrhiza glabra. Curr Top Med Chem. 2015;15(11):1043-9.
    30. Gaur R, Yadav DK, Kumar S, Darokar MP, Khan F, Bhakuni RS. (2015) Molecular modeling based synthesis and evaluation of in vitro anticancer activity of indolyl chalcones. Curr Top Med Chem. 2015, 15(11):1003-12.
    31. B. Sharma, H. K. Srivastava, G. Gayatri and G. N. Sastry (2015) Energy Decomposition Analysis of Cation-p, Metal Ion-Lone Pair, Hydrogen Bonded, Charge Assisted Hydrogen Bonded and p-p Interactions. J. Comp. Chem., 2015, 36, 529-538.
    32. C. Choudhury, U. D. Priyakumar and G. N. Sastry, (2015) Dynamics Based Pharmacophore Models for Screening Potential Inhibitors of Mycobacterial Cyclopropane Synthase. J. Chem. Inf. Model., 2015, 55, 848-860.
    33. Singh N, Tiwari S, Srivastava KK, Siddiqi MI. (2015) Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological evaluation. J. Chem Inf Model. 2015 Jun 22;55(6
    34. Suryanaryana Murty U, Srinivasa Rao Mutheneni, Sumana Chenna, Vaideesh Parasaram, Madhusudhan Rao Kadiri (2015) Climate drivers on malaria transmission in Arunachal Pradesh, India. PLOS ONE. 10(3): e0119514. doi:10.1371/journal.pone.0119514.
    35. Gaur R, Cheema HS, Kumar Y, Singh SP, Yadav DK, Darokar MP, Khan F, Bhakuni RS (2015) In vitro antimalarial activity and molecular modeling studies of novel artemisinin derivatives. RSC Adv., 2015, 5:47959
    36. Kalani K, Cheema HS, Tripathi H, Khan F, Darokar MP, Srivastava SK. (2015) QSAR guided semi-synthesis and in vitro validation of antiplasmodial activity in Ursolic acid derivatives. RSC Advances, 2015, 5: 32133-32143.
    37. M. Mujahid, P. Yogeeswari, D. Sriram, U. M. V. Basavanag, E. D. Cervantes, L. C. Bahena, J. Robles, R. G. Gonnade, M. Karthikeyan, R. Vyas, M. Muthukrishnan,* (2015) Spirochromone-chalcone conjugates as antitubercular agents: synthesis, bio evaluation and molecular modeling studies. RSC Adv., 2015, 5, 106448.
    38. Mushtaq K, Sheikh JA, Amir M, Khan N, Singh B, Agrewala JN (2015) Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028Rv2031 (HspX) operon. Frontiers in Microbiology 1(0.3389/fmicb.2015.00351.
    39. Kumar, Dhirendra; Jain, Aradhya; Dash, Debasis; (2015) Probing the Missing Human Proteome: A Computational Perspective . Journal of Proteome Research 14:12 4949-4958 2015.
    40. Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R, Raghava GP. (2015) Peptide toxicity prediction. Methods Mol Biol.
    41. Shrivastava N, Nag JK, Pandey J, Tripathi RP, Shah P, Siddiqi MI, Misra-Bhattacharya S. (2015) Homology modeling of NAD+-dependent DNA ligase of the Wolbachia endosymbiont of Brugia malayi and its drug target potential using dispiro-cycloalkanones. Antimicrob Agents.
    42. Kaur, G., Subramanian, S. (2015) A novel RING finger in the C-terminal domain of the coatomer protein alpha-COP. Biology direct 10, 70.
    43. Singh S, Singh H, Tuknait A, Chaudhary K, Singh B, Kumaran S, Raghava GP (2015) PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biol Direct. 2015 Dec 21;10:73.
    44. Kaur, G., Subramanian, S. (2015) The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers. Biology direct 10, 36.
    45. Nizamuddin S, Govindaraj P, Saxena S, Kashyap M, Mishra A, Singh S, Rotti H, Raval R, Nayak J, Bhat BK, Prasanna BV, Dhumal VR, Bhale S, Joshi KS, Dedge AP, Bharadwaj R, Gangadharan GG, Nair S, Gopinath PM, Patwardhan B, Kondaiah P, Satyamoorthy K, Valiathan MS, Thangaraj K (2015) A novel gene THSD7A is associated with obesity. Int J Obes. 39: 1662-1665.
    46. Kumar R, Chaudhary K, Singh Chauhan J, Nagpal G, Kumar R, Sharma M, Raghava GP. (2015) An in silico platform for predicting, screening and designing of antihypertensive peptides. Sci Rep. 2015 Jul 27;5:12512.
    47. Govindaraj P, Nizamuddin S, Sharath A, Jyothi V, Rotti H, Raval R, Nayak J, Bhat BK, Prasanna BV, Shintre P, Sule M, Joshi KS, Dedge AP, Bharadwaj R, Gangadharan GG, Nair S, Gopinath PM, Patwardhan B, Kondaiah P, Satyamoorthy K, Valiathan MV, Thangaraj K (2015) Genome-wide analysis correlates Ayurveda Prakriti. Sci Rep. 5: 15786.
    48. Mandloi, S. and Chakrabarti, S. (2015) PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool.  Sci Rep, 5, 10021.
    49. Anoop S. Chauhan, Pooja Rawat, Himanshu Malhotra, Navdeep Sheokand, Manoj Kumar, Anil Patidar, Surbhi Chaudhary, Priyanka Jakhar, Chaaya I.Raje and Manoj Raje(2015) Secreted multifunctional Glyceraldehyde-3-phosphate dehydrogenase sequesters lactoferrin and iron into cells via a non-canonical pathway. Scientific Reports 5, 18465.
    50. Jain, C.K., Pradhan, B.S., Banerjee, S., Mondal, N.B.,Majumder, S.S., Bhattacharyya, M., Chakrabarti, S., Roychoudhury, S. and Majumder, H.K. (2015) Sulfonoquinovosyldiacylglyceride selectively targets acute lymphoblastic leukemia cells and exerts potent anti-leukemic effects in vivo. Sci Rep, 5, 12082.
    51. Nagpal G, Gupta S, Chaudhary K, Kumar Dhanda S, Prakash S, Raghava GP (2015) VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants. Sci Rep. 2015 Jul 27;5:12478.
    52. Tyagi A, Tuknait A, Anand P, Gupta S, Sharma M, Mathur D, Joshi A, Singh S, Gautam A, Raghava GP. (2015) CancerPPD: a database of anticancer peptides and proteins.  Nucleic Acids Res. 2015 Jan;43.
    53. Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenauer O, Vera J (2015) Personalized cancer immunotherapy using systems medicine approaches. Briefings in Bioinformatics 2015. doi: 10.1093/bib/bbv046.
    54. Schmitz U, NAderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J. (2015) The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions. Briefings in Bioinformatics 2015. doi: 10.1093/bib/bbv061.
    55. Pal, U.; Pramanik, S, Bhattacharya, B; Banerji, B and Maiti, N. C. (2015) Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis. SpringerPlus 2015, 4:548.
    56. Rupa Bhowmick, Abhishek Subramanian And Ram Rup Sarkar* (2015) Exploring the differences in metabolic behavior of astrocyte and glioblastoma: A flux balance analysis approach. Systems and Synthetic Biology, 9, 159 - 177.
    57. Piyali Ganguli, Saikat Chowdhury, Shomeek Chowdhury And Ram Rup Sarkar* (2015) Identification of Th1/Th2 regulatory switch to promote healing response during Leishmaniasis: a computational approach. EURASIP Journal on Bioinformatics and Systems Biology, 2015:13.
    58. Kalia VC (2015) Let's explore the latent features of genes to identify bacteria. J Mol Genet Med 9:e105.
    59. Rajput NK, Singh V, Bhardwaj A* (2015) mTORC2 Controls Cancer Cell Survival by Modulating Gluconeogenesis. Nature: Cell Death Discovery 2015.
    60. 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.
    61. 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.
    62. 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.
    63. Sampada Sontakke, Kishan K. Khetan, Subhodeep Banerjee, Tanmoy Mondal, Jagamohan Chhatai, Manika Pal-Bhadra and Utpal Bhadra. (2015). Different types of transgene silencing in animals: a natural foundation for RNAi technology. Journal of Molecular Biology 4: 137. doi:10.4172/2168-9547.1000137.
    64. Sarma P, Bag I, Ramaiah, MJ, Kamal, A, Bhadra Utpal, Pal Bhadra M (2015). PBD regulates breast cancer cell proflieration via SIRT-p53 axis. Cancer Biology and Therapy 16(10): 1486-501. doi: 10.1080/15384047.2015.1071731.
    65. Shinde Santosh P. and Utpal Bhadra (2015). A Complex genome-microRNA interplay in Human mitochondria. BioMed Research International (JBB) Volume 2015, Article ID 206382, 13 pages
    66. Rana S, Datta K. Reddy T.L., Chatterjee E., Sen P. Pal Bhadra Manika, Utpal Bhadra, Paramanik A., Paramanik P Sarkar M.C. and Sarkar S. (2015). A spatio-temporal cardiomyocyte targeted vector system for Efficient Delivery of therapeutic payloads to regress cardiac hypertrophy abating bystander effect. Journal of Controlled Release 200: 167-178.
    67. Santosh P. Shinde, Amit Kumar Banerjee, Neelima Arora, U.S.N Murty, Venkateswara Rao Sripathi, Manika Pal-Bhadra, Utpal Bhadra (2015). Computational approach for elucidating interactions of cross-species miRNAs and their targets in Flaviviruses. Journal of Vector Borne Diseases (JVBD) 52: 11-22
    68. 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.
    69. 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.
    70. 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.
    71. 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.
    72. 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.
    73. 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.
    74. 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.
    75. 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.
    76. 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
    77. 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
    78. 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.
    79. 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.
    80. 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
    81. 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.
    82. 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.
    83. 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.
    84. 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.
    85. 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.
    86. 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.
    87. 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.
    88. 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.
    89. 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.
    90. 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.
    91. 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.
    92. 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.
    93. 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.
    94. 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.
    95. 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.
    96. 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.
    97. 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
    98. 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.
    99. 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.
    100. 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.
    101. 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
    102. 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.
    103. 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.
    104. 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.
    105. Abinaya E, Narang P, Bhardwaj A.(2015).FROG - Fingerprinting Genomic Variation Ontology. PLoS One.10(8):e0134693. doi: 10.1371/journal.pone.0134693.
    106. 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.
    88. 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.
    89. 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.
    90. 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.
    91. 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.
    92. 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 .
    93. 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.
    94. 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.
    95. 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.
    96. 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
    97. 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/j.tube.2013.08.001.
    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). http://doi.org/10.1128/genomeA.00005-13
    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. 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.
    70. 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.