Publications

• Rajput A, Thakur A, Sharma S, Kumar M*.  aBiofilm: a resource of anti-biofilm agents and their potential implications in targeting antibiotic drug resistance. Nucleic Acids Res. 2017 Nov 16. doi: 10.1093/nar/gkx1157.
  (Impact Factor 11.561)


• Monga I, Qureshi A, Thakur N, Gupta AK, Kumar M*.  ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy. G3 (Bethesda). 2017 Sep 7;7(9):2931-2943. doi: 10.1534/g3.117.044024.
  (Impact Factor 2.861)


• Rajput A, Kumar M*.   In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria. Sci Rep. 2017 Aug 1;7(1):6969. doi: 10.1038/s41598-017-07241-5.
  (Impact Factor 4.259)


• Thakur A, Qureshi A, Kumar M*.  vhfRNAi: a web-platform for analysis of host genes involved in viral infections discovered by genome wide RNAi screens. Mol Biosyst. 2017 Jun 27;13(7):1377-1387. doi: 10.1039/c6mb00841k.
  (Impact Factor 2.30)


• Rajput A and Kumar M*.  Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing. Front Microbiol. 2017 May 3;8:798. doi: 10.3389/fmicb.2017.00798.
  (Impact Factor 4.167)


• Qureshi A, Kaur G, Kumar M*.  AVCpred: an integrated web server for prediction and design of antiviral compounds. Chem Biol Drug Des. 2017 Jan;89(1):74-83. doi: 10.1111/cbdd.12834.
  (Impact Factor 2.40)


• Dar SA, Gupta AK, Thakur A, Kumar M*.  SMEpred workbench: a web server for predicting efficacy of chemically modified siRNAs. RNA Biol. 2016 Sep 7:0.
  (Impact Factor 4.076)


• 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*.  ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis. Sci Rep. 2016 Sep 16;6:32713. doi: 10.1038/srep32713
  (Impact Factor 5.228)


• Kaur K^#, Gupta AK^#, Rajput A^#, Kumar M*.  ge-CRISPR- An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system. Sci Rep. 2016 Sep 1;6:30870. doi: 10.1038/srep30870.
  (Impact Factor 5.228)


• Qureshi A, Kaur G, Kumar M*. AVCpred: An integrated web server for prediction and design of antiviral compounds. Chem Biol Drug Des. 2016 Aug 4. doi: 10.1111/cbdd.12834.
  (Impact Factor 2.802)


• Thakur A, Rajput A, Kumar M*.  MSLVP: prediction of multiple subcellular localization of viral proteins using a support vector machine. Mol Biosyst. 2016 Jul 19;12(8):2572-86. doi: 10.1039/c6mb00241b.
  (Impact Factor 3.210)


• Dar SA, Thakur A, Qureshi A, Kumar M*. siRNAmod: A database of experimentally validated chemically modified siRNAs.Sci Rep. 2016 Jan 28;6:20031. doi: 10.1038/srep20031.
  (Impact Factor 5.228)


• Khan MS, Gupta AK, Kumar M*. ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases. Epigenomics. 2016 Jan;8(1):67-75. doi: 10.2217/epi.15.95. Epub 2015 Dec 18.
  (Impact Factor 4.649)


• Rajput A, Kaur K, Kumar M*. 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.
  (Impact Factor 9.112)


• Qureshi A, Tandon H, Kumar M*.  AVP-IC50 Pred: Multiple machine learning techniques based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50). Biopolymers. 2015 Nov;104(6):753-63. doi: 10.1002/bip.22703.
  (Impact Factor 2.385)


• Kumar Gupta A, Kumar M*.  HPVbase-- a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep. 2015 Jul 24;5:12522. doi: 10.1038/srep12522.
  (Impact Factor 5.578)


• Kaur K, Tandon H, Gupta AK, Kumar M*.  CrisprGE: a central hub of CRISPR/Cas-based genome editing. Database (Oxford). 2015 Jun 27;2015:bav055. doi: 10.1093/database/bav055.
  (Impact Factor 3.372)


• Rajput A, Gupta AK, Kumar M*.  Prediction and analysis of quorum sensing peptides based on sequence features. PLoS One. 2015 Mar 17;10(3):e0120066. doi: 10.1371/journal.pone.0120066.
  (Impact Factor 3.234)


• Qureshi A, Thakur N, Monga I, Thakur A, Kumar M*.  VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. Database (Oxford). 2014 Nov 7; 2014. doi: 10.1093/database/bau103.
  (Impact Factor 4.457)


• Qureshi A, Thakur N, Tandon H, Kumar M*.  AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Res. 2014 Jan;42(Database issue):D1147-53. doi: 10.1093/nar/gkt1191. Epub 2013 Nov 26.
  (Impact Factor 8.026)


• Qureshi A, Thakur N, Kumar M*.  VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses. J Transl Med. 2013 Dec 11;11:305. doi: 10.1186/1479-5876-11-305.
  (Impact Factor 3.460)


• Qureshi A, Thakur N, Kumar M*.  HIPdb: A database of experimentally validated HIV inhibiting peptides. PLoS ONE, 2013. 8(1): e54908. doi:10.1371/journal.pone.0054908.
  (Impact Factor 4.092)


• Thakur N, Qureshi A, Kumar M*.  AVPpred: Collection and prediction of highly effective antiviral peptides. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W199-204. Epub 2012 May 25. doi: 10.1093/nar/gks450.
  (Impact Factor 8.026)


• Thakur N, Qureshi A, Kumar M*.  VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res., 2012, 40(D1): D230-D236 doi:10.1093/nar/gkr1147.
  (Impact Factor 8.026)


• Tyagi A, Ahmed F, Thakur N, Sharma A, Raghava GPS and Kumar M*.  HIVsirDB: A Database of HIV Inhibiting siRNAs. PLoS ONE, 2011, 6(10): e25917. doi:10.1371/journal.pone.0025917.
  (Impact Factor 4.411)


• Kukreti H, Mittal V, Chaudhary A, Rautela RS, Kumar M, Chauhan S, Bhat S, Chhabra M, Bhattacharya D, Pasha ST, Kumar D, Gomber S, Lal S, Rai A*.  Continued persistence of a single genotype of dengue virus type-3 (DENV-3) in Delhi, India since its re-emergence over the last decade. J Microbiol Immunol Infect. 2010 Feb;43(1):53-61. doi: 10.1016/S1684-1182(10)60008-4. Epub 2010 Mar 29.
  


• Kumar M, Jain SK, Pasha ST, Chattopadhaya D, Lal S, Rai A*.  Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV type 1: emergence of a distinct subclade and predicted implications. AIDS Res Hum Retroviruses. 2006 Dec;22(12):1206-19.
  (Impact Factor 2.325)


• Kumar M, Pasha ST, Mittal V, Rawat DS, Arya SC, Agarwal N, Bhattacharya D, Lal S and Rai, A*.  Unusual emergence of guate98-like molecular subtype of DEN-3 during 2003 dengue outbreak in Delhi. Dengue Bulletins, 2004, 28, 161-167.
  


• Dash PK, Parida MM, Saxena P, Kumar M, Rai A, Pasha ST, Jana AM*.  Emergence and continued circulation of dengue-2 (genotype IV) virus strains in northern India. J Med Virol. 2004 Oct ;74(2):314-22.
  (Impact Factor 1.998)


• Anand R, Ghosh D, Bhupatiraju AV, Broor S, Pasha ST, Khare S, Kumar M, Dutta KK, Rai A*.  Partial VP1/2A gene sequence based molecular epidemiology of wild type 1 poliovirus isolates from some parts of India. Epidemiol Infect. 2002 Aug;129(1):107-12.
  (Impact Factor 2.515)


• Arvind Rai, Ranjana Anand, Manoj Kumar, D.S. Rawat, S.T. Pasha and Jotna Sokhey.  Molecular subtyping of Hepatitis B Virus (HBV) by partial genome sequencing of HBV. Journal of Basic Applied Biomedicine, 1999, 6(2): 27-29.
  


• Arvind Rai, Ranjana Anand, Manoj Kumar, ST Pasha, DS Rawat, Jotna Sokhey.  VP1/2A gene sequence based molecular epidemiology wild poliovirus Type 1 isolated circulating in India. Journal of Basic and Applied Biomedicine, 1999, 6 (3): 21-24.