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Date: May 25, 2017
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Publications

   
NGS data analysis:
Firoz A , Malik A, Singh SK, Jha V, and Ali A. Identification of hub glycogenes and their nsSNP analysis from mouse RNA-Seq data. Gene. 2015 Dec 15; 574(2):235-46. PMID: 26260015
Tayubi I. A, Barukab O. M, Firoz A, Malik A. Identification of hub genes and their SNP analysis in West Nile Virus infection for designing therapeutic methodologies using RNA-Seq data. Genes & Genomics. 2015 Aug 15; 37(8):679-91.
Firoz A , Malik A , Singh SK, Jha V, and Ali A. Comparative analysis of glycogene expression in different mouse tissues using RNA-Seq data. International journal of genomics, vol. 2014, Article ID 837365, 18 pages, 2014. PMID: 25121089
   
Databases / Tools:
Malik A, Firoz A, Lee EJ, Jha V, and Choi I. Protein-carbohydrate interactions: Motif analysis and atom-wise statistics. Indian Journal of Biochemistry and Biophysics. 2015. (Accepted).
Singh SK, Malik A, Firoz A, Jha V. CDKD: A Clinical Database of Kidney Disease. BMC Nephrol. 2012 Apr 27; 13(1):23 PMID: 22540288
Firoz A, Malik A, Jolpin KH, Ahmad Z, Ahmad S. Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC Biochemistry 2011, 12:20 PMID: 21569447
Firoz A, Malik A, Afzal O, Jha V. ContPro: A web tool for calculating amino acid contact distances in protein from 3D – structures at different distance threshold. Bioinformation 5(2):55-57 (2010) PMID: 21346863
Malik A, Firoz A, Jha V, Ahmad S. PROCARB: A database of known and modelled carbohydrate-binding protein structures with sequence-based prediction tools. Advances in Bioinformatics 2010:436036. Epub 2010 Jun 29. PMID: 20671979
   
Molecular Modeling:
Afzal O, Kumar S, Kumar R, Firoz A, Jaggi M, and Bawa S. Docking based virtual screening and molecular dynamics study to identify potential monoacylglycerol lipase inhibitors. Bioorganic & Medicinal Chemistry Letters. 2014 Aug 15;24(16):3986-96. PMID: 25011912
Malik A, Firoz A, Jha V, Sunderasan E, Ahmad S. Modeling the three dimensional structure and complex of single-chain variable fragment (scFv) specific to Corynespora cassiicola toxin, cassiicolin. J Mol Model. 2010 Mar 16. PMID: 20232097
   
   
Book chapters:
Tayaubi IA, Firoz A, Malik A. Protein Misfolding and Amyloid formation in Alzheimer's disease. Proteiostasis and Chaperone Surveillance, Publisher, Springer.
Malik A, Firoz A, Afzal O, Jha V and Choi I. Protein Structure Databases and 3D Structure Prediction Tools. Advances in Protein Chemistry, OMICS Group eBooks, 2013
Singh SK, Malik A, Firoz A. Computer aided drug discovery (CADD): A QSAR approach. Advanced Pharmacology. 2014. (pp. 450-475). Hyderabad, Andhra Pradesh, India: PharmaMed Press/BSP Books
   
   
Oral/poster in National/International Conference:
Firoz A, Malik A, Singh SK, Jha V, Ali A. Accelerating Biology 2016: Decoding the Deluge. January 19 - 21, 2016 organized by Bioinformatics Group, C-DAC, Pune. Poster presentation: Computational analysis and identification of hub glycogenes from mouse RNA-Seq data
Ali SA, Firoz A, Islam A, Hassan I and Ahmad F. ProStab: An online tool for predicting the stability of protein using its atomic coordinates in protein data bank (PDB). [Presented at The National Conference on Recent trends in Protein Structure Biology, (16-18 Dec 2013) JMI. New Delhi, India] Journal of Proteins and Proteomics, Vol 4, No 2, 2013
Firoz A, Singh S, Jha V, Ali A, malik A: NucleoProtDb: a database of experimentally determined three-dimensional structures of protein-adenine/guanine phosphate complexes [Oral presentation at National Conference on Innovative Molecules for Sustainable Future (NCIMSF-2013) October 24th -26th, 2013, Thapar University, Patiala, Punjab, India].
Firoz A, Malik A, Jolpin KH, Ahmad Z, Jha V and Ahmad S. Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates [ Poster at The 11th KIAS Conference on Protein Structure and Function, (6-8 OCT 2011) KIAS, Seoul, Korea]
Singh S, Malik A, Firoz A, Jha V: CDKD: A Clinical Database of Kidney Diseases. [Presented paper at International Conference on Bioinformatics and System Biology (INCOBS-2011), Annamalai University, Chidambaram, Tamilnadu, India]
Firoz A, Jha V. Analysis of inter base parameters of single stranded DNA. [Presented Poster at International Conference on Bioinformatics and System Biology (INCOBS-2011), Annamalai University, Chidambaram, Tamilnadu, India]
Malik A, Firoz A, Jha V, Ahmad S. Prediction of carbohydrate-binding sites in proteins from amino acid sequences using neural networks. [Presented Poster at International Conference on Open Source for Computer Aided Drug Discovery (OSCADD-2009), IMTECH, Chandigarh, India].
   
   
   
   

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