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Sankara Nethralaya
Sankara Nethralaya
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Centre For Bioinformatics

Publications

INVITED BOOK CHAPTERS (Dr.V.Umashankar):

Insilico Tools of Molecular Modeling, in Handbook of Systems Toxicology, V.Umashankar and S.Gurunathan, edited by Daniel A. Casciano and SauraC.Sahu. Chichester, UK: John Wiley & Sons, Ltd,pp 579-590. (2011)
Cheminformatics and its Applications, in Handbook of Systems Toxicology, edited by Daniel A. Casciano and SauraC.Sahu. Chichester,V.Umashankar and S.Gurunathan,UK: John Wiley & Sons, Ltd,pp 347-360.(2011)
Tools and Databases for Computational Epigenomics, Toxicology and Epigenetics, Edited by SauraC.Sahu. Chichester, V.Umashankar and S.Gurunathan, UK: John Wiley & Sons, Ltd,pp. 595-614.(2011)
 
LIST OF RESEARCH PUBLICATIONS:
2017
Ornithine and its role in metabolic diseases: An appraisal.MuthukumaranSivashanmugam, JaidevJa, Umashankar V., Sulochana K.N. Article in Biomedicine & Pharmacotherapy 86:185–194 • February 2017 DOI: 10.1016/j.biopha.2016.12.024
Inhibition of IKKβ by celastrol and its analogues – an in silico and in vitro approach. KarpagamVeerappan, Sathishkumar Natarajan, PurushothEthiraj, UmashankarVetrivel&Shila Samuel. Article in Pharmaceutical Biology 55(1):368-373 • January 2017. DOI: 10.1080/13880209.2016.1241809
2016
Unraveling Genomic and Phenotypic nature of Multidrug-Resistant (MDR) Pseudomonas aeruginosa VRFPA04 Isolated from Keratitis Patient.N. Murugan, J. Malathi, V. Umashankar, H.N. Madhavan.MicrobiologicalResearch. 2016; 193. DOI:10.1016/j.micres.2016.10.002.PMID: 27825482
InSilico Structure Prediction of Human Fatty Acid Synthase–Dehydratase: A Plausible Model for Understanding Active Site Interactions. Perinkulam Ravi Deepa, John Arun, VetrivelUmashankar, ASamdani, ManoharanSangeetha, Subramanian Krishnakumar.Bioinformatics and biology insights 2016; DOI:10.4137/BBI.S38317.2016. PMID: 27559295
Virtual Screening, Molecular dynamics and binding free energy calculations on Human Carbonic Anhydrase IX catalytic domain for deciphering potential leads. Arun John, MuthukumaranSivashanmugam, VetrivelUmashankar, SulochanaKonerirajapuram Natarajan.Journal of Biomolecular Structure & Dynamics.2016; DOI:10.1080/07391102.2016.1207565. PMID: 27373313
Multilevel Precision-Based Rational Design of Chemical Inhibitors Targeting the Hydrophobic Cleft of Toxoplasma gondii Apical Membrane Antigen 1 (AMA1). UmashankarVetrivel, ShaliniMuralikumar, B Mahalakshmi, K Lily Therese, HN Madhavan, Mohamed Alameen, IndhujaThirumudi.Genomics & Informatics. 2016; 14(2). DOI:10.5808/GI.2016.14.2.53. PMID: 27445648
Comparative docking of dual conformations in human fatty acid synthase thioesterase domain reveals potential binding cavity for virtual screening of ligands. Arun John, UmashankarVetrivel, Krishnakumar Subramanian, Perinkulam Ravi Deepa.Journal of Biomolecular Structure & Dynamics2016; DOI:10.1080/07391102.PMID: 27145135
Targeting CD44, ABCG2 and CD133 markers using aptamers: in silico analysis of CD133 extracellular domain 2 and its aptamer. Subramanian N, Akilandeswari B, Bhutra A, Alameen M, Vetrivel U, Khetan V et al,. RSC Advances. 2016;6(38):32115-32123. DOI: 10.1039/C5RA27072C
Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient. Murugan N, Malathi J, Umashankar V, Madhavan H.Gene. 2016;578(1):105-111. PMID: 26692145
Bio-conjugation of antioxidant peptide on surface-modified gold nanoparticles: a novel approach to enhance the radical scavenging property in cancer cell.Kalmodia S, Vandhana S, Tejaswini Rama B, Jayashree B, SreenivasanSeethalakshmi T, Umashankar V et al,.Cancer Nanotechnology. 2016;7(1).PMID: 26900409
Probing the biophysical interaction between Neocarzinostatin toxin and EpCAM RNA aptamer.Athyala PK, Kanwar JR, Alameen M, Kanwar RK, Krishnakumar S, Watson J,Vetrivel U, Narayanan J. BiochemBiophys Res Commun. 2016;469(2):257-62. PMID: 26642954
2015
Homozygosity mapping in Leber congenital amaurosis and autosomal recessive retinitis pigmentosa in South Indian families.SundaramurthySrilekha,TharigopalaArokiasamy,Natarajan N. Srikrupa,VetrivelUmashankar,SwaminathanMeenakshi,ParveenSen,SumanKapur,NagasamySoumittra.PLOS ONE. 2015.PMID: 26147992
Draft genome sequence of blaVeb-1, blaoxa-10producing multi-drug resistant (MDR) Pseudomonas aeruginosastrain VRFPA09 recovered from bloodstream infection.NandagopalMurugan, JambulingamMalathi, VetrivelUmashankar, HajibNarahari Rao Madhavan.Brazilian Journal of Microbiology. 2015; vol.46, n.3, pp. 639-640.PMID: 26413042
Comparative Modeling and Molecular Dynamics Simulation of Substrate Binding in Human Fatty Acid Synthase: EnoylReductase and β-KetoacylReductase Catalytic Domains.Arun John, VetrivelUmashankar, SubramanianKrishnakumar, and Perinkulam Ravi Deepa.Genomics & Informatics.2015;13(1):15-24. PMID: 25873848
Insights on Drug Targeting ofToxoplasma gondiiHost Invasion Proteins: A Review. IndhujaThirumudi, UmashankarVetrivel, Mahalakshmi B, Lily Therese K, Madhavan HN. Asian Journal of Pharmaceutical and Clinical Research. 2015; 8:3
Drug Discovery: an appraisal.Umashankar, V., and S. Gurunathan. International Journal of Pharmacy and Pharmaceutical Sciences.2015; 7.4.
Virtual screening studies of seaweed metabolites for predicting potential pparγ agonists. Gurula, H., Loganathan, T.,Krishnamoorthy, T., Vetrivel, U., & Samuel, S. International Journal of Pharmacy and Pharmaceutical Sciences.20157(11).
2014
Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort. SathyaPriya C, P. Sen, V. Umashankar, N. Gupta, M. Kabra, G. Kumaramanickavel, C. Stoetzel, H. Dollfus and S. Sripriya.Clin Genet. 2014. doi: 10.1111/cge.12342. PMID: 24400638
In Silico analysis and prioritization of drug targets in Fusariumsolani. MuthukumaranSivashanmmugam,HemavathyNagarajam, UmashankarVetrivel, GayathriRamasubban, KL therese, Madhavan HN,UmashankarVetrivel.Medical Hypotheses, Elsevier.2014;84(2). PMID: 25555413
Computational docking studies reveal the potential inhibitory binding mode of Curcumin and its analogues on Lung Resistance Protein. SeethalakshmiSreenivasan, Mohamed al ameen, Subramanian Krishnakumarand UmashankarVetrivel.International Journal of Pharmacy and Pharmaceutical Sciences. 2014
Whole-Genome Sequencing and Mutation Analysis of Two Extensively Drug-Resistant Sputum Isolates of Mycobacterium tuberculosis (VRFCWCF XDRTB 232 and VRFCWCF XDRTB 1028) from Chennai, India. Lakshmipathy D, Vetrivel U, Ramasubban G, Kulandai LT, Madhavan HN, Sridhar R, Meenakshi N. Genome Announcements, American Society of Microbiology.2014;2(6).PMCID: PMC4241668
Whole genome sequence of polyresistant Mycobacterium tuberculosis CWCFVRF PRTB 19 sputum isolate from Chennai, India, closely clustering with East African Indian 5 genogroup. Lakshmipathy D, Vetrivel U, Ramasubban G, Kulandai LT, Madhavan HN, Sridhar R, Meenakshi N.Genome Announcements, American Society of Microbiology.2014; 2(4):e00702-14. PMCID: PMC4102868
Draft Genome Sequence of sputum isolate of Multidrug resistant Mycobacterium tuberculosis CWCFVRF MDRTB 670 strain from Chennai, India.GayathriRamasubban, DhanurekhaLakshmipathy, UmashankarVetrivel, Lily Therese Kulandai, HajibNarahariMadhavan, R Sridhar, N Meenakshi.Genome announcements, American Society of Microbiology.2014; Vol 2. Issue 3.PMID: 24855307
Importance of ABC transporters in different tissues. UmashankarVetrivel and Gurunathan Subramanian. Drug metabolism and drug interactions 29.2 2014; 65-66.
Comparative genomic analysis of multidrug-resistant Pseudomonas aeruginosa clinical isolates VRFPA06 and VRFPA08 with VRFPA07.Murugan, Nandagopal, JambulingamMalathi, VetrivelUmashankar, and HajibNarahari Rao Madhavan.Genome announcements, American Society of Microbiology.2014; no. 2 (2014): e00140-14.PMCID: PMC3945505
2013
Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets Towards Prediction of Novel Serum Biomarkers.Madhu Beta, NaliniVenkatesan, MadavanVasudevan, UmashankarVetrivel, VikasKhetan, Subramanian Krishnakumar, Bioinformatics and Biology Insights.2013; Vol 7, 21-34,PMID: 23400111.
Modulation of MDR1 expression and function in retinoblastoma cells by curcumin.SeethalakshmiSreenivasan, SathyabaarathiRavichandran, UmashankarVetrivel,Subramanian Krishnakumar, Journal of Pharmacology and Pharmacotherapeutics.2013 doi: 10.4103/0976-500X.110882.PMCID: PMC3669568
Insilico Analysis of Novel Mutation ala102pro Targeting pncA Gene of M. Tuberculosis.DhanurekhaLakshmipathy, GayathriRamasubban, Lily Therese*, UmashankarVetrivel, MuthukumaranSivashanmugam, SunithaRajendiran, Sridhar R, Madhavan HN, and Meenakshi N. J ComputSciSyst Biol.2013, 6:2.
Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India.Malathi J, Murugan N, Umashankar V, Bagyalakshmi R, Madhavan HN. Genome Announc.American Society of Microbiology.2013; 1(4). PMCID: PMC3703595
Elucidation Of IRON Binding Patterns Through Insilico Approaches In Human Iron Binding Proteins.MuthukumaranSivashanmugam, AnushaKuppuswamy, UmashankarVetrivel, K.N. Sulochana. International Journal of Therapeutic Applications, Volume 10, 2013, 11-18.
Structural studies on AIPL1 and its functional interactions with NUB1 to identify key interacting residues in LCA4. S. Muthukumaran,V. Umashankar,MeenaRevathiValliappan. Journal of Ocular Biology, Diseases, and Informatics.2013 April.Springer.PMID: 24596939
Virtual screening studies reveal linarin as a potential natural inhibitor targeting cdk-4 in retinoblastoma. S. Muthukumaran& R. Chandana, V.Umashankar.Journal of Pharmacology and Pharmacotherapeutics. 2013. PMID: 24250202
Novel Mutations in the thymidne kinase gene of ocular herpes simplex virus isolate responsible for acyclovir resistance by in silico analysis. Samson Moses Y, Malathi J, UmashankarV, Sherlin and Madhavan H.N, International Journal of Computational Bioinformatics and In Silico Modeling.2013 2(4): 158-165
2012
ICAM-1 K469E polymorphism is a genetic determinant for the clinical risk factors of T2D subjects with retinopathy in Indians: a population-based case–control study.Kumari Vinita1, Sarangapani Sripriya1, Krishnamurthy Prathiba, KulothunganVaitheeswaran, RavichandranSathyabaarathi, Mahendran Rajesh, John Amali, VetrivelUmashankar, GovindasamyKumaramanickavel, SwakshyarSaumya Pal, Rajiv Raman, Tarun Sharma, British Medical Journal Open. 2012; 2:e001036. PMID: 22904330.
Agonistic effect of polyunsaturated fatty acids (PUFAs) and its metabolites on brain-derived neurotrophic factor (BDNF) through molecular docking simulation. UmashankarVetrivelet al.,BMCLipids in Health and Disease.2012 11:109.PMCID: PMC3477081.
In vitro and In silico studies on inhibitory effects of curcumin on multi drug resistance associated protein (MRP1) in retinoblastoma cells.SeethalakshmiSreenivasan, SathyabaarathiRavichandran, UmashankarVetrivel, and Subramanian Krishnakumar, Bioinformation. 2012; 8(1): 13–19. 2012. PMID: 22359429
Phylogenetic comparison of exonic US4, US7 and UL44 regions of clinical herpes simplex virus type 1 isolates showed lack of association between their anatomic sites of infection and genotypic/sub genotypic classification.Harishankar A, Jambulingam M, Gowrishankar R, Venkatachalam A, VetrivelUmashankar,Ravichandran S, Yesupadam SM and Madhavan HN,Virology Journal,BMC.2012; 9:65.PMID: 22416856
Studies on New Delhi Metallo-Beta-Lactamse-1 producing Acinetobacterbaumannii isolated from donor swab in a tertiary eye care centre, India and structural analysis of its antibiotic binding interactions.MuraliSowmiya, VetrivelUmashankar, SivashanmuganMuthukumaran, HajibNarahariraoMadhavan, and JambulingamMalathi, Bioinformation. 2012; 8(10): 445–452.PMID: 22715297
2011
A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens.UmashankarVetrivelGurunathan Subramanian SudarsanamDorairaj.HUGO Journal (Official Journal of Human Genome Organization).2011;DOI 10.1007/s11568-011-9152-7.Springer.PMID:PMC3238024
Insilico Identification of Novel Inhibitors for Emphysema through Structure Based Drug Design Approaches.Raghavanrajashekaran, Charanyamuralidharan, Sathyabaarthiravichandran,Umashankarvetrivel.Journal of Biology and Life Sciences. 2011; Vol 2, No 1.
Detection of novel coupled mutations in the katG gene (His276Met, Gln295His and Ser315Thr) in a multidrug-resistant Mycobacterium tuberculosis strain from Chennai, India, and insight into the molecular mechanism of isoniazid resistance using structural bioinformatics approaches.GayathriRamasubbana, Kulandai Lily Theresea, UmashankarVetrivel, MuthukumaranSivashanmugamb, ParvathyRajanc, R. Sridhard, Hajib N. Madhavana, N. Meenakshie. International Journal of Antimicrobial Agents. Elsevier.2011PMID: 21330112
Functional characterization of novel mutations in UL54 of ganciclovir resistant HCMV strain using structural analysis.JambulingamMalathi, VetrivelUmashankar, RavichandranSathyabaarathi, SivashanmuganMuthukumaran, MuraliIshwarya, HajibNarahariMadhavan.Bioinformation.2011.PMID: 21383907
Molecular screening of the CYP4V2 gene in Bietti crystalline dystrophy that is associated with choroidal neovascularization.GandraMamatha, VetrivelUmashankar, NachiappanKasinathan, Tandava Krishnan, RavichandranSathyabaarathi, Thirumalai Karthiyayini,1 John Amali,1 Chetan Rao,3 Jagadeesan Madhavan1.Molecular Vision.2011; 17:1970-1977. PMID: 21850171.
Chemical inhibition of Fatty Acid Synthase: molecular docking analysis and biochemical validation in ocular cancer cells. P. R. Deepa, S. Vandhana, S. Muthukumaran,V.Umashankar, U. Jayanthi, S. Krishnakumar, J OculBiol Dis Infor. Springer,2011. PMID: 23181152
Comparative modeling of PON2 and analysis of its substrate binding interactions using computational methods. Subramanian Barathi&MuralidaranCharanya&ShivashanmugamMuthukumaran&NarayanasamyAngayarkanni&VetrivelUmashankar.J OculBiol Dis Infor,springer.2011; DOI 10.1007/s12177-011-9057-7.PMID: 22319641
2010
Ab initio model of HIV’s Vifand simulation studies of APOBEC3G-Vif complex.UmashankarVetrivel. International Journal of Integrative Biology (IJIB). 2010, Vol. 10, No. 1, 29.
LIST OF CONFERENCE ABSTRACTS:
Probing the plausible structural conformations of ROCK1 towards enabling efficient screening of ligands. Samdani.A and Umashankar V. The Society of Biological Chemists.(2016)
Structure-function relationship studies on human fatty acid synthase thioesterase domain and its inhibitors: an in silico approach.Arun John, Umashankar V.,Deepa P. R., Krishnakumar S. International Conference on Crystal Growth and Bimolecular Crystallography (ICCGBC-2014) at Sastra University, Thanjavur (2014)
Virtual Screening of small molecules and Insilico designing of peptides targeting HistidineDecarboxyalse for anticancer activity.Muthukumaran S,Arun john, Umashankar V, K.N. Sulochana. The Society of Biological Chemists.(2013)
Multi- faceted utility of in silico tools to explore structure- function relationships: A case-study of human FASN (Fatty acid synthase) multi-catalytic domain protein.Arun John, Umashankar V., Deepa P. R., Krishnakumar S. Recent Advances in Computational Drug Design at IISC, Bangalore. (2013)
Family of Small Leucine Rich Repeats Proteoglycans binds to TGF-Beta1 throughtheirLRR Domain:Insilico Analysis.S.JagaVeeraPandiyan, S.Muthukumaran, V.Umashankar, K.N Sullochana. Presented at the The Society of Biological Chemists, Lucknow, India(2011)
CONFERENCES ATTENDED:
Dr.V.Umashankar attended the workshop on "Advanced techniques in protein design and engineering" held at Indian Institute of Science and Research (IISER), Mohali, 15th March - 19th March 2016.
Dr.V.Umashankar, Samdani.A and Muthukumaran.S attended the 41st IndianSociety of Human Genetics Annual meeting& International Conference conducted by the Genetics Department, Vision Research Foundation on 3rd- 5th March,2016.
Dr.V.Umashankar attended the talk given by Dr.MichaelLelivit, Director of Bioinformatics, Ion torrent Inc USA on “Roadmap to $1000 genome” on 7-3-2012 held at Bangalore.
Dr.V.Umashankar attended the workshop on Next Generation Sequencing Data Analysis conducted by European Molecular Biology Laboratory (EMBL) and National Centre for Biological Sciences on 13-01-2013 at Centre for Cellular and Molecular Platforms(C-CAMP) Bangalore
LIST OF INVITED TALKS:
DrV.Umasshankar gave an invited talk on Ocular Bioinformatics in the workshop organised by the INAE-NATF (indo-french) at Indian Institute of Science held on 15th -17th April, 2015
Dr.V.Umashankar gave an invited talk on “Insilico tools for Bioinformatics at National Workshop on “Recent Trends in Computer Aided Drug Design' on conducted by SriVenkateswara Engineering of College on 27th& 29th September 2014
Dr.V.Umashankar gave an invited talk on “Bioinformatics & Molecular Diagnostics, VRR Institute of Biomedical Sciences, Chennai on 26-11-2014.
Dr.V.Umashankar delivered invited talk on “Bioinformatics and bioactive compounds” at the National Level Conference on Bioactive compounds held at meenakshi college, Chennai on 24-01-2013.
Dr.V.Umashankar delivered an Invited talk on Bioinformatics & Open source tools at the National Level Bioinformatics Workshop held at TamilnaduVetinary University on 08-05-2013.
Dr.V.Umashankar delivered an Invited talk on Bioinformatics in a Seminar on Bioinformatics at Sathyabama University on 26-07-2013.
Dr.V.Umashankar delivered an Invited talk at CME programme on Next Generation Sequencing at MicroLabs, Coimbatore on 22-09-2013.
Dr.V.Umashankar delivered an Invited talk on “Introduction to Sequence Analysis and Biological Databases” at the CME program on Biomedical Informatics conducted by Aravind Eye Hospital, Madurai on 13-10-2013
Dr.V.Umashankar delivered an invited talk on “Bioinformatics and Data Analysis Challenges” and also chaired a technical session at the International Conference on “Recent Advances on High Dimensional Data Analysis” conducted by International biometry society and National Institute for Tuberculosis Research on 27-12-2013
Dr.V.Umashankardelivered invited talk on “Opensource tools for Bioinformatics at the National conference on “mathematical computing” at Vellore Institute of technology, Chennai on 30-11-2012.
Dr.V.Umashankar delivered an invited talk on “Genotype to phenotype analysis of SNPs” at IERG 2011conference held at Hyderabad.
Dr.V.Umashankar delivered an invited talk on “Open source Software for Bioinformatics” at National Level Conference on Statistical Methods for Bioinformatics 2011 conducted by National Institute of Tuberculosis Research, Chennai.