Vinod Scaria

Summary

Publications

  1. pmc lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
    Deeksha Bhartiya
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
    Database (Oxford) 2013:bat034. 2013
  2. pmc Long Non-Coding RNAs in Infection Biology
    Vinod Scaria
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research Delhi, India
    Front Genet 3:308. 2012
  3. pmc High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region
    Satish Sati
    CSIR Institute of Genomics and Integrative Biology, Delhi, India
    PLoS ONE 7:e31621. 2012
  4. pmc tbvar: A comprehensive genome variation resource for Mycobacterium tuberculosis
    Kandarp Rakeshkumar Joshi
    CSIR Open Source Drug Discovery Unit, Anusandhan Bhawan, Delhi 110001, India Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhawan, Delhi 110001, India Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India and GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Mall Road, Delhi 110007, India
    Database (Oxford) 2014:bat083. 2014
  5. pmc Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana
    Salma Jamal
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
    BMC Bioinformatics 14:329. 2013
  6. pmc Predictive modeling of anti-malarial molecules inhibiting apicoplast formation
    Salma Jamal
    CSIR Open Source Drug Discovery Unit, Anusandhan Bhavan, Delhi 110001, India
    BMC Bioinformatics 14:55. 2013
  7. pmc Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity
    Mukesh Kumar Lalwani
    Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
    PLoS ONE 7:e52588. 2012
  8. pmc Systematic transcriptome wide analysis of lncRNA-miRNA interactions
    Saakshi Jalali
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Delhi, India
    PLoS ONE 8:e53823. 2013
  9. pmc Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci
    Satish Sati
    Genomics and Molecular Medicine Unit and GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi 110007, India
    Nucleic Acids Res 40:10018-31. 2012
  10. doi request reprint Conceptual approaches for lncRNA drug discovery and future strategies
    Deeksha Bhartiya
    CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
    Expert Opin Drug Discov 7:503-13. 2012

Collaborators

Detail Information

Publications32

  1. pmc lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
    Deeksha Bhartiya
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
    Database (Oxford) 2013:bat034. 2013
    ..To the best of our knowledge, lncRNome is one of the largest and most comprehensive resources for lncRNAs. Database URL: http://genome.igib.res.in/lncRNome...
  2. pmc Long Non-Coding RNAs in Infection Biology
    Vinod Scaria
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research Delhi, India
    Front Genet 3:308. 2012
    ....
  3. pmc High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region
    Satish Sati
    CSIR Institute of Genomics and Integrative Biology, Delhi, India
    PLoS ONE 7:e31621. 2012
    ....
  4. pmc tbvar: A comprehensive genome variation resource for Mycobacterium tuberculosis
    Kandarp Rakeshkumar Joshi
    CSIR Open Source Drug Discovery Unit, Anusandhan Bhawan, Delhi 110001, India Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhawan, Delhi 110001, India Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India and GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Mall Road, Delhi 110007, India
    Database (Oxford) 2014:bat083. 2014
    ..To the best of our knowledge, tbvar is the largest and most comprehensive genome variation resources for MTBC. Database URL: http://genome.igib.res.in/tbvar/ ..
  5. pmc Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana
    Salma Jamal
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
    BMC Bioinformatics 14:329. 2013
    ....
  6. pmc Predictive modeling of anti-malarial molecules inhibiting apicoplast formation
    Salma Jamal
    CSIR Open Source Drug Discovery Unit, Anusandhan Bhavan, Delhi 110001, India
    BMC Bioinformatics 14:55. 2013
    ....
  7. pmc Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity
    Mukesh Kumar Lalwani
    Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
    PLoS ONE 7:e52588. 2012
    ..The miR142a-3p mediated control of cdh5 constitutes an additional layer of regulation for maintaining vascular integrity and developmental angiogenesis. These findings have implications in development, wound repair and tumor growth...
  8. pmc Systematic transcriptome wide analysis of lncRNA-miRNA interactions
    Saakshi Jalali
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Delhi, India
    PLoS ONE 8:e53823. 2013
    ..The availability of genome-scale datasets for Argonaute targets across human transcriptome has prompted us to reconstruct a genome-scale network of interactions between miRNAs and lncRNAs...
  9. pmc Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci
    Satish Sati
    Genomics and Molecular Medicine Unit and GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi 110007, India
    Nucleic Acids Res 40:10018-31. 2012
    ..Thus, our observation suggests that epigenetic regulation of lncRNA shares common features with mRNA except the role of DNA methylation which is markedly dissimilar...
  10. doi request reprint Conceptual approaches for lncRNA drug discovery and future strategies
    Deeksha Bhartiya
    CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
    Expert Opin Drug Discov 7:503-13. 2012
    ..Recent evidence also suggests the role of lncRNAs in the pathophysiology of disease processes...
  11. pmc A sequence-based variation map of zebrafish
    Ashok Patowary
    CSIR Institute of Genomics and Integrative Biology, Delhi, India
    Zebrafish 10:15-20. 2013
    ..We also show that human disease gene orthologs in the sequenced wild zebrafish genome show a lower ratio of nonsynonymous to synonymous single nucleotide variations...
  12. pmc Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish
    Kriti Kaushik
    Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhavan, New Delhi, India
    PLoS ONE 8:e83616. 2013
    ..Our study is thus a starting point and opens a way towards discovering new molecular interactions of gene expression within the specific adult tissues in the context of maintenance of organ form and function. ..
  13. doi request reprint Systematic analysis and functional annotation of variations in the genome of an Indian individual
    Ashok Patowary
    Genomics and Molecular Medicine, CSIR Institute of Genomics and IntegrativeBiology, Council of Scientific and Industrial Research, Delhi, India
    Hum Mutat 33:1133-40. 2012
    ..This study thus provides the template for genome-scale analysis of personal genomes for personalized medicine...
  14. pmc The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation
    Meghna Singh
    CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Mall Road, Delhi 110007, India, Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhawan, Delhi 110001, India, Acharya Narendra Dev College, Delhi University, Govindpuri, Kalkaji, New Delhi 110019, India, Dr B R Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India, Department of Genetics, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India and Mayo Clinic, Rochester, MN, USA
    Database (Oxford) 2014:bau011. 2014
    ..The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search. Database URL: http://genome.igib.res.in/twiki. ..
  15. pmc Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain
    Rhishikesh Bargaje
    Institute of Genomics and Integrative Biology CSIR, Mall Road, Delhi 110 007, India
    Nucleic Acids Res 40:8965-78. 2012
    ..Our results suggest that gene expression levels in vivo are determined by accessibility of the TSS and proximity of H2A.Z...
  16. ncbi request reprint Time for the zebrafish ENCODE
    Sridhar Sivasubbu
    Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Mall Road, Delhi 110 007, India
    J Genet 92:695-701. 2013
    ..We discuss how the present understanding and genome-scale methodologies available in this model organism could be effectively used towards realizing this goal. ..
  17. pmc Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets
    Vinita Periwal
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology CSIR, New Delhi 110007, India
    BMC Pharmacol 12:1. 2012
    ..In addition, this approach would save significantly on the cost, effort and time required to run high throughput screens...
  18. doi request reprint Distinct patterns of genetic variations in potential functional elements in long noncoding RNAs
    Deeksha Bhartiya
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhawan, Delhi, 110001, India
    Hum Mutat 35:192-201. 2014
    ..We further examined signals of selections and allele frequencies of these prioritized set of lncRNAs. To the best of our knowledge, this is the first and comprehensive large-scale analysis of genetic variations in long ncRNAs. ..
  19. doi request reprint miRvar: A comprehensive database for genomic variations in microRNAs
    Deeksha Bhartiya
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology CSIR, Mall Road, Delhi 110007
    Hum Mutat 32:E2226-45. 2011
    ..The data is made available on the Leiden Open (source) Variation Database (LOVD) platform at http://genome.igib.res.in/mirlovd to provide ease of aggregation and analysis and is open for community curation efforts...
  20. doi request reprint Antagonism of microRNA function in zebrafish embryos by using locked nucleic acid enzymes (LNAzymes)
    Hemant Suryawanshi
    CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi 110007, India
    Chembiochem 13:584-9. 2012
    ..We demonstrate that LNAzyme can efficiently knockdown miRNAs with minimal toxicity to the zebrafish embryos...
  21. pmc Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs
    Saakshi Jalali
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
    Biol Direct 7:25. 2012
    ..We hypothesized that some lncRNAs could potentially be processed to small RNA and thus could have a dual regulatory output...
  22. doi request reprint FishMap Zv8 update--a genomic regulatory map of zebrafish
    Deeksha Bhartiya
    Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research, Delhi, India
    Zebrafish 7:179-80. 2010
    ..FishMap Zv8 update is available at http://fishmap2.igib.res.in...
  23. pmc Computational analysis and predictive modeling of small molecule modulators of microRNA
    Salma Jamal
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Mall Road, Delhi, 110007, India
    J Cheminform 4:16. 2012
    ..abstract:..
  24. doi request reprint Insights into structural variations and genome rearrangements in prokaryotic genomes
    Vinita Periwal
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Delhi 110007 and Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhawan, New Delhi 110001, India GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Delhi 110007 and Academy of Scientific and Innovative Research AcSIR, Anusandhan Bhawan, New Delhi 110001, India
    Bioinformatics 31:1-9. 2015
    ..We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing...
  25. pmc Cheminformatics models for inhibitors of Schistosoma mansoni thioredoxin glutathione reductase
    Sonam Gaba
    GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
    ScientificWorldJournal 2014:957107. 2014
    ..We show that a combined approach of machine learning and other cheminformatics approaches such as substructure comparison and molecular docking is efficient to prioritise molecules from large molecular datasets. ..
  26. doi request reprint Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci
    Deeksha Bhartiya
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology CSIR, Mall Road, Delhi 110007, India
    Hum Mutat 33:E2367-74. 2012
    ..The compilation is available at the snoRNA locus specific variation database: http://genome.igib.res.in/snolovd conforming to the HGVS standards for nomenclature of genomic variants...
  27. pmc Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis
    Rohit Vashisht
    Council of Scientific and Industrial Research, Delhi, India
    PLoS ONE 7:e39808. 2012
    ..The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach...
  28. pmc De novo identification of viral pathogens from cell culture hologenomes
    Ashok Patowary
    CSIR Institute of Genomics and Integrative Biology CSIR IGIB, Mall Road, Delhi 110007, India
    BMC Res Notes 5:11. 2012
    ..abstract:..
  29. doi request reprint Pharmacogenetic landscape of clopidogrel in north Indians suggest distinct interpopulation differences in allele frequencies
    Anil K Giri
    Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
    Pharmacogenomics 15:643-53. 2014
    ..We built an allele frequency map of variants affecting clopidogrel response in north Indians...
  30. pmc Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21
    Rubina Tabassum
    Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research Institute of Genomics and Integrative Biology, Delhi, India
    Diabetes 62:977-86. 2013
    ..Our study suggests that common susceptibility variants for T2D are largely the same across populations, but also reveals a population-specific locus and provides further insights into genetic architecture and etiology of T2D...
  31. pmc A case for pharmacogenomics in management of cardiac arrhythmias
    Gaurav Kandoi
    Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi, India
    Indian Pacing Electrophysiol J 12:54-64. 2012
    ..We also discuss potential issues that need to be resolved before personalized pharmacogenomics becomes a reality in regular clinical practice...