Raja Mazumder

Summary

Affiliation: Georgetown University
Country: USA

Publications

  1. pmc The Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 31:345-7. 2003
  2. pmc PIRSF: family classification system at the Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 32:D112-4. 2004
  3. pmc Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets
    Peter B McGarvey
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
    PLoS ONE 4:e7162. 2009
  4. ncbi request reprint UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
  5. pmc SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways
    Konstantinos Karagiannis
    Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA
    Genomics Proteomics Bioinformatics 11:122-6. 2013
  6. pmc Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data
    Charles Cole
    Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
    BMC Bioinformatics 15:28. 2014
  7. pmc The Universal Protein Resource (UniProt): an expanding universe of protein information
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057 1414, USA
    Nucleic Acids Res 34:D187-91. 2006
  8. doi request reprint Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins
    Hayley Dingerdissen
    Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA
    FEBS J 280:1542-62. 2013
  9. doi request reprint Protein functional annotation by homology
    Raja Mazumder
    Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA
    Methods Mol Biol 484:465-90. 2008
  10. ncbi request reprint Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes
    Winona C Barker
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Virus Genes 39:1-9. 2009

Collaborators

Detail Information

Publications26

  1. pmc The Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 31:345-7. 2003
    ..The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files...
  2. pmc PIRSF: family classification system at the Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 32:D112-4. 2004
    ..PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes...
  3. pmc Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets
    Peter B McGarvey
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
    PLoS ONE 4:e7162. 2009
    ....
  4. ncbi request reprint UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
    ..Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences...
  5. pmc SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways
    Konstantinos Karagiannis
    Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA
    Genomics Proteomics Bioinformatics 11:122-6. 2013
    ..The underlying datasets are updated once every 3months. SNVDis is freely available at http://hive.biochemistry.gwu.edu/tool/snvdis...
  6. pmc Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data
    Charles Cole
    Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
    BMC Bioinformatics 15:28. 2014
    ..It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it...
  7. pmc The Universal Protein Resource (UniProt): an expanding universe of protein information
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057 1414, USA
    Nucleic Acids Res 34:D187-91. 2006
    ..A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/...
  8. doi request reprint Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins
    Hayley Dingerdissen
    Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA
    FEBS J 280:1542-62. 2013
    ....
  9. doi request reprint Protein functional annotation by homology
    Raja Mazumder
    Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA
    Methods Mol Biol 484:465-90. 2008
    ..These protocols rely on publicly available computational resources and tools and can be utilized by anyone with an Internet access...
  10. ncbi request reprint Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes
    Winona C Barker
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Virus Genes 39:1-9. 2009
    ..These findings should help predicting the disease potential of emerging and re-emerging flaviviruses and understanding the relationship between protein structure and disease outcome...
  11. ncbi request reprint Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines
    Raja Mazumder
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Virus Genes 35:175-86. 2007
    ....
  12. pmc Computational identification of strain-, species- and genus-specific proteins
    Raja Mazumder
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057 1414, USA
    BMC Bioinformatics 6:279. 2005
    ..Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets...
  13. pmc Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function
    Raja Mazumder
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D C USA
    PLoS Comput Biol 4:e1000151. 2008
  14. pmc A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs
    Hayley Dingerdissen
    Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
    Biol Direct 9:9. 2014
    ..Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV...
  15. pmc Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes
    Phuc Vinh Nguyen Lam
    Life Sciences Department, Paris Diderot University, Paris 75013, France
    Genomics Proteomics Bioinformatics 11:96-104. 2013
    ..The tool, Structure Feature Analysis Tool (SFAT), is freely available to the public at http://hive.biochemistry.gwu.edu/tools/sfat...
  16. pmc Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes
    Raja Mazumder
    Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, USA
    PLoS ONE 7:e36212. 2012
    ....
  17. pmc A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
    Tsung Jung Wu
    Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037, USA, Data Systems and Technology Jet Propulsion Laboratory 4800 Oak Grove Drive Pasadena, CA 91109 Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20852, USA and McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA
    Database (Oxford) 2014:bau022. 2014
    ..Database URL: BioMuta: http://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu...
  18. pmc Community annotation in biology
    Raja Mazumder
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Biol Direct 5:12. 2010
    ..Based on this study we propose community annotation projects should devote resources to direct solicitation for input and streamlining of the processes or interfaces used to collect this input...
  19. pmc CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes
    Nikhat Zafar
    School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110 USA
    BMC Bioinformatics 3:12. 2002
    ..A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining...
  20. ncbi request reprint Trends in protein evolution inferred from sequence and structure analysis
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Struct Biol 12:392-9. 2002
    ....
  21. pmc Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily
    Raja Mazumder
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:5229-43. 2002
    ..Initially, this domain appears to have been involved in RNA processing and it appears to have been recruited to perform various other functions in later stages of evolution...
  22. pmc CDD: a curated Entrez database of conserved domain alignments
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 31:383-7. 2003
    ..This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members...
  23. pmc MMDB: Entrez's 3D-structure database
    Jie Chen
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 31:474-7. 2003
    ..MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html...
  24. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
    ..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...
  25. pmc A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 5:R7. 2004
    ....
  26. pmc GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes
    Srikanth Celamkoti
    Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
    BMC Bioinformatics 5:52. 2004
    ..It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb...