Research Topics
| Raja MazumderSummaryAffiliation: Georgetown University Country: USA Publications
| Collaborators
|
Detail Information
Publications
The Protein Information ResourceCathy 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...- PIRSF: family classification system at the Protein Information ResourceCathy 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... - Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targetsPeter 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.... 
Protein functional annotation by homologyRaja 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...- Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromesWinona 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... 
UniRef: comprehensive and non-redundant UniProt reference clustersBaris 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...- Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccinesRaja Mazumder
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
Virus Genes 35:175-86. 2007.... 
Computational identification of strain-, species- and genus-specific proteinsRaja 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...- The Universal Protein Resource (UniProt): an expanding universe of protein informationCathy 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/... - Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting functionRaja Mazumder
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C. USA
PLoS Comput Biol 4:e1000151. 2008 - Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genesRaja Mazumder
Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, USA
PLoS ONE 7:e36212. 2012.... - Community annotation in biologyRaja Mazumder
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
Biol Direct 5:12. 2010..REVIEWERS: This article was reviewed by I. King Jordan, Daniel Haft and Yuriy Gusev... - A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomesEugene V Koonin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Genome Biol 5:R7. 2004.... - The COG database: an updated version includes eukaryotesRoman 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... - MMDB: Entrez's 3D-structure databaseJie 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... - CDD: a curated Entrez database of conserved domain alignmentsAron 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... - Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamilyRaja 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... - Trends in protein evolution inferred from sequence and structure analysisL 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.... - CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomesNikhat 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... - GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomesSrikanth 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...