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Raja Mazumder

Raja Mazumder

Associate Professor of Biochemistry and Molecular Medicine

Office Phone: 202-994-5004
Email:
Department: Biochemistry and Molecular Medicine

Education

  • B.Sc., Calcutta University, 1991
  • M.Sc, Calcutta University, 1991
  • MS, University of Mississippi, 1994
  • PhD, Virginia Polytechnic Institute and State University, 2000

Research

Applied bioinformatics and computational biochemistry strongly rooted in evolutionary biology form the basis of my research program. Many of our bioinformatics predictions have been validated in the laboratory, and there are currently a few that are in the wet-lab testing phase. Our current research goals includes conducting a comprehensive comparative analysis at the genomic level, the development of methods to perform analysis of extra-large data sets (such as next generation data and proteomics data) within the context of evolutionary systems biology to identify experimental therapeutic targets, and to create a bioinformatics data-warehouse for “omics” data integration for cancer research. We use bioinformatic approaches in conjunction with experimental data to identify potential experimental targets for development of diagnostics/therapeutics. Our objective is to perform predictive modeling of cancer pathways, systems-level evolutionary analysis of genes, proteins and their regulation, spanning major oncovirus pathogen groups. Ongoing research includes development of High-performance Integrated Virtual Environment (HIVE)< http://hive.biochemistry.gwu.edu/>, a cloud-based environment that contains various bio-scientific tools for analysis of extra-large data; identification of vaccine and therapeutic targets for Hepatitis C Virus; identification of non-synonymous Single Nucleotide Variations (nsSNV) that affect post-translational modifications and their relationship to cancer and other diseases.

Publications

View publications by this faculty member from January 1, 2013 - present

Yan C, Pattabiraman N, Goecks J, Lam P, Nayak A, Pan Y, Torcivia-Rodriquez J, Voskanian A, Wan Q, and Mazumder R. Impact of germline and somatic missense variations on drug binding sites. Pharmacogenomics J. 2016 Jan 26. PMID: 26810135

Wu T-J, Schriml LM, Chen Q-R, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, and Mazumder R. Generating a focused view of Disease Ontology cancer terms for pan-cancer data integration and analysis. Database (Oxford). 2015 Apr 4. pii: bav032. PMID: 25841438.

Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu T-J, Yang C, Zhang H, and Mazumder R. BioXpress: An integrated RNA-seq derived gene expression database for pan-cancer analysis. Database (Oxford). 2015 Mar 28. pii: bav019. PMID: 25819073.

Kumari P, Mazumder R, Simonyan V, and Krampis K. Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. [v1; ref status: awaiting peer review,http://f1000r.es/4yw] F1000Research 2015, 4:20 . doi: 10.12688/f1000research.6016.1.

Simonyan V and Mazumder R. High-performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes, 2014 Sep 30;5(4):957-81. PMID: 25271953.

Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, and Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics, 2014 Oct 21;15(1):918. PMID: 25336203.

Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, and Mazumder R. Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Research, 2014 Sep 17. PMID: 25232094.

Nayak A, Pattabiraman N, Fadra N, Goldman R, Pond S, and Mazumder R. Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2. J Biomol Struct Dyn. 2014 Sep 23:1-30. PMID: 25245635.

Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, and Mazumder R. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Genomics. 2014 June 12. PMID: 24930720.

Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, and Simonyan V. HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis. PLOS One. 2014 June 11; 9(6). PMID: 24918764.

Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, and Mazumder R. A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biol Direct. 2014 June 03. PMID: 24894379.

Abunimer A, Smith K, Wu T-J, Lam P, Simonyan V, and Mazumder R. Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based variation detection. Genes. 2014. PMID:24705329.

Wu T-J, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, and Mazumder R. A framework for organizing cancer related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). Database. 2014. PMID: 24667251.

Cole C, Krampis K, Karagiannis K, Almeida J, Faison JW, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, and Mazumder R. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinformatics. 2014 Jan 27;15:28. PMID: 24467687.

Adhikari S, Chetram MA, Woodrick J, Mitra PS, Manthena PV, Khatkar P, Dakshanamurthy S, Dixon M, Karmahapatra SK, Nuthalapati NK, Gupta S, Narasimhan G, Mazumder R, Loffredo CA, Uren A, and Roy R. Germ-line variants of human N-methylpurine DNA glycosylase show impaired DNA repair activity and facilitate 1,N6 ethenoadenine induced mutations. J Biol Chem. 2014 Dec 23. pii: jbc.M114.627000. PMID: 25538240.

Mudvari P, Kowsari K, Cole C, Mazumder R, and Horvath A. Extraction of molecular features through exome to transcriptome alignment. J Metabol Sys Biol. July 2013 Issue:1, Vol.1.

Basuchoudhary A, Simonyan V, and Mazumder R. Community annotation and the evolution of cooperation: How patience matters. Open Bioinformatics Journal. 2013 7:9-18.

Karagiannis K, Simonyan V, and Mazumder R. SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways. Genomics Proteomics Bioinformatics. 2013 Apr;11(2):122-6. PMID: 23618375.

Lam PV, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, and Mazumder R. Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes. Genomics Proteomics Bioinformatics. 2013 Apr;11(2):96-104. PMID: 23459159.

Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, and Mazumder R. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins. FEBS J. 2013 Mar;280(6):1542-62. PMID: 23350563.

Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, and Mazumder R. Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference. Database (Oxford). 2012 Oct 29;2012:bas036. doi: 10.1093/database/bas036. Print 2012. PubMed PMID: 23110974.

Mazumder R, Morampudi KS, Motwani M, Vasudevan S, and Goldman R. Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes. PLoS One. 2012;7(5):e36212. PMID: 22586465.

Gaudet P, Mazumder R . Foreward Biocuration Virtual Issue 2012. Database. Article ID bas011.

Mazumder R, Morampudi KS, Motwani M, Vasudevan S, Goldman, R. Proteome-wide Analysis of Single-nucleotide Variations in the N-glycosylation sequon of human genes. PLoS One. 2012;7(5): e36212. Epub 2012 May 7.

Amino acid sites in Flavivirus E proteins useful for development of diagnostics and vaccines. Inventors: J-L Sagripanti , Cathy Wu and Raja Mazumder. Patent Application number 60,921,747 Serial # 12,061,067. Approved May 17, 2011. Number: 7943148

Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R (corresponding). Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One. 2011 Apr 27;6(4):e18910. PMCID: PMC3083393

Mazumder R, Natale DA, Julio JA, Yeh LS, Wu CH. Community annotation in biology. Biol Direct. 2010 Feb 18;5:12.

UniProt Consortium,..Mazumder R (multiple co-authors). The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010 Jan;38 (Database issue):D142-8. Epub 2010 Oct 20.

Barker WC, Mazumder R, Vasudevan S, Sagripanti JL, Wu CH. Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes. Virus Genes. 2009 Mar 13.

Mazumder R, Vasudevan S, Nikolskaya AN. Protein functional annotation by homology. Methods Mol Biol. 2008;484:465-90.

Mazumder R, Vasudevan S. Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. PLoS Comput Biol. 26;4(9):e1000151, 2008.

Mazumder R, Hu ZZ, Vinayaka CR, Sagripanti JL, Frost SD, Kosakovsky Pond SL and Wu CH. 2007. Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. Virus Genes 35(2):175-186, 2007.

Mazumder R, Zafar N and Seto D. Finding Order. 2001. Science. 292:749 (Reviewed by RL Bernstein and JB Spalding for the New Products section of Science).

Additional publications published before January 1, 2013 may be available within Himmelfarb Library's database.

Industry Relationships and Collaborations

This faculty member (or a member of their immediate family) has reported a financial interest with the healthcare related companies listed below. These relations have been reported to the University and, when appropriate, management plans are in place to address potential conflicts.

  • None