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Raja Mazumder

Research Profile

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Chemicals & Drugs

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Evolution, Molecular

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Genes & Molecular Sequences

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Eukaryotic Cells

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Publications

TOP 3
Konstantinos Karagiannis; Vahan Simonyan; Raja Mazumder
SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways.
Phuc Vinh Nguyen Lam; Radoslav Goldman; Konstantinos Karagiannis; Tejas Narsule; Vahan Simonyan; Valerii Soika; Raja Mazumder
Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes.
Hayley Dingerdissen; Konstantinos Karagiannis; Mona Motwani; Vahan Simonyan; Raja Mazumder
Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

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All Publications

2013: Konstantinos Karagiannis; Vahan Simonyan; Raja Mazumder
SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways.
Genomics, proteomics & bioinformatics 2013;11(2):122-6.
2013: Phuc Vinh Nguyen Lam; Radoslav Goldman; Konstantinos Karagiannis; Tejas Narsule; Vahan Simonyan; Valerii Soika; Raja Mazumder
Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes.
Genomics, proteomics & bioinformatics 2013;11(2):96-104.
2013: Hayley Dingerdissen; Konstantinos Karagiannis; Mona Motwani; Vahan Simonyan; Raja Mazumder
Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.
The FEBS journal 2013;280(6):1542-62.
2012: Raja Mazumder; Krishna Sudeep Morampudi; Mona Motwani; Sona Vasudevan; Radoslav Goldman
Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes.
PloS one 2012;7(5):e36212.
2011: Hongzhan Huang; Peter B McGarvey; Baris E Suzek; Raja Mazumder; Jian Zhang; Yongxing Chen; Cathy H Wu
A comprehensive protein-centric ID mapping service for molecular data integration.
Bioinformatics (Oxford, England) 2011;27(8):1190-1.
2011: Chuming Chen; Darren A Natale; Robert D Finn; Hongzhan Huang; Jian Zhang; Cathy H Wu; Raja Mazumder
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.
PloS one 2011;6(4):e18910.
2010: Raja Mazumder; Darren A Natale; Jessica Anne Ecalnir Julio; Lai-Su Yeh; Cathy H Wu
Community annotation in biology.
Biology direct 2010;5():12.
2009: Winona C Barker; Raja Mazumder; Sona Vasudevan; Jose-Luis Sagripanti; Cathy H Wu
Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes.
Virus genes 2009;39(1):1-9.
2009: Peter B McGarvey; Hongzhan Huang; Raja Mazumder; Jian Zhang; Yongxing Chen; Chengdong Zhang; Stephen Cammer; Rebecca Will; Margie Odle; Bruno Sobral; Margaret Moore; Cathy H Wu
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.
PloS one 2009;4(9):e7162.
2008: Raja Mazumder; Sona Vasudevan; Anastasia N Nikolskaya
Protein functional annotation by homology.
Methods in molecular biology (Clifton, N.J.) 2008;484():465-90.
2008: C Zhang; Oswald R Crasta; S Cammer; R Will; R Kenyon; D Sullivan; Q Yu; W Sun; R Jha; D Liu; T Xue; Y Zhang; M Moore; P McGarvey; Hongzhan Huang; Yongxing Chen; J Zhang; Raja Mazumder; Chengcang Wu; Bruno Sobral
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
Nucleic acids research 2008;36(Database issue):D884-91.
2007: Raja Mazumder; Zhang-Zhi Hu; CR Vinayaka; Jose-Luis Sagripanti; Simon D W Frost; Sergei L Kosakovsky Pond; Cathy H Wu
Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines.
Virus genes 2007;35(2):175-86.
2007: Baris E Suzek; Hongzhan Huang; Peter McGarvey; Raja Mazumder; Cathy H Wu
UniRef: comprehensive and non-redundant UniProt reference clusters.
Bioinformatics (Oxford, England) 2007;23(10):1282-8.
2006: Cathy H Wu; Rolf Apweiler; Amos Bairoch; Darren A Natale; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Raja Mazumder; Claire O'Donovan; Nicole Redaschi; Baris E Suzek
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic acids research 2006;34(Database issue):D187-91.
2005: Raja Mazumder; Darren A Natale; Sudhir Murthy; Rathi Thiagarajan; Cathy H Wu
Computational identification of strain-, species- and genus-specific proteins.
BMC bioinformatics 2005;6():279.
2004: Eugene V Koonin; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Igor Rogozin; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Genome biology 2004;5(2):R7.
2004: Cathy H Wu; Anastasia N Nikolskaya; Hongzhan Huang; Lai-Su L Yeh; Darren A Natale; CR Vinayaka; Zhang-Zhi Hu; Raja Mazumder; Sandeep Kumar; Panagiotis Kourtesis; Robert S Ledley; Baris E Suzek; Leslie Arminski; Yongxing Chen; Jian Zhang; Jorge Louie Cardenas; Sehee Chung; Jorge Castro-Alvear; Georgi Dinkov; Winona C Barker
PIRSF: family classification system at the Protein Information Resource.
Nucleic acids research 2004;32(Database issue):D112-4.
2003: Roman L Tatusov; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Boris Kiryutin; Eugene V Koonin; Dmitri M Krylov; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Sergei Smirnov; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale
The COG database: an updated version includes eukaryotes.
BMC bioinformatics 2003;4():41.
2003: Igor Rogozin; Vladimir N Babenko; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Boris G Mirkin; Anastasia N Nikolskaya; B Sridhar Rao; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale; Eugene V Koonin
Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.
Cold Spring Harbor symposia on quantitative biology 2003;68():293-301.
2003: Jie Chen; John B Anderson; Carol DeWeese-Scott; Natalie Fedorova Abrams; Lewis Y Geer; Siqian He; David I Hurwitz; John D Jackson; Aviva R Jacobs; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Thomas Madej; Aron Marchler-Bauer; Gabriele H Marchler; Raja Mazumder; Anastasia N Nikolskaya; B Sridhar Rao; Anna R Panchenko; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Sona Vasudevan; Yanli Wang; Roxanne A Yamashita; Jodie Yin; Stephen H Bryant
MMDB: Entrez's 3D-structure database.
Nucleic acids research 2003;31(1):474-7.
2003: Aron Marchler-Bauer; John B Anderson; Carol DeWeese-Scott; Natalie Fedorova Abrams; Lewis Y Geer; Siqian He; David I Hurwitz; John D Jackson; Aviva R Jacobs; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Thomas Madej; Gabriele H Marchler; Raja Mazumder; Anastasia N Nikolskaya; Anna R Panchenko; B Sridhar Rao; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Sona Vasudevan; Yanli Wang; Roxanne A Yamashita; Jodie Yin; Stephen H Bryant
CDD: a curated Entrez database of conserved domain alignments.
Nucleic acids research 2003;31(1):383-7.
2002: Raja Mazumder; Lakshminarayan M Iyer; Sona Vasudevan; L Aravind
Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.
Nucleic acids research 2002;30(23):5229-43.
2002: L Aravind; Raja Mazumder; Sona Vasudevan; Eugene V Koonin
Trends in protein evolution inferred from sequence and structure analysis.
Current opinion in structural biology 2002;12(3):392-9.