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Raja Mazumder, Ph.D. - Publications

Affiliations: 
2000 Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
Microbiology Biology
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48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, ... ... Mazumder R, et al. Baseline human gut microbiota profile in healthy people and standard reporting template. Plos One. 14: e0206484. PMID 31509535 DOI: 10.1371/Journal.Pone.0206484  0.323
2019 Kim B, Ali T, Dong C, Lijeron C, Mazumder R, Wultsch C, Krampis K. miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 30653336 DOI: 10.1089/Cmb.2018.0218  0.372
2019 Torcivia-Rodriguez J, Dingerdissen H, Chang TC, Mazumder R. A Primer for Access to Repositories of Cancer-Related Genomic Big Data. Methods in Molecular Biology (Clifton, N.J.). 1878: 1-37. PMID 30378067 DOI: 10.1007/978-1-4939-8868-6_1  0.345
2018 Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, ... ... Mazumder R, et al. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. Plos Biology. 16: e3000099. PMID 30596645 DOI: 10.1371/Journal.Pbio.3000099  0.337
2018 Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. Nucleic Acids Research. 46: D1128-D1136. PMID 30053270 DOI: 10.1093/Nar/Gkx907  0.35
2018 Fan Y, Hu Y, Yan C, Goldman R, Pan Y, Mazumder R, Dingerdissen HM. Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. Scientific Reports. 8: 4322. PMID 29531238 DOI: 10.1038/S41598-018-22345-2  0.355
2017 Karagiannis K, Simonyan V, Chumakov K, Mazumder R. Separation and assembly of deep sequencing data into discrete sub-population genomes. Nucleic Acids Research. PMID 28977510 DOI: 10.1093/Nar/Gkx755  0.326
2017 Pan Y, Yan C, Hu Y, Fan Y, Pan Q, Wan Q, Torcivia-Rodriguez J, Mazumder R. Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids. Scientific Reports. 7: 42169. PMID 28176830 DOI: 10.1038/Srep42169  0.316
2017 Gulzar N, Dingerdissen H, Yan C, Mazumder R. Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins. Methods in Molecular Biology (Clifton, N.J.). 1558: 159-190. PMID 28150238 DOI: 10.1007/978-1-4939-6783-4_8  0.352
2016 Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH. Computational clustering for viral reference proteomes. Bioinformatics (Oxford, England). PMID 27153712 DOI: 10.1093/Bioinformatics/Btw110  0.338
2016 Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S, Golikov A, Gulzar N, Karagiannis K, Vinh Nguyen Lam P, Maudru T, Muravitskaja O, Osipova E, Pan Y, Pschenichnov A, Rostovtsev A, ... ... Mazumder R, et al. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database : the Journal of Biological Databases and Curation. 2016. PMID 26989153 DOI: 10.1093/Database/Baw022  0.314
2015 Wu TJ, Schriml LM, Chen QR, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, ... ... Mazumder R, et al. Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis. Database : the Journal of Biological Databases and Curation. 2015: bav032. PMID 25841438 DOI: 10.1093/Database/Bav032  0.302
2015 Kumari P, Mazumder R, Simonyan V, Krampis K. Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. F1000research. 4: 20. DOI: 10.12688/F1000Research.6016.1  0.327
2014 Simonyan V, Mazumder R. High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes. 5: 957-81. PMID 25271953 DOI: 10.3390/Genes5040957  0.337
2014 Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R. Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Research. 42: 11570-88. PMID 25232094 DOI: 10.1093/Nar/Gku772  0.311
2014 Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Genomics. 104: 1-7. PMID 24930720 DOI: 10.1016/J.Ygeno.2014.06.001  0.33
2014 Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, Simonyan V. HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis. Plos One. 9: e99033. PMID 24918764 DOI: 10.1371/Journal.Pone.0099033  0.321
2014 Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R. A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biology Direct. 9: 9. PMID 24894379 DOI: 10.1186/1745-6150-9-9  0.319
2014 Abunimer A, Smith K, Wu TJ, Lam P, Simonyan V, Mazumder R. Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based biomarker discovery and diagnostics. Genes. 5: 254-69. PMID 24705329 DOI: 10.3390/Genes5020254  0.316
2014 Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, 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 : the Journal of Biological Databases and Curation. 2014: bau022. PMID 24667251 DOI: 10.1093/Database/Bau022  0.394
2014 Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, 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. 15: 28. PMID 24467687 DOI: 10.1186/1471-2105-15-28  0.351
2013 Karagiannis K, Simonyan V, Mazumder R. SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways. Genomics, Proteomics & Bioinformatics. 11: 122-6. PMID 23618375 DOI: 10.1016/J.Gpb.2012.10.003  0.364
2013 Lam PV, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, Mazumder R. Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes. Genomics, Proteomics & Bioinformatics. 11: 96-104. PMID 23459159 DOI: 10.1016/J.Gpb.2012.11.003  0.304
2013 Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, Mazumder R. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins. The Febs Journal. 280: 1542-62. PMID 23350563 DOI: 10.1111/Febs.12155  0.33
2013 Kumar R, Horvath A, Mazumder R, Toi M, Sato F, Pillai MR, Costa L, Carmo-Fonseca M, Knapp S, Dutt A, Gupta S, Badwe R. The Global Cancer Genomics Consortium's Second Annual Symposium: Genomics Medicine in Cancer Research Genes and Cancer. 4: 196-200. DOI: 10.1177/1947601913484582  0.309
2012 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. 7: e36212. PMID 22586465 DOI: 10.1371/Journal.Pone.0036212  0.332
2012 Gaudet P, Mazumder R. Biocuration Virtual Issue 2012. Database : the Journal of Biological Databases and Curation. 2012: bas011. PMID 22434845 DOI: 10.1093/Database/Bas011  0.362
2011 Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. Plos One. 6: e18910. PMID 21556138 DOI: 10.1371/Journal.Pone.0018910  0.36
2010 Mazumder R, Natale DA, Julio JA, Yeh LS, Wu CH. Community annotation in biology. Biology Direct. 5: 12. PMID 20167071 DOI: 10.1186/1745-6150-5-12  0.327
2009 McGarvey PB, Huang H, Mazumder R, Zhang J, Chen Y, Zhang C, Cammer S, Will R, Odle M, Sobral B, Moore M, Wu CH. Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. Plos One. 4: e7162. PMID 19779614 DOI: 10.1371/Journal.Pone.0007162  0.349
2008 Mazumder R, Vasudevan S. Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. Plos Computational Biology. 4: e1000151. PMID 18818720 DOI: 10.1371/Journal.Pcbi.1000151  0.353
2008 Mazumder R, Vasudevan S, Nikolskaya AN. Protein functional annotation by homology. Methods in Molecular Biology (Clifton, N.J.). 484: 465-90. PMID 18592196 DOI: 10.1007/978-1-59745-398-1_28  0.36
2008 Zhang C, Crasta O, Cammer S, Will R, Kenyon R, Sullivan D, Yu Q, Sun W, Jha R, Liu D, Xue T, Zhang Y, Moore M, McGarvey P, Huang H, ... ... Mazumder R, et al. An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Research. 36: D884-91. PMID 17984082 DOI: 10.1093/Nar/Gkm903  0.352
2007 Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (Oxford, England). 23: 1282-8. PMID 17379688 DOI: 10.1093/Bioinformatics/Btm098  0.337
2006 Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research. 34: D187-91. PMID 16381842 DOI: 10.1093/Nar/Gkj161  0.36
2005 Mazumder R, Natale DA, Murthy S, Thiagarajan R, Wu CH. Computational identification of strain-, species- and genus-specific proteins. Bmc Bioinformatics. 6: 279. PMID 16305751 DOI: 10.1186/1471-2105-6-279  0.338
2004 Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C, Seto D. GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. Bmc Bioinformatics. 5: 52. PMID 15128433 DOI: 10.1186/1471-2105-5-52  0.346
2004 Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biology. 5: R7. PMID 14759257 DOI: 10.1186/Gb-2004-5-2-R7  0.342
2004 Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, et al. PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Research. 32: D112-4. PMID 14681371 DOI: 10.1093/Nar/Gkh097  0.315
2003 Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, et al. The COG database: an updated version includes eukaryotes. Bmc Bioinformatics. 4: 41. PMID 12969510 DOI: 10.1186/1471-2105-4-41  0.337
2003 Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, et al. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Research. 31: 383-7. PMID 12520028 DOI: 10.1093/Nar/Gkg087  0.315
2002 Aravind L, Mazumder R, Vasudevan S, Koonin EV. Trends in protein evolution inferred from sequence and structure analysis. Current Opinion in Structural Biology. 12: 392-9. PMID 12127460 DOI: 10.1016/S0959-440X(02)00334-2  0.343
2002 Zafar N, Mazumder R, Seto D. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. Bmc Bioinformatics. 3: 12. PMID 11972896 DOI: 10.1186/1471-2105-3-12  0.355
2002 Zafar N, Mazumder R, Seto D. Application of global computational tools GeneOrder and CoreGenes to the comparative analyses of chordopoxvirus genomes Information Sciences. 146: 127-135. DOI: 10.1016/S0020-0255(02)00220-7  0.351
2001 Zafar N, Mazumder R, Seto D. Comparisons of gene colinearity in genomes using GeneOrder2.0 Trends in Biochemical Sciences. 26: 514-516. PMID 11504629 DOI: 10.1016/S0968-0004(01)01881-3  0.344
2001 Mazumder R, Kolaskar A, Seto D. GeneOrder: Comparing the order of genes in small genomes Bioinformatics. 17: 162-166. PMID 11238072 DOI: 10.1093/Bioinformatics/17.2.162  0.364
2000 Mazumder R, Pinkart HC, Alban PS, Phelps TJ, Benoit RE. Low-substrate regulated microaerophilic behavior as a stress response of aquatic and soil bacteria. Current Microbiology. 41: 79-83. PMID 10856370 DOI: 10.1007/S002840010097  0.646
1999 Mazumder R, Phelps TJ, Krieg NR, Benoit RE. Determining chemotactic responses by two subsurface microaerophiles using a simplified capillary assay method. Journal of Microbiological Methods. 37: 255-63. PMID 10480269 DOI: 10.1016/S0167-7012(99)00072-X  0.643
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