High-performance Integrated Virtual Environment
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PUBLICATIONS

Please cite use of HIVE with:

 

  1. Simonyan V and Mazumder R. High-performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes, ;5(4): 957-981. PMID: 25271953.
  2. 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, Pschenichov A, Rostovtsev A, Santana-Quintero L, Smith K, Thompson EE, Tkachenko V, Torcivia-Rodriguez J, Voskanian A, Wan Q, Wang J, Wu TJ, Wilson C, Mazumder R. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database (Oxford). 2016;2016:baw022. PMID: 26989153.

 

Additional HIVE Team publications:   

 
  1. Dingerdissen H, Torcivia-Rodriguez J, Hu Y, Chang T-C, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. Nucleic Acids Research. 2017

  2. Karagiannis K, Simonyan V, Chumakov K, Mazumder R. Separation and assembly of deep sequencing data into discrete sub-population genomes. Nucleic Acids Research. 2017;45(19):10989-11003. PMID: 28977510.

  3. Chen J, Zaidi S, Rao S, Chen J-S, Phan L, Farci P, Su X, Shetty K, White J, Zamboni F, Wu X, Rashid A, Pattabiraman N, Mazumder R, Horvath A, Wu R-C, Li S, Xiao C, Deng C-X, Wheeler D A, Mishra B, Akbani R, Mishra L. Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor beta Pathway. Gastroenterology. 2017;S0016-5085(17)36144-9. PMID: 28918914.

  4. Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics. 2017;18(1):391. PMID: 28865429.

  5. Gannavaram S, Torcivia J, Gasparyan L, Kaul A, Ismail N, Simonyan V, Nakhasi HL. Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization. Sci Rep. 2017;7(1):4718. PMID: 28680050.

  6. Simonyan V, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A. HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls. Genomics. 2017;109(3-4):131-140. PMID: 28188908.

  7. Pan Y, Yan C, Fan Y, Pan Q, Wan Q, Torcivia-Rodriquez J, Mazumder R. Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids. Scientific Reports. 2017;7:42169 PMID: 28176830.

  8. Gulzar N, Dingerdissen H, Yan C, Mazumder R. Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins. Methods Mol Biol. 2017;1558:159-190. PMID: 28150238.

  9. Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 PMID: 27974626.

  10. Yan C, Pattabiraman N, Goecks J, Lam P, Nayak A, Pan Y, Torcivia-Rodriquez J, Voskanian A, Wan Q, Mazumder R. Impact of germline and somatic missense variations on drug binding sites. Pharmacogenomics J. 2017;17(2):128-136 PMID: 26810135.

  11. Novatt H, Theisen TC, Massie T, Simonyan V, Voskanian-Kordi A, Renn LA, Rabin RL. Distinct Patterns of Expression of Transcription Factors in Response to Interferon Beta and Interferon lambda-1. J Interferon Cytokine Res. 2016;36(10):589-598 PMID: 27447339.

  12. Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Poison SW, Wang Y, Wu CH, UniProt Consortium. Computational clustering for viral reference proteomes. Bioinformatics. 2016;32(13):2041-3 PMID: 27153712.

  13. Mahmood AS, Wu TJ, Mazumder R, Vijay-Shanker K. DiMex: A text-mining system for mutation-disease association extraction. PLoS One. 2016;11(4):e0152725 PMID: 27073839.

  14. Goldweber S, Theodore J, Torcivia-Rodriquez J, Simonyan V, Mazumder R. Pubcast and Genecast: Browsing and exploring publications and associated curated content in biology through mobile devices. IEEE/ACM Trans Comput Biol Bioinform. 2016;14(2):498-500 PMID: 27019500.

  15. Majid L, Zagorodnyaya T, Plant EP, Petrovskaya S, Bidzhieva B, Ye Z, Simonyan V, Chumakov K. Deep Sequencing for Evaluation of Genetic Stability of Influenza A/California/07/2009 (H1N1) Vaccine Viruses. PLoS One. 2015;10(9):e0138650. PMID: 26407068.

  16. Sauder CJ, Ngo L, Simonyan V, Cong Y, Zhang C, Link M, Malik T, Rubin SA. Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal. Virus Genes. 2015;51(1):12-24. PMID: 25962759.

  17. 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, Mazumder R. Generating a focused view of Disease Ontology cancer terms for pan-cancer data integration and analysis. Database (Oxford). 2015;2015:bav032. PMID: 25841438.

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

  19. 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. 2015;4(20)

  20. Abunimer A, Dingerdissen H, Torcivia-Rodriguez J, Vinh Nguyen Lam P, Mazumder R. Non-synonymous Single-Nucleotide Variations as Cardiovascular System Disease Biomarkers and Their Roles in Bridging Genomic and Proteomic Technologies. Biomarkers in Cardiovascular Disease. 2015

  21. 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, 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;290(8):4966-80. PMID: 25538240.

  22. Wilson CA and Simonyan V. FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies. PDA J Pharm Sci Technol. 2014;68(6):626-630. PMID: 25475637.

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

  24. 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. 2014;42(18):11570-88. PMID: 25232094.

  25. Nayak A, Pattabiraman N, Fadra N, Goldman R, Pond S, Mazumder R. Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2. J Biomol Struct Dyn. 2014;33(8):1682-94. PMID: 25245635.

  26. 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. 2014;104(1):1-7. PMID: 24930720.

  27. 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. 2014;9(6):e99033. PMID: 24918764.

  28. 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. Biol Direct. 2014;9:9. PMID: 24894379.

  29. Bidzhieva B, Zagorodnyaya T, Karagiannis K, Simonyan V, Laassri M, Chumakov K. Deep sequencing approach for genetic stability evaluation of influenza A viruses. J Virol Methods. 2014;199(68):75. PMID: 24406624.

  30. Abunimer A, Smith K, Wu T-J, Lam P, Simonyan V, Mazumder R. Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based variation detection. Genes. 2014;5(2):254-69. PMID: 24705329.

  31. Wu T-J, 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. 2014;2014:bau022. PMID: 24667251.

  32. Dabrazhynetskaya A, Soika V, Volokhov D, Simonyan V, Chizhikov V. Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050. Genome Announce. 2014;2(2):pii: e00127-14. PMID: 24604646.

  33. Cole C, Krampis K, Karagiannis K, Almeida J, Faison JW, 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. 2014;15:28. PMID: 24467687.

  34. Mudvari P, Kowsari K, Cole C, Mazumder R, Horvath A. Extraction of molecular features through exome to transcriptome alignment. J Metabol Sys Biol. 2013;1(1):7. PMID: 24791251.

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

  36. Karagiannis K, Simonyan V, Mazumder R. SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways. Genomics Proteomics Bioinformatics. 2013;11(2):122-126. PMID: 23618375.

  37. 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. 2013;11(2):96-104. PMID: 23459159.

  38. Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, Mazumder R. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins. FEBS J. 2013;280(6):1542-1562. PMID: 23350563.

  39. 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, Mazumder R. Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference. Database (Oxford). 2012;2012:bas036. PMID: 23110974.

  40. Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE. RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene forphylogenetic analysis and identification of the species of the family Mycoplasmataceae. Mol Phylogenet Evol. 2012;62(1):515-28. PMID: 22115576.

  41. 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. PMID: 22586465.

 

Posters  

 
  1. HIVE Pathogen Detection Pipeline, presented by Ekaterina Osipova at the 1st Annual Office of Biostatistics and Epidemiology (OBE) Research Day: Advancing Regulatory Sciences, November 16, 2015, Silver Spring, MD. (view as pdf)

  2. Assessing the Immunoglobulin Repertoire by Next-Generation Sequencing using HIVE tools, presented by HIVE user Andrea Siegel at the 3rd Annual Scientific Computing Day, September 8-9, 2015, Silver Spring, MD. (view as pdf)

  3. HIVE Genomic Comparator: Mycoplasma Use Case, presented by HIVE user Alena Debrazhynetskaya at the 3rd Annual Scientific Computing Day, September 8-9, 2015, Silver Spring, MD. (view as pdf)

  4. HIVE Platform for Next-Generation Sequencing Analysis, presented by Konstantinos Karagiannis at the 3rd Annual Scientific Computing Day, September 8-9, 2015, Silver Spring, MD. (view as pdf)

  5. High-performance Integrated Virtual Environment (HIVE) Proteomics: Integrated, cloudbased RNA-Seq and proteomics analysis of prostate adenocarcinoma samples, presented by Hayley Dingerdissen at the American Association for Cancer Research Annual Meeting, April 18-22, 2015, Philadelphia, PA.(view as pdf)

  6. Human pan-cancer variomes and their epigenetic profiles: Extending beyond the coding region, presented by John Torcivia at the American Association for Cancer Research Annual Meeting, April 18-22, 2015, Philadelphia, PA. (view as pdf)

  7. Development of HIVE Database and Analytics for Regulatory Applications to Orthopedic Devices, presented by Ekaterina Osipova at the 2nd Annual FDA Scientific Computing Day, September 18, 2014, Silver Spring, MD. (view as pdf)

  8. A framework for organizing cancer related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE), presented by Raja Mazumder at the Seventh International Biocuration Conference, April 6-9, 2014, Toronto, Canada. (view as pdf)

  9. Novel HIVE methods in cancer genomics: Mutation detection, phylogentic analysis of patients, scanning against a comprehensive curated cancer database BioMuta, presented by John Torvicia and Haitchen Zhang at the Third Symposium on Translational Genomics Conference, March 20-21, 2014, Bethesda, Maryland. (view as pdf)

  10. HIVE Viral Detection, presented by Vahan Simonyan at 2013 PDA/FDA Advanced Technologies for Virus Detection in the Evaluation of Biologicals Conference, November 13-14, 2013, Bethesda, MD. (view as pdf)

  11. Application of Metabolic Modeling to Predict the Effects of Human nsSNV Orthologs in Yeast, presented by Hayley Dingerdissen at NIH Research Festival 2013, October 7-11, Bethesda, MD. (view as pdf)

  12. Clone Discovery Algorithm for High-Throughput Sequencing Data, presented by Konstantinos Karagiannis at NIH Research Festival 2013, Bethesda, MD. (view as pdf)

  13. Utilizing HIVE: RNA-Seq High Throughput Expression Analysis Study Of A Model Disease Schizophrenia, presented by Olesja Muravitskaja at NIH Research Festival 2013, October 7-11, Bethesda, MD. (view as pdf)

  14. HIVE-Seq: Sequence Manipulation Tools for FastA and FastQ Files, presented by Luis Santana-Quintero at NIH Research Festival 2013, October 7-11, Bethesda, MD. (view as pdf)

  15. Assessing SNP using the KPGP-38 Human Genomes next-generation sequencing data from CAMDA, presented by Valerii Soika at NIH Research Festival 2013, October 7->11, Bethesda, MD. (view as pdf)

  16. HIVE Infrastructures, winner of Poster Award at 1st Annual FDA Scientific Computing Day, July 15, 2013, presented by Alin Voskanian. Also presented by Vahan Simonyan at Next Generation Sequencing Data Congress, June 17-18, London, UK. Also presented by Alin Voskanian at 2013 NIH Research Festival, October 7-11, Bethesda, MD. (view as pdf)

  17. HIVE Algorithms, presented by Alin Voskanian at 1st Annual FDA Scientific Computing Day, July 15, 2013. Also presented by Vahan Simonyan at Next Generation Sequencing Data Congress, June 17-18, London, UK. (view as pdf)

 

Other  

 
  1. HIVE White Paper, updated October 2015.

  2. HIVE Brochure, updated October 2015.

  3. Glycosciences and BioCompute Objects, updated June 2017.

  4. Cancer Genomics Standarization Grant, updated May 2017.