BPG is committed to discovery and dissemination of knowledge
Cited by in F6Publishing
For: 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:e99033. [PMID: 24918764 DOI: 10.1371/journal.pone.0099033] [Cited by in Crossref: 27] [Cited by in F6Publishing: 20] [Article Influence: 3.4] [Reference Citation Analysis]
Number Citing Articles
1 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;51:12-24. [DOI: 10.1007/s11262-015-1204-y] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 0.6] [Reference Citation Analysis]
2 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;7:4718. [PMID: 28680050 DOI: 10.1038/s41598-017-05088-4] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 1.4] [Reference Citation Analysis]
3 Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu TJ, Yan C, Zhang H, Mazumder R. BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. Database (Oxford) 2015;2015:bav019. [PMID: 25819073 DOI: 10.1093/database/bav019] [Cited by in Crossref: 53] [Cited by in F6Publishing: 49] [Article Influence: 7.6] [Reference Citation Analysis]
4 Hopson LM, Singleton SS, David JA, Basuchoudhary A, Prast-Nielsen S, Klein P, Sen S, Mazumder R. Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application. Prog Mol Biol Transl Sci 2020;176:141-78. [PMID: 33814114 DOI: 10.1016/bs.pmbts.2020.08.011] [Reference Citation Analysis]
5 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;15:918. [PMID: 25336203 DOI: 10.1186/1471-2164-15-918] [Cited by in Crossref: 13] [Cited by in F6Publishing: 12] [Article Influence: 1.6] [Reference Citation Analysis]
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;109:131-40. [PMID: 28188908 DOI: 10.1016/j.ygeno.2017.01.002] [Cited by in Crossref: 8] [Cited by in F6Publishing: 9] [Article Influence: 1.6] [Reference Citation Analysis]
7 Hora B, Gulzar N, Chen Y, Karagiannis K, Cai F, Su C, Smith K, Simonyan V, Shah SA, Ahmed M, Sanchez AM, Stone M, Cohen MS, Denny TN, Mazumder R, Gao F. Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing. mSphere 2020;5:e00551-20. [PMID: 33055255 DOI: 10.1128/mSphere.00551-20] [Reference Citation Analysis]
8 Simonyan V, Mazumder R. High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes (Basel) 2014;5:957-81. [PMID: 25271953 DOI: 10.3390/genes5040957] [Cited by in Crossref: 44] [Cited by in F6Publishing: 36] [Article Influence: 5.5] [Reference Citation Analysis]
9 Hutchins JR. Genomic Database Searching. Methods Mol Biol 2017;1525:225-69. [PMID: 27896724 DOI: 10.1007/978-1-4939-6622-6_10] [Cited by in Crossref: 2] [Article Influence: 0.3] [Reference Citation Analysis]
10 Hadley S. King C, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discovery Today 2022. [DOI: 10.1016/j.drudis.2022.01.007] [Reference Citation Analysis]
11 Tohma K, Saito M, Mayta H, Zimic M, Lepore CJ, Ford-Siltz LA, Gilman RH, Parra GI. Complete Genome Sequence of a Nontypeable GII Norovirus Detected in Peru. Genome Announc 2018;6:e00095-18. [PMID: 29519825 DOI: 10.1128/genomeA.00095-18] [Cited by in Crossref: 7] [Cited by in F6Publishing: 4] [Article Influence: 1.8] [Reference Citation Analysis]
12 Kurtz SL, Voskanian-Kordi A, Simonyan V, Elkins KL. Sequence comparison of Francisella tularensis LVS, LVS-G and LVS-R. Pathog Dis 2018;76. [PMID: 30137434 DOI: 10.1093/femspd/fty067] [Reference Citation Analysis]
13 Lypaczewski P, Hoshizaki J, Zhang WW, McCall LI, Torcivia-Rodriguez J, Simonyan V, Kaur A, Dewar K, Matlashewski G. A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence. Sci Rep 2018;8:16549. [PMID: 30409989 DOI: 10.1038/s41598-018-34812-x] [Cited by in Crossref: 19] [Cited by in F6Publishing: 14] [Article Influence: 4.8] [Reference Citation Analysis]
14 Yao Q, Tian Y, Li PF, Tian LL, Qian YM, Li JS. Design and development of a medical big data processing system based on Hadoop. J Med Syst 2015;39:23. [PMID: 25666927 DOI: 10.1007/s10916-015-0220-8] [Cited by in Crossref: 48] [Cited by in F6Publishing: 19] [Article Influence: 6.9] [Reference Citation Analysis]
15 Sauder CJ, Simonyan V, Ngo L, Karagiannis K, Cong Y, Zhang C, Wang R, Wu WW, Malik T, Rubin SA. Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication. Virology 2016;493:173-88. [PMID: 27058764 DOI: 10.1016/j.virol.2016.03.021] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
16 Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford) 2021;2021:baab008. [PMID: 33784373 DOI: 10.1093/database/baab008] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
17 Gu S, Zaidi S, Hassan MI, Mohammad T, Malta TM, Noushmehr H, Nguyen B, Crandall KA, Srivastav J, Obias V, Lin P, Nguyen BN, Yao M, Yao R, King CH, Mazumder R, Mishra B, Rao S, Mishra L. Mutated CEACAMs Disrupt Transforming Growth Factor Beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis. Gastroenterology 2020;158:238-52. [PMID: 31585122 DOI: 10.1053/j.gastro.2019.09.023] [Cited by in Crossref: 13] [Cited by in F6Publishing: 13] [Article Influence: 4.3] [Reference Citation Analysis]
18 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, 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 DOI: 10.1093/database/baw022] [Cited by in Crossref: 32] [Cited by in F6Publishing: 31] [Article Influence: 5.3] [Reference Citation Analysis]
19 Wang Z, Hopson LM, Singleton SS, Yang X, Jogunoori W, Mazumder R, Obias V, Lin P, Nguyen BN, Yao M, Miller L, White J, Rao S, Mishra L. Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU. Biochim Biophys Acta Mol Basis Dis 2021;1867:166179. [PMID: 34082069 DOI: 10.1016/j.bbadis.2021.166179] [Reference Citation Analysis]
20 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, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R. Baseline human gut microbiota profile in healthy people and standard reporting template. PLoS One 2019;14:e0206484. [PMID: 31509535 DOI: 10.1371/journal.pone.0206484] [Cited by in Crossref: 31] [Cited by in F6Publishing: 28] [Article Influence: 10.3] [Reference Citation Analysis]
21 Bosma TJ, Karagiannis K, Santana-Quintero L, Ilyushina N, Zagorodnyaya T, Petrovskaya S, Laassri M, Donnelly RP, Rubin S, Simonyan V, Sauder CJ. Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm. PLoS One 2019;14:e0216944. [PMID: 31100083 DOI: 10.1371/journal.pone.0216944] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
22 Karagiannis K, Simonyan V, Chumakov K, Mazumder R. Separation and assembly of deep sequencing data into discrete sub-population genomes. Nucleic Acids Res 2017;45:10989-1003. [PMID: 28977510 DOI: 10.1093/nar/gkx755] [Cited by in Crossref: 8] [Cited by in F6Publishing: 6] [Article Influence: 1.6] [Reference Citation Analysis]