| Year |
Citation |
Score |
| 2019 |
Malania L, Bai Y, Khanipov K, Tsereteli M, Metreveli M, Tsereteli D, Sidamonidze K, Imnadze P, Fofanov Y, Kosoy M. species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis. Infectious Disease Reports. 11: 8132. PMID 31579471 DOI: 10.4081/Idr.2019.8132 |
0.387 |
|
| 2019 |
Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN. 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. Plos One. 14: e0213869. PMID 30889210 DOI: 10.1371/Journal.Pone.0213869 |
0.365 |
|
| 2019 |
Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Global Transcriptomic Profiling of Pulmonary Gene Expression in an Experimental Murine Model of Infection. Genes. 10. PMID 30857242 DOI: 10.3390/Genes10030204 |
0.336 |
|
| 2018 |
Chowdhury IH, Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Enhancer Associated Long Non-coding RNA Transcription and Gene Regulation in Experimental Models of Rickettsial Infection. Frontiers in Immunology. 9: 3014. PMID 30687302 DOI: 10.3389/Fimmu.2018.03014 |
0.354 |
|
| 2018 |
Hegde S, Khanipov K, Albayrak L, Golovko G, Pimenova M, Saldaña MA, Rojas MM, Hornett EA, Motl GC, Fredregill CL, Dennett JA, Debboun M, Fofanov Y, Hughes GL. Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected , , and Mosquito Vectors. Frontiers in Microbiology. 9: 2160. PMID 30250462 DOI: 10.3389/Fmicb.2018.02160 |
0.308 |
|
| 2018 |
Kalesinskas L, Cudone E, Fofanov Y, Putonti C. S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences. Evolutionary Bioinformatics Online. 14: 1176934318797354. PMID 30245567 DOI: 10.1177/1176934318797354 |
0.652 |
|
| 2018 |
Albayrak L, Khanipov K, Golovko G, Fofanov Y. Broom: Application for non-redundant storage of High Throughput Sequencing data. Bioinformatics (Oxford, England). PMID 30010786 DOI: 10.1093/Bioinformatics/Bty580 |
0.33 |
|
| 2018 |
Webb MS, Miller AL, Howard TL, Johnson BH, Chumakov S, Fofanov Y, Nguyen-Vu T, Lin CY, Thompson EB. Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells:interactions of MAPK, MYC and glucocorticoid pathways. Molecular and Cellular Endocrinology. PMID 29596968 DOI: 10.1016/J.Mce.2018.03.004 |
0.301 |
|
| 2018 |
Patterson EI, Khanipov K, Rojas MM, Kautz TF, Rockx-Brouwer D, Golovko G, Albayrak L, Fofanov Y, Forrester NL. Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity. Virus Evolution. 4: vey001. PMID 29479479 DOI: 10.1093/Ve/Vey001 |
0.318 |
|
| 2018 |
Robeson MS, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ. Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa). Ecology and Evolution. 8: 185-196. PMID 29321862 DOI: 10.1002/Ece3.3638 |
0.316 |
|
| 2017 |
Wu YW, Shao Y, Khanipov K, Golovko G, Pimenova M, Fofanov Y, Chu KH. Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing Poly(3-Hydroxybutyrate). Genome Announcements. 5. PMID 28883143 DOI: 10.1128/Genomea.00948-17 |
0.396 |
|
| 2017 |
Kosoy M, McKee C, Albayrak L, Fofanov Y. Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives. Parasitology. 1-20. PMID 28764816 DOI: 10.1017/S0031182017001263 |
0.352 |
|
| 2017 |
Schroeder CLC, Narra HP, Sahni A, Khanipov K, Patel J, Fofanov Y, Sahni SK. Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions. Ticks and Tick-Borne Diseases. PMID 28709615 DOI: 10.1016/J.Ttbdis.2017.06.008 |
0.343 |
|
| 2016 |
Albayrak L, Khanipov K, Pimenova M, Golovko G, Rojas M, Pavlidis I, Chumakov S, Aguilar G, Chávez A, Widger WR, Fofanov Y. The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome. Bmc Genomics. 17: 1017. PMID 27955616 DOI: 10.1186/S12864-016-3375-X |
0.315 |
|
| 2016 |
Narra HP, Schroeder CL, Sahni A, Rojas M, Khanipov K, Fofanov Y, Sahni SK. Small Regulatory RNAs of Rickettsia conorii. Scientific Reports. 6: 36728. PMID 27834404 DOI: 10.1038/Srep36728 |
0.32 |
|
| 2016 |
Schroeder CL, Narra HP, Sahni A, Rojas M, Khanipov K, Patel J, Shah R, Fofanov Y, Sahni SK. Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii. Frontiers in Microbiology. 7: 859. PMID 27375581 DOI: 10.3389/Fmicb.2016.00859 |
0.313 |
|
| 2016 |
Kosoy M, Bai Y, Enscore R, Rizzo MR, Bender S, Popov V, Albayrak L, Fofanov Y, Chomel B. Bartonella melophagi in blood of domestic sheep (Ovis aries) and sheep keds (Melophagus ovinus) from the southwestern US: Cultures, genetic characterization, and ecological connections. Veterinary Microbiology. 190: 43-9. PMID 27283855 DOI: 10.1016/J.Vetmic.2016.05.009 |
0.325 |
|
| 2015 |
Schroeder CL, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK. Bacterial small RNAs in the Genus Rickettsia. Bmc Genomics. 16: 1075. PMID 26679185 DOI: 10.1186/S12864-015-2293-7 |
0.41 |
|
| 2015 |
Loeffelholz M, Fofanov Y. The main challenges that remain in applying high-throughput sequencing to clinical diagnostics. Expert Review of Molecular Diagnostics. 15: 1405-8. PMID 26394651 DOI: 10.1586/14737159.2015.1088385 |
0.303 |
|
| 2015 |
Sible E, Cooper A, Malki K, Bruder K, Watkins SC, Fofanov Y, Putonti C. Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches. Data in Brief. 5: 9-12. PMID 26380839 DOI: 10.1016/J.Dib.2015.08.001 |
0.581 |
|
| 2015 |
Rojas M, Golovko G, Khanipov K, Albayrak L, Chumakov S, Pettitt BM, Strongin AY, Fofanov Y. Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines. Plos One. 10: e0127799. PMID 26039084 DOI: 10.1371/Journal.Pone.0127799 |
0.405 |
|
| 2015 |
Chernov AV, Reyes L, Xu Z, Gonzalez B, Golovko G, Peterson S, Perucho M, Fofanov Y, Strongin AY. Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells. Epigenetics : Official Journal of the Dna Methylation Society. 10: 303-18. PMID 25695131 DOI: 10.1080/15592294.2015.1020000 |
0.359 |
|
| 2015 |
Be NA, Thissen JB, Fofanov VY, Allen JE, Rojas M, Golovko G, Fofanov Y, Koshinsky H, Jaing CJ. Metagenomic analysis of the airborne environment in urban spaces. Microbial Ecology. 69: 346-55. PMID 25351142 DOI: 10.1007/S00248-014-0517-Z |
0.356 |
|
| 2014 |
Stepanov VG, Xiao Y, Tran Q, Rojas M, Willson RC, Fofanov Y, Fox GE, Roberts DJ. The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions. Bmc Microbiology. 14: 225. PMID 25194715 DOI: 10.1186/S12866-014-0225-3 |
0.318 |
|
| 2013 |
Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus. Bmc Evolutionary Biology. 13: 184. PMID 24007216 DOI: 10.1186/1471-2148-13-184 |
0.66 |
|
| 2012 |
Saxer G, Havlak P, Fox SA, Quance MA, Gupta S, Fofanov Y, Strassmann JE, Queller DC. Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum. Plos One. 7: e46759. PMID 23056439 DOI: 10.1371/Journal.Pone.0046759 |
0.311 |
|
| 2012 |
Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, Howard JJ, Ballesteros E, Gupta S, Widger W, Fofanov Y. Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation. Bmc Bioinformatics. 13: 166. PMID 22800377 DOI: 10.1186/1471-2105-13-166 |
0.325 |
|
| 2012 |
Gijavanekar C, Drabek R, Soni M, Jackson GW, Strych U, Fox GE, Fofanov Y, Willson RC. Detection and typing of viruses using broadly sensitive cocktail-PCR and mass spectrometric cataloging: demonstration with dengue virus. The Journal of Molecular Diagnostics : Jmd. 14: 402-7. PMID 22579629 DOI: 10.1016/J.Jmoldx.2012.02.006 |
0.324 |
|
| 2012 |
Gijavanekar C, Strych U, Fofanov Y, Fox GE, Willson RC. Rare target enrichment for ultrasensitive PCR detection using cot-rehybridization and duplex-specific nuclease. Analytical Biochemistry. 421: 81-5. PMID 22155054 DOI: 10.1016/J.Ab.2011.11.010 |
0.339 |
|
| 2012 |
McCue KF, Ponciano G, Rockhold DR, Whitworth JL, Gray SM, Fofanov Y, Belknap WR. Generation of PVY Coat Protein siRNAs in Transgenic Potatoes Resistant to PVY American Journal of Potato Research. 89: 374-383. DOI: 10.1007/S12230-012-9257-0 |
0.334 |
|
| 2011 |
Zhu B, Kuriakose JA, Luo T, Ballesteros E, Gupta S, Fofanov Y, McBride JW. Ehrlichia chaffeensis TRP120 binds a G+C-rich motif in host cell DNA and exhibits eukaryotic transcriptional activator function. Infection and Immunity. 79: 4370-81. PMID 21859854 DOI: 10.1128/Iai.05422-11 |
0.35 |
|
| 2011 |
Gijavanekar C, Añez-Lingerfelt M, Feng C, Putonti C, Fox GE, Sabo A, Fofanov Y, Willson RC. PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'. The Febs Journal. 278: 1676-87. PMID 21410643 DOI: 10.1111/J.1742-4658.2011.08091.X |
0.579 |
|
| 2011 |
Medina RA, Rojas M, Tuin A, Huff S, Ferres M, Martinez-Valdebenito C, Godoy P, García-Sastre A, Fofanov Y, SantaLucia J. Development and characterization of a highly specific and sensitive SYBR green reverse transcriptase PCR assay for detection of the 2009 pandemic H1N1 influenza virus on the basis of sequence signatures. Journal of Clinical Microbiology. 49: 335-44. PMID 21084522 DOI: 10.1128/Jcm.01142-10 |
0.364 |
|
| 2010 |
Colborn JM, Kosoy MY, Motin VL, Telepnev MV, Valbuena G, Myint KS, Fofanov Y, Putonti C, Feng C, Peruski L. Improved detection of Bartonella DNA in mammalian hosts and arthropod vectors by real-time PCR using the NADH dehydrogenase gamma subunit (nuoG). Journal of Clinical Microbiology. 48: 4630-3. PMID 20926707 DOI: 10.1128/Jcm.00470-10 |
0.568 |
|
| 2010 |
Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, Goldman TD, Feldgarden M, Birren BW, Fofanov Y, Boos J, et al. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proceedings of the National Academy of Sciences of the United States of America. 107: 4371-6. PMID 20142485 DOI: 10.1073/Pnas.0911295107 |
0.402 |
|
| 2009 |
Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y. PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics (Oxford, England). 25: 2438-9. PMID 19602525 DOI: 10.1093/Bioinformatics/Btp429 |
0.384 |
|
| 2009 |
Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M, Jayaraman K, Fofanov Y. Ultraspecific probes for high throughput HLA typing. Bmc Genomics. 10: 85. PMID 19232123 DOI: 10.1186/1471-2164-10-85 |
0.632 |
|
| 2008 |
Añez M, Putonti C, Fox GE, Fofanov Y, Willson RC. Exhaustive computational identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers. Journal of Biotechnology. 133: 267-76. PMID 17996971 DOI: 10.1016/J.Jbiotec.2007.09.007 |
0.643 |
|
| 2007 |
Putonti C, Pettitt B, Reid J, Fofanov Y. PIDA:A new algorithm for pattern identification. Online Journal of Bioinformatics : Ojb. 8: 30-40. PMID 19834570 |
0.529 |
|
| 2007 |
Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y. Effect of the mutation rate and background size on the quality of pathogen identification. Bioinformatics (Oxford, England). 23: 2665-71. PMID 17881407 DOI: 10.1093/Bioinformatics/Btm420 |
0.599 |
|
| 2007 |
Tucker DL, Ott CM, Huff S, Fofanov Y, Pierson DL, Willson RC, Fox GE. Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment. Bmc Microbiology. 7: 15. PMID 17343762 DOI: 10.1186/1471-2180-7-15 |
0.311 |
|
| 2007 |
Putonti C, Meizhuo Z, Johnsson L, Fofanov Y. Two challenges in genomics that can benefit from petascale platforms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4375: 313-322. |
0.588 |
|
| 2006 |
Chumakov S, Ballesteros E, Rodriguez Sanchez JE, Chavez A, Zhang M, Pettit BM, Fofanov Y. Using Mutual Information to Discover Temporal Patterns in Gene Expression Data. Medical Physics : ... Mexican Symposium. Mexican Symposium On Medical Physics. 854: 25-30. PMID 20428481 DOI: 10.1063/1.2356392 |
0.494 |
|
| 2006 |
Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D, Fofanov Y. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Molecular Biology and Evolution. 23: 1863-8. PMID 16829541 DOI: 10.1093/Molbev/Msl053 |
0.646 |
|
| 2006 |
Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, Fofanov Y. Human-blind probes and primers for dengue virus identification. The Febs Journal. 273: 398-408. PMID 16403026 DOI: 10.1111/J.1742-4658.2005.05074.X |
0.663 |
|
| 2006 |
Putonti C, Chumakov S, Chavez A, Luo Y, Graur D, Fox GE, Fofanov Y. Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli Aip Conference Proceedings. 854: 126-128. DOI: 10.1063/1.2356423 |
0.527 |
|
| 2006 |
Zhang M, Putonti C, Chumakov S, Gupta A, Fox GE, Graur D, Fofanov Y. Statistical properties of short subsequences in microbial genomes and their link to pathogen identification and evolution Aip Conference Proceedings. 854: 13-18. DOI: 10.1063/1.2356390 |
0.684 |
|
| 2005 |
Chumakov S, Belapurkar C, Putonti C, Li TB, Pettitt BM, Fox GE, Willson RC, Fofanov Y. The theoretical basis of universal identification systems for bacteria and viruses. Journal of Biological Physics and Chemistry : Jbpc. 5: 121-128. PMID 20428334 DOI: 10.4024/40501.Jbpc.05.04 |
0.613 |
|
| 2005 |
Tucker DL, Karouia F, Wang J, Luo Y, Li TB, Willson RC, Fofanov Y, Fox GE. Effect of an artificial RNA marker on gene expression in Escherichia coli. Applied and Environmental Microbiology. 71: 4156-9. PMID 16000839 DOI: 10.1128/Aem.71.7.4156-4159.2005 |
0.35 |
|
| 2004 |
Thompson EB, Webb MS, Miller AL, Fofanov Y, Johnson BH. Identification of genes leading to glucocorticoid-induced leukemic cell death. Lipids. 39: 821-5. PMID 15638253 DOI: 10.1007/S11745-004-1302-7 |
0.301 |
|
| 2004 |
Fofanov Y, Luo Y, Katili C, Wang J, Belosludtsev Y, Powdrill T, Belapurkar C, Fofanov V, Li TB, Chumakov S, Pettitt BM. How independent are the appearances of n-mers in different genomes? Bioinformatics (Oxford, England). 20: 2421-8. PMID 15087315 DOI: 10.1093/Bioinformatics/Bth266 |
0.376 |
|
| 2004 |
Putonti C, Fofanov Y. Analysis of promoter regions for essential genes of bacillus subtilis using PIDA Proceedings of the International Conference On Mathematics and Engineering Techniques in Medicine and Biological Sciences, Metmbs'04. 276-282. |
0.514 |
|
| 2004 |
Chumakov S, Putonti C, Pettitt BM, Fox G, Willson RC, Fofanov Y. Using statistical properties of short subsequences in microbial identification Proceedings of the International Conference On Mathematics and Engineering Techniques in Medicine and Biological Sciences, Metmbs'04. 363-367. |
0.519 |
|
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