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• Article

  16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics

  Peterson, C. T., Sharma, V., Iablokov, S. N., Albayrak, L., Khanipov, K., Uchitel, S., Chopra, D., Mills, P. J., Fofanov, Y., Rodionov, D. A. & Peterson, S. N., Mar 2019, In: PloS one. 14, 3, e0213869.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Neurodegenerative diseases
  • Nootropic Agents
  • Prebiotics
  • neurodegenerative diseases
  • prebiotics
  5 Scopus citations

• Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

  Robeson, M. S., Khanipov, K., Golovko, G., Wisely, S. M., White, M. D., Bodenchuck, M., Smyser, T. J., Fofanov, Y., Fierer, N. & Piaggio, A. J., Jan 2018, In: Ecology and Evolution. 8, 1, p. 185-196 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Sus scrofa
  • pig
  • diet
  • stomach content
  • animal
  14 Scopus citations

• Broom: application for non-redundant storage of high throughput sequencing data

  Albayrak, L., Khanipov, K., Golovko, G. & Fofanov, Y., Jan 1 2019, In: Bioinformatics (Oxford, England). 35, 1, p. 143-145 3 p.

  Research output: Contribution to journal › Article › peer-review

  • High Throughput
  • Sequencing
  • Computational Biology
  • Information Storage and Retrieval
  • Research Personnel
  2 Scopus citations

• Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects of ⁵⁶Fe, ¹⁶O, and ²⁸Si irradiation on the induction of murine hepatocellular carcinoma

  Nia, A. M., Khanipov, K., Barnette, B. L., Ullrich, R. L., Golovko, G. & Emmett, M. R., Jul 1 2020, In: BMC Genomics. 21, 1, 453.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Gene Expression Profiling
  • Hepatocellular Carcinoma
  • RNA
  • Ions
  • Acute-Phase Reaction

• Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

  Narra, H. P., Sahni, A., Alsing, J., Schroeder, C. L. C., Golovko, G., Nia, A. M., Fofanov, Y., Khanipov, K. & Sahni, S. K., Sep 25 2020, In: BMC Genomics. 21, 1, 665.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Rickettsia conorii
  • Ticks
  • 6S RNA
  • Transcriptome
  • Infection

• Detection of multi-dimensional co-exclusion patterns in microbial communities

  Albayrak, L., Khanipov, K., Golovko, G. & Fofanov, Y., 2018, In: Bioinformatics. 34, 21, p. 3695-3701 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Probiotics
  • Microbiota
  • Community
  • Pipelines
  • Microorganisms
  4 Scopus citations

• Efficient identification of multiple pathways: RA-Seq analysis of livers from ⁵⁶Fe ion irradiated mice

  ia, A. M., Chen, T., Barnette, B. L., Khanipov, K., Ullrich, R. L., Bhavnani, S. K. & Emmett, M. R., Mar 20 2020, In: BMC bioinformatics. 21, 1, 118.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Liver
  • Mouse
  • Pathway
  • Network Analysis
  • Gene
  1 Scopus citations

• Enhancer associated long non-coding RNA transcription and gene regulation in experimental models of rickettsial infection

  Chowdhury, I. H., Narra, H. P., Sahni, A., Khanipov, K., Fofanov, Y. & Sahni, S. K., 2019, In: Frontiers in immunology. 10, JAN, 3014.

  Research output: Contribution to journal › Article › peer-review

  • Long Noncoding RNA
  • Theoretical Models
  • Spotted Fever Group Rickettsiosis
  • Infection
  • Rickettsia
  3 Scopus citations

• Global transcriptomic profiling of pulmonary gene expression in an experimental murine model of Rickettsia conorii infection

  Narra, H. P., Sahni, A., Khanipov, K., Fofanov, Y. & Sahni, S. K., Mar 2019, In: Genes. 10, 3, 204.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Boutonneuse Fever
  • Gene Expression Profiling
  • Theoretical Models
  • aconitate decarboxylase
  • Lung
  1 Scopus citations

• Identification and characterization of novel small RNAs in Rickettsia prowazekii

  Schroeder, C. L. C., Narra, H. P., Sahni, A., Rojas, M., Khanipov, K., Patel, J., Shah, R., Fofanov, Y. & Sahni, S. K., 2016, In: Frontiers in Microbiology. 7, JUN, 859.

  Research output: Contribution to journal › Article › peer-review

  • Rickettsia prowazekii
  • Bacterial RNA
  • RNA
  • 6S RNA
  • 4.5S RNA
  13 Scopus citations

• Identification of multidimensional Boolean patterns in microbial communities

  Golovko, G., Kamil, K., Albayrak, L., Nia, A. M., Duarte, R. S. A., Chumakov, S. & Fofanov, Y., Sep 11 2020, In: Microbiome. 8, 1, 131.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Microbiota
  • Secondary Metabolism

• Janibacterspecies with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis

  Malania, L., Bai, Y., Khanipov, K., Tsereteli, M., Metreveli, M., Tsereteli, D., Sidamonidze, K., Imnadze, P., Fofanov, Y. & Kosoy, M., 2019, In: Infectious Disease Reports. 11, 2, p. 22-25 4 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Aortic Valve Stenosis
  • Bacteria
  • Whole Genome Sequencing
  • Aortic Valve
  • Agar

• Measuring alphavirus fidelity using non-infectious virus particles

  Patterson, E. I., Khanipov, K., Swetnam, D. M., Walsdorf, S., Kautz, T. F., Thangamani, S., Fofanov, Y. & Forrester, N. L., May 2020, In: Viruses. 12, 5, v12050546.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Alphavirus
  • Mutation Rate
  • Venezuelan Equine Encephalitis Viruses
  • Virion
  • Mutation
  2 Scopus citations

• Microbiome interaction networks and community structure from laboratory-reared and field-collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus mosquito vectors

  Hegde, S., Khanipov, K., Albayrak, L., Golovko, G., Pimenova, M., Saldaña, M. A., Rojas, M. M., Hornett, E. A., Motl, G. C., Fredregill, C. L., Dennett, J. A., Debboun, M., Fofanov, Y. & Hughes, G. L., Sep 10 2018, In: Frontiers in Microbiology. 9, SEP, 2160.

  Research output: Contribution to journal › Article › peer-review

  • Culex
  • Mosquito Vectors
  • Aedes
  • Microbiota
  • Culicidae
  24 Scopus citations

• Microbiota dysbiosis and its pathophysiological significance in bowel obstruction

  Hegde, S., Lin, Y. M., Golovko, G., Khanipov, K., Cong, Y., Savidge, T., Fofanov, Y. & Shi, X. Z., Dec 1 2018, In: Scientific reports. 8, 1, 13044.

  Research output: Contribution to journal › Article › peer-review

  • Dysbiosis
  • Microbiota
  • Proteobacteria
  • Anti-Bacterial Agents
  • Colon
  9 Scopus citations

• Novel wolbachia strains in anopheles malaria vectors from sub-saharan africa [version 2; referees: 3 approved]

  Jeffries, C. L., Lawrence, G. G., Golovko, G., Kristan, M., Orsborne, J., Spence, K., Hurn, E., Bandibabone, J., Tantely, L. M., Raharimalala, F. N., Keita, K., Camara, D., Barry, Y., Wat’senga, F., Manzambi, E. Z., Afrane, Y. A., Mohammed, A. R., Abeku, T. A., Hegde, S., Khanipov, K. & 6 others, Pimenova, M., Fofanov, Y., Boyer, S., Irish, S. R., Hughes, G. L. & Walker, T., 2018, In: Wellcome Open Research. 3, 113.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Wolbachia
  • Anopheles
  • Africa South of the Sahara
  • Malaria
  • Bacteria
  21 Scopus citations

• Small Regulatory RNAs of Rickettsia conorii

  Narra, H. P., Schroeder, C. L. C., Sahni, A., Rojas, M., Khanipov, K., Fofanov, Y. & Sahni, S. K., Nov 11 2016, In: Scientific reports. 6, 36728.

  Research output: Contribution to journal › Article › peer-review

  • Rickettsia conorii
  • Boutonneuse Fever
  • RNA
  • Ticks
  • Endothelial Cells
  19 Scopus citations

• The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome

  Albayrak, L., Khanipov, K., Pimenova, M., Golovko, G., Rojas, M., Pavlidis, I., Chumakov, S., Aguilar, G., Chávez, A., Widger, W. R. & Fofanov, Y., Dec 12 2016, In: BMC Genomics. 17, 1, 1017.

  Research output: Contribution to journal › Article › peer-review

  • Mitochondrial Genome
  • Mitochondrial DNA
  • DNA
  • Mutation
  • Genome
  11 Scopus citations

• Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts

  Lane Warmbrod, K., Patterson, E. I., Kautz, T. F., Stanton, A., Rockx-Brouwer, D., Kalveram, B. K., Khanipov, K., Thangamani, S., Fofanov, Y. & Forrester, N. L., 2019, In: PLoS pathogens. 15, 4, e1007610.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Replicase
  • Viral RNA
  • Culicidae
  • Vertebrates
  • Mutation Rate
  7 Scopus citations