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• 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

• 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

• Draft genome sequence of Zobellella denitrificans ZD1 (JCM 13380), a salt-tolerant denitrifying bacterium capable of producing poly(3-hydroxybutyrate)

  Wu, Y. W., Shao, Y., Khanipov, K., Golovko, G., Pimenova, M., Fofanov, Y. & Chu, K. H., 2017, In: Genome Announcements. 5, 36, e00948-17.

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

  • poly-beta-hydroxybutyrate
  • Biopolymers
  • Base Composition
  • Ecosystem
  • Taiwan
  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

• Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis

  Albayrak, L., Khanipov, K., Rojas, M., Golovko, G., Pimenova, M., Fofanov, Y. & Kosoy, M., Jul 1 2017, Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017. Institute of Electrical and Electronics Engineers Inc., p. 249-254 6 p. (Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017; vol. 2018-January).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Scoring
  • Alignment
  • Genome
  • Gene
  • Clustering
  1 Scopus citations

• Expression Profiling of Long Noncoding RNA Splice Variants in Human Microvascular Endothelial Cells: Lipopolysaccharide Effects in Vitro

  Chowdhury, I. H., Narra, H. P., Sahni, A., Khanipov, K., Schroeder, C. L. C., Patel, J., Fofanov, Y. & Sahni, S. K., 2017, In: Mediators of inflammation. 2017, 3427461.

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

  • Long Noncoding RNA
  • Lipopolysaccharides
  • Endothelial Cells
  • In Vitro Techniques
  • Genome
  11 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 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

• Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media

  Chonmaitree, T., Jennings, K., Golovko, G., Khanipov, K., Pimenova, M., Patel, J. A., McCormick, D. P., Loeffelholz, M. J. & Fofanov, Y., Jul 2017, In: PloS one. 12, 7, e0180630.

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

  • Probiotics
  • otitis media
  • Pathogens
  • Bacteria
  • Otitis Media
  36 Scopus citations

• Novel computational approach for identification of highly mutated integrated HIV genomes

  Khanipov, K., Albayrak, L., Golovko, G., Pimenova, M., Ioannis, P., Fofanov, Y., Khanipov, K. & Pavlidis, I., Jul 1 2017, Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017. Institute of Electrical and Electronics Engineers Inc., p. 246-248 3 p. (Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017; vol. 2018-January).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Viruses
  • Genome
  • Virus
  • Genes
  • Human

• Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions

  Schroeder, C. L. C., Narra, H. P., Sahni, A., Khanipov, K., Patel, J., Fofanov, Y. & Sahni, S. K., Oct 2017, In: Ticks and Tick-borne Diseases. 8, 6, p. 827-836 10 p.

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

  • Rickettsia prowazekii
  • pathogens
  • Epidemic Louse-Borne Typhus
  • In Vitro Techniques
  • infection
  10 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