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• 2020

  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

• 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

• Endothelial exosome plays functional role during rickettsial infection

  Liu, Y., Zhou, C., Su, Z., Chang, Q., Qiu, Y., Bei, J., Gaitas, A., Xiao, J., Drelich, A., Khanipov, K., Jin, Y., Golovko, G., Saito, T. B. & Gong, B., Nov 17 2020, In: Unknown Journal.

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

  • rickettsial diseases
  • Endothelial cells
  • exosomes
  • Exosomes
  • endothelial cells

• 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

• 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
• 2018

  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
  16 Scopus citations

• Broom: Application for non-redundant storage of High Throughput Sequencing data

  Albayrak, L., Khanipov, K., Golovko, G. & Fofanov, Y., May 2 2018, In: Unknown Journal.

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

  • brooms
  • information storage
  • application coverage
  • Information Storage and Retrieval
  • researchers

• Detection of Multidimensional Co-Exclusion Patterns in Microbial Communities

  Albayrak, L., Khanipov, K., Golovko, G. & Fofanov, Y., May 5 2018, In: Unknown Journal.

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

  • Microorganisms
  • Microbiota
  • microbiome
  • microbial communities
  • Probiotics

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

  Albayrak, L., Khanipov, K., Golovko, G. & Fofanov, Y., Nov 1 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

• 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
  26 Scopus citations

• Microbiome interaction networks and community structure from lab-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., Jun 4 2018, In: Unknown Journal.

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

  • Culex
  • Mosquito Vectors
  • Aedes
  • Aedes albopictus
  • Culex quinquefasciatus

• 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

  Jeffries, C. L., Lawrence, G. G., Golovko, G., Kristan, M., Orsborne, J., Spence, K., Hurn, E., Bandibabone, J., Tantely, M. L., 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. & Walker, T., Jun 7 2018, In: Unknown Journal.

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

  Open Access

  • Wolbachia
  • Anopheles
  • Sub-Saharan Africa
  • Africa South of the Sahara
  • malaria

• 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
  22 Scopus citations

• Using High Throughput DNA Sequencing to Evaluate the Accuracy of Serial Dilution Based Tests of Microbial Activities in Oil Pipelines

  Khanipov, K., Golovko, G., Rojas, M., Pimenova, M., Albayrak, L., Chumakov, S., Duarte, R., Widger, W. R., Pickthall, T. & Fofanov, Y., May 16 2018, In: Unknown Journal.

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

  • high-throughput nucleotide sequencing
  • High-Throughput Nucleotide Sequencing
  • Dilution
  • microbial activity
  • Oils
• 2017

  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

• 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
  12 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
  37 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