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Items: 23

1.

Janibacter species 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.

Infect Dis Rep. 2019 Sep 18;11(2):8132. doi: 10.4081/idr.2019.8132. eCollection 2019 Sep 18.

2.

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

Warmbrod KL, Patterson EI, Kautz TF, Stanton A, Rockx-Brouwer D, Kalveram BK, Khanipov K, Thangamani S, Fofanov Y, Forrester NL.

PLoS Pathog. 2019 Apr 4;15(4):e1007610. doi: 10.1371/journal.ppat.1007610. eCollection 2019 Apr.

3.

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 CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.

PLoS One. 2019 Mar 19;14(3):e0213869. doi: 10.1371/journal.pone.0213869. eCollection 2019.

4.

Global Transcriptomic Profiling of Pulmonary Gene Expression in an Experimental Murine Model of Rickettsia conorii Infection.

Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK.

Genes (Basel). 2019 Mar 8;10(3). pii: E204. doi: 10.3390/genes10030204.

5.

Enhancer Associated Long Non-coding RNA Transcription and Gene Regulation in Experimental Models of Rickettsial Infection.

Chowdhury IH, Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK.

Front Immunol. 2019 Jan 9;9:3014. doi: 10.3389/fimmu.2018.03014. eCollection 2018.

6.

Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa.

Jeffries CL, Lawrence GG, Golovko G, Kristan M, Orsborne J, Spence K, Hurn E, Bandibabone J, Tantely LM, Raharimalala FN, Keita K, Camara D, Barry Y, Wat'senga F, Manzambi EZ, Afrane YA, Mohammed AR, Abeku TA, Hedge S, Khanipov K, Pimenova M, Fofanov Y, Boyer S, Irish SR, Hughes GL, Walker T.

Version 2. Wellcome Open Res. 2018 Nov 27 [revised 2018 Jan 1];3:113. doi: 10.12688/wellcomeopenres.14765.2. eCollection 2018.

7.

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 MA, Rojas MM, Hornett EA, Motl GC, Fredregill CL, Dennett JA, Debboun M, Fofanov Y, Hughes GL.

Front Microbiol. 2018 Sep 10;9:2160. doi: 10.3389/fmicb.2018.02160. eCollection 2018.

8.

Microbiota dysbiosis and its pathophysiological significance in bowel obstruction.

Hegde S, Lin YM, Golovko G, Khanipov K, Cong Y, Savidge T, Fofanov Y, Shi XZ.

Sci Rep. 2018 Sep 3;8(1):13044. doi: 10.1038/s41598-018-31033-0.

9.

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

Albayrak L, Khanipov K, Golovko G, Fofanov Y.

Bioinformatics. 2019 Jan 1;35(1):143-145. doi: 10.1093/bioinformatics/bty580.

PMID:
30010786
10.

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

Albayrak L, Khanipov K, Golovko G, Fofanov Y.

Bioinformatics. 2018 Nov 1;34(21):3695-3701. doi: 10.1093/bioinformatics/bty414.

PMID:
29878050
11.

Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy.

Kautz TF, Guerbois M, Khanipov K, Patterson EI, Langsjoen RM, Yun R, Warmbrod KL, Fofanov Y, Weaver SC, Forrester NL.

Virus Evol. 2018 Mar 6;4(1):vey004. doi: 10.1093/ve/vey004. eCollection 2018 Jan.

12.

Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity.

Patterson EI, Khanipov K, Rojas MM, Kautz TF, Rockx-Brouwer D, Golovko G, Albayrak L, Fofanov Y, Forrester NL.

Virus Evol. 2018 Feb 15;4(1):vey001. doi: 10.1093/ve/vey001. eCollection 2018 Jan.

13.

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

Robeson MS 2nd, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ.

Ecol Evol. 2017 Nov 26;8(1):185-196. doi: 10.1002/ece3.3638. eCollection 2018 Jan.

14.

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

Chowdhury IH, Narra HP, Sahni A, Khanipov K, Schroeder CLC, Patel J, Fofanov Y, Sahni SK.

Mediators Inflamm. 2017;2017:3427461. doi: 10.1155/2017/3427461. Epub 2017 Sep 25.

15.

Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing Poly(3-Hydroxybutyrate).

Wu YW, Shao Y, Khanipov K, Golovko G, Pimenova M, Fofanov Y, Chu KH.

Genome Announc. 2017 Sep 7;5(36). pii: e00948-17. doi: 10.1128/genomeA.00948-17.

16.

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

Schroeder CLC, Narra HP, Sahni A, Khanipov K, Patel J, Fofanov Y, Sahni SK.

Ticks Tick Borne Dis. 2017 Oct;8(6):827-836. doi: 10.1016/j.ttbdis.2017.06.008. Epub 2017 Jun 29.

17.

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 JA, McCormick DP, Loeffelholz MJ, Fofanov Y.

PLoS One. 2017 Jul 14;12(7):e0180630. doi: 10.1371/journal.pone.0180630. eCollection 2017.

18.

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 WR, Fofanov Y.

BMC Genomics. 2016 Dec 12;17(1):1017.

19.

Small Regulatory RNAs of Rickettsia conorii.

Narra HP, Schroeder CL, Sahni A, Rojas M, Khanipov K, Fofanov Y, Sahni SK.

Sci Rep. 2016 Nov 11;6:36728. doi: 10.1038/srep36728.

20.

Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii.

Schroeder CL, Narra HP, Sahni A, Rojas M, Khanipov K, Patel J, Shah R, Fofanov Y, Sahni SK.

Front Microbiol. 2016 Jun 8;7:859. doi: 10.3389/fmicb.2016.00859. eCollection 2016.

21.

Bacterial small RNAs in the Genus Rickettsia.

Schroeder CL, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK.

BMC Genomics. 2015 Dec 18;16:1075. doi: 10.1186/s12864-015-2293-7.

22.

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.

Rojas M, Golovko G, Khanipov K, Albayrak L, Chumakov S, Pettitt BM, Strongin AY, Fofanov Y.

PLoS One. 2015 Jun 3;10(6):e0127799. doi: 10.1371/journal.pone.0127799. eCollection 2015.

23.

Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation.

Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, Howard JJ, Ballesteros E, Gupta S, Widger W, Fofanov Y.

BMC Bioinformatics. 2012 Jul 16;13:166. doi: 10.1186/1471-2105-13-166.

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