Works by Fofanov, Yuriy

Results: 39

A Computational Tool for the Genomic Identification of Regions of Unusual Compositional Properties and Its Utilization in the Detection of Horizontally Transferred Sequences.

Published in:

Molecular Biology & Evolution, 2006, v. 23, n. 10, p. 1863, doi. 10.1093/molbev/msl053

By:

Putonti, Catherine;
Yi Luo;
Katili, Charles;
Chumakov, Sergey;
Fox, George E.;
Graur, Dan;
Fofanov, Yuriy

Publication type:

Article

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

Published in:

Ecology & Evolution (20457758), 2018, v. 8, n. 1, p. 185, doi. 10.1002/ece3.3638

By:

Robeson, II, Michael S.;
Khanipov, Kamil;
Golovko, George;
Wisely, Samantha M.;
White, Michael D.;
Bodenchuck, Michael;
Smyser, Timothy J.;
Fofanov, Yuriy;
Fierer, Noah;
Piaggio, Antoinette J.

Publication type:

Article

Measuring Alphavirus Fidelity Using Non-Infectious Virus Particles.

Published in:

Viruses (1999-4915), 2020, v. 12, n. 5, p. 546, doi. 10.3390/v12050546

By:

Patterson, Edward I.;
Khanipov, Kamil;
Swetnam, Daniele M.;
Walsdorf, Samantha;
Kautz, Tiffany F.;
Thangamani, Saravanan;
Fofanov, Yuriy;
Forrester, Naomi L.

Publication type:

Article

Janibacter species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis.

Published in:

Infectious Disease Reports, 2019, v. 11, n. 2, p. 22, doi. 10.4081/idr.2019.8132

By:

Malania, Lile;
Ying Bai;
Khanipov, Kamil;
Tsereteli, Marika;
Metreveli, Mikheil;
Tsereteli, David;
Sidamonidze, Ketevan;
Imnadze, Paata;
Fofanov, Yuriy;
Kosoy, Michael

Publication type:

Article

The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions.

Published in:

BMC Microbiology, 2014, v. 14, n. 1, p. 1, doi. 10.1186/s12866-014-0225-3

By:

Stepanov, Victor G.;
Yeyuan Xiao;
Quyen Tran;
Rojas, Mark;
Willson, Richard C.;
Fofanov, Yuriy;
Fox, George E.;
Roberts, Deborah J.

Publication type:

Article

Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment.

Published in:

BMC Microbiology, 2007, v. 7, p. 1, doi. 10.1186/1471-2180-7-15

By:

Tucker, Don L.;
Ott, C. Mark;
Huff, Stephen;
Fofanov, Yuriy;
Pierson, Duane L.;
Willson, Richard C.;
Fox, George E.

Publication type:

Article

PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'.

Published in:

FEBS Journal, 2011, v. 278, n. 10, p. 1676, doi. 10.1111/j.1742-4658.2011.08091.x

By:

Gijavanekar, Charul;
Añez-Lingerfelt, Maria;
Feng, Chen;
Putonti, Catherine;
Fox, George E.;
Sabo, Aniko;
Fofanov, Yuriy;
Willson, Richard C.

Publication type:

Article

Human-blind probes and primers for dengue virus identification.

Published in:

FEBS Journal, 2006, v. 273, n. 2, p. 398, doi. 10.1111/j.1742-4658.2005.05074.x

By:

Putonti, Catherine;
Chumakov, Sergei;
Mitra, Rahul;
Fox, George E.;
Willson, Richard C.;
Fofanov, Yuriy

Publication type:

Article

Effect of the mutation rate and background size on the quality of pathogen identification.

Published in:

Bioinformatics, 2007, v. 23, n. 20, p. 2665, doi. 10.1093/bioinformatics/btm420

By:

Reed, Chris;
Fofanov, Viacheslav;
Putonti, Catherine;
Chumakov, Sergei;
Slezak, Tom;
Fofanov, Yuriy

Publication type:

Article

How independent are the appearances of n-mers in different genomes?

Published in:

Bioinformatics, 2004, v. 20, n. 15, p. 2421, doi. 10.1093/bioinformatics/bth266

By:

Yuriy Fofanov;
Yi Luo;
Charles Katili;
Jim Wang;
Yuri Belosludtsev;
Thomas Powdrill;
Chetan Belapurkar;
Viacheslav Fofanov;
Tong-Bin Li;
Sergey Chumakov;
B. Montgomery Pettitt

Publication type:

Article

Identification of multidimensional Boolean patterns in microbial communities.

Published in:

Microbiome, 2020, v. 8, n. 1, p. N.PAG, doi. 10.1186/s40168-020-00853-6

By:

Golovko, George;
Kamil, Khanipov;
Albayrak, Levent;
Nia, Anna M.;
Duarte, Renato Salomon Arroyo;
Chumakov, Sergei;
Fofanov, Yuriy

Publication type:

Article

Matrix metalloproteinases cleave membrane-bound PD-L1 on CD90+ (myo-)fibroblasts in Crohn's disease and regulate Th1/Th17 cell responses.

Published in:

International Immunology, 2020, v. 32, n. 1, p. 57, doi. 10.1093/intimm/dxz060

By:

Aguirre, Jose E;
Beswick, Ellen J;
Grim, Carl;
Uribe, Gabriela;
Tafoya, Marissa;
Palma, Gabriela Chacon;
Samedi, Von;
McKee, Rohini;
Villeger, Romain;
Fofanov, Yuriy;
Cong, Yingzi;
Yochum, Gregory;
Koltun, Walter;
Powell, Don;
Pinchuk, Irina V

Publication type:

Article

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

Published in:

Genes, 2019, v. 10, n. 3, p. 204, doi. 10.3390/genes10030204

By:

Narra, Hema P.;
Sahni, Abha;
Khanipov, Kamil;
Fofanov, Yuriy;
Sahni, Sanjeev K.

Publication type:

Article

Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus.

Published in:

BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-184

By:

Putonti, Catherine;
Nowicki, Bogdan;
Shaffer, Michael;
Fofanov, Yuriy;
Nowicki, Stella

Publication type:

Article

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

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0180630

By:

Chonmaitree, Tasnee;
Jennings, Kristofer;
Golovko, Georgiy;
Khanipov, Kamil;
Pimenova, Maria;
Patel, Janak A.;
McCormick, David P.;
Loeffelholz, Michael J.;
Fofanov, Yuriy

Publication type:

Article

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

Published in:

PLoS Pathogens, 2019, v. 15, n. 4, p. 1, doi. 10.1371/journal.ppat.1007610

By:

Warmbrod, K. Lane;
Patterson, Edward I.;
Kautz, Tiffany F.;
Stanton, Adam;
Rockx-Brouwer, Dedeke;
Kalveram, Birte K.;
Khanipov, Kamil;
Thangamani, Saravanan;
Fofanov, Yuriy;
Forrester, Naomi L.

Publication type:

Article

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

Published in:

Bioinformatics, 2019, v. 35, n. 1, p. 143, doi. 10.1093/bioinformatics/bty580

By:

Albayrak, Levent;
Golovko, George;
Fofanov, Yuriy;
Khanipov, Kamil

Publication type:

Article

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

Published in:

Bioinformatics, 2018, v. 34, n. 21, p. 3695, doi. 10.1093/bioinformatics/bty414

By:

Albayrak, Levent;
Golovko, George;
Fofanov, Yuriy;
Khanipov, Kamil

Publication type:

Article

4471 Interactions of the Infant Nasopharyngeal Microbiota and Subjects' Clinical Traits in Development of Viral Upper Respiratory Tract Infections and Acute Otitis Media.

Published in:

2020

By:

Khanipov, Kamil;
Golovko, George;
Nia, Anna;
Evangelista, Lorraine;
Fofanov, Yuriy

Publication type:

Abstract

Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00859

By:

Schroeder, Casey L. C.;
Narra, Hema P.;
Sahni, Abha;
Rojas, Mark;
Khanipov, Kamil;
Patel, Jignesh;
Shah, Riya;
Fofanov, Yuriy;
Sahni, Sanjeev K.

Publication type:

Article

Bacterial small RNAs in the Genus Rickettsia.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2293-7

By:

Schroeder, Casey L. C.;
Narra, Hema P.;
Rojas, Mark;
Sahni, Abha;
Patel, Jignesh;
Khanipov, Kamil;
Wood, Thomas G.;
Fofanov, Yuriy;
Sahni, Sanjeev K.

Publication type:

Article

Microbiota dysbiosis and its pathophysiological significance in bowel obstruction.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-31033-0

By:

Hegde, Shrilakshmi;
Lin, You-Min;
Golovko, George;
Khanipov, Kamil;
Cong, Yingzi;
Savidge, Tor;
Fofanov, Yuriy;
Shi, Xuan-Zheng

Publication type:

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.

Published in:

PLoS ONE, 2019, v. 14, n. 3, p. 1, doi. 10.1371/journal.pone.0213869

By:

Peterson, Christine Tara;
Sharma, Vandana;
Iablokov, Stanislav N.;
Albayrak, Levent;
Khanipov, Kamil;
Uchitel, Sasha;
Chopra, Deepak;
Mills, Paul J.;
Fofanov, Yuriy;
Rodionov, Dmitry A.;
Peterson, Scott N.

Publication type:

Article

Impairment of Tissue-Resident Mesenchymal Stem Cells in Chronic Ulcerative Colitis and Crohn's Disease.

Published in:

Journal of Crohn's & Colitis, 2021, v. 15, n. 8, p. 1362, doi. 10.1093/ecco-jcc/jjab001

By:

Grim, Carl;
Noble, Robert;
Uribe, Gabriela;
Khanipov, Kamil;
Johnson, Paul;
Koltun, Walter A;
Watts, Tammara;
Fofanov, Yuriy;
Yochum, Gregory S;
Powell, Don W;
Beswick, Ellen J;
Pinchuk, Irina V

Publication type:

Article

Epigenetic alteration by DNA-demethylating treatment restores apoptotic response to glucocorticoids in dexamethasone-resistant human malignant lymphoid cells.

Published in:

Cancer Cell International, 2014, v. 14, n. 1, p. 1, doi. 10.1186/1475-2867-14-35

By:

Miller, Aaron L.;
Chuandong Geng;
Golovko, Georgiy;
Sharma, Meenakshi;
Schwartz, Jason R.;
Jiabin Yan;
Sowers, Lawrence;
Widger, William R.;
Fofanov, Yuriy;
Vedeckis, Wayne V.;
Thompson, E. Brad

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2012, v. 13, n. 1, p. 166, doi. 10.1186/1471-2105-13-166

By:

Golovko, Georgiy;
Khanipov, Kamil;
Rojas, Mark;
Martinez-Alcántara, Antonio;
Howard, Jesse J.;
Ballesteros, Efren;
Gupta, Sharu;
Widger, William;
Fofanov, Yuriy

Publication type:

Article

Metagenomic Analysis of the Airborne Environment in Urban Spaces.

Published in:

Microbial Ecology, 2015, v. 69, n. 2, p. 346, doi. 10.1007/s00248-014-0517-z

By:

Be, Nicholas;
Thissen, James;
Fofanov, Viacheslav;
Allen, Jonathan;
Rojas, Mark;
Golovko, George;
Fofanov, Yuriy;
Koshinsky, Heather;
Jaing, Crystal

Publication type:

Article

Generation of PVY Coat Protein siRNAs in Transgenic Potatoes Resistant to PVY.

Published in:

American Journal of Potato Research, 2012, v. 89, n. 5, p. 374, doi. 10.1007/s12230-012-9257-0

By:

McCue, Kent;
Ponciano, Grisel;
Rockhold, David;
Whitworth, Jonathan;
Gray, Stewart;
Fofanov, Yuriy;
Belknap, William

Publication type:

Article

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

Published in:

BMC Genomics, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s12864-020-07077-w

By:

Narra, Hema P.;
Sahni, Abha;
Alsing, Jessica;
Schroeder, Casey L. C.;
Golovko, George;
Nia, Anna M.;
Fofanov, Yuriy;
Khanipov, Kamil;
Sahni, Sanjeev K.

Publication type:

Article

Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected Aedes aegypti , Aedes albopictus , and Culex quinquefasciatus Mosquito Vectors.

Published in:

Frontiers in Microbiology, 2018, p. N.PAG, doi. 10.3389/fmicb.2018.02160

By:

Hegde, Shivanand;
Khanipov, Kamil;
Albayrak, Levent;
Golovko, George;
Pimenova, Maria;
Saldaña, Miguel A.;
Rojas, Mark M.;
Hornett, Emily A.;
Motl, Greg C.;
Fredregill, Chris L.;
Dennett, James A.;
Debboun, Mustapha;
Fofanov, Yuriy;
Hughes, Grant L.

Publication type:

Article

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.

Published in:

PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0127799

By:

Rojas, Mark;
Golovko, Georgiy;
Khanipov, Kamil;
Albayrak, Levent;
Chumakov, Sergei;
Pettitt, B. Montgomery;
Strongin, Alex Y.;
Fofanov, Yuriy

Publication type:

Article

Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum.

Published in:

PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0046759

By:

Saxer, Gerda;
Havlak, Paul;
Fox, Sara A.;
Quance, Michael A.;
Gupta, Sharu;
Fofanov, Yuriy;
Strassmann, Joan E.;
Queller, David C.

Publication type:

Article

S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences.

Published in:

Evolutionary Bioinformatics, 2018, n. 14, p. 1, doi. 10.1177/1176934318797354

By:

Kalesinskas, Laurynas;
Cudone, Evan;
Fofanov, Yuriy;
Putonti, Catherine

Publication type:

Article

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

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-3375-x

By:

Albayrak, Levent;
Khanipov, Kamil;
Pimenova, Maria;
Golovko, George;
Rojas, Mark;
Pavlidis, Ioannis;
Chumakov, Sergei;
Aguilar, Gerardo;
Chávez, Arturo;
Widger, William R.;
Fofanov, Yuriy

Publication type:

Article

Small Regulatory RNAs of Rickettsia conorii.

Published in:

Scientific Reports, 2016, p. 36728, doi. 10.1038/srep36728

By:

Narra, Hema P.;
Schroeder, Casey L. C.;
Sahni, Abha;
Rojas, Mark;
Khanipov, Kamil;
Fofanov, Yuriy;
Sahni, Sanjeev K.

Publication type:

Article

Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells.

Published in:

Epigenetics, 2015, v. 10, n. 4, p. 303, doi. 10.1080/15592294.2015.1020000

By:

Chernov, Andrei V;
Reyes, Leticia;
Xu, Zhenkang;
Gonzalez, Beatriz;
Golovko, Georgiy;
Peterson, Scott;
Perucho, Manuel;
Fofanov, Yuriy;
Strongin, Alex Y

Publication type:

Article

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

Published in:

Mediators of Inflammation, 2017, p. 1, doi. 10.1155/2017/3427461

By:

Chowdhury, Imran H.;
Narra, Hema P.;
Sahni, Abha;
Khanipov, Kamil;
Schroeder, Casey L. C.;
Patel, Jignesh;
Fofanov, Yuriy;
Sahni, Sanjeev K.

Publication type:

Article

The main challenges that remain in applying high-throughput sequencing to clinical diagnostics.

Published in:

2015

By:

Loeffelholz, Michael;
Fofanov, Yuriy

Publication type:

Editorial

Ultraspecific probes for high throughput HLA typing.

Published in:

BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-85

By:

Chen Feng;
Putonti, Catherine;
Meizhuo Zhang;
Eggers, Rick;
Mitra, Rahul;
Hogan, Mike;
Jayaraman, Krishna;
Fofanov, Yuriy

Publication type:

Article