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Bacteriophages of the lower urinary tract.

Garretto A, Miller-Ensminger T, Wolfe AJ, Putonti C.

Nat Rev Urol. 2019 May 9. doi: 10.1038/s41585-019-0192-4. [Epub ahead of print] Review.


Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429.

Zilliox MJ, Schreckenberger PC, Putonti C.

Microbiol Resour Announc. 2019 May 9;8(19). pii: e00439-19. doi: 10.1128/MRA.00439-19.


virMine: automated detection of viral sequences from complex metagenomic samples.

Garretto A, Hatzopoulos T, Putonti C.

PeerJ. 2019 Apr 10;7:e6695. doi: 10.7717/peerj.6695. eCollection 2019.


Pseudomonas Diversity Within Urban Freshwaters.

Batrich M, Maskeri L, Schubert R, Ho B, Kohout M, Abdeljaber M, Abuhasna A, Kholoki M, Psihogios P, Razzaq T, Sawhney S, Siddiqui S, Xoubi E, Cooper A, Hatzopoulos T, Putonti C.

Front Microbiol. 2019 Feb 15;10:195. doi: 10.3389/fmicb.2019.00195. eCollection 2019.


Characterization of a protozoan Phosducin-like protein-3 (PhLP-3) reveals conserved redox activity.

Kooistra RL, David R, Ruiz AC, Powers SW, Haselton KJ, Kiernan K, Blagborough AM, Solamen L, Olsen KW, Putonti C, Kanzok SM.

PLoS One. 2018 Dec 31;13(12):e0209699. doi: 10.1371/journal.pone.0209699. eCollection 2018.


Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.


Freshwater Viromes: From Sampling to Evaluation.

Putonti C, Diener Z, Watkins SC.

Methods Mol Biol. 2018;1849:17-27. doi: 10.1007/978-1-4939-8728-3_2.


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

Kalesinskas L, Cudone E, Fofanov Y, Putonti C.

Evol Bioinform Online. 2018 Sep 17;14:1176934318797354. doi: 10.1177/1176934318797354. eCollection 2018.


Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages.

Watkins SC, Sible E, Putonti C.

Viruses. 2018 Jun 16;10(6). pii: E331. doi: 10.3390/v10060331.


Detecting viral genomes in the female urinary microbiome.

Garretto A, Thomas-White K, Wolfe AJ, Putonti C.

J Gen Virol. 2018 Aug;99(8):1141-1146. doi: 10.1099/jgv.0.001097. Epub 2018 Jun 11.


The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.

Kula A, Saelens J, Cox J, Schubert AM, Travisano M, Putonti C.

Sci Rep. 2018 May 29;8(1):8350. doi: 10.1038/s41598-018-25914-7.


Culturing of female bladder bacteria reveals an interconnected urogenital microbiota.

Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ, Lawley TD.

Nat Commun. 2018 Apr 19;9(1):1557. doi: 10.1038/s41467-018-03968-5.


Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution.

Shapiro JW, Putonti C.

MBio. 2018 Mar 20;9(2). pii: e01870-17. doi: 10.1128/mBio.01870-17.


Draft Genome Sequence of the Siderophore-Degrading Soil Bacterium Mesorhizobium loti Strain LU.

Castignetti D, Polley N, Putonti C.

Genome Announc. 2018 Feb 8;6(6). pii: e00029-18. doi: 10.1128/genomeA.00029-18.


Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1.

Putonti C, Polley N, Castignetti D.

Genome Announc. 2018 Feb 8;6(6). pii: e00028-18. doi: 10.1128/genomeA.00028-18.


Bacteriophages of the Urinary Microbiome.

Miller-Ensminger T, Garretto A, Brenner J, Thomas-White K, Zambom A, Wolfe AJ, Putonti C.

J Bacteriol. 2018 Mar 12;200(7). pii: e00738-17. doi: 10.1128/JB.00738-17. Print 2018 Apr 1.


Draft Genome Sequence of Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990).

Putonti C, Kalesinskas L, Cudone E, Engelbrecht KC, Koenig DW, Wolfe AJ.

Genome Announc. 2017 Jul 6;5(27). pii: e00619-17. doi: 10.1128/genomeA.00619-17.


Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains.

Putonti C, Kalesinskas L, Cudone E, Engelbrecht KC, Koenig DW, Wolfe AJ.

Genome Announc. 2017 Jul 6;5(27). pii: e00618-17. doi: 10.1128/genomeA.00618-17.


Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698).

Putonti C, Cudone E, Kalesinskas L, Engelbrecht KC, Koenig DW, Wolfe AJ.

Genome Announc. 2017 Jul 6;5(27). pii: e00576-17. doi: 10.1128/genomeA.00576-17.


Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128.

Putonti C, Kalesinskas L, Cudone E, Engelbrecht KC, Koenig DW, Wolfe AJ.

Genome Announc. 2017 Jul 6;5(27). pii: e00575-17. doi: 10.1128/genomeA.00575-17.


Draft Genome Sequence of Escherichia coli K-12 (ATCC 29425).

Engelbrecht KC, Putonti C, Koenig DW, Wolfe AJ.

Genome Announc. 2017 Jul 6;5(27). pii: e00574-17. doi: 10.1128/genomeA.00574-17.


Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798).

Dimitrova D, Engelbrecht KC, Putonti C, Koenig DW, Wolfe AJ.

Genome Announc. 2017 Jul 6;5(27). pii: e00573-17. doi: 10.1128/genomeA.00573-17.


The use of informativity in the development of robust viromics-based examinations.

Watkins SC, Putonti C.

PeerJ. 2017 May 2;5:e3281. doi: 10.7717/peerj.3281. eCollection 2017.


PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets.

Hatzopoulos T, Watkins SC, Putonti C.

Microb Genom. 2016 Mar 10;2(3):e000053. doi: 10.1099/mgen.0.000053. eCollection 2016 Mar.


Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus.

Price TK, Shaheen M, Kalesinskas L, Malki K, Hilt EE, Putonti C, Wolfe AJ.

Genome Announc. 2016 Dec 1;4(6). pii: e01278-16. doi: 10.1128/genomeA.01278-16.


Seven Bacteriophages Isolated from the Female Urinary Microbiota.

Malki K, Sible E, Cooper A, Garretto A, Bruder K, Watkins SC, Putonti C.

Genome Announc. 2016 Nov 23;4(6). pii: e01003-16. doi: 10.1128/genomeA.01003-16.


Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome.

Malki K, Shapiro JW, Price TK, Hilt EE, Thomas-White K, Sircar T, Rosenfeld AB, Kuffel G, Zilliox MJ, Wolfe AJ, Putonti C.

PLoS One. 2016 Nov 18;11(11):e0166757. doi: 10.1371/journal.pone.0166757. eCollection 2016.


Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae.

Hilt EE, Price TK, Diebel K, Putonti C, Wolfe AJ.

Genome Announc. 2016 Nov 17;4(6). pii: e01248-16. doi: 10.1128/genomeA.01248-16.


Genome sequences and annotation of two urinary isolates of E. coli.

Price TK, Mehrtash A, Kalesinskas L, Malki K, Hilt EE, Putonti C, Wolfe AJ.

Stand Genomic Sci. 2016 Oct 12;11:79. eCollection 2016.


Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers.

Ziccardi W, Zhao C, Shepelev V, Uralsky L, Alexandrov I, Andreeva T, Rogaev E, Bun C, Miller E, Putonti C, Doering J.

Chromosome Res. 2016 Sep;24(3):421-36. doi: 10.1007/s10577-016-9530-z. Epub 2016 Jul 18.


Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges.

Bruder K, Malki K, Cooper A, Sible E, Shapiro JW, Watkins SC, Putonti C.

Evol Bioinform Online. 2016 Jun 20;12(Suppl 1):25-33. doi: 10.4137/EBO.S38549. eCollection 2016. Review.


Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches.

Malki K, Bruder K, Putonti C.

Data Brief. 2015 Oct 19;5:556-9. doi: 10.1016/j.dib.2015.10.005. eCollection 2015 Dec.


18S rDNA dataset profiling microeukaryotic populations within Chicago area nearshore waters.

Searle D, Sible E, Cooper A, Putonti C.

Data Brief. 2016 Jan 7;6:526-9. doi: 10.1016/j.dib.2015.12.042. eCollection 2016 Mar.


A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1.

Reisman S, Hatzopoulos T, Läufer K, Thiruvathukal GK, Putonti C.

Evol Bioinform Online. 2016 Jan 18;12:23-7. doi: 10.4137/EBO.S32757. eCollection 2016.


Assessment of microbial populations within Chicago area nearshore waters and interfaces with river systems.

Sible E, Cooper A, Malki K, Bruder K, Hatzopoulos T, Watkins SC, Putonti C.

Data Brief. 2015 Sep 25;5:305-8. doi: 10.1016/j.dib.2015.09.004. eCollection 2015 Dec.


Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla.

Malki K, Kula A, Bruder K, Sible E, Hatzopoulos T, Steidel S, Watkins SC, Putonti C.

Virol J. 2015 Oct 9;12:164. doi: 10.1186/s12985-015-0395-0.


Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches.

Sible E, Cooper A, Malki K, Bruder K, Watkins SC, Fofanov Y, Putonti C.

Data Brief. 2015 Aug 13;5:9-12. doi: 10.1016/j.dib.2015.08.001. eCollection 2015 Dec.


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

Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S.

BMC Evol Biol. 2013 Sep 4;13:184. doi: 10.1186/1471-2148-13-184.


The evolution and putative function of phosducin-like proteins in the malaria parasite Plasmodium.

Putonti C, Quach B, Kooistra RL, Kanzok SM.

Infect Genet Evol. 2013 Jan;13:49-55. doi: 10.1016/j.meegid.2012.08.023. Epub 2012 Sep 17.


CBDB: the codon bias database.

Hilterbrand A, Saelens J, Putonti C.

BMC Bioinformatics. 2012 Apr 26;13:62. doi: 10.1186/1471-2105-13-62.


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

Gijavanekar C, Añez-Lingerfelt M, Feng C, Putonti C, Fox GE, Sabo A, Fofanov Y, Willson RC.

FEBS J. 2011 May;278(10):1676-87. doi: 10.1111/j.1742-4658.2011.08091.x. Epub 2011 Apr 18.


Improved detection of Bartonella DNA in mammalian hosts and arthropod vectors by real-time PCR using the NADH dehydrogenase gamma subunit (nuoG).

Colborn JM, Kosoy MY, Motin VL, Telepnev MV, Valbuena G, Myint KS, Fofanov Y, Putonti C, Feng C, Peruski L.

J Clin Microbiol. 2010 Dec;48(12):4630-3. doi: 10.1128/JCM.00470-10. Epub 2010 Oct 6.


Adaptive evolution and inherent tolerance to extreme thermal environments.

Cox J, Schubert AM, Travisano M, Putonti C.

BMC Evol Biol. 2010 Mar 12;10:75. doi: 10.1186/1471-2148-10-75.


Mechanisms responsible for a PhiX174 mutant's ability to infect Escherichia coli by phosphorylation.

Cox J, Putonti C.

J Virol. 2010 May;84(9):4860-3. doi: 10.1128/JVI.00047-10. Epub 2010 Feb 10.


Evolution of the sequence composition of Flaviviruses.

Schubert AM, Putonti C.

Infect Genet Evol. 2010 Jan;10(1):129-36. doi: 10.1016/j.meegid.2009.11.004. Epub 2009 Nov 13.


Ultraspecific probes for high throughput HLA typing.

Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M, Jayaraman K, Fofanov Y.

BMC Genomics. 2009 Feb 20;10:85. doi: 10.1186/1471-2164-10-85.


The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.

Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E, Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, Caballero J, Siefert J, Eguiarte L, Vielle JP, Martínez O, Souza V, Herrera-Estrella A, Herrera-Estrella L.

Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5803-8. doi: 10.1073/pnas.0800981105. Epub 2008 Apr 11.


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

Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y.

Bioinformatics. 2007 Oct 15;23(20):2665-71. Epub 2007 Sep 19.


The diverse and informative future of microarray applications.

Putonti C.

Pharmacogenomics. 2007 Feb;8(2):137-40. No abstract available.


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